San FranciSco EStuary invasive Spartina project 2014 isp Monitoring and treatment report

Transcription

1 2014 San FranciSco EStuary invasive Spartina project 2014 isp Monitoring and treatment report

2 San Francisco Estuary Invasive Spartina Project 2014 ISP Monitoring and Treatment Report Prepared by: Tobias Rohmer Olofson Environmental, Inc. Drew Kerr & Ingrid Hogle 1830 Embarcadero Cove, Suite 100 Oakland, California For the State Coastal Conservancy San Francisco Estuary Invasive Spartina Project 1330 Broadway, 13 th Floor Oakland, CA August 2015

3 Cover Photos: (clockwise from top left) Airboat shown on the mudflats of San Pablo Marsh. These watercrafts allow for inventory and treatment on low tides, which is essential for thorough detection of all hybrid Spartina, and to allow for sufficient dry time for the herbicide to enter the plants before the next tidal inundation. ISP biologist wading through a meadow of Spartina in the far South Bay. Manual removal of Spartina densiflora is being used to complete the eradication of this species around the Estuary after successful reductions using imazapyr in the initial years of the ISP. The plant shown is typical of the size found by biologists at this stage in the effort as the ISP partners work to exhaust the seed bank. This report was prepared with funding provided by: California State Coastal Conservancy and California Wildlife Conservation Board (MOU # and subsequent)

4 Table of Contents 1. Introduction and Summary of Progress Through Treatment and Monitoring Completed in Bay-wide Inventory Regional Inventory and Treatment Activities Region 1: Marin Region 2: San Francisco Peninsula Region 3: San Mateo Region 4: Dumbarton South Region 5: Union City Region 6: Hayward Region 7: San Leandro Bay Region 8: Bay Bridge North Region 9: Suisun Region 10: Vallejo Region 11: Petaluma Region 12: Outer Coast Special Topics South Bay Salt Pond Restoration Project Knapp Tract Island Ponds Newer Breaches SBSP Monitoring Strategy Central Bair Island Restoration Restricted Treatment Sites New Infestations and Sub-areas Added in ISP Genetics Program Spartina Patens Update Considerations for Earlier Entry to the Fringe Marsh at Five Sites Increased Use of Airboat for ISP Inventory Enhanced DNA Sampling in the Far South Bay Summary of 2014 Inventory Monitoring and Treatment References Appendix 1. Target Species Descriptions Appendix 2. ISP Program Areas Invasive Spartina Project i 2014 Monitoring and Treatment Report

5 Figures Figure 1. ISP Reporting Regions and 2014 survey efforts throughout San Francisco Bay Estuary Figure hybrid Spartina alterniflora x foliosa presence throughout San Francisco Bay Estuary by ISP Reporting Region and sub-area Figure Spartina densiflora presence throughout San Francisco Bay Estuary by ISP Reporting Region and sub-area Figure Spartina densiflora x foliosa hybrid, S. anglica, and S. patens presence throughout San Francisco Bay Estuary by ISP Reporting Region and sub-area Figure 5. Bay-wide trend of invasive Spartina from by net cover and treatment cover Figure 6. Bay-wide trends of invasive Spartina infestation from by Reporting Region Figure 7. Bay-wide trend of invasive Spartina by treatment authorization since Figure 8. Distribution of invasive Spartina in 2014 across the 32 sub-areas of Reporting Region 1: Marin Figure 9. Distribution of invasive Spartina in 2014 within the Corte Madera Creek Watershed of Marin Region Figure 10. Hybrid Spartina alterniflora in the foreground growing in a brackish section of upper San Bruno Creek with Typha sp Figure 11. USFWS-certified California red-legged frog biologist using a stick to check the hybrid Spartina alterniflora stand for amphibian presence ahead of treatment Figure 12. Distribution of invasive Spartina in 2013 across the 35 sub-areas of Reporting Region 2: San Francisco Peninsula Figure 13. Distribution of invasive Spartina in 2014 across the 26 sub-areas of Reporting Region 3: San Mateo Figure 14. Two applicators navigating the challenging mudflat terrain of Cooley Landing to haul hose out to some outlier clones of hybrid Spartina alterniflora Figure 15. Distribution of invasive Spartina in 2014 across the 25 sub-areas of Reporting Region 4: Dumbarton South Figure 16. Hybrid Spartina alterniflora established at Eden Landing Pond E9, with two larger clones on the mudflat in the distance Figure 17. Distribution of invasive Spartina in 2014 across the 21 sub-areas of Reporting Region 5: Union City Figure 18. Distribution of invasive Spartina in 2014 across the 27 sub-areas of Reporting Region 6: Hayward Figure 19. Distribution of invasive Spartina in 2014 across the 19 sub-areas of Reporting Region 7: San Leandro Bay Figure 20. Distribution of invasive Spartina in 2014 across the 12 sub-areas of Reporting Region 8: Bay Bridge North Invasive Spartina Project ii 2014 Monitoring and Treatment Report

6 Figure 21. Distribution of invasive Spartina in 2014 across the single sub-area and adjacent shoreline of Reporting Region 9: Suisun Figure 22. Distribution of invasive Spartina in 2014 across the four sub-areas of Reporting Region 10: Vallejo Figure 23. Distribution of invasive Spartina in 2014 across the four sub-areas of Reporting Region 11: Petaluma Figure 24. Distribution of invasive Spartina in 2014 across the five sub-areas of Reporting Region 12: Outer Coast Figure 25. Native Spartina establishment along elevated areas where mud has accreted on old manmade structures within Knapp Tract/Pond A Figure 26. The largest hybrid Spartina alterniflora clone found in Knapp Tract/Pond A6 in 2014 (5 meter diameter), with numerous S. foliosa clones establishing in the background Figure 27. Map of the South Bay Salt Ponds and neighboring recent restoration projects in South San Francisco Bay Figure 28. Distribution map of the 11 ISP sub-areas in which treatment of hybrid S. alterniflora has been restricted since Figure 29. Bay-wide trend of invasive Spartina net area, by treatment authorization since Figure 30. Density plot of discriminant function scores for two genetic clusters of Spartina Figure 31. Seedling of Chloropyron molle molle growing amongst the wispy spring growth of a Spartina patens clone Figure 32. Backpack application to stand of Spartina patens along a channel bank Figure 33. Applying herbicide mixture to a sponge for wicking onto Spartina patens within one meter of the endan-gered Chloropyron molle molle Invasive Spartina Project iii 2014 Monitoring and Treatment Report

7 Tables Table Bay-wide summary of invasive Spartina area by species Table Bay-wide summary of invasive Spartina area by ISP Reporting Region Table 3. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 1: Marin Table 4. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 2: San Francisco Peninsula Table 5. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 3: San Mateo Table 6. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 4: Dumbarton South Table 7. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 5: Union City Table 8. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 6: Hayward 36 Table 9. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 7: San Leandro Bay Table 10. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 8: Bay Bridge North Table 11. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 9: Suisun Table 12. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 10: Vallejo Table 13. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 11: Petaluma Table 14. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 12: Outer Coast Table 15. Biennial hybrid S. alterniflora quantities and trends from at the 11 ISP sub-areas where treatment has been restricted since Invasive Spartina Project iv 2014 Monitoring and Treatment Report

8 1. Introduction and Summary of Progress Through 2013 Since the early 1970s, four non-native cordgrasses, including Spartina alterniflora (Atlantic smooth cordgrass), S. densiflora (Chilean cordgrass), S. anglica (English cordgrass), and S. patens (salt meadow cordgrass), were introduced to the San Francisco Estuary (Estuary or Bay throughout this report). Each of these species is known to be invasive outside of its native range, and each has demonstrated varying degrees of invasiveness since establishing in the Estuary. Spartina species are closely related, and both S. alterniflora and S. densiflora subsequently hybridized with native S. foliosa (Daehler and Strong 1996; Ayres, Strong et al. 2003; Ayres, Grotkopp et al. 2008). Offspring of hybrid S. alterniflora x foliosa backcrossed with the parent species and with one another, producing an extremely robust and fertile hybrid swarm, which invaded habitat throughout the Estuary, threatening the ecological integrity of the existing tidal wetlands and mudflats as well as the potential for future restoration efforts (Daehler and Strong 1996; Goals 1999; Ayres, Strong et al. 2003; State Coastal Conservancy 2003; Ayres, Zaremba et al. 2004; Ayres, Grotkopp et al. 2008). For further detail on each species of Spartina found in the Estuary, see Appendix 1. The San Francisco Estuary Invasive Spartina Project (ISP) was established in 2000 by the California State Coastal Conservancy (Conservancy), in partnership with the U.S. Fish and Wildlife Service (USFWS), in response to the invasion of non-native Spartina. Non-native Spartina had been determined to pose many serious threats to the Estuary, as was described in the ISP s Programmatic Environmental Impact Statement/Environmental Impact Report (PEIS/EIR; (State Coastal Conservancy 2003). Predicted impacts of non-native Spartina in the Estuary included the destruction or degradation of endangered species habitat, loss of flood control capacity, creation of mosquitobreeding areas, corruption of salt marsh restoration efforts, and the possible eventual extinction of native Spartina foliosa. The purpose of the ISP is to implement a regional program to eradicate nonnative Spartina species from the Estuary. This goal is accomplished through a highly-coordinated program of inventory mapping and treatment that is planned and supervised by ISP biologists, and implemented with input and on-the-ground actions by a bay-wide network of partners including dozens of landowners, resource agencies, contractors, grantees, and stakeholder groups throughout the nine county Bay Area. The project has been supported over the years by a combination of state (74%), federal (22%), and local and other funds (4%). The 2014 expenditure for monitoring and treatment was roughly $1,500,000, a 20% reduction from prior years, due to decreasing availability of State of California funds. Working within very limited annual windows of opportunity (due to tides, stage of plant grown, and presence of endangered species in the work area), the ISP conducts mapping and treatment of invasive Spartina each year throughout 60,000 acres of potential habitat. Since 2008, inventory efforts have been conducted primarily on the ground on foot or using various boats. Sites are inventoried each year prior to treatment to allow thorough and focused mapping and collection of DNA samples, and to collect accurate current locations of invasive Spartina plants to inform treatment. Having the target plant locations confirmed and mapped in advance allows treatment crews to focus on thorough treatment without having to hunt for plants at the same time. It also enhances worker safety, reduces the amount of ground crews must cover, and reduces disturbance to the marsh. Biologists map found invasive Spartina plants as points, lines, or polygons using handheld data loggers with Global Positioning System (GPS), and spatially demarcate each feature. A cover class is assigned to each feature to record the density of live invasive Spartina within that feature s delineated boundary (see inset: Defining Area ). Invasive Spartina Project Monitoring and Treatment Report

9 Defining Area The ISP uses the terms net area and treatment area to define the extent of non-native Spartina. Net area refers to the size of the infestation if the space between stems were subtracted from the overall footprint of the plant or clump of plants. Net area is the metric typically used in botanical surveys. Treatment area describes the area that will be directly affected by treatment. Treatment area is a separate measurement used for planning, and it is generally five to seven times greater than the net area of During treatment, ISP biologists guide agency personnel or contracted herbicide applicators to each previously-mapped invasive Spartina feature and update that feature in the data logger to record that day s treatment activity (e.g. treated, not treated, sub-optimally treated etc.). This method of treatment survey has been implemented by ISP since 2010, and it has greatly improved the ability of field staff to accomplish thorough treatment of sites in the limited amount of time available with the treatment crew(s) for a given day. For further detail on the methods employed by ISP for treatment, monitoring, and other work, please see Appendix 2. The ISP has made tremendous progress toward eradication since 2000, controlling non-native Spartina throughout the San Francisco Estuary and in the neighboring coastal areas of Point Reyes National Seashore and Bolinas Lagoon. In 2013, the ISP mapped a total of 32.8 net acres of non-native Spartina 1, a 96% estuary-wide reduction since the peak of the invasion at 805 acres in Since 2011, treatment restrictions have been in place at eleven sub-areas, and in 2013 a total of 20.9 acres of non-native Spartina (nearly two thirds of the Bay-wide total) remained untreated in those eleven marshes. ISP and its partners treated the remaining 11.9 acres of non-native Spartina in the sub-areas where treatment was authorized. For further information on the invasion histories and treatment activities around the Bay, see the 2013 ISP Monitoring and Treatment Report (Rohmer, Kerr et al. 2014). 1 This is a corrected value from the originally reported 38.4 acres for 2013 inventory. The discrepancy arose from the coarse method of mapping used by ISP staff when inventorying the large amounts of Spartina in sub-areas with treatment restrictions. More detail of these mapping methods is presented in Section 2.1. Invasive Spartina Project Monitoring and Treatment Report

10 2. Treatment and Monitoring Completed in 2014 The ISP s activities and progress are described in this section, first from a bay-wide perspective, and then in more detail for each of 12 Reporting Regions (see inset this page). The Reporting Regions are based on regions initially defined by USFWS for assessment of California Ridgway s rail (Rallus obsoletus obsoletus) populations. The Reporting Region boundaries also take into consideration natural and political landscape features, similarity in land management issues, geographic proximity and ecological connectedness of the treatment sub-areas, and general impact of non-native Spartina invasion on the region. ISP uses these Reporting Regions to cohesively present treatment and monitoring data in a manner more suitable for correlation with California Ridgway s rail ( Ridgway s rail ) data Bay-wide Inventory In 2014, the ISP prioritized inventory of sites bay-wide based on local invasion pressure, which led to very similar site prioritization as that in Prior to the beginning of the season, biologists reviewed historical bay-wide inventory data, and determined the relative invasion pressure or impact risks according to the following set of criteria: historic presence of non-native Spartina, proximity to seed source from nearby infestations, and habitat suitability for colonization by non-native Spartina. Sub-areas were then divided into categories: sites for full inventory, sites for partial inventory, and sites to be coarsely inventoried in Sites selected for full inventory have historic infestation or a high risk of colonization due to inviting ISP Reporting Regions Region 1. Marin Region 2. San Francisco Peninsula Region 3. San Mateo Region 4. Dumbarton South Region 5. Union City Region 6. Hayward Region 7. San Leandro Bay Region 8. Bay Bridge North Region 9. Vallejo Region 10. Suisun Region 11. Petaluma Region 12. Outer Coast habitat conditions and nearby seed source. Marshes selected for partial inventory are characterized by remote infestations in portions of very large sub-areas; the historically colonized areas were thoroughly surveyed, though the remainder of the site was not. The 11 sites where treatment was precluded or restricted in 2014 were mapped on a coarse level using 25x25 meter grids, a survey method that has been frequently employed by ISP when mapping heavy infestations since Mapping by grid follows the rationale that detailed locations of plants would neither inform current year treatment nor inventory for the following year, and the time saved mapping by grid can be better allocated to areas that will receive treatment. All of ISP s 211 defined treatment sub-areas were at least partially inventoried in This amounts to approximately 35,000 acres, or 60% of the Estuary s potential invasive Spartina habitat that was surveyed in its entirety most recently in Figure 1 shows the location of the ISP Reporting Regions and status of inventory completion by inventory boundary for Inventory and treatment efficiency increased in 2014 as a result of technological advancements in ISP s data sharing capabilities. ISP staff collect field data during inventory using Trimble Yuma2 tablets running ESRI ArcPad GIS software. Later during treatment, that data is updated to record timing and type of treatment applications. The data is housed in geodatabases, and all data layers associated with a day s field work are checked out to transfer them onto the Yuma 2 tablets. Prior to this season, this data was then kept independently on each tablet in the field with no way to com- Invasive Spartina Project Monitoring and Treatment Report

11 Figure 1. ISP Reporting Regions and 2014 survey efforts throughout San Francisco Bay Estuary. Invasive Spartina Project Monitoring and Treatment Report

12 municate or share data with coworkers without returning to the office to check all data into the geodatabase, and re-check it out. Beginning in 2014, this is no longer the case, as biologists now have the ability to conduct two way, real-time synchronization of data in the field. With the push of a button, field staff can now see where others have completed inventory and which plants have been treated, and more importantly, they are better able to identify areas that have not received adequate survey and/or plants that have been missed during treatment. Similarly, senior staff in the office can now view the data as it is synchronized, and can alert field staff of any data discrepancies or oversights while staff are still on site. This new capability greatly increases the efficiency with which staff can coordinate and complete thorough inventory and treatment, and contributes greatly to the project having been able to survey a greater number of sites than initially anticipated. ISP was also featured in ESRI s ArcNews (Winter 2014/2015) providing testimony on the benefits of another innovative tool called Data Reviewer that has reduced the time needed for staff to perform data quality checks by 75% through new automations ( The ISP inventoried a total of 28.9 acres of hybrid S. alterniflora bay-wide, which marks a decline of 96.4% since peak infestation of 805 acres in Where full treatment has been authorized since at least 2012, net cover has reduced by 48% between 2013 and 2014, which reflects a 99% decline in those sub-areas since peak infestation (Table 1). However, the bay-wide infestation decreased by only 12% since 2013, due to the 1.8-acre increase (8%) persisting in the 11 sub-areas with treatment prohibitions and restrictions. Four regions continue to contain the vast majority (98%) of remaining non-native Spartina in the Estuary (Table 2). Listed here in decreasing order of cordgrass cover, they are: Region 7: San Leandro Bay (12.0 acres) Region 6: Hayward (9.1 acres) Region 3: San Mateo (4.7 acres) Region 4: Dumbarton South (2.6 acres) Each of the three most infested regions have some level of treatment restriction placed on them, and the 22.7 acres of hybrid S. alterniflora present in restricted sub-areas accounts for almost 80% of the 2014 bay-wide total (Table 1, Figure 2). More specific inventory methods, results, and treatment activities are detailed by Reporting Region in Section 2.2. As mentioned above, sub-areas with treatment restrictions were mapped by grid in 2014, while in 2013 they were mapped using a coarser method so that resources could be diverted to inventory and treat elsewhere. The 2013 method assigned cover classes to large, coarse polygons, and groundtruthed them by re-surveying portions of two sub-areas by the same biologists using standard point/line/polygon methods. A review of the results indicated an underestimation of cover class in the very large polygons. To account for this, the cover classes of these polygons were adjusted to reflect a larger amount of error; that is, the minimum and maximum levels of non-native Spartina were amplified to reflect the decreased precision, and the average net cover also increased. Inventory of these same sub-areas using the standard grid method in 2014 showed that this data scaling in 2013 seems to have overshot the mark. As a result, 2014 inventory data falsely showed an 11% decrease of invasive Spartina cover in these marshes since 2013, despite there having been no treatment, and with visual assessments indicating that invasive Spartina had indeed increased in these marshes. With this information, the scaled results reported previously for 2013 have been discarded, and moving forward, only un-scaled 2013 data will be reported and used in annual trends. Grids will continue to Invasive Spartina Project Monitoring and Treatment Report

13 Table Bay-wide summary of invasive Spartina area by species. S. alterniflora x foliosa Peak Amount Sub-areas with 2014 Treatment Authorization 6.2 ac 11.9 ac -5.7 ac -48% ac ac -99.0% 1.0% Sub-areas with 2014 Treatment Restrictions 22.7 ac 20.9 ac 1.8 ac 8.5% ac ac -86.1% 13.9% S. alterniflora x foliosa TOTAL 28.9 ac 32.8 ac -3.9 ac -12% ac ac -96.4% 3.6% S. densiflora S. densiflora x foliosa S. anglica S. patens Spartina species Net Cover 2014 Net Cover 2013 Change Since 2013 % Change Since 2013 Peak Year Change Since Peak % Change Since Peak % Remaining since Peak 24.2 m m m 2-48% ac -4.2 ac % 0.14% 17.1 m m m 2 5% m m % 4.9% 5.6 m m m 2 39% m m % 1.5% 75 m 2 91 m 2-16 m 2-13% ac ac -96.9% 3.1% Table Bay-wide summary of invasive Spartina area by ISP Reporting Region. Region # Region Name # Sub- Areas Potential Invasive Spartina Habitat (ac) Proportion of Region Authorized for Treatment (by acreage) Net Cover 2014 (ac) % Baywide Total Change Since 2013 (ac) % Change Peak Amount Change Since Since 2013 Peak Year (ac) Peak (ac) % Decline Since Peak 1 Marin 32 4,182 All % % % 0.6% 2 SF Peninsula 35 1,219 All % % % 0.1% 3 San Mateo* 26 5,821 97% % % % 3.5% 4 Dumbarton South 25 9,194 All % % % 6.5% 5 Union City 21 3,741 All % % % 0.01% 6 Hayward* 27 1,482 72% % % % 4.0% 7 San Leandro Bay* % % % % 14.2% 8 Bay Bridge North 12 1,796 All % % % 2.0% 9 Suisun 1 1,555 All % % % 3.1% 10 Vallejo 4 18,908 All % % % 3.5% 11 Petaluma 4 6,252 All % % % 10.3% 12 Outer Coast 5 3,028 All % % % 37.2% ALL SFB Estuary , % % % % 3.6% * This region has treatment restrictions in at least one sub-area. The amount of the region that is authorized for full treatment is calculated by area in column 5. % Remaining since Peak Invasive Spartina Project Monitoring and Treatment Report

14 be used as the standard method for coarser inventory monitoring when more spatially explicit information is not needed to inform treatment. Since 2013, the ISP has conducted secondary rounds of inventory and treatment at select sites. This is a critical action as the timing of the growing season can vary by site, with some sites or portions of sites emerging and/or maturing later in the season, and thorough detection can also be hampered by herbivory. This requires more funding to visit a site twice, so this approach is only applied to prioritized sites and could be applied to additional sites with increased budget. All sub-areas chosen for a second round are approaching eradication and many contain linear stretches of marsh that can be treated early because they do not provide habitat for Ridgway s rails. This allows sufficient time for the treated plants to exhibit signs from the imazapyr before returning for the second round. However, some hybrid S. alterniflora plants have not yet emerged by the first inventory, usually because these sites have been intensively treated for years, and remaining rhizomes are down to their last reserves. Also at this early time in the year, young plants may have been grazed or mowed by herbivores (mainly geese), causing biologists to miss plants that are still alive below-ground. Individual small plants may also be missed during the first round of inventory due to the tall pickleweed (Sarcocornia pacifica) and other native vegetation present, or due to the amount of effort needed to successfully cover the enormous size of some sites. In 2014, secondary rounds of inventory were conducted mostly in the latter half of October, after most other sites had been inventoried and treated, and managers could assess the availability of time and resources to proceed. Figures 2-4 show the Reporting Regions and provide graphic summaries of the distribution of each non-native Spartina species within each Reporting Region and each sub-area. Figure 2 shows that the greatest presence of hybrid S. alterniflora is congregated around the Central and South Bay, but is still present at low levels in all other regions. Region 1 is the source of the S. densiflora infestation and where that species remains at its highest (Figure 3). Figure 4 shows that S. densiflora x foliosa hybrid is no longer found in Region 2 and continues to be exclusively in Region 1 for the second consecutive year. There were far more historical S. densiflora sites in Region 1, the site of the introduction in the 1970s, than anywhere else in the Estuary, and many of these infestations were growing adjacent to S. foliosa, so it is not surprising that this area would be the final stronghold for this hybrid. There were 25 sub-areas across ten Reporting Regions with prior invasion history in which no nonnative Spartina was found in 2014, including: Murphy s Creek (04i), Brickyard Cove (23a), Novato (23m), and China Camp (23o) in Region 1; India Basin (12c), Hunter s Point Naval Reserve (12d), Crissy Field (12g), Yerba Buena Island (12h), Mission Creek (12i), Old Shipyard (18c), Inner Harbor (18d), Fisherman's Park (19m), and Anza Lagoon (19r) in Region 2; Foster City (19q) and Maple Street Channel (19s) in Region 3; Coyote Creek-Alameda County (05f, Region 4); Upstream of 20 Tide Gates (13g; Region 5); Sulphur Creek (20j, Region 6); Hoffman Marsh (212e; Region 8); two subareas in Region 10, White Slough/Napa River (26a) and Sonoma Baylands (26d); Grey s Field (24b, Region 11); and three sub-areas in Region 12, Limantour Estero (25b), Drakes Estero (25c), and Bolinas Lagoon, South (25e). Re-occurrence of hybrid S. alterniflora occurred in one sub-area, Triangle Marsh (20w; Region 6: Marin), where no invasive Spartina was found in 2013, but where one 0.01 m 2 plant was found in Infestations were discovered in two freshly breached sites: Central Bair (2o) in the San Mateo Region, and Pond E8A, E9, E8X (13m) in Eden Landing Ecological Reserve of the Union City Region. Invasive Spartina Project Monitoring and Treatment Report

15 Figure hybrid Spartina alterniflora x foliosa presence throughout San Francisco Bay Estuary by ISP Reporting Region and sub-area. Invasive Spartina Project Monitoring and Treatment Report

16 Figure Spartina densiflora presence throughout San Francisco Bay Estuary by ISP Reporting Region and sub-area. Invasive Spartina Project Monitoring and Treatment Report

17 Figure Spartina densiflora x foliosa hybrid, S. anglica, and S. patens presence throughout San Francisco Bay Estuary by ISP Reporting Region and sub-area. Invasive Spartina Project Monitoring and Treatment Report

18 Bay-wide and Regional Trends since 2005 Figures 5-7 show bay-wide and Regional trends of invasive Spartina over the years. Since the peak infestation of 805 acres in 2005, cover has dropped to 28.9 acres in 2014, but annual rates of decline have been leveling out (Figure 5). As Figure 7 shows, the hybrid S. alterniflora within the sites where treatment was authorized continues to decline, though that is offset somewhat by increases in invasive Spartina in those 11 sites where full treatment has not been authorized since These trends are expected to continue until treatment is reauthorized, as is discussed in greater detail in Section 3.2 of this report. Figure 5. Bay-wide trend of invasive Spartina from by net cover and treatment cover. * Treatment acre measurements began in 2008 **2007 data were artificially low due to constraints of aerial photo interpretation that year. Invasive Spartina Project Monitoring and Treatment Report

19 Figure 6. Bay-wide trends of invasive Spartina infestation from by Reporting Region. Figure 7. Bay-wide trend of invasive Spartina by treatment authorization since 2010, the most recent year the ISP was allowed to treat all detected invasive Spartina. Invasive Spartina Project Monitoring and Treatment Report

20 2.2. Regional Inventory and Treatment Activities Region 1: Marin The Marin Region (Region 1) is composed of 32 sub-areas in Marin County, and extends from the Golden Gate Bridge to the mouth of the Petaluma River. It includes several large, contiguous tracts of marsh, most notably those in the Novato Creek, Corte Madera Creek and Las Gallinas Creek Watersheds. Relative to regions in the Central and South Bays, the Marin Region has never had a very sizeable infestation in terms of acreage, but had many small infestations scattered throughout the marshes and tidal channels. However, four non-native Spartina species are present (S. alterniflora x foliosa hybrids, S. densiflora, S. densiflora x foliosa hybrids, and S. anglica), the majority occurring in the Corte Madera Creek Watershed. Creekside Park (04g) on upper Corte Madera Creek is the original introduction site for both S. densiflora and S. anglica to the Estuary. Spartina anglica has been contained to this original site, while S. densiflora had already spread to five other regions prior to the ISP initiating treatment there in The ISP thoroughly inventoried 27 of this region s 32 sub-areas on foot when accessible, and supplemented by kayak on jagged shorelines and upstream portions of the watershed. Four sub-areas (Bothin Marsh [23j], Sausalito [23k], Novato [23m], and China Camp [23o]) were not fully surveyed because they are comparatively time consuming to survey, and they are under low invasion pressure. Local areas around historic infestations at these sites were thoroughly surveyed. No non-native Spartina was found at Novato and China Camp. This was the first year of zero detect for Novato, and there has been no non-native Spartina detected in China Camp since A combined total area of 3.5 m² persisted in Bothin Marsh and Sausalito, all within the footprint of recent infestations. The fifth sub-area that was not thoroughly inventoried this year was San Rafael Canal Mouth-West (23d.2), where a miscommunication regarding site boundaries resulted in only the creek mouth being inventoried. The upper and central reaches of this creek will be surveyed extensively in The ISP inventoried a total of 145 m² (0.036 acre) of non-native cordgrass of four species in the Marin Region in This reflects a 74 m² (33%) decline from 2013 inventory and a reduction of 6.07 acres (>99%) since peak infestation in 2005 (Figures 8 & 9, Table 3). A total of 98 m 2 (0.024 acre) of hybrid S. alterniflora was inventoried, distributed throughout 19 subareas of the region. Thirteen sub-areas had no hybrid S. alterniflora in Marin marshes have never been heavily infested by hybrid S. alterniflora, but eradication efforts here are complicated by the landscape of intricate, privately owned shorelines, which also support abundant S. foliosa. The ISP and the Friends of Corte Madera Creek Watershed have adapted inventory methods to address these areas, including shifting from kayak surveys conducted from the creek, to ground surveys, which enable more thorough detection but which require contacting each landowner to survey along long stretches of private properties. The Marin infestation of Spartina densiflora remains the largest in the Estuary, and occurred in 24 of 32 sub-areas. ISP inventoried a total of 24 m² cover, which accounts for 99% of the 2014 bay-wide total, and reflects a 47% decrease from 2013 inventory. The greatest decline occurred in College of Marin Ecological Study Area (04b), where in m² of mature S. densiflora plants were discovered hidden in dense brackish vegetation and removed, leaving only 0.09 m² to be mapped and dug there in While the amount of S. densiflora continued to decline at most sub-areas, ten sub-areas had increases, although only two of those had expansions greater than 1 m². Every instance of S. densiflora found in 2014 was subsequently treated either with herbicide application, by manual digging, or both. Invasive Spartina Project Monitoring and Treatment Report

21 Figure 8. Distribution of invasive Spartina in 2014 across the 32 sub-areas of Reporting Region 1: Marin. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

22 Figure 9. Distribution of invasive Spartina in 2014 within the Corte Madera Creek Watershed of ISP's Marin Region. To best manage S. densiflora, the ISP conducts two rounds of inventory and removal each year, one in May/June and the other in January. Two surveys allows for the greatest possible detection of the target plants; in May and June, the S. densiflora will often have a flower stalk sticking up above the surrounding vegetation, and in January, the dark green S. densiflora visually stands out from the pickleweed, which is either red or fully senescent. There are no large, mature S. densiflora plants remaining in the Estuary, so the ISP focus is to exhaust the seed bank, which is viable for approximately 3-5 years. For the second consecutive year in 2014, hybrid Spartina densiflora foliosa was found only in the Marin Region, after having been removed from San Francisco Peninsula (Region 2) in The area of hybrid S. densiflora mapped totaled 17.1 m², an increase of 6% over Over 90% of the increase of hybrid S. densiflora was in recently proliferating patches in Upper Corte Madera Creek (above Bon Air Rd) (04h), and all instances of the plants were treated. Hybrid S. densiflora has a sprawling, rhizomatous growth pattern that makes it laborious to dig, and in prior years, it was predominantly been treated with herbicide, with good success. However, in 2014, the ISP shifted to a more aggressive approach, digging out greater than 75% of the plants. The remaining plants were treated with herbicide early in the season and revisited late summer to verify mortality. A final species, Spartina anglica, has only ever been found in the Marin Region, and only at one subarea, Creekside Park (04g). Although the population is small, with only 5.6 m 2 mapped in 2014, it has increased by 40% over the past two years. This year extra effort was made to thoroughly identify and Invasive Spartina Project Monitoring and Treatment Report

23 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 3. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 1: Marin. REGION 1: MARIN Split Sub-Area 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species Since Peak Since a: Blackie's Creek (above bridge) 6/4, 8/1, 1/19/15 Dug, Backpack m² 0.1 m² 0.8 m² 2005 >99% 17% 03b: Blackie's Creek Mouth 6/4, 8/1, 1/19/15 Dug, Backpack <0.01 m² 2 m² m² 2 m² 14 m² 2005 >99% 46% 04a: Corte Madera Ecological Reserve 6/10, 10/22, 1/28/15 Dug, Backpack 0 2 m² 0.1 m² 2 m² 17 m² 2005 >99% 30% 04b: College of Marin Ecological Study Area 6/5, 1/16/15 Dug <0.01 m² m² 0.09 m² 1 m² 2004 >99% 99% 04c: Piper Park East 6/2, 1/23/15 Dug 0.11 m² m² 0.3 m² 4 m² 2005 >99% 24% 04d: Piper Park West 6/2, 1/23/15 Dug m² 0.4 m² 2 m² 2005 >99% 540% increase (0.3 m²) 04e: Larkspur Ferry Landing Area 6/5, 10/15, 1/26/15 Dug, Backpack 0 13 m² 0.03 m² 13 m² 23 m² % 1712% increase (13 m²) 04f: Riviera Circle 6/23-6/24, 7/21, 11/3, 2/5/15 Dug, Backpack m² 7 m² 7 m² 53 m² 2005 >99% 50% 6 m² 04g: Creekside Park 6/17, 12/15-12/16 Dug, Backpack 0.9 m² 0.3 m² 8 m² 15 m² 135 m² 2005 >99% 2% 04h: Upper Corte Madera Creek (Above Bon Air Rd) 6/5, 6/17, 7/29, 9/18, 11/3, 1/16/15 Dug, Backpack 16 m² 5 m² 1 m² 21 m² 117 m² 2006 >99% 7% increase (1 m²) 04i: Lower Corte Madera Creek (Bon Air Rd to HWY 101) 6/5 & 16, 7/21 & 29, 11/3, 1/26 & 1/29/15 Dug, Backpack 0.02 m² 15 m² 2 m² 16 m² 125 m² % 45% 04j.1: Corte Madera Creek Mouth - North Bank 6/17, 10/15, 1/30/15 Dug, Backpack 0.26 m² 16 m² 3 m² 19 m² 145 m² 2007 >99% 65% 04j.2: Corte Madera Creek Mouth - South Bank 6/16, 11/24, 1/29/15 Dug, Backpack m² 0.2 m² 0.9 m² 12 m² 2007 >99% 72% 04k: Boardwalk No. 1 (Arkites) 6/16, 1/29/15 Dug m² 0.2 m² 4 m² 2006 >99% 89% 04l: Murphy Creek No invasive Spartina 2013 or % n/a 09: Tiscornia Marsh / Pickleweed Park 6/3, 10/15, 1/21/15 Dug, Backpack 0.17 m² 0.09 m² 1 m² 1 m² 4 m² 2004 >99% 634% increase (1 m²) 23a: Brickyard Cove No invasive Spartina % 100% 23b: Beach Drive 8/1 Backpack 0 5 m² 0 5 m² 82 m² 2006 >99% 10% 23c: Loch Lomond Marina 7/17 Dug m² 0.1 m² 0.4 m² 2004 >99% 86% 23d.1: San Rafael Canal Mouth East 6/4, 1/15/15 Dug, Backpack 0 5 m² 0 5 m² 40 m² % 2% 23d.2: San Rafael Canal Mouth West 10/15 Backpack m² m² 0.01 m² 0.03 m² 2004 >99% 99% 23e: Muzzi and Martas Marsh 6/10, 8/18, 10/22, 10/24, 1/28/15 Dug, Backpack <0.01 m² 29 m² 0.2 m² 30 m² 319 m² % 33% increase (8 m²) 23f: Paradise Cay 7/21, 12/23 Dug m² 0.1 m² 0.4 m² 2004 >99% 52% 23g: Greenwood Cove 7/2 Dug <0.01 m² m² 0.1 m² 1 m² 2006 >99% 68% 23h: Strawberry Point 7/2 Dug m² 0.05 m² 0.09 m² 2 m² 2005 >99% 71% 23i: Strawberry Cove 8/1, 9/5, 12/13 (R2) Backpack m² m² 24 m² 2007 >99% 94% 23j: Bothin Marsh 9/18 Backpack 0 3 m² 0 3 m² 57 m² 2006 >99% 339% increase (3 m²) 23k: Sausalito 9/18 Backpack m² m² 0.1 m² 2004 >99% 92% 23l: Starkweather Park 6/3, 1/21/15 Dug m² 0.03 m² 2 m² 2006 >99% 1207% increase (0.03 m²) 23m: Novato No invasive Spartina % 100% 23n: Triangle Marsh and shoreline 10/24, 2/9/15 Dug, Backpack m² 0.2 m² 2 m² 13 m² % 506% increase (2 m²) 23o: China Camp 3 years with no invasive Spartina ( ) % n/a 6 m² REGION 1 TOTAL 17 m² 98 m² 24 m² 145 m² 0.3 acres 2005 >99% 33% Invasive Spartina Project Monitoring and Treatment Report Net Area Treatment Area All Invasive Spartina Cover Net Area Decline Peak Year

24 treat all instances of the plant. The increase in this population is likely due to the tendency of S. anglica to grow low and virtually undetectable under and within dense bands of S. foliosa that exist at Creekside Park. Even with the second year of increase, however, the remaining S. anglica at Creekside Park is only 0.01% of its 2006 peak of 383 m 2. Four sub-areas in the Marin Region that were previously infested with non-native cordgrass had none in These sub-areas included Brickyard Cove (23a) and Novato (23m) for the first year, Murphy s Creek (04l) for the second year, and China Camp (23o) for the third year, which qualifies it for local eradication status. Ridgway s rail populations in the Marin Region are supported by abundant large intact native marshes of high quality habitat, and are not expected to be impacted by the removal of the remaining 146 m 2 of non-native Spartina in this region. As a result, the ISP has not targeted Region 1 for habitat enhancement with the exception of planting Grindelia stricta for nesting substrate and cover at Creekside Park, where the previously rampant infestation by multiple non-native Spartina species displaced many native marsh plants. Surveys for Ridgway s rails conducted by the ISP and Point Blue Conservation Science have shown slight declines in Marin rail populations over the last four years, the cause of which is unknown. The low remaining invasion pressure in the Marin Region has preserved abundant S. foliosa that the ISP can harvest for propagation and outplanting to regions that do not have native cordgrass propagule sources. To date, the ISP has collected S. foliosa from four Marin County marshes: Strawberry Cove (23i), Coyote Creek (a part of Bothin [23j]), Starkweather Park (23l), and Upper Gallinas Creek (a part of Novato [23m]). These plants have been outplanted into the four Reporting Regions where the ISP has been actively planting S. foliosa: Region 2: San Francisco Peninsula, Region 5: Union City, Region 6: Hayward, and Region 7: San Leandro Bay. Invasive Spartina Project Monitoring and Treatment Report

25 Region 2: San Francisco Peninsula The San Francisco Peninsula Region (Region 2) includes 35 sub-areas, and extends from the Golden Gate Bridge to the San Mateo Bridge. Once very highly infested by hybrid S. alterniflora, successful treatment has returned the sub-areas predominantly to mudflat and riprap-lined shoreline, as they were prior to invasion. The three most prominent marsh habitats in the region are found at the confluence of Colma Creek and San Bruno Creek (site 18) in South San Francisco, the shoreline of the San Francisco Airport (SFO, 19h), and the mouth of Seal Slough (19p) in San Mateo. Only one subarea, comprised of Treasure, Yerba Buena and Angel Islands (12h), was not thoroughly inventoried in 2014, because the predominantly unsuitable habitat along the shorelines provide minimal opportunity for colonization. A small area of prior infestation on Yerba Buena Island was surveyed on foot and no invasive Spartina was found. The remaining 34 sub-areas were surveyed completely on foot and 0.18 acre of non-native cordgrass was mapped. This is 0.1 acre (35%) less than 2013, and amounts to 0.14% of the footprint ( acres) at the peak in 2004 (Table 2). Hybrid S. alterniflora is now scarce or absent in the majority of sub-areas in the San Francisco Peninsula Region, since over 99% of the remaining population now occurs in only six of its 35 sub-areas (Figure 12, Table 4). The remaining 29 sub-areas each have less than 2 m² of net cover, with nine of those sub-areas having no invasive Spartina found in Only two sub-areas, Sanchez Marsh (19k) and Seal Slough Mouth-Central Marsh (19p.1), contained greater than 100 m² net cover, and this accounts for 79% of the region s total inventory. Sanchez Marsh (19k), which had only a modest reduction in hybrid S. alterniflora between 2013 and 2014 (34 m 2, 7.5%), was aggressively treated in 2014 and the infestation is expected to decrease substantially by 2015 inventory. Sanchez Marsh is also the only remaining sub-area in Region 2 containing S. densiflora, and there were six detected instances totaling m 2 mapped and removed by digging in Sanchez Marsh also historically contained hybrid Spartina densiflora foliosa, and 2014 marked the second consecutive year in which it has not been found anywhere in the San Francisco Peninsula Region. Formerly a stronghold for hybrid S. alterniflora, SFO (19h) was thoroughly inventoried and carefully treated in 2013, which resulted in a 58% reduction and a 2014 inventory of 57 m 2 net cover. Similarly, a shift in treatment methods from manual removal to herbicide application at Pier 98/Heron s Head (12b) and Crissy Field (12g) reduced the hybrid infestation to 1.1 m 2 and no detected invasive Spartina, respectively. Figure 10. Hybrid Spartina alterniflora in the foreground growing in a brackish section of upper San Bruno Creek with Typha sp. A stretch of upper San Bruno Creek referred to as Cupid s Row contained several large stands of hybrid S. alterniflora that were first discovered in 2008 (Figure 10). Treatment of this area is complicated by the presence of remnant populations of two special status species, the Threatened California red-legged frog (Rana draytonii, CRLF) and the Endangered San Francisco garter snake (Thamnophis Invasive Spartina Project Monitoring and Treatment Report

26 Figure 11. USFWS-certified California red-legged frog biologist using a stick to check the hybrid Spartina alterniflora stand for amphibian presence ahead of treatment. sirtalis tetrataenia). For several years, a federal injunction on the use of imazapyr around California red-legged frog precluded any treatment of this infestation. The injunction was finally lifted in late 2013, making the use of imazapyr herbicide a possibility. Treating this 33 m 2 population was a priority for the ISP because of the threat it posed to the downstream area, the Colma/San Bruno marshes, where 55 acres of hybrid S. alterniflora existed at peak, but was nearing local eradication in Treating the Cupid s Row area required a separate Biological Opinion evaluation and amendment letter from USFWS Ecological Services. On August 14, 2014, the stands were surveyed and cleared by a Service-approved CRLF biologist, and subsequently treated by a backpack application of imazapyr (Figure 11). In mid-october 2014, ISP conducted a second round of inventory over 18 sub-areas to detect and treat new sprouts and regrowth that may have appeared since the original rounds of inventory and treatment in June, July and August. This resulted in 24 new instances of hybrid S. alterniflora totaling 0.79 m 2, most of which was subsequently treated. One plant was not treated because genetic data that identified the plant as hybrid were not received until after the completion of the treatment season. This plant will be targeted in was a milestone year for the San Francisco Peninsula Region in that the following seven subareas achieved zero detect status for the first time: India Basin (12c), Crissy Field (12g), Yerba Buena Island (12h), Mission Creek (12i), Old Shipyard (18c), Inner Harbor (18d), and Anza Lagoon (19r). Hunters Point Naval Reserve (12d) also had its second year of zero detect, and Fisherman's Park (19m) achieved local eradication status with no invasive Spartina found for three years. The major reduction in hybrid S. alterniflora in this region has also resulted in reduced numbers of California Ridgway s rails, which have little native habitat available in the San Francisco Peninsula Region. Rail numbers were high when hybrid S. alterniflora was at its peak and provided a large amount of non-native habitat at the Colma Creek/San Bruno complex. With the removal of invasive hybrid monocultures from this area, the mudflats have now restored to near their original extent, and the region is once again limited in the amount of tidal area that is at suitable elevation for native tidal marsh vegetation to establish. There is little opportunity to enhance habitat that could support California Ridgway s rail in this region, and the ISP s restoration efforts here have been limited and experimental. A pilot project to reintroduce S. foliosa along Colma Creek (18a) and in San Bruno Marsh (18g) was begun by Whitney Thornton (San Francisco State University s Romberg Tiburon Center) in 2011 and continued through 2014, and is beginning to show some potential for creating habitat, but its utility for rails is not yet apparent. Invasive Spartina Project Monitoring and Treatment Report

27 Figure 12. Distribution of invasive Spartina in 2013 across the 35 sub-areas of Reporting Region 2: San Francisco Peninsula. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

28 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 4. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 2: San Francisco Peninsula. Split Sub-Area REGION 2: SAN FRANCISCO PENINSULA 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species All Invasive Spartina Cover Net Area Decline Since Peak Since a: Pier 94 8/18 Backpack m² m² 0.3 m² 2005 >99% 85% increase (0.01 m²) 12b: Pier 98 / Heron's Head 10/1 Backpack 0 1 m² 0 1 m² 10 m² 2008 >99% 97% 12c: India Basin No invasive Spartina % 100% 12d: Hunters Point Naval Reserve No invasive Spartina 2013 or % n/a 12e: Yosemite Channel 10/1 Backpack 0 2 m² 0 2 m² 9 m² 2004 >99% 12% 12f: Candlestick Cove 7/16 Backpack 0 0 m² 0 0 m² m² 2006 >99% 100% 12g: Crissy Field No invasive Spartina % 100% 12h: Yerba Buena Island No invasive Spartina % 100% 12i: Mission Creek No invasive Spartina % 100% 18a: Colma Creek 7/16 Backpack m² m² 0.2 m² 2005 >99% 100% 18b: Navigable Slough 7/16 Backpack m² m² 0.8 m² 2006 >99% 99% 18c: Old Shipyard No invasive Spartina % 100% 18d: Inner Harbor No invasive Spartina % 100% 18e: Sam Trans Peninsula 7/16, 9/17, 11/26 (R2) Backpack, Airboat m² m² 6 m² 2004 >99% 20% increase (0.1 m²) 18f: Confluence Marsh 11/26 (R2) Backpack 0 0 m² 0 0 m² m² 2004 >99% 100% 18g: San Bruno Marsh 7/16, 9/17, 11/26 (R2) Backpack, Airboat m² m² 9 m² 2004 >99% 96% 18h: San Bruno Creek 7/16, 8/26, 9/17, 11/26 (R2) Backpack 0 35 m² 0 35 m² 117 m² 2006 >99% 51% 19a: Brisbane Lagoon 7/16, 11/26 (R2) Backpack m² m² 0.4 m² 2006 >99% 95% 19b: Sierra Point 7/16 Backpack m² m² 2 m² 2004 >99% 95% 19c: Oyster Cove 7/16 Backpack m² m² 0.2 m² 2006 >99% 100% 19d: Oyster Point Marina 11/26 (R2) Backpack 0 0 m² 0 0 m² 0.03 m² 2006 >99% 100% 19e: Oyster Point Park 11/26 (R2) Backpack m² m² 0.1 m² 2005 >99% 100% 19f: Point San Bruno 7/16 Backpack m² m² 0.1 m² 2005 >99% 100% 19g: Seaplane Harbor 10/29 Backpack m² m² 0.9 m² 2004 >99% 67% 19h: SFO 10/29 Backpack, Airboat 0 57 m² 0 57 m² 864 m² 2004 >99% 60% 19i: Mills Creek Mouth 7/16, 9/17 Backpack, Airboat 0 1 m² 0 1 m² 13 m² 2005 >99% 23% 19j: Easton Creek Mouth 7/16, 9/17 Backpack, Airboat m² m² 10 m² 2004 >99% 38% 19k: Sanchez Marsh 6/2, 9/29, 1/22/15 Dug, Backpack, Airboat m² m² 420 m² 0.6 ac % 9% 19l: Burlingame Lagoon 6/2, 10/8 Dug, Backpack 0 13 m² 0 13 m² 57 m² 2004 >99% 36% increase (3 m²) 19m: Fisherman's Park 3 years with no invasive Spartina ( ) % n/a 19n: Coyote Point Marina / Marsh 7/16, 11/4 (R2) Backpack m² m² 1 m² 2004 >99% 90% 19o: San Mateo Creek / Ryder Park 11/4 (R2) Backpack m² m² 2 m² 2006 >99% 75% 19p.1: Seal Slough Mouth - Central Marsh 10/30 Backpack, Airboat m² m² 793 m² 2004 >99% 24% 19p.2: Seal Slough Mouth - Peripheral Marshes 7/17, 10/30 Backpack, Airboat 0 44 m² 0 44 m² 446 m² 2004 >99% 72% 19r: Anza Lagoon No invasive Spartina % 100% Net Area Treatment Area Peak Year REGION 2 TOTAL m² m² 747 m² 1.1 acres 2004 >99% 35% Invasive Spartina Project Monitoring and Treatment Report

29 Region 3: San Mateo The San Mateo Region (Region 3) consists of 26 sub-areas that line the western South Bay shoreline between the San Mateo and Dumbarton Bridges. Control of hybrid S. alterniflora in this region is essential to protect some large historic tracts of native marsh (Greco Island [02f, 02h]), extensive tracts of restored marsh (Bair Island [02c, 02d, 02k, 02m, 02o]), and remaining large commercial salt ponds that are slated for restoration to tidal activity. This region was heavily impacted by hybrid S. alterniflora invasion, which colonized the shoreline and marshes, and quickly invaded newly-breached areas undergoing restoration to tidal marsh. Two sub-areas in this region were not thoroughly inventoried in 2014: Central Bair (02o) and B2 North Quadrant East (02c.1b). Central Bair was breached in early 2013 and its interior was visually assessed in 2014 as not yet suitable for invasive Spartina colonization, and so only a portion of its perimeter was surveyed. B2 North Quadrant East, though substantially invaded, is not authorized for full treatment, and inventory there was delayed until after treatment season was completed. By the time inventory was conducted at B2 North Quadrant East, plants on one third of the site were too senescent to be accurately identified during inventory. In this area, therefore, 2013 inventory data has been referenced as an underestimate of 2014 inventory, with the expectation that in the absence of full treatment, no decrease in infestation would occur. The remaining 24 sub-areas were extensively surveyed on foot or by various boats (kayak, Whaler, or Achilles inflatable boat). A total of 4.7 net acres of hybrid S. alterniflora was mapped in the San Mateo Region, which reflects a 51% reduction since 2013 (Figure 13, Table 5). Aggressive treatment in this region yielded by far the largest reduction in invasive Spartina cover in the Bay between 2013 and 2014 a five-acre reduction compared to less than one half acre in all other regions. This strong effect was largely due to a few factors: 1. The San Mateo Region had (and still has) the third largest infestation in the estuary and has full treatment authorization at all but one sub-area. 2. The other two regions with larger infestations (Region 6: Hayward, and Region 7: San Leandro Bay) have treatment restrictions placed on the sub-areas with the most hybrid Spartina, and 3. Within the San Mateo Region, thorough inventory and treatment facilitated by multiple airboats is quickly bringing this region s infestation under control and closer to eradication. Over half (62%) of the remaining infestation in Region 3 is located in two sub-areas of Bair Island: B2 North Quadrant East (02c.1b) and B2 North Quadrant South (02c.2). As mentioned above, the infestation at B2 North Quadrant East will persist until full treatment is re-authorized. Full treatment is permitted at B2 North Quadrant South, and its infestation was reduced by 0.83 acres since 2013 inventory. However, in comparison with other sub-areas receiving full treatment, the infestation at B2 North South Quadrant remains the largest in the Estuary, and is one of only two populations with greater than one net acre of cover. Two other sub-areas in Region 3, Ravenswood Slough and Mouth (02i) and Upper Belmont Slough and Redwood Shores (02a.2), experienced the two largest reductions in hybrid S. alterniflora in the Estuary with a combined decrease of 2.7 acres. The reduction in the infestation level of Ravenswood Slough over the past two years has been dramatic, and an encouraging demonstration of what can be accomplished with the proper tools and timing. Herbicide application methods used at this sub-area have shifted over the years from aerial application by helicopter for the initial infestation, followed by ground-based Argo amphibious Invasive Spartina Project Monitoring and Treatment Report

30 Figure 13. Distribution of invasive Spartina in 2014 across the 26 sub-areas of Reporting Region 3: San Mateo. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

31 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 5. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 3: San Mateo. Split Sub-Area REGION 3: SAN MATEO 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species Net Area Treatment Area All Invasive Spartina Cover Net Area Decline Peak Year Since Peak Since a.1a: Belmont Slough Mouth 8/29, 9/2, 9/4, 9/15 Truck, Backpack, Airboat m² m² 0.3 ac % 80% 02a.1b: Belmont Slough Mouth South 8/29, 9/2, 9/4, 9/15 Truck, Backpack, Airboat 0 92 m² 0 92 m² 0.3 ac 2004 >99% 73% 02a.2: Upper Belmont Slough and Redwood Shores 8/29 Backpack, Airboat m² m² 1.5 ac % 83% 02a.3: Bird Island 9/15-9/16 Backpack, Airboat 0 85 m² 0 85 m² 743 m² % 52% 02a.4: Redwood Shores Mitigation Bank 7/31 Backpack 0 4 m² 0 4 m² 32 m² % 37% 02b.1: Corkscrew Slough 8/29, 10/2, 10/14, 11/13, 12/1 Backpack, Airboat m² m² 0.9 ac % 20% increase (108 m²) 02b.2: Steinberger Slough South, Redwood Creek Northwest 8/1, 8/29, 12/1 Backpack, Airboat m² m² 1 ac % 42% 02c.1a: B2 North Quadrant West 8/13, 8/29, 9/16, 11/17 Backpack, Airboat m² m² 1.7 ac % 80% 02c.1b: B2 North Quadrant East 8/27 Aerial: Broadcast ac ac 11.5 ac % 7% 02c.2: B2 North Quadrant South 10/15-10/16, 10/29, 11/14, 11/17 Backpack, Airboat ac ac 6.3 ac % 42% 02d.1a: B2 South Quadrant West 8/14 Backpack, Airboat m² m² 0.6 ac 2004 >99% 67% 02d.1b: B2 South Quadrant East 8/14 Backpack, Airboat 0 5 m² 0 5 m² 132 m² 2004 >99% 54% 02d.2: B2 South Quadrant (2) 8/14 Backpack, Airboat m² m² 883 m² % 26% increase (29 m²) 02d.3: B2 South Quadrant (3) 10/2 Backpack 0 3 m² 0 3 m² 48 m² 2009 >99% 98% 02e: West Point Slough NW 10/14, 11/14 Airboat 0 50 m² 0 50 m² 163 m² % 68% 02f: Greco Island North 9/30,10/1, 10/14, 11/14 Backpack, Airboat m² m² 1.5 ac % 34% 02g: West Point Slough SW and East 9/30, 10/1, 10/14, 11/4 Backpack 0 83 m² 0 90 m² 696 m² 2005 >99% 24% increase (17 m²) 02h: Greco Island South 9/30-10/1, 11/14 Backpack, Airboat m² m² 0.7 ac 2005 >99% 30% increase (72 m²) 02i: Ravenswood Slough and Mouth 8/13, 9/22 Truck, Backpack, Airboat m² m² 0.6 ac 2004 >99% 94% 02j.1: Ravenswood Open Space Preserve (N of Hwy 92) 7/16, 9/22 Backpack, Airboat 0 14 m² 0 14 m² 120 m² % 96% 02k: Redwood Creek and Deepwater Slough 7/16, 10/2, 11/14, 12/1 Backpack, Airboat m² m² 0.7 ac % 45% 02l: Inner Bair 7/31 Backpack 0 5 m² 0 5 m² 62 m² 2006 >99% 79% 02m: Pond B3 8/20, 10/3, 10/17 Airboat ac ac 2.7 ac 2014 n/a 184% increase (984 m²) 02o: Central Bair 11/14 Backpack m² m² 0.09 m² 2014 n/a n/a 19q: Foster City No invasive Spartina % 100% 19s: Maple Street Channel No invasive Spartina % 100% REGION 3 TOTAL acres acres 31 acres % 51% Invasive Spartina Project Monitoring and Treatment Report

32 tracked vehicles and backpack application, which worked well for parts of the remaining population, but proved insufficient for accessing and treating the remaining large mudflat clones at the slough mouth. Although the San Mateo County Mosquito and Vector Control District (SMCMVCD) purchased an airboat in 2010 that was expected to provide access to the mudflat clones, due to various equipment, permitting, and planning difficulties (including suspension of treatment authorization in 2011), the bulk of the Ravenswood Slough infestation went untreated in 2011 and In 2013, airboats were used very effectively for treatment on the mudflats, resulting in a substantial reduction of 1.7 acres in the hybrid Spartina. This reduction in 2013 enabled the use of trucks with 600-foot hoses to be incorporated into the treatment strategy in 2014, greatly reducing cost and freeing up the SMCMVCD airboat for other treatment sites where it was required. Having flexibility to adapt and evolve treatment methods over time has been key to effective treatment at this site. Two sub-areas in this region experienced their first year of zero detect in 2014: Foster City (19q) and Maple Street Channel (19s). The 2014 inventory also marked the first season in which no Spartina densiflora was found with the San Mateo Region. This species has been removed from all three subareas in which it has been found (West Point Slough NW [02e], Redwood Creek [02k], and Maple Street Channel [19s]), though the potential for a three to five year seed bank requires continued targeted surveys. Annual surveys for Ridgway s rails by the ISP have shown that, despite the steadily decreasing infestation, rail populations in the region have been steadily increasing over the last four years. Rails currently occupy the heavily infested B2 North Quadrant sub-areas (02c1.a-c) in low density, and those sub-areas with the highest densities of rails, Greco Island South (02h) and Deepwater Slough (02k) have minimal remaining infestations. These combined factors should minimize potential detrimental impacts to rails from continued hybrid S. alterniflora treatment. The presence of abundant S. foliosa and persisting hybrid S. alterniflora in this region leave the ISP Restoration Program little need, and few opportunities, to plant native cordgrass. However, high tide refuge islands, intended to provide rails with extra cover during extreme tide events, have now been installed in eight Region 3 sub-areas: two along Belmont Slough (02a.1-2), one on Bird Island (02a.3), four in Corkscrew Slough (02b.1), four within B2 North Quadrant (02c.1), and four in Deepwater Slough (02k). Additionally, the ISP has installed approximately 15,000 Grindelia stricta plants to provide rails with increased cover from predators, and potential substrate for nesting. Until the infestation of hybrid S. alterniflora in this region can be reduced to a minimal level, the ISP cannot safely install S. foliosa where it was extirpated by the hybrid swarm and subsequent treatment, and will continue to explore other options for enhancing habitat for the San Mateo Ridgway s rail population. Invasive Spartina Project Monitoring and Treatment Report

33 Region 4: Dumbarton South The Dumbarton South Region (Region 4) includes 25 sub-areas and is comprised of all tidal wetlands south of the Dumbarton Bridge. This includes freshly breached restoration sites, salt evaporator ponds that are slated for restoration to tidal marsh, large expanses of marsh protected and managed by the USFWS as part of San Francisco Bay Don Edwards National Wildlife Refuge (DENWR), and the marsh fringes that provide connectivity between them. Much of this region is a focal area for restoration by the South Bay Salt Pond Restoration Project (SBSP), and control of invasive Spartina here is key to the SBSP achieving its long term goals. All but one of the region s 25 sub-areas were thoroughly inventoried on the ground, either on foot, by kayak, or by airboat. A portion of Coyote Creek to Artesian Slough (15a.5) was not surveyed the less saline upper reaches, where there is no history of invasion and the threat of new infestation is minor. Pond A17 (15a.7), which was restored to tidal action in 2013, was surveyed on foot for the first time and was confirmed to have Spartina foliosa (and no detectable hybrid) establishing. The hybrid S. alterniflora infestation in the Dumbarton South Region amounts to 9% of the Estuary total, placing this region as the fourth most infested, behind San Leandro Bay, Hayward, and San Mateo Regions. Hybrid S. alterniflora is the only species of non-native cordgrass that has been found in Region 4, and in 2014 ISP mapped a total of 2.6 net acres, an increase of acres from 2013 (Figure 15, Table 6). This 3% increase is due in part to Cooley Landing West (16.2), which is one of the only two sub-areas (B2 North Quadrant South being the other) in the Estuary with both an infestation greater than one acre and authorization for full treatment. Between 2013 and 2014, this marsh experienced a 0.4-acre increase in hybrid S. alterniflora, which was the largest Estuary-wide increase observed in a sub-area undergoing full treatment. This expansion was quickly identified during inventory and then followed by a full four days of aggressive treatment by airboat, truck and backpack in order to regain control over the site. The ground-based work incorporated 600-foot hoses from two trucks to allow for efficient treatment of extensive stands located far from the levee where backpacking would be prohibitive (Figure 14). This is by far the most thorough treatment Figure 14. Two applicators navigating the challenging mudflat terrain of Cooley Landing to haul hose out to some outlier clones of hybrid Spartina alterniflora. Invasive Spartina Project Monitoring and Treatment Report

34 this challenging site has received. Other large infestations also remain in two neighboring marshes along Coyote Creek, Calaveras Marsh (05a.2) and Alviso Slough (15a.4) each with 0.4 acres. Smaller but noteworthy hybrid S. alterniflora expansions were documented in two sub-areas: Coyote Creek to Artesian Slough (15a.5) and Knapp Tract (15a.6). The increase at Coyote Creek is due almost entirely to three large clones (combined 175 m² net area) developing in an expansive S. foliosa meadow along the sub-area s western border with Alviso Slough. Identity was confirmed via genetic testing and more extensive genetic sampling will be conducted in this area in 2015 to discern the extent of nascent infestation that might be present. The expansion at Knapp Tract (aka Pond A6) was not as big, but it was surprising in its suddenness. The site was restored to tidal action in 2010, and between the 2013 and 2014 growing seasons, both S. foliosa and hybrid S. alterniflora rapidly established on its mudflat interior. Although invasive Spartina totaled only net 18 m² in 2014, this was an expansion from just a few stems in 2013, and amounted to an increase of more than 160,000% in one year; by far the greatest increase ever measured by the ISP. In order to inventory the full extent of this site that is predominantly soft and unconsolidated mud, an airboat was used for the first time. Knapp Tract will be discussed in more detail in Section 3.1 of this report. Coyote Creek-Alameda County (05f) maintains its status of local eradication as no invasive Spartina has been found here in four years. In 2014, ISP experienced an additional setback at five sub-areas in the Dumbarton South Region that precluded thorough treatment of the infestations there [Mowry Marsh & Slough (05a.1), Calaveras Marsh (05a.2), Dumbarton Marsh (05b), Palo Alto Baylands (8) and Alviso Slough & Ogilvie Island (15a.4)]. Much of the remaining hybrid Spartina growing amongst the native cordgrass on the fringe of these five sub-areas was senesced by the time ISP surveyed them ahead of the August 12 entry date specified for treatment in the Biological Opinion. In the case of Dumbarton and Mowry Marshes, where the infestation is largely under control, this meant that a significant portion of the known infestation within the sub-area went untreated for another year, and may have produced viable seed that may take several seasons to mature before it can be detected and treated. To prevent this from happening again, during discussions for the 2015 Biological Opinion, ISP requested an earlier entry date of July 20 for the fringe marsh portions of these sub-areas. These fringe areas will be approached from the water by airboat so as not to potentially disturb Ridgway s rails at the end of their nesting season by traversing the marsh with a treatment crew. The number of California Ridgway s rails in this region continue to increase, despite the ISP s success in continuing to reduce hybrid S. alterniflora in the marshes that support the majority of this region s rail population. This region includes some of the highest quality Ridgway s rail habitat in the Estuary, and survey results revealed detection increases over the last three years (McBroom 2014). Marshes in this region generally have abundant S. foliosa and Grindelia stricta and are therefore not a high priority for ISP restoration efforts. However, the ISP and partners have constructed high tide refuge islands at Cooley Landing (16.2) and Palo Alto Baylands (08). Invasive Spartina Project Monitoring and Treatment Report

35 Figure 15. Distribution of invasive Spartina in 2014 across the 25 sub-areas of Reporting Region 4: Dumbarton South. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

36 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 6. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 4: Dumbarton South. Split Sub-Area REGION 4: DUMBARTON SOUTH 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species All Invasive Spartina Cover Net Area Decline Since Peak Since j.2: Ravenswood Open Space Preserve (S of Hwy 92) 7/16, 8/7 Backpack 0 13 m² 0 13 m² 140 m² 2006 >99% 7% increase (0.8 m²) 02n: SF2 8/7 Backpack 0 1 m² 0 1 m² 16 m² % 30% 05a.1: Mowry Marsh and Slough 8/28, 9/29, 11/10, 11/12 Backpack, Airboat m² m² 0.4 ac % 56% 05a.2: Calaveras Marsh 9/15-9/16, 10/2 Backpack, Amphibious vehicle, Airboat ac ac 3.4 ac % 17% 05b: Dumbarton/Audubon 9/12, 9/29, 10/29, 11/10, 11/12 Backpack, Airboat m² m² 0.7 ac % 5% increase (25 m²) 05c.1: Newark Slough West 11/12 Backpack, Airboat 0 5 m² 0 5 m² 51 m² 2004 >99% 84% 05c.2: Newark Slough East 9/13 Backpack, Airboat 0 16 m² 0 16 m² 270 m² 2005 >99% 16% 05d: LaRiviere Marsh 9/13 Backpack 0 19 m² 0 19 m² 205 m² 2006 >99% 81% 05e: Mayhew's Landing 9/13 Backpack 0 60 m² 0 60 m² 469 m² 2005 >99% 5% 05f: Coyote Creek - Alameda County 4 years with no invasive Spartina ( ) % n/a 05g: Cargill Pond (W Hotel) 8/7 Backpack 0 45 m² 0 45 m² 152 m² % 553% increase (38 m²) 05h: Plummer Creek Mitigation Marsh 11/5 Backpack 0 15 m² 0 15 m² 103 m² % 26% 05i: Island Ponds 10/2, 10/23 Airboat m² m² 2 m² 2013 >99% 100% 08: Palo Alto Baylands 9/29, 10/3 Truck, Backpack m² m² 1.1 ac % 4% 15a.1: Charleston Slough to Mountainview Slough 9/29-9/30 Truck, Backpack 0 29 m² 0 29 m² 418 m² 2004 >99% 31% 15a.2: Stevens Ck to Guadalupe Sl 9/30 Truck, Backpack 0 31 m² 0 31 m² 188 m² % 4% 15a.3: Guadalupe Slough 9/30-10/1, 11/18 Truck, Backpack m² m² 0.3 ac % 50% increase (49 m²) 15a.4: Alviso Slough 8/28, 9/16, 10/1, 10/23, 11/18 Backpack, Airboat ac ac 2.2 ac % 27% 15a.5: Coyote Creek to Artesian Slough 8/28 Backpack, Airboat m² m² 446 m² % 367% increase (150 m²) 15a.6: Knapp Tract 10/2, 10/16, 10/23, 11/18 Airboat 0 18 m² 0 18 m² 87 m² 2014 n/a 163,255% increase (18 m²) 15a.7: Pond 17 New Subarea - No invasive Spartina n/a n/a 15b: Faber / Laumeister Marsh 10/28, 11/4 Backpack 0 56 m² 0 57 m² 669 m² % 32% 15c: Shoreline Regional Park 10/2 Backpack 0 42 m² 0 42 m² 725 m² % 80% 16.1: Cooley Landing Central 8/14-8/15, 9/3, 9/17 Truck, Backpack, Airboat m² m² 1.6 ac % 2% 16.2: Cooley Landing West 8/14-8/15, 9/17 Truck, Backpack, Airboat 0 1 ac 0 1 ac 7.2 ac % 67% increase (0.4 ac) Net Area Treatment Area Peak Year REGION 4 TOTAL acres acres 17.8 acres % 3% increase (344 m²) Invasive Spartina Project Monitoring and Treatment Report

37 Region 5: Union City The Union City Region (Region 5) includes 21 sub-areas and extends along the East Bay from the San Mateo Bridge to the Dumbarton Bridge. This region includes the original introduction site for S. alterniflora to San Francisco Bay, Pond 3 adjacent to the north bank of the Alameda Flood Control Channel (AFCC; 01f, also known as Ecology Marsh), where it was planted in the early 1970s by the Army Corps of Engineers as part of a restoration effort. These plantings later hybridized with native S. foliosa and eventually resulted in the bay-wide spread of their highly invasive generations of offspring. The 21 sub-areas of Region 5 have experienced the most dramatic turn in invasive Spartina presence witnessed in the estuary. This region once harbored 233 acres of hybrid S. alterniflora, and after extensive survey on foot or by kayak of every site in this region, a total of 0.03 net acre of hybrid (0.013% of the peak amount) was mapped in 2014 (Figure 17, Table 7). Continued declines and small amounts of hybrid S. alterniflora were observed at 17 sub-areas, while minute increases (<1 m²) were observed in another three. The remaining sub-area, Eden Landing-Ponds E8A, E9, and E8X (13m), was restored to tidal action in 2012 and experienced its first detection of invasive Spartina in 2014 when a total of 34 m² (27% of regional total) was mapped (Figure 16). The elevation of this young marsh is appropriate for establishment of both S. foliosa and hybrid S. alterniflora, and establishing plants were genetically tested to verify ancestry. All detected invasive clones were treated with herbicide via airboat in These restorations marshes will be discussed in more detail in Section 3.1 Figure 16. Hybrid Spartina alterniflora established at Eden Landing Pond E9, with two larger clones on the mudflat in the distance of this report. One sub-area within the Eden Landing Ecological Reserve, known as Upstream of 20 Tide Gates (13g), had no invasive Spartina in 2014, marking its initial year of zero detect. The six sub-areas of AFCC (01a-f) contained 17 m² of invasive Spartina at the time of initial inventory and treatment. This is a reduction by 86% from 2013 inventory, and the 2014 level of infestation represents less than 0.01% of the historic 141-acre footprint here at its peak. The secondary round of inventory at AFCC and its neighbor Ideal Marsh North (21a) yielded an additional, previously undetected 171 instances of hybrid S. alterniflora totaling 2.7 m², all of which was sprayed and prevented from proliferating through the winter. ISP s recent incorporation of a second round of inventory and treatment at sites approaching eradication is proving to be an important tool in moving sites towards zero detection more rapidly, and the progress at AFCC in 2014 may provide one of the best examples of the value of this tool. As detailed above, the entire AFCC site complex is very close to eradication. However, the sub-area at the upstream extent of hybrid Spartina habitat (1d) is much more brackish than the rest of the complex, and normally supports tall, dense stands of cattails and bulrush that obstruct detection of scattered hybrid Spartina plants. It is very difficult for biologists to even walk through this section during the summer in ISP s standard inventory window. Round two inventory at this sub-area over the past two years has helped discover several pockets of hybrid Spartina that were quite large relative to the remaining infestation throughout AFCC. In 2014, this upstream sub-area contained 7 m 2 of hybrid Spartina, while the entire rest of the complex had just 10 m 2. These late-season surveys are Invasive Spartina Project Monitoring and Treatment Report

38 Figure 17. Distribution of invasive Spartina in 2014 across the 21 sub-areas of Reporting Region 5: Union City. Subareas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

39 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 7. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 5: Union City Split Sub-Area REGION 5: UNION CITY 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species Since Peak Since a: Channel Mouth 7/18, 12/18 (R2) Backpack 0 2 m² 0 2 m² 10 m² 2004 >99% 7% 01b: Lower Channel 8/15, 12/18 (R2) Backpack 0 5 m² 0 5 m² 42 m² 2004 >99% 92% 01c: Upper Channel 7/18, 12/18 (R2) Backpack 0 2 m² 0 2 m² 29 m² 2004 >99% 89% 01d: Upper Channel - Union City Blvd to I /18, 12/18 (R2) Backpack 0 7 m² 0 7 m² 109 m² 2005 >99% 80% 01e: Strip Marsh No. of Channel Mouth 7/18, 12/18 (R2) Backpack m² m² 3 m² 2004 >99% 77% 01f: Pond 3 - AFCC 8/15, 12/18 (R2) Backpack m² m² 2 m² 2005 >99% 77% 13a: Old Alameda Creek North Bank 9/17 Backpack m² m² 0.5 m² 2005 >99% 81% 13b: Old Alameda Creek Island 9/17 Backpack 0 2 m² 0 2 m² 26 m² 2005 >99% 93% 13c: Old Alameda Creek South Bank 8/12 Backpack 0 0 m² 0 0 m² m² 2005 >99% 100% 13d: Whale's Tail North Fluke 9/17 Backpack 0 4 m² 0 4 m² 18 m² 2005 >99% 7% increase (0.3 m²) 13e: Whale's Tail South Fluke 8/12 Backpack m² m² 4 m² 2005 >99% 84% 13f: Cargill Mitigation Marsh 8/12 Backpack m² m² 4 m² 2004 >99% 96% 13g: Upstream of 20 Tide Gates No invasive Spartina % 100% 13h: Eden Landing - North Creek 8/11 Backpack m² m² 1 m² 2007 >99% 44% increase (0.009 m²) 13i: Eden Landing - Pond 10 8/11 Backpack m² m² 0.3 m² 2008 >99% 97% 13j: Eden Landing - Mt Eden Creek 8/11 Backpack 0 2 m² 0 2 m² 12 m² 2009 >99% 11% 13k: Eden Landing Reserve South - North Creek Marsh 8/11 Backpack 0 5 m² 0 5 m² 29 m² % 10% increase (0.4 m²) 13l: Eden Landing Reserve North - Mt Eden Creek Marsh 8/11 Backpack 0 2 m² 0 2 m² 17 m² % 70% 13m: Eden Landing - Ponds E8A, E9, and E8X 9/17, 12/1 Backpack, Airboat 0 34 m² 0 34 m² 113 m² 2014 n/a n/a 21a: Ideal Marsh North 7/18, 12/18 (R2) Backpack 0 7 m² 0 7 m² 124 m² 2005 >99% 98% 21b: Ideal Marsh South 8/15, 9/2 Backpack, Airboat 0 53 m² 0 53 m² 528 m² 2006 >99% 70% Net Area Treatment Area All Invasive Spartina Cover Net Area Decline Peak Year REGION 5 TOTAL m² m² 0.3 acres 2004 >99% 82%. Invasive Spartina Project Monitoring and Treatment Report

40 conducted after much of this brackish vegetation biomass has senesced, and in 2014 early autumn rain cleared away dead stalks, greatly enhancing the visibility and allowing thorough detection of hybrid Spartina. This enabled treatment of these targets before they could expand further over the winter and before they dispersed hybrid seed to the four-mile stretch of AFCC downstream. Invasive Spartina and its treatment have little to no effect on California Ridgway s rail populations in Region 5, as only 0.01% of the peak infestation remains. Despite this, 2014 rail surveys by ISP and DENWR revealed a slightly declining four-year population trend for the birds (McBroom 2014). Rail habitat in this region could be greatly improved, both to attract Ridgway s rails where they currently do not occur, and to increase numbers in marshes where they are present. This region has many young restoration marshes and large areas that were heavily impacted by the initial hybrid S. alterniflora infestation. Now that invasion pressure is minimal, these marshes provide ample opportunity for S. foliosa [re]introduction to hasten restoration toward becoming mature native marshes. As of the completion of the restoration season, more than 90,000 S. foliosa and 16, 000 Grindelia plantings have been installed across ten sub-areas in the Alameda Flood Control Channel (1a, 1b, 1c, 1f) and Eden Landing Ecological Reserve (13d, 13e, 13f, 13j, 13k, and 13l) complexes. This includes approximately 6,050 S. foliosa stems within Mt. Eden Creek Marsh (13l) for the first time in Established S. foliosa that was planted in the first year, , was measured for size and cover, and a total of 165 m 2 was present in Eden Landing, while AFCC boasted 187 m 2 net cover. This amount of S. foliosa is almost three times the amount of hybrid S. alterniflora inventoried across the entire region, and that is a measurement only of plants installed during the season. Continued plantings in later years have also been establishing well and will be assessed for size and cover in future monitoring seasons (see for Revegetation Program plans and monitoring reports). Invasive Spartina Project Monitoring and Treatment Report

41 Region 6: Hayward The Hayward Region (Region 6) extends from the San Mateo Bridge to Oakland Airport on the east side of the San Francisco Bay. It is heavily urbanized and consists of 27 sub-areas clustered around three relatively young but large restoration marsh complexes, the oldest of which (Cogswell Marsh [20m-o]) was restored in All sites in this region were mapped on foot and a total of 9.1 acres of non-native cordgrass, all hybrid S. alterniflora, were detected, which is 32% of the Estuary total. Treatment was not permitted in six sub-areas of Region 6: Cogswell B (20n), Cogswell C (20o), Citation Marsh North (20d.2), North Marsh (20f), Bunker Marsh (20g), and San Lorenzo Creek Mouth North (20h.1) (See Section 3.2 for further discussion). These sites were inventoried more coarsely in order to concentrate inventory efforts on sites where treatment would be implemented in These six marshes, hold nine acres of hybrid S. alterniflora, which comprises >99% of the Region 6 total invasive cordgrass inventory. There was virtually no change (0.2% decrease) in Region 6 Spartina cover between 2013 and 2014, despite continued reductions in 19 sub-areas (Figure 18, Table 8). Three sub-areas (Oyster Bay Regional Shoreline [20a], Hayward Landing [20k], and Estudillo Creek Channel [20u]) experienced proportionally large increases in hybrid S. alterniflora, though it only amounted to a combined 35 m² increase. These increases are due to the proximity to restricted treatment sites at Robert s Landing and Cogswell Marsh. Sub-areas where treatment has been authorized continuously contained only 262 m² of hybrid cordgrass, and only two of those sub-areas (Oyster Bay Regional Shoreline [20a] and San Leandro Shoreline Outliers [20q]) contained more than 50 m². Many sub-areas in the Hayward Region are approaching zero detection of invasive Spartina, though none are expected to achieve local eradication while prohibition of treatment at neighboring sites promote annual production of invasive Spartina seed. One sub-area in particular, Sulphur Creek (20j), experienced its first year in which no hybrid S. alterniflora was detected, though it is unlikely that this will be maintained considering its location between the Robert s Landing and Cogswell complexes. Round two inventory and treatment will not be conducted in these areas adjacent to restricted treatment sites. Despite an autumn follow-up treatment at Estudillo Creek in 2013, the proliferation of seed from uncontrolled hybrid in Citation Marsh served to negate these efforts, and the subsequent 2014 inventory found both sides of this previously well-controlled channel lined with invasive cordgrass seedlings. In 2014 the ISP surveyed 25 California Ridgway s rail sites in the Hayward Region. Rail detections were roughly the same as those from 2013, though these were well below the level detected in 2012 and prior years. There is little vegetation to provide habitat for rails in these marshes besides invasive cordgrass, and potential impacts of treatment on local rail populations remain high. The large amount of remaining invasive Spartina here precludes the reintroduction of S. foliosa as a habitat enhancement for Ridgway s rails. However, most of the region s marshes could greatly benefit from additional vegetative cover and Grindelia, which has not naturally established due to the young nature of these marshes and likely out-competition by the hybrid infestation. The ISP Restoration Program has to date installed approximately 20,000 Grindelia plants (sometimes paired with Distichlis spicata), across eleven sub-areas in the Cogswell, Oro Loma, and Robert s Landing marsh complexes, and a total of eight high tide refuge islands have been installed in Cogswell B, Cogswell C, and Bunker Marsh. The large infestation of hybrid S. alterniflora precludes the planting of S. foliosa in most subareas, though a total of approximately 10,370 stems were installed across H.A.R.D. Marsh (20s), Triangle Marsh (20w), and on the marsh plain of Cogswell Marsh Quadrant A (20m) for the first time in Invasive Spartina Project Monitoring and Treatment Report

42 Figure 18. Distribution of invasive Spartina in 2014 across the 27 sub-areas of Reporting Region 6: Hayward. Subareas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

43 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 8. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 6: Hayward Split Sub-Area REGION 6: HAYWARD 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species All Invasive Spartina Cover Net Area Decline Since Peak Since a: Oro Loma Marsh - East 9/2-9/3 Backpack, Airboat 0 3 m² 0 3 m² 68 m² 2008 >99% 95% 07b: Oro Loma Marsh - West 9/2-9/3 Backpack, Airboat 0 40 m² 0 40 m² 366 m² 2005 >99% 93% 20a: Oyster Bay Regional Shoreline 7/17, 10/10 (R2) Backpack, Airboat 0 54 m² 0 54 m² 532 m² 2004 >99% 103% increase (27 m²) 20b: Oakland Metropolitan Golf Links 7/17 Backpack 0 32 m² 0 32 m² 422 m² % 92% 20c: Dog Bone Marsh 7/17 Backpack m² m² 7 m² 2006 >99% 95% 20d.1: Citation Marsh South 9/2 Backpack 0 1 m² 0 1 m² 13 m² 2004 >99% 65% 20d.2: Citation Marsh North No Treatment Authorized since ac ac 8.3 ac % 15% increase (0.3 ac) 20e: East Marsh 7/18 Backpack m² m² 3 m² 2004 >99% 92% 20f: North Marsh No Treatment Authorized since ac ac 22.8 ac % 3% 20g: Bunker Marsh No Treatment Authorized since ac ac 7.6 ac % 32% 20h.1: San Lorenzo Creek and Mouth North No Treatment Authorized since m² m² 7 m² 2004 >99% 99% 20h.2: San Lorenzo Creek and Mouth South 7/18 Backpack 0 5 m² 0 5 m² 129 m² 2004 >99% 84% 20i: Bockmann Channel 7/14, 10/16 (R2) Backpack m² m² 0.3 m² 2004 >99% 14% increase (0.01 m²) 20j: Sulphur Creek No invasive Spartina % 100% 20k: Hayward Landing 7/14, 10/16 (R2) Backpack m² m² 2 m² 2004 >99% 6867% increase (0.5 m²) 20l: Johnson's Landing 7/14, 10/16 (R2) Backpack m² m² 2 m² 2005 >99% 56% 20m: Cogswell Marsh, Quadrant A 7/14, 10/16 (R2) Backpack 0 4 m² 0 7 m² 75 m² 2005 >99% 34% 20n: Cogswell Marsh, Quadrant B No Treatment Authorized since ac ac 21.4 ac % 11% increase (0.4 ac) 20o: Cogswell Marsh, Quadrant C No Treatment Authorized since ac ac 1.2 ac % 9% increase (165 m²) 20p: Hayward Shoreline Outliers 7/14, 10/16 (R2) Backpack m² m² 3 m² 2008 >99% 93% 20q: San Leandro Shoreline Outliers 7/18 Backpack 0 56 m² 0 56 m² 732 m² % 27% 20r: Oakland Airport Shoreline and Channels 7/31 Backpack 0 47 m² 0 47 m² 315 m² 2006 >99% 76% 20s: H.A.R.D. Marsh 8/14, 10/16 (R2) Backpack m² m² 6 m² 2006 >99% 85% 20t: San Leandro Marina 7/17 Backpack m² m² 0.1 m² 2009 >99% 91% 20u: Estudillo Creek Channel 7/17 Backpack 0 12 m² 0 12 m² 99 m² % 131% increase (7 m²) 20v: Hayward Landing Canal 8/7, 10/16 (R2) Backpack 0 2 m² 0 2 m² 44 m² 2006 >99% 89% 20w: Triangle Marsh 7/14 Backpack m² m² 0.2 m² 2007 >99% n/a Net Area Treatment Area Peak Year. REGION 6 TOTAL acres acres 61.9 acres % 0.2% Invasive Spartina Project Monitoring and Treatment Report

44 Region 7: San Leandro Bay The San Leandro Bay Region (Region 7) is an exceptionally urbanized portion of the East Bay that extends north from the Oakland Airport to the Bay Bridge. Its 19 sub-areas consist of long thin tidal areas along rip-rap shorelines and open mudflats, punctuated by fragmented areas of extant marsh habitat. All sub-areas of Region 7 (Figure 19, Table 9) were monitored on foot in 2014, with the exceptions of Oakland Inner Harbor (17f), Crab Cove, and some inland channels by Elsie Roemer (both are small portions of 17a), which were surveyed on foot and also by boat. Since 2010, this region has four sub-areas that maintain treatment prohibitions: Arrowhead Marsh-East (17c.2), MLK New Marsh (17h), Fan Marsh (17j), and MLK Regional Shoreline-Damon Marsh (17d.4) (see Section 3.2 for further discussion). Although inventory was not needed to inform treatment, these sites were coarsely mapped in order to prioritize inventory at sites where treatment would be implemented in Hybrid S. alterniflora was the only non-native cordgrass species found in Region 7, with a net cover of 12 acres, an 11% increase since This increase is driven entirely by expansion of untreated Spartina in Arrowhead Marsh East, MLK New Marsh and Damon Marsh where treatment was not authorized. Ninety-eight percent of hybrid S. alterniflora found in Region 7 is located in the four subareas where treatment has not been authorized since This area represents 42% of the total amount of invasive Spartina remaining in the entire Estuary. The San Leandro Bay Region contains no sub-areas where invasive Spartina is absent. Annual inventory and treatment in the San Leandro Bay Region allows ISP to control the proliferation of hybrid S. alterniflora, but will not allow for local eradication. The presence of Arrowhead Marsh East, the single largest infestation in the Estuary, in the center of the region alone makes local eradication impossible while treatment restrictions all but guarantee annual production of invasive Spartina seed. Despite the high invasion pressure throughout much of the region, a secondary round of inventory and treatment was conducted over a single day at two sub-areas that were close to eradication: Alameda Island South (Elsie Roemer Bird Sanctuary, Crown Memorial State Beach, Crab Cove) (17a) and Bay Farm Island (17b). This allows the City of Alameda, the ISP partner on the site, to maintain progress and not allow reinfestation from the restricted treatment sites in San Leandro Bay to establish a new propagules source. A total of 53 new instances totaling 1.2 m² of invasive Spartina were detected and subsequently treated. A similar secondary round of inventory was conducted over most of the region in 2013, though it was not followed up with treatment since it was recognized that a secondary round of treatment would be insufficient to offset the high level of seed dispersal from the contiguous restricted treatment sites. In 2013, a total of 490 new instances of hybrid S. alterniflora totaling 9 m² were mapped during the secondary round of inventory. Left to proliferate untreated over the winter, those same plants were mapped in 2014, but had exploded to 123 m² net cover (>1,000% increase). This highlights the utility of secondary inventory and treatment in areas where the infestation pressure has already been reduced to manageable levels (e.g. in 2014 within Region 2: San Francisco Peninsula and Region 5: Union City). The high level of infestation in San Leandro Bay marshes has supported a local high-density Ridgway s rail population for the past couple decades, and the lack of appropriate native marsh structure in these marshes makes the rails here dependent upon hybrid S. alterniflora. Surveys by ISP staff in 2014 show that the population has been relatively stable since 2011, though at reduced numbers from the levels observed in 2010 and prior years, despite the lack of treatment since Invasive Spartina Project Monitoring and Treatment Report

45 The treatment restrictions at the four key marshes in this region currently leave few opportunities for rail habitat enhancement, due to risk of hybrid S. alterniflora encroaching on and overwhelming new plantings in the absence of control efforts. Plantings of S. foliosa in these areas would likely be pollinated by the hybrids, which would promote production of hybridized seed. As a result, the ISP Restoration Program has exerted limited efforts to enhance habitat in this region. From 2011 to 2014, more than 3,000 Grindelia plantings have been installed at Arrowhead West (17c.1), MLK New Marsh, and Damon Marsh, and 2,950 experimental S. foliosa stems have been installed at Elsie Roemer where hybrid presence has been minimal since Additionally, a total of five high tide refuge islands have been constructed within MLK New Marsh and Arrowhead West to provide protective cover for rails. Due to the continued and growing threat of encroaching hybrid S. alterniflora, no further island construction or plantings are planned within the San Leandro Bay Region. Invasive Spartina Project Monitoring and Treatment Report

46 Figure 19. Distribution of invasive Spartina in 2014 across the 19 sub-areas of Reporting Region 7: San Leandro Bay. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

47 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 9. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 7: San Leandro Bay Split Sub-Area REGION 7: SAN LEANDRO BAY 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species All Invasive Spartina Cover Net Area Decline Since Peak Since a: Alameda Island South (Elsie Roemer Bird Sanctuary, Crown Memorial State Beach, Crab Cove) 7/30, 9/30 (R2) Backpack m² m² 772 m² 2006 >99% 0.3% increase (0.6 m²) 17b: Bay Farm Island 7/30, 9/30 (R2) Backpack 0 2 m² 0 2 m² 32 m² 2005 >99% 18% 17c.1: Arrowhead Marsh West 9/15-9/16, 10/16 Backpack, Airboat m² m² 1.4 ac % 71% 17c.2: Arrowhead Marsh East No Treatment Authorized since ac ac 15.7 ac % 4% increase (0.3 ac) 17d.1: MLK Regional Shoreline - Fan Marsh Shoreline 7/30-7/31 Airboat 0 59 m² 0 59 m² 582 m² 2004 >99% 11% increase (6 m²) 17d.2: Airport Channel - MLK Shoreline 7/30-7/31 Backpack 0 22 m² 0 22 m² 313 m² 2005 >99% 162% increase (14 m²) 17d.3: East Creek - MLK Shoreline 7/30-7/31 Backpack 0 19 m² 0 19 m² 162 m² 2004 >99% 52% 17d.4: MLK Regional Shoreline - Damon Marsh No Treatment Authorized since ac ac 4.6 ac % 48% increase (634 m²) 17d.5: Damon Slough / Elmhurst Creek - MLK Shoreline 7/30-7/31 Backpack 0 9 m² 0 9 m² 83 m² 2005 >99% 75% 17e.1: San Leandro Creek North 7/30-7/31 Backpack 0 2 m² 0 2 m² 18 m² 2005 >99% 951% increase (2 m²) 17e.2: San Leandro Creek South 7/17 Backpack 0 28 m² 0 28 m² 254 m² 2005 >99% 247% increase (20 m²) 17f: Oakland Inner Harbor 8/18 Backpack, Airboat 0 6 m² 0 6 m² 51 m² 2007 >99% 61% 17g: Coast Guard Island 7/31 Backpack m² m² 0.5 m² 2007 >99% 91% 17h: MLK New Marsh No Treatment Authorized since ac ac 18.3 ac % 51% increase (1.2 ac) 17i: Coliseum Channels 7/16-7/17 Backpack 0 28 m² 0 28 m² 393 m² 2005 >99% 1% 17j: Fan Marsh No Treatment Authorized since ac ac 5.5 ac % 22% 17k: Airport Channel 7/30-7/31 Backpack, Airboat m² m² 16 m² 2005 >99% 74% 17l: Doolittle Pond 7/30-7/31 Backpack 0 5 m² 0 5 m² 59 m² 2004 >99% 394% increase (4 m²) 17m: Alameda Island (Aeolian Yacht Club and East Shore) 7/31 Backpack 0 18 m² 0 18 m² 163 m² 2006 >99% 47% Net Area Treatment Area Peak Year REGION 7 TOTAL acres 0 12 acres 46.2 acres % 11% increase (1.2 acres) Invasive Spartina Project Monitoring and Treatment Report

48 Region 8: Bay Bridge North The Bay Bridge North Region (Region 8) is composed of 12 sub-areas including all East Bay shoreline marshes north of the Bay Bridge and southwest of the Carquinez Strait. This region is typified by riprap shorelines and fragmented marshes with little or no room for expansion due to urban development. The exceptions are intact historic Whittell Marsh (10a) and Giant Marsh (10c), and the large and partially-brackish Wildcat Marsh (22a) and San Pablo Marsh (22b). ISP surveyed the 12 sub-areas in Region 8 on foot in 2014, except for the shorelines and ponds adjacent to Wildcat Marsh, which were surveyed by kayak. A total of 0.13 acre of hybrid S. alterniflora was found, which represents 0.5% of the estuary total (Figure 20, Table 10). This marks a minor decrease of 7% from 2013 inventory, which is the result of the greater than 200 m 2 reduction in hybrid S. alterniflora within San Pablo Marsh West (22b.2) being offset by approximately 50 m 2 increases in hybrid at each of four sub-areas: Wildcat Marsh (22a), Emeryville Crescent East and West (06a, 06b), and Breuner Marsh (Rheem Creek, 22c). Rheem Creek and San Pablo Marsh East (22b.1) are the only sub-areas in this region with infestations larger than 100 m 2 (with 115 m 2 and 111 m 2 hybrid S. alterniflora, respectively). One sub-area, Hoffman Marsh (22e) regained its status of zero detect after a single hybrid clone had reappeared in 2013 and was immediately treated. Multiple genetic samples were collected from regrowth in the proximity of that former clone to verify no hybrid S. alterniflora remained in Spartina densiflora has been present in this region since it was first detected here in 2004, having been inventoried and manually removed from four sub-areas: Whittell Marsh (10a), Southern Marsh (10b), Giant Marsh (10c), and Richmond/Albany/Pinole Shoreline (22f). The 2014 inventory season marks the first year that S. densiflora was not detected in any sub-area in the Bay Bridge North Region. However, persistent inventory monitoring is required in order to achieve local eradication of this species considering that it can develop a seed bank that remains viable for an estimated three to five years. Due to the limited potential habitat along stretches of this region s hardscape shoreline and ISP budget constraints, portions of one sub-area, Richmond/Albany Shoreline/Pinole (22f), were not surveyed in 2014 so that ISP efforts could be focused in areas of potentially higher risk and impact (See Figure 1). Shorelines proximal to historic infestations were revisited on foot, but areas that lacked recent detection of infestation were not thoroughly inventoried. Since 2008, treatment has consistently reduced hybrid S. alterniflora cover in this region, while California Ridgway s rail surveys over the same time period indicate a positive five-year trend (Elrod, Wood et al. 2014; McBroom 2014). Ample well-developed native rail habitat exists at the region s two largest marshes, Wildcat Marsh (22a) and San Pablo Marsh (22b), which support the bulk of the region s rail population. There is little need for enhancement at these two marshes, and there is little opportunity for planting at other marshes in the Region; the ISP has not implemented any restoration projects in this region. Invasive Spartina Project Monitoring and Treatment Report

49 Figure 20. Distribution of invasive Spartina in 2014 across the 12 sub-areas of Reporting Region 8: Bay Bridge North. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

50 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 10. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 8: Bay Bridge North. Split Sub-Area REGION 8: BAY BRIDGE NORTH 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species All Invasive Spartina Cover Net Area Decline Since Peak Since a: Emeryville Crescent East 9/30 Backpack 0 70 m² 0 70 m² 648 m² % 163% increase (44 m²) 06b: Emeryville Crescent West 7/18, 10/1 (R2) Backpack 0 49 m² 0 49 m² 253 m² 2004 >99% 1621% increase (46 m²) 10a: Whittel Marsh 11/25 Dug m² m² 5 m² 2005 >99% 4% increase (0.01 m²) 10b: Southern Marsh 9/30 Dug, Backpack m² m² 11 m² 2010 >99% 87% 10c: Giant Marsh 9/30 Backpack 0 2 m² 0 2 m² 47 m² 2010 >99% 83% 22a: Wildcat Marsh 9/4, 11/21 Backpack, Airboat 0 85 m² 0 85 m² 422 m² % 198% increase (57 m²) 22b.1: San Pablo Marsh East 9/2, 9/4 Backpack, Airboat m² m² 779 m² 2009 >99% 5% 22b.2: San Pablo Marsh West 9/2, 9/4 Backpack, Airboat 0 87 m² 0 87 m² 0.4 ac % 71% 22c: Breuner Marsh (Rheem Creek) 9/30 Backpack m² m² 963 m² % 72% increase (48 m²) 22d: Stege Marsh 9/1 Backpack 0 6 m² 0 6 m² 54 m² % 0.2% increase (0.01 m²) 22e: Hoffman Marsh No invasive Spartina % 100% 22f: Richmond / Albany / Pinole Shoreline 9/30, 11/21 Backpack 0 9 m² 0 9 m² 72 m² 2005 >99% 5% increase (0.4 m²) Net Area Treatment Area Peak Year REGION 8 TOTAL m² m² 1.2 acres % 7% Invasive Spartina Project Monitoring and Treatment Report

51 Region 9: Suisun The Suisun Region (Region 9) is bounded on the west by the Carquinez Strait and extends east approximately to Antioch, where the salinity level transitions to freshwater within the San Joaquin-Sacramento Delta. The Suisun Region consists of a single sub-area, Southampton Marsh (11), which was surveyed thoroughly on foot in 2014 for two species of invasive Spartina: hybrid S. alterniflora and S. patens. Southampton Marsh, a part of the Benicia State Recreation Area, is the only location in the Estuary where S. patens has been documented, and it has persisted there since the early 1960s. In 2014, ISP staff mapped a total of 81 m 2 of non-native cordgrass in this marsh, 75.3 m 2 of which was S. patens and 5.5 m 2 of which was hybrid S. alterniflora (Figure 21, Table 11). The long rocky shoreline that lines the Carquinez Strait provides minimal opportunity for Spartina establishment and was not surveyed in 2013 so that resources could be focused on portions of the bay with more invasion pressure. Presence of hybrid S. alterniflora increased since 2013 at this sub-area by a little more than 2 m 2 due to the development of some new clones along the shoreline. Most hybrid S. alterniflora plants were treated with herbicide, although a couple of mapped plants were already senescent by the time treatment occurred and the efficacy of treatment will be assessed during 2015 inventory. Similarly, one new patch amounting to 2.5 m 2 was identified as invasive through genetic testing, but the results had not been received prior to 2014 treatment, and the plant was not treated. In 2014, after a four-year hiatus of treatment on the S. patens infestation, a new plan was finalized and approved by USFWS Ecological Services and an herbicide application was conducted in April. Please see Section 3.5 for a detailed account of the development of the plan that protects three special-status species while moving forward with the eradication of S. patens from California. The Suisun Region, with its extensive brackish and freshwater marshes, has a very low density of California Ridgway s rails, which generally prefer more saline conditions, and the nominal infestation by invasive cordgrass has not seemed to have any impacts on rail populations. Ridgway s rail have not been detected at Southampton Marsh since 2011 despite annual surveys by Avocet Research Associates. As such, no habitat enhancement efforts have been undertaken here by the ISP to date. California Department of Parks & Recreation has been implementing a very successful Lepidium latifolium treatment program at this site that is restoring the channel bank vegetation (e.g. Grindelia stricta) of this brackish marsh. Invasive Spartina Project Monitoring and Treatment Report

52 Figure 21. Distribution of invasive Spartina in 2014 across the single sub-area and adjacent shoreline of Reporting Region 9: Suisun. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green.. Invasive Spartina Project Monitoring and Treatment Report

53 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 11. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 9: Suisun. REGION 9: SUISUN Split Sub-Area 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species Since Peak Since : Southampton Marsh 4/29, 10/1, 1/8/15 Dug, Backpack 75 m² 5 m² 0 81 m² 411 m² % 14% Net Area Treatment Area All Invasive Spartina Cover Net Area Decline Peak Year REGION 9 TOTAL 75 m² 5 m² 0 81 m² 411 m² % 14% Invasive Spartina Project Monitoring and Treatment Report

54 Region 10: Vallejo The Vallejo Region (Region 10) is composed of four sub-areas, and covers the northern portion of San Pablo Bay, bounded by the mouth of the Petaluma River to the west, the City of Vallejo to the east, and extending eight miles inland to the north. Due to the region s large size, several methods were employed to complete inventory at its four sub-areas. Portions of the shoreline at San Pablo Bay NWR and Mare Island (26b) and Sonoma Creek (26c) were surveyed by airboat. The main portion of Sonoma Creek proper was inventoried by kayak. Sonoma Baylands (26d), including Tolay Creek, was thoroughly inventoried by airboat, thanks to a joint effort with staff from California Department of Food and Agriculture. Mare Island was also inventoried on foot for both S. densiflora and hybrid S. alterniflora, using all-terrain vehicles provided by USFWS San Pablo Bay National Wildlife Refuge. The expansive White Slough/Napa River sub-area (26a) is under very low invasion pressure by non-native Spartina, and was therefore not surveyed, except for 128 acres that comprise White Slough Marsh, which was surveyed by kayak. The total amount of non-native Spartina mapped in this region was 44 m 2, 0.03 m 2 of which was six instances of S. densiflora along the Mare Island shoreline that were manually removed and disposed of offsite (Figure 22, Table 12). The remainder of invasive cordgrass in this region was hybrid S. alterniflora: 39 m 2 along the shoreline of Mare Island and 6 m 2 along Sonoma Creek, both of which mark 80% or greater reductions since 2013 inventory and treatment. In 2012, a rapid expansion (889% increase) of hybrid S. alterniflora was detected along the Mare Island shoreline, and after heavy treatment for two years in a row, this infestation seems to be under control. The infestation along Sonoma Creek has centered on two patches, both of which senesce early, which previously resulted in reduced efficacy of treatment. In 2013, these patches were sprayed earlier in the season (August 7), which resulted in an 87% reduction in cover. Based on that success, treatment in 2014 was again scheduled early (July 28), well ahead of early senescence. The significant reductions at Sonoma Creek and Mare Island contribute to the current Region 10 infestation now totaling less than 4% of the 0.32-acre footprint at peak in The infested area on Mare Island is quite remote, making inventory and treatment time consuming. In recent years, the remote location combined with the relatively large size of the infestation and the fact that it is growing in a matrix of S. foliosa, necessitated treatment by airboat that can carry sufficient herbicide. However in 2014, a significant portion of the detected hybrids occurred at a low elevation out on the mudflats, requiring treatment to be conducted at a low tide when the plants are exposed. Unfortunately, the substrate in this area is very sandy and not suitable for an airboat at low tide, so although treatment by airboat was attempted, it had to be abandoned. With the infestation greatly reduced, ISP was instead able to transport the herbicide and personnel to the site using an ATV. This treatment method will be utilized for future applications until local eradication is achieved. The impact of non-native Spartina on Ridgway s rails in the Vallejo Region is minimal at most because rail and non-native Spartina occurrences are geographically disparate. Annual rail surveys by ISP and San Pablo Bay NWR detect relatively low numbers of rail, though detections are increasing as younger restoration marshes mature and develop. No rails have been detected in the portions of Mare Island and along Sonoma Creek where the infestation and treatment have occurred. This region has abundant native cordgrass, which has established very successfully at recent restoration sites like Tolay Creek and Sonoma Baylands (each are portions of 26d), where rail numbers are increasing. No ISP restoration efforts have been directed towards this region due to the observed abundance of native plants in established marshes and their natural recruitment in younger ones. Invasive Spartina Project Monitoring and Treatment Report

55 Figure 22. Distribution of invasive Spartina in 2014 across the four sub-areas of Reporting Region 10: Vallejo. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

56 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 12. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 10: Vallejo. REGION 10: VALLEJO Split Sub-Area 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species All Invasive Spartina Cover Net Area Decline Since Peak Since a: White Slough / Napa River 4 years with no invasive Spartina ( ) % n/a 26b: San Pablo Bay NWR and Mare Island 6/3, 10/18, 2/10/15 Dug, Backpack 0 39 m² 0.03 m² 39 m² 422 m² % 80% 26c: Sonoma Creek 7/28 Backpack 0 6 m² 0 6 m² 90 m² % 88% 26d: Sonoma Baylands 4 years with no invasive Spartina ( ) % n/a Net Area Treatment Area Peak Year REGION 10 TOTAL 0 44 m² 0.03 m² 44 m² 511 m² % 81% The ISP Restoration Program has, however, harvested plants from the plentiful bands of S. foliosa along the Napa River for propagation at The Watershed Nursery. Since initial collections in 2011, the ISP has outplanted native cordgrass from this region in three Reporting Regions: Region 5: Union City, Region 6: Hayward, and Region 7: San Leandro Bay. Invasive Spartina Project Monitoring and Treatment Report

57 Region 11: Petaluma The Petaluma Region (Region 11) is composed of four sub-areas, and includes the wetlands lining the tidal portions of the Petaluma River and its tributaries in Marin and Sonoma Counties, from downtown Petaluma to the river s mouth in northwestern San Pablo Bay. The historic infestation of this region by hybrid S. alterniflora, which peaked in 2007 at 0.15 acre, has been fairly localized to the upper reaches of the Petaluma River and was very possibly brought about by propagules transported here via uncleaned dredge equipment. Each of this region s four sub-areas were inventoried in 2014, though to varying degrees of thoroughness and utilizing different methods. Grey s Field (24b) and all major waterways of Upper Petaluma River-Upstream of Grey s Field (24a) were surveyed via airboat and on foot. The portions of Petaluma Marsh (24c) and Lower Petaluma River-Downstream of San Antonio Creek (24d) that are boat accessible and west of Petaluma River were surveyed by whaler, though the eastern bank and its tributaries were not surveyed in No instance of nonnative Spartina has ever been detected within the un-surveyed portions of 24c and 24d, despite thorough monitoring in previous years. Inventory of this region yielded 64 m 2 of hybrid S. alterniflora and no other non-native cordgrass species (Figure 23, Table 13). This represents a 61% increase over 2013, more than 99% of which was within 24a (Upper Petaluma River-Upstream of Grey's Field). After an expansion of the infestation in this site during the 2012 season, late treatment in November that year resulted in greatly reduced efficacy, and much of the infestation remained in Treatment in 2013 was then bumped up to early October in an attempt to improve efficacy, but the treatment still was not effective, as the 2014 inventory showed expansion of plants mapped and sprayed in Possible causes of the low efficacy include again spraying too late in the season, or making an error in preparing the herbicide mix (e.g. insufficient herbicide concentration, or lack of surfactant), which might have resulted in the plants not absorbing and translocating enough herbicide to achieve mortality. In 2014, treatment was conducted even earlier, in September, and extra attention was paid to mixing and applying the herbicide. The expanded infestation in the Petaluma Region has insignificant impact on the local rail population; the persisting hybrid S. alterniflora exists along the narrow shoreline of Petaluma River, while the rail population is supported in the marsh interior where hybrid cordgrass has never been detected. The region s high quality rail habitat was largely surveyed by Point Blue Conservation Science, who reported a continued decline in this region s California Ridgway s rail population (Elrod, Wood et al. 2014). The cause of continued decline is unknown, but invasive Spartina and its treatment are not indicated as factors. Since the occurrence and control of hybrid Spartina has been very limited in this region, and there is both abundant S. foliosa and Grindelia, no ISP restoration projects have been implemented here. No infestation has been ever been found in the southern reaches of Petaluma River, and ISP s Restoration Program has collected S. foliosa from Sonoma Marina since Native cordgrass from this region has then been outplanted into the four Reporting Regions where the ISP has been actively planting S. foliosa: Region 2: San Francisco Peninsula, Region 5: Union City, Region 6: Hayward, and Region 7: San Leandro Bay. Invasive Spartina Project ISP Monitoring and Treatment Report

58 Figure 23. Distribution of invasive Spartina in 2014 across the four sub-areas of Reporting Region 11: Petaluma. Subareas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project ISP Monitoring and Treatment Report

59 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 13. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 11: Petaluma. Split Sub-Area REGION 11: PETALUMA 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species Since Peak Since a: Upper Petaluma River - Upstream of Grey's Field 9/11 Backpack, Airboat 0 64 m² 0 64 m² 381 m² % 71% increase (27 m²) 24b: Grey's Field 4 years with no invasive Spartina ( ) % n/a 24c: Petaluma Marsh 9/11 Backpack, Airboat m² m² 0.02 m² 2010 >99% 100% 24d: Lower Petaluma River - Downstream of San Antonio Creek No invasive Spartina ever detected n/a n/a Net Area Treatment Area All Invasive Spartina Cover Net Area Decline Peak Year REGION 11 TOTAL 0 64 m² 0 64 m² 381 m² % 61% increase (24 m²) Invasive Spartina Project Monitoring and Treatment Report

60 Region 12: Outer Coast The Outer Coast Region (Region 12) includes the geographically-isolated watersheds on the western border of Marin County. This region is composed of remote coastal estuaries and bays, several of which have been colonized by a couple of instances of hybrid S. alterniflora. In 2014, each of the five sub-areas in this region were thoroughly inventoried on foot or by boat (kayak, Whaler, or Achilles), except for Estero de Limantour (25b), which was surveyed on foot near the historic infestation zone only. Invasive Spartina currently exists in the Outer Coaster Region in two instances: Spartina densiflora in two small marshes of Tom s Point/Tomales Bay (25a) and hybrid S. alterniflora in Bolinas Lagoon, North (25d) (Figure 24, Table 14). Presence of S. densiflora persists at both Tom s Point and Hog Island Oyster Company, both of which only contained seedlings. Through two rounds of inventory, ISP staff mapped and dug 10 instances totaling 0.1 m² net cover of S. densiflora at Tom s Point and 4 instances (0.02 m²) at Hog Island Oyster Company. No mature plants remained, and ISP conducts two rounds of surveys there each year to ensure that all detections are removed before they can set seed. With virtually no re-invasion potential, it is simply a matter of time until the S. densiflora seed bank is exhausted and local eradication achieved. Two large hybrid Spartina clones were discovered in 2011 out on the unconsolidated mudflat of Bolinas Lagoon North, where tarping would not be an effective treatment method. This infestation of hybrid S. alterniflora expanded as expected between 2013 and 2014, because treatment by herbicide had not yet been authorized at this site. Until 2014, these clones had been treated by mowing the above ground biomass in order to preclude seed dispersal, but this also triggered increased vegetative growth in the plants (358% increase since 2013), allowing them to coalesce into a single giant stand. During this time, two other instances of hybrid Spartina sprung up near these mudflat clones, bringing the sub-area infestation to 72 m 2. After a multi-year process of CEQA review, public meetings in the community with presentations by ISP, and permitting by the Gulf of the Farallones National Marine Sanctuary and others, Marin County Parks and Open Space finally conducted the first imazapyr applications to hybrid Spartina at the site with assistance from ISP. The final permit process took longer than anticipated, which delayed treatment until well into autumn (October 21) and resulted in a significant portion of the infestation being senesced at treatment. ISP will assist Marin County in 2015 to make sure treatment is optimized to eliminate this threat to a very sensitive lagoon and the California coast. All other occurrences of hybrid S. alterniflora have been removed from the region, with no invasive Spartina being found in Drakes Estero (25c) for two years, or in Limantour Estero (25b) and Bolinas Lagoon, South (25e) for three years (achieving local eradication status). Cordgrass growing near the historic infestation in Limantour was genetically sampled, and determined to indeed be an expanding population of native S. foliosa. The few occurrences of hybrid S. alterniflora in the region have had no impact on Ridgway s rails, as their observed geographic range is limited to the tidal marshes of the San Francisco Estuary, with the exception of occasional fall and winter observations along the Outer Coast. As an example, ISP staff detected a rail in Tomales Bay during an October 2012 Spartina survey, but there has been no evidence of any breeding population. As such, no annual Ridgway s rail surveys have been conducted in the Outer Coast Region. No ISP restoration projects have been implemented here to date. Invasive Spartina Project Monitoring and Treatment Report

61 Figure 24. Distribution of invasive Spartina in 2014 across the five sub-areas of Reporting Region 12: Outer Coast. Sub-areas with current infestation are labeled in pink, while those with no detection of invasive Spartina are labeled in green. Invasive Spartina Project Monitoring and Treatment Report

62 anglica patens densiflora x foliosa alterniflora x foliosa densiflora Table 14. Summary of 2014 invasive Spartina area by sub-area within Reporting Region 12: Outer Coast. Split Sub-Area REGION 12: OUTER COAST 2014 Treatment Dates 2014 Treatment Method Net Spartina Coverage By Species Since Peak Since a: Tom's Point, Tomales 6/6, 2/12/15 Dug m² 0.1 m² 0.5 m² % 84% 25b: Limantour Estero 3 years with no invasive Spartina ( ) % n/a 25c: Drakes Estero No invasive Spartina 2013 or % n/a 25d: Bolinas Lagoon, North 10/21 Backpack 0 72 m² 0 72 m² 180 m² % 358% increase (57 m²) 25e: Bolinas Lagoon, South No invasive Spartina 2013 or % n/a Net Area Treatment Area All Invasive Spartina Cover Net Area Decline Peak Year REGION 12 TOTAL 0 72 m² 0.1 m² 73 m² 181 m² % 338% increase (56 m²) Invasive Spartina Project Monitoring and Treatment Report

63 3. Special Topics 3.1. South Bay Salt Pond Restoration Project The South Bay Salt Pond Restoration Project (SBSP), managed by the Conservancy in partnership with USFWS DENWR and California Department of Fish and Wildlife (CDFW), is the largest tidal marsh restoration effort on the West Coast. The goal of the project is to restore and enhance wetlands in the South San Francisco Bay, while providing for flood management and wildlife-oriented public access and recreation. As the foundation for the effort, in 2003 the State and Federal governments acquired 15,100 acres of commercial salt ponds from Cargill and initiated planning for largescale restoration. This ambitious project has a timeline of approximately 50 years to restore the decommissioned salt ponds to salt marsh and a variety of other tidal habitats. As these systems mature, they promise to provide much-needed support to a variety of species that have been seriously impacted by the loss of 85-90% of the historic wetlands around the Estuary since the turn of the 20 th Century. Experience with tidal marsh restorations in the South Bay since the late 1980s has shown conclusively that, soon after tidal connection is reestablished at sites that have appropriate elevations, they are populated and rapidly dominated by hybrid S. alterniflora. While the initial ground surface elevation of the restoration sites varies greatly due to subsidence or the import of fill, they all initially lack significant vegetation, although some may have sparse remnants of pickleweed on mounds or around the perimeter. With the absence of competition and biotic resistance, hybrid S. alterniflora can quickly colonize and expand vegetatively through the soft mud. Once hybrid S. alterniflora is well established, it can significantly alter the hydrology and further development of the plant community, pushing the site off of a regionally normal tidal marsh development trajectory Knapp Tract One such site is Knapp Tract (aka Pond A6; 15a.6), a site in the Alviso complex that was breached in 2010 (See Figure 27). During treatment of hybrid Spartina along Coyote Creek in October 2014, the ISP s Treatment Program Manager scanned the northern portion of A6 from a levee and discovered rapid and previously undetected Spartina and pickleweed colonization in the marsh interior (only the perimeter had previously been surveyed). The SBSP Executive Director and Conservancy managers were alerted to this discovery, and the ISP mobilized an airboat contractor on October 30 to conduct a thorough survey and DNA sampling throughout the site. Figure 25. Native Spartina establishment along elevated areas where mud has accreted on old manmade structures within Knapp Tract/Pond A6 (looking northeast) ISP staff found invasive Spartina established around the spines of old manmade structures in the northern portion of the site, along the decommissioned road bisecting the southern portion of the site, and on the islands constructed to support high tide shorebird roosting (Figure 25, 26). Surveyors mapped a total of 44 invasive Invasive Spartina Project Monitoring and Treatment Report

64 Figure 26. The largest hybrid Spartina alterniflora clone found in Knapp Tract/Pond A6 in 2014 (5 meter diameter), with numerous S. foliosa clones establishing in the background (looking southwest) Spartina features during inventory including 15 hybrid S. alterniflora clones (18.3 m 2 ) and 29 features totaling 73.4 m 2 of Spartina that was identified as likely to be S. foliosa 2. Genetic sampling of a total of 20 mapped features confirmed accurate field identification (15 S. foliosa, 5 hybrid S. alterniflora) of all sampled plants, which bolsters confidence that the remaining un-sampled cordgrass in the site, both mapped and un-mapped, is likely S. foliosa. Sampling was conducted on plants that represented all various forms of Spartina found throughout the site, and because results from 75% of samples confirmed native ancestry, S. foliosa is believed to comprise the vast majority of cordgrass throughout the site. The site was treated by airboat on November 18. To achieve maximum efficacy, the target plants were sprayed early in a receding tide cycle to maximize herbicide dry time. By the time the local tide had receded to approximately 6 feet, all Spartina was fully exposed within the site because the relic manmade structures had served to elevate the substrate above the surrounding mudflat. Cordgrass establishment on these features may serve to expedite sediment retention and accretion in directly adjacent areas. The majority of the low-elevation mudflat at this young marsh will likely accrete sediment more slowly, taking a longer time before elevations are suitable for widespread native Spartina colonization Island Ponds The ISP has been monitoring the Island Ponds (aka A19-A21; 05i) on the northern bank of Coyote Creek since the site was breached in The western-most area, Pond A21, greatly exceeded the expected rate of sediment accretion, and by 2012 the site had established extensive salt marsh vegetation throughout. The vegetation included many acres of native S. foliosa, and only a few hybrid S. alterniflora clones, that were subsequently treated by airboat that year. This quickly-maturing marsh contains Spartina clones in all stages of development and maturation, greatly complicating identification of hybrid S. alterniflora plants, and its large size and very soft sediment pose access challenges as well. In 2014, ISP conducted an early-season DNA sampling in an effort to ensure an accurate understanding of the level of hybrid Spartina infestation at A21. Surveyors sampled ten plants that represented many of the varying morphologies (plant forms and structures) of the Spartina population, mostly in the western portion of the marsh, and all samples were genetically identified as native cordgrass. The site was inventoried later in the growing season to allow ISP to better discern hybrid from native Spartina, and only a single patch of hybrid Spartina (0.14 m 2 ), regrowth from a large, DNA-confirmed clone treated in 2013, was mapped throughout Pond A21. In early October 2014, the Santa Clara Valley Water District (SCVWD) alerted the ISP of some suspicious Spartina clones in A21. During mitigation monitoring work at the site, the SCVWD botanist found three patches of concern. The botanist noted that, while the plants did not possess a signature 2 Note that the ISP did not map or estimate all areas of Spartina identified with high confidence as S. foliosa. Invasive Spartina Project Monitoring and Treatment Report

65 Figure 27. Map of the South Bay Salt Ponds and neighboring recent restoration projects in South San Francisco Bay. Sites are differentiated based on whether they have been restored to tidal action and if so, whether they have been infested with hybrid S. alterniflora or not as of Sites are labeled with the year in which they were restored to tidal action. red culm or large inflorescences of many hybrid S. alterniflora, they appeared different from the predominant S. foliosa at the site, still having green leaves, where most of the native cordgrass had already turned yellow-brown with senescence. ISP staff investigated the clones by airboat, sampled them for genetic analysis, and preemptively treated them with imazapyr. Late in October, the ISP mobilized additional inventory and DNA collection at the site. No additional hybrid S. alterniflora were identified in the field, and 10 additional DNA samples further supported the belief that the expanding robust Spartina population in the pond is native. Samples taken from the neighboring Mud Slough, also were confirmed as native S. foliosa Newer Breaches Since 2011, more than 1,350 acres of diked salt ponds in the South Bay have been breached and restored to twice-daily tidal exchange, expanding the potential habitat for hybrid S. alterniflora and necessitating some level of monitoring by the ISP (as well as the potential for follow-up treatment). These new restorations include large ponds within existing ISP site complexes: Eden Landing Ponds E8A/E9 - part of sub-area 13m totaling 633 acres, adjoining the 32- acre E8X, which was breached in 2008, within the Union City Region, Pond A17 sub-area 15a.7, breached in 2012, comprising 136 acres along Coyote Creek in the Dumbarton South Region. Invasive Spartina Project Monitoring and Treatment Report

66 Ponds E8A, E9, E8X In August 2014, ISP found two small hybrid S. alterniflora clones adjacent to the levee in the northern portion of Pond E9, both of which were treated the next day. Uncertain whether the interior mudflat was yet at an elevation appropriate for Spartina colonization, the ISP waited until the end of the season to conduct a more complete survey. A thorough survey in November 2014 found additional hybrid S. alterniflora clones in E9, and most were greater than four meters in diameter. This level of infestation was surprising, considering the high degree of invasive Spartina control that had been achieved throughout the Eden Landing complex, where for the previous two seasons, all invasive cordgrass had been fully treated well ahead of seed production or dispersal, and there should have been minimal invasion pressure from within the complex itself. The new plants discovered in the Eden ponds were more than double the total amount of remaining hybrid S. alterniflora (16 m 2 ) found throughout the rest of the 1360-acre Eden Landing complex in Based on the size of the largest of the new E9 clones, it was suspected that they likely established the first winter after the pond was breached (2011), possibly from propagules within the Eden Landing Complex or possibly from seeds dispersed from Cogswell B or C (20n, 20o), three kilometers to the north where treatment is suspended. This is significant in that it suggests there is not always a lag time after breaching before invasive Spartina can establish in a new restoration. Pond A17 ISP surveyed Pond A17 and two adjacent areas, the managed wet pond A16 and muted New Chicago Marsh, in the Alviso/Coyote Creek area, in November No suspected hybrid S. alterniflora was detected, and three DNA samples confirmed the native field identifications. To date hybrid S. alterniflora has never been found within Pond A17, however a clone was found in 2013 only 100 meters from the breach to the pond, which highlights the need for continued thorough monitoring of the site SBSP Monitoring Strategy Experience with these challenging SBSP restoration sites, many of which are large and remote, led the ISP to develop a new strategy for conducting inventory that will be implemented in Few of these sites can be accessed on foot, and those that can are far too large to be adequately inventoried simply from the levee. Accessing the sites by outboard motorboat requires water too deep to permit full detection of colonizing young Spartina or regrowth from treated plants, which can be short in stature and would be submerged at higher tide. Other island infestations at more mature restoration marshes (e.g. Bair Island) are similarly accessible only by boat, which again puts surveyors on site when tides are too high for effective detection of small and low elevation plants, and they are very expansive, requiring many person-hours to fully inventory. The ISP expects to address these problems in 2015 by expanding the use of airboats both for providing site access and for transporting surveyors across the mud flats and low marsh plains during lower tide to conduct surveys. The DENWR and SPBNWR have committed the use of their airboats with pilots for Refuge sites, and the Conservancy has set aside funds within the budgets of two ISP grant recipients, the San Mateo County Mosquito & Vector Control District and the California Wildlife Foundation (CWF), specifically for airboats. With the expanded use of airboats, ISP anticipates conducting improved surveys in significantly less time, which may allow the ISP to expand surveys to some lower risk sites, and to conduct additional Invasive Spartina Project Monitoring and Treatment Report

67 second rounds of monitoring and treatment at sites near eradication. This method may have additional benefits of improved safety for surveyors who will not need to work at these remote locations during the more dangerous high tides Central Bair Island Restoration This 598-acre site on Bair Island in the San Mateo Region was breached in 2013, and ISP did not expect its open mudflats to be at the appropriate elevation for immediate colonization by Spartina. However, while surveying the adjacent marsh Deepwater Slough (02k) in October 2014, biologists found a single, small new Spartina recruit at the toe of the levee within the newly-breached Central Bair (02o). The plant was DNA sampled, identified as hybrid S. alterniflora, and treated shortly thereafter. Budget did not allow for a more complete low-tide survey of Central Bair in autumn 2014, but it is clear that Spartina is colonizing the site on some level, and inventory there will be a priority in 2015, as well as follow up treatment if necessary. The site s proximity to several significant hybrid S. alterniflora infestations, including the restricted treatment site of B2 North Quadrant East (2c.1b), along with this young marsh s elevation already being suitable for vegetation establishment, means it is likely that Central Bair is already colonized by both native and invasive cordgrass. ISP monitoring and treatment will need to increase here in future years to enable this marsh to develop along a trajectory towards an intact native plant community. This will require more thorough coverage of the nearly 600 acres by airboat on a tide that allows for both full exposure of young plants as well as safe navigation over the open marsh plain. To achieve both of these conflicting objectives over such a large area will likely take two or more inventory events of several hours each during the proper tide window, the same strategy employed at the neighboring Bair Island restoration site of Pond B3 (02m) Restricted Treatment Sites The 2012 USFWS Biological Opinion (BO; USFWS Memorandum, Aug 21, 2012) authorized full treatment at 200 of ISP s 211 treatment sub-areas. Treatment restrictions were placed on the remaining 11 sub-areas, allowing treatment for seed suppression at one sub-area, and prohibiting treatment at the remaining ten sub-areas. B2 North Quadrant East (02c.1b) in the San Mateo Region (Region 3) was authorized to receive an aerially-applied, sub-lethal concentration of herbicide to halt production and dispersal of hybrid S. alterniflora seed, while maintaining aboveground biomass to provide endangered California Ridgway s rails with cover from predators and nesting substrate. The ten subareas in which no treatment was authorized are: Citation Marsh North (20d.2), North Marsh (20f), Bunker Marsh (20g), San Lorenzo Creek Marsh North (20h.1), Cogswell Quadrant B (20n), and Cogswell Quadrant C (20o) in the Hayward Region (Region 6); Arrowhead Marsh East (17c.2), MLK Regional Shoreline-Damon Marsh (17d.4), MLK New Marsh (17h), and Fan Marsh (17j) in San Leandro Bay (Region 7). Subsequent BO amendments in 2013 and 2014 have maintained these restrictions at these eleven sites, and the restrictions will be reevaluated once Ridgway s rail population numbers increase enough bay-wide that reduction of cordgrass in these marshes is not expected to put the species at increased risk. Distribution of these sites is shown in Figure 28. To focus inventory efforts in other marshes that would inform treatment for 2014, these 11 sites were surveyed on a coarser level to ascertain the general distribution and abundance of non-native cordgrass without the level of detail required to relocate individual plants for treatment purposes. In 2014, these marshes were predominantly surveyed by grid, which entails dividing each marsh into 25mx25m grids and assessing cover classes for each. The results total 22.7 acres of hybrid S. alterni- Invasive Spartina Project Monitoring and Treatment Report

68 Figure 28. Distribution map of the 11 ISP sub-areas in which treatment of hybrid S. alterniflora has been restricted since Invasive Spartina Project Monitoring and Treatment Report

69 Table 15. Biennial hybrid S. alterniflora quantities and trends from at the 11 ISP sub-areas where treatment has been restricted since Spartina amounts presented in this table are mean values within the range of estimated net cover area with minima and maxima in parentheses. The seemingly steady trends (symbolized as ) denote that an annual net change could not be accurately determined due to overlaps in the minima and maxima of these cover ranges. ISP Reporting Region Subarea # Sub-area Name 2010 net ac. (min-max) 2012 net ac. (min-max) 2014 net ac. (min-max) Landowner 3 02c.1b B2 North Quadrant East* ( ) 1.51 ( )* 1.83 ( ) CDFW d.2 Citation Marsh North 0.46 ( ) 1.11 ( )* 2.31 ( )* City of San Leandro 20f North Marsh 0.57 ( ) 0.71 ( ) 1.76 ( )* City of San Leandro -- 7 flora, which is a 1.7-acre increase from 2013 levels 3. This inventory reflects an 8.5% increase over 2013 levels of infestation, which is slightly higher than the 5% and 4% increases observed between the prior two monitoring seasons ( and ). The 22.7 acres of hybrid S. alterniflora in the restricted treatment zones account for 79% of the total remaining invasive Spartina in the Bay in 2014 (Tables 1 and 15, Figure 29). Four-year trends shown in Table 15 illustrate that the footprint of the infestations in five out of six Hayward Region (Region 6) restricted sub-areas have been detectably increasing. Biennial trends were determined by comparing the upper and lower limits of net invasive Spartina inventoried in a given year, and determining if the area ranges overlap or if they are distinctly higher or lower than prior years. The four restricted sub-areas within San Leandro Bay (Region 7) have experienced no detectable changes in the area of non-native Spartina, which means only that the maxima and minima within each sub-area overlap with those of prior years. All Region 6 restricted sub-areas are relatively young restoration marshes that were quickly dominated by hybrid S. alterniflora shortly after being reopened to tidal action, and the lack of mature marsh vegetative structure in these sites might facilitate more rapid infestation regrowth in the absence of treatment. By the 2014 monitoring season, the sub-areas with no treatment allowance had been untreated for four full growing seasons, and their combined invasive Spartina footprint continues to steadily grow an average of approximately one acre per year. Besides the obvious complications that this poses to achieving local eradication once treatment is eventually re-authorized, the unchecked production of seeds and propagules in these marshes complicates all current eradication efforts in their neighboring sub areas. Within the Hayward and San Leandro Bay Regions, there were a total of 22 sub-areas that contained less than 10 m 2 of invasive cordgrass in If these marshes were located elsewhere in the Bay, ISP would expect treatment to reduce the cover to zero within a couple of years Trend Trend 20g Bunker Marsh 0.37 ( ) 0.29 ( ) 0.8 ( )* City of San Leandro -- 20h.1 San Lorenzo Creek and Mouth North 0.04 ( ) 0.02 ( )* 0.6 m 2 (.2-1m 2 )* City of San Leandro 20n Cogswell Marsh, Quadrant B 0.58 ( ) 4.25 ( )* 3.69 ( ) EBRPD -- 20o Cogswell Marsh, Quadrant C 0.25 ( ) 0.37 ( ) 0.5 ( ) EBRPD c.2 Arrowhead Marsh East 8.57 ( ) 7.39 ( ) 7.3 ( ) EBRPD MLK Regional Shoreline - Damon 17d.4 Marsh 0.37 ( ) 0.34 ( ) 0.48 ( ) EBRPD h MLK New Marsh 3.39 ( ) 3.91 ( ) 3.65 ( ) EBRPD j Fan Marsh 0.28 ( ) 0.19 ( ) 0.34 ( ) Port of Oakland Total ( ) ( ) 22.7 ( ) *02c.1b has been authorized for seed suppression only since 2012 Four year Trend 3 This references a corrected value of 20.9 acres from the originally reported 38.4 acres for 2013 inventory. The discrepancy arose from the course method of mapping used by ISP staff used in 2013 when inventorying the large amounts of Spartina in sub-areas with treatment restrictions. More detail of these mapping methods was presented in Section 2.1. Invasive Spartina Project Monitoring and Treatment Report

70 Figure 29. Bay-wide trend of invasive Spartina net area, by treatment authorization since An annual decline in bay-wide infestation has been observed since 2006 when estuary-wide treatment began, though the amount of hybrid S. alterniflora is slowly increasing in the sites where treatment is restricted. However, constant invasion pressure from the nearby sites with treatment restrictions precludes this from happening. This has been demonstrated in San Leandro Bay, where no sub-area has ever achieved zero detection since treatment restrictions have been in place, despite the high level of control that had been achieved through previous years of full treatment. In the Hayward Region, no hybrid S. alterniflora was detected in Triangle Marsh (20w) in 2012 and 2013, but the marsh was again re-infested in As such, the single Region 6 sub-area free from hybrid in 2014, Sulphur Creek (20j), is expected to again be infested by 2015 considering its position between the no-treatment sub-areas in the Robert s Landing and the Cogswell Complexes (collectively site 20). Annual inventory and treatment within sub-areas of these two regions achieves control at best, and until nearby treatment restrictions are lifted, no progress can be made towards eradication in this portion of the Estuary. For this reason, the ISP is not conducting second rounds of inventory or treatment in these areas, so that limited resources can be focused in locations where true local eradication can be achieved New Infestations and Sub-areas Added in 2014 There were no new invasive Spartina infestations discovered in ISP defines a new infestation as a freshly discovered instance of invasive Spartina greater than one kilometer from any historic location. Invasive Spartina Project Monitoring and Treatment Report

71 No new treatment sub-areas were added in However, the two most recently added sub-areas, Pond A17 (15a.7) in Region 4: Dumbarton South, and Central Bair (02o) in Region 3: San Mateo, began to receive invasive Spartina recruits in 2014 (see previous discussions in Sections and 3.1) ISP Genetics Program The ISP relies heavily on genetic analysis to help identify native and non-native Spartina. Each year before inventory season begins, ISP staff review and evaluate the previous year s genetic findings and develop a genetic sampling plan that will provide meaningful information to the treatment and restoration programs, and assure efficient use of resources. The most common reasons for collecting DNA samples are to aid identification of specific plants, guide hybrid treatment and native cordgrass reintroduction, and monitor new or changing plant morphologies. Collected leaf samples are shipped to a commercial laboratory, Genome Advisors, for the extraction of DNA. Extractions are forwarded to the UCLA Department of Human Genetics GenoSeq Laboratory where they are analyzed and scored using Simple Sequence Repeats (SSRs; aka microsatellites ). Genotype data are returned to the ISP, where they are run through a quality assurance protocol before a laboratory identification (LID) is assigned to each sample using the statistical models implemented in the software Structure (Pritchard, Stephens et al. 2000). For each sample, Structure returns an estimate of the proportion of ancestry derived from either S. foliosa or non-native sources, as well as a 95% credibility interval. Based on the estimate of ancestry, each plant gets a laboratory identification of S. foliosa, hybrid/s. alterniflora, or Uncertain. In addition, each LID is described as high, moderate, or low confidence, based on the 95% credibility interval. The ISP incorporates the results from Structure into its GIS database for further inspection and for reference in the field during treatment and inventory events in current and future years. These designations provide ISP biologists with valuable information for making species identifications in the field. Over 3,500 plants have been collected and analyzed in this manner since the ISP started using SSRs in 2010, allowing the identification and rapid treatment of many hybrid S. alterniflora plants that may have otherwise been missed for a period of time. Confirmation of S. foliosa ancestry has preserved many native cordgrass stands, allowing them to continue to provide critical habitat features as well as maintaining a propagule source that can revegetate areas after hybrid S. alterniflora removal. Just as hybrid S. alterniflora is more morphologically diverse than S. foliosa, and yet sometimes appears quite similar, hybrid genotypes occupy a wider range of values compared to native Spartina genotypes, with considerable overlap between them (Figure 30). The overlap between native and nonnative Spartina, in both genetics and morphology, is what makes identifying hybrid S. alterniflora so difficult. The use of the Uncertain LID range and credibility intervals are a necessary concession to this situation. ISP biologists weigh the bulk of evidence genetics, morphology, location, environment, and history to arrive at a final decision to treat or not treat every plant. Receiving results from the genetics laboratory in time to inform the same year s treatment creates opportunities to treat genetically identified hybrid S. alterniflora populations before they can disperse seeds, and to protect S. foliosa from being misidentified and treated as hybrid. Improving the turnaround time for receiving results was therefore a high priority for During the height of the 2014 field season, the average time from shipping samples to receiving results was 18 days, and the median was 13 days. Over the entire season, the average was 25 days, compared to an average of more than 14 weeks in In most cases, the faster turnaround allowed genetic results to be considered Invasive Spartina Project Monitoring and Treatment Report

72 Figure 30. Density plot of discriminant function scores for two genetic clusters of Spartina. Spartina genotypes sampled in were analyzed by Discriminant Analysis of Principle Components using the R module adegenet. The analysis, which collapses genotype information into principle components, sorted samples into a sharply peaked S. foliosa cluster and a broad, relatively undefined S. alterniflora hybrid cluster. The area of overlap between the two curves illustrates the difficulty in clearly identifying some plants. when making decisions for the 2014 treatment season. These improvements were achieved through better communication with the laboratory regarding the ISP s need for quick data turnaround, updates on the status of samples, providing advance notice of planned shipments, and helping the lab increase capacity by replacing some broken analytical equipment. In 2014 the ISP conducted very early-season sampling at four marshes with a history of cryptic hybrid morphologies resulting from introgression: (Calaveras Marsh [05a.2], Palo Alto Baylands [08], Dumbarton [05b], and Belmont Slough [02a.1a, 02b.2]) before distinguishing field characteristics were apparent, in hopes of receiving results before inventory at these sites. Later, during inventory at these marshes, ISP staff revisited the same plants with genetic results in hand, in order to calibrate their concept of what morphologies of S. foliosa and hybrid S. alterniflora looked like at these marshes. This was the first time same-year genetic data was used to inform inventory as well as treatment, made possible through the collection of these early-season DNA samples, and the process resulted in more accurate field identifications without the need for additional DNA sampling, leading to treatment of many non-native plants a year in advance of when they otherwise would have been detected. Early season sampling will be repeated in 2015, but with the shorter lab turnaround times achieved in 2014 expected to continue, the sampling will take place slightly later in the season, giving the plants more time to manifest useful characteristics for field identification. The ISP made some adjustments over the last two seasons regarding how many and which SSR markers to use. Three markers, SPAR9, SPAR22, and SPAR28, were added in the second half of the 2012 season, bringing the number of markers in use to 16. These three markers were chosen because published work and advice from UC Davis researchers showed that they would likely be very informative in discerning native Spartina from non-native. After two full seasons of use, the ISP has collected enough data to assess if these markers have improved species identification capabilities. Of the 1,147 samples analyzed from 2013 and 2014 seasons, only 14 recorded a change in the species Invasive Spartina Project Monitoring and Treatment Report

73 identification when run with or without the three newest markers. All of these changes were between an Uncertain laboratory identification and either hybrid or S. foliosa. No identifications involved a switch between hybrid and S. foliosa. However, the 95% credibility intervals were about 1.5% narrower with the new markers (paired T-test, P = 0.032). As such, the addition of the three markers does not appear to change identifications, but does improve confidence in the identifications. Going forward, restricting statistical analyses to the years after 2013with the current, full suite of SSR markers will improve, simplify, and speed analyses, and will avoid having to record genotypes as containing missing data for the three newer markers. In the later part of the 2013 season, the determination was made to drop one of the 16 SSR markers, SPAR15, in use at that time, due to inconsistencies in genotype scores. Data for that marker was removed from genotypes for which values had been recorded, 2013 results were calculated without SPAR15, and the marker was permanently dropped from further use, leaving ISP with 15 SSR markers going forward. In 2014, the ISP began a program of focused sampling to augment the library of genetic alleles that are associated with the different types of Spartina. A robust library of known native and non-native samples with which to compare unknown samples improves the statistical performance of Structure and increases confidence in the results. Forty unmistakably hybrid samples were added to the genetic database at the end of the 2014 season, and further sampling of high-confidence S. foliosa and hybrid S. alterniflora is planned for Preliminary runs of Structure with and without the 40 hybrid reference samples indicate that including these samples improves genetic identifications when analyses are performed on a regional scale, e.g., South Bay or North Bay. An understanding of regional differences in population genetics may ultimately play a role in the final eradication of invasive Spartina Spartina Patens Update The ISP has been working with California Department of Parks and Recreation (State Parks) since 2004 to control and eventually eradicate Spartina patens from Southampton Marsh at Benicia State Recreation Area (BSRA). Herbicide treatment yielded great progress initially, and by 2008 the infestation had been reduced by over 90%, mainly through the elimination of a group of large clones on the marsh plain. However, since that time there had been little progress towards eradication, mainly due to treatment restrictions related to the presence of an endangered annual plant, Chloropyron molle (soft bird s beak, formerly Cordylanthus mollis mollis) (Figure 31). The growing season for soft bird s beak begins in early spring, and treatment of S. patens was restricted until after October/November, when the soft bird s beak plants set seed, so that treatment would not interrupt reproduction. However, by autumn, S. patens is senescent, which decreases the plants ability to uptake herbicide and significantly reduces treatment efficacy. The optimal treatment timing for S. patens is in spring, when the plants are green and actively growing, and prior to flowering to avoid formation of seeds. Treatment by herbicide application is the most appropriate treatment method available, because large-scale digging or tarping presents unacceptable impacts to the high-quality habitat where much of the Figure 31. Seedling of Chloropyron molle molle growing amongst the wispy spring growth of a Spartina patens clone. Invasive Spartina Project Monitoring and Treatment Report

74 remaining S. patens was located. In the absence of treatment over multiple years, seed set by the Spartina contributed to building a seed bank, exacerbating the infestation and contributing to the minimal reduction in the cover of mature S. patens each year since In 2011, just as a new strategy was being developed, California Ridgway s rails were detected during pre-breeding season call counts after many years of absence from the marsh. The detection of the rails resulted in the establishment of Ridgway s rail breeding habitat conservation zones in the marsh to avoid impacts to the endangered birds. State Parks and USFWS jointly restricted entry into these zones between February 1 and October 1. This timing restriction further precluded the opportunity for effective herbicide application to patches of S. patens that occurred within the Ridgway s rail zones. Southampton Marsh also supports a relatively high density of the threatened California black rail (Laterallus jamaicensis coturniculus) and, given its location in the Carquinez Strait, may provide this bird an important dispersal link between the San Pablo Bay and Suisun Bay tidal marshlands. Black rail habitat conservation zones had been previously delineated in the marsh as part of State Parks management program for control of Lepidium latifolium (perennial pepperweed), and no entry was allowed to these zones during the bird s breeding season from March to August. The black rail conservation zones include approximately 16% of the S. patens infestation at Southampton Marsh. By 2014, with Ridgway s rails not being detected since 2011, the exclusion measures for this species were lifted, allowing for a potential herbicide treatment of S. patens at the proper spring timing at areas not still covered by the black rail conservation zones. ISP worked with State Parks, USDA-ARS researcher Brenda Grewell (who has studied the Chloropyron at BSRA for many years), and ornithologist Jules Evens (Avocet Research Associates) to develop a treatment plan that would remove the invasive cordgrass while reducing potential impacts on the three special status species to acceptable levels. The plan requires a USFWS-approved Ridgway s rail biologist to survey the Ridgway s rail conservation zones along the channels for the bird, clearing them ahead of the treatment crew. This allows treatment of about 84% of the S. patens population. In areas where the target S. patens is greater than one meter from Chloropyron, the herbicide will be sprayed onto the plants in the standard manner, utilizing a 4-gallon backpack sprayer or smaller 1-2 gallon handheld sprayer (Figure 32). But in areas where the S. patens is less than one meter from Chloropyron or is growing interspersed, the herbicide must be wicked or wiped onto the Spartina leaves (Figure 33). This approach is expected eliminate collateral damage to Chloropyron in cases where it is simply near S. patens but not growing directly in a clone, and to limit the impacts where the two plants are interspersed. In cases where Chloropyron is located in a monotypic stand of S. patens, it can be assumed that the hemiparasitic Chloropyron has formed a haustorial connection to Figure 32. Backpack application to stand of Spartina patens along a channel bank. Herbicide was selected as the lowest impact treatment method since tarping or digging would destroy the integrity of the bank and eliminate the mature hedge of Grindelia stricta in the background that is important Ridgway s rail habitat. the roots of S. patens, allowing it to absorb nutrients from its host. In these cases, mortality of the weed is expected to induce mortality of the hemiparasite since Chloropyron typically does not survive without a live host plant connection under field conditions. However, since the interaction zone Invasive Spartina Project Monitoring and Treatment Report

75 Figure 33. Applying herbicide mixture to a sponge for wicking onto Spartina patens within one meter of the endan-gered Chloropyron molle molle. between S. patens and Chloropyron over the entirety of Southampton Marsh involves just 1.2% of a thriving Chloropyron population, the proportion potentially impacted by the careful wicking application should be very small. In addition, controlling the adjacent S. patens may directly benefit the Chloropyron by removing the competition and allowing more appropriate native hosts to establish through natural succession, providing more opportunities for Chloropyron seedlings to flourish in future years. Within the black rail conservation zones, treatment of the other 16% of the S. patens population is to be conducted in the late Autumn and Winter using only manual removal or tarping, since the Spartina plants are senescent and not able to translocate the herbicide. This plan was reviewed by USFWS Ecological Services and a Biological Opinion amendment letter was generated to permit the work. The California Department of Fish & Wildlife s Native Plant Program also evaluated the plan s impacts to the listed Chloropyron and approved the new strategy. On April 29, 2014, ISP was finally able to conduct an herbicide application to S. patens for the first time since Brenda Grewell accompanied the treatment crew to help identify Chloropyron seedlings, the presence of which determines the method of herbicide application as detailed above. In January 2015, a crew revisited the site to assess potential for manual S. patens removal in the black rail zones. They found that, with the invasive cordgrass just starting to emerge, it was impossible to accurately determine the extent of each clone or new patch, and many of the discernable features were too large to dig without causing long-term damage to the marsh plain. The largest polygons of S. patens were found to be barely within a black rail conservation zone line that had been roughly delineated on the map without GPS; many of the interaction areas were out on the open pickleweed plain and could potentially be navigated carefully without great risk of harm to black rails since the vegetation was neither of the density nor height preferred by the birds. Jules Evens conducted a site visit with the team and agreed that it should be safe to have a rail biologist clear these areas ahead of the applicator as has been done for Ridgway s rail, enabling the use of herbicide during the active growing season and avoiding the longer-term impacts to the marsh from manual treatment. In spring 2015, Evens will set up listening stations near the interaction zones between S. patens and black rail habitat to determine if they are currently being used by the birds, and the team should be able to treat all S. patens throughout the Recreation Area on a single day without the level of marsh plain damage that would have resulted from manual removal and hauling the material off site. Invasive Spartina Project Monitoring and Treatment Report

76 4. Considerations for Earlier Entry to the Fringe Marsh at Five Sites During the 2014 Treatment Season, ISP found that hybrid S. alterniflora clones growing in the S. foliosa fringe in several South Bay sites had senesced prior to the dates treatment was permitted by the Biological Opinion. Since herbicide treatment of senesced plants is not effective, ISP was not able to control entire large areas, and the opportunity to eliminate those clones and maintain progress towards eradication was lost. This is especially problematic in high-quality marshes approaching eradication, such as Mowry and Dumbarton marshes, where these senescent plants represent a significant proportion of the total remaining infestation. In addition, the location of the hybrid S. alterniflora clones within a matrix of S. foliosa increases the potential for a flowering hybrid to swamp the S. foliosa with pollen and produce hybrid seed. ISP rail biologists determined that the S. foliosa fringe was too low in elevation to provide Ridgway s rail with breeding habitat, so earlier entry should not have an impact on rail breeding at the site. This is especially true if treatment crews approach from the mudflat by airboat as opposed to traversing the marsh plain where nests are more likely to be located. DENWR and the Conservancy submitted a request to USFWS Ecological Services that ISP be permitted to begin treating these limited portions of the sites in question in mid-july, and return to treat the interior of the marsh after August 12 (the standard BO entry date for Refuge marshes). This request was granted and pertains to the following five ISP sub-areas: Mowry Marsh & Slough (5a.1), Calaveras Marsh (5a.2), Dumbarton Marsh (5b), Palo Alto Baylands (8), and Alviso Slough/Ogilvie Island (15a.4). As is standard ISP procedure for all treatment in RIRA habitat, the applicator will be accompanied by a RIRA biologist who will suspend treatment if nests or agitated birds are encountered Increased Use of Airboat for ISP Inventory As discussed in Section 3.1.3, an airboat survey and DNA collection was mobilized in 2014 after the discovery of rapid invasive Spartina colonization within Knapp Tract and to investigate a report of infestation in the Island Ponds (A21) from SCVWD. In both cases, using the airboat for access at a low tide provided full exposure of all Spartina plants and allowed completion of a full survey of the site in a fraction of the time it could have been done with a standard boat or kayaks. In an effort to improve efficiency in completing thorough inventory of new restoration sites, and also to improve worker health and safety during inventory at large island sites such as Bair & Greco, the ISP is planning to increase airboat use in 2015 to facilitate these surveys. Inventory at the large island sites has been conducted by deploying personnel from a boat with an outboard motor, which requires a significant amount of water to be present throughout much of the work day. This tide level also fills channels and often floods the marshplain, which limits surveyor mobility, makes the work slow and tedious, and decreases the likelihood of detecting invasive Spartina at lower tidal elevations. With such a limited number of airboats in the Bay Area, it is challenging to mobilize enough of these essential platforms to accomplish ISP s goals over the course of the inventory and treatment season. The DENWR and SPBNWR have committed the use of their airboats with pilots for Refuge sites, and the Conservancy has set aside funds within the budgets of two ISP grant recipients, the San Mateo County Mosquito & Vector Control District and the California Wildlife Foundation (CWF), specifically for airboats. Not only will this allow for inventory to be conducted on a lower tide, but the airboat can also shuttle biologists over impassable channels or to yet-unmapped portions of the Invasive Spartina Project Monitoring and Treatment Report

77 site, greatly reducing worker fatigue while also reducing the time required to complete thorough inventory. With the expanded use of airboats, ISP anticipates conducting improved surveys in significantly less time, which may result in having time available to survey some lower risk sites, and to conduct additional second rounds of monitoring and treatment at sites near eradication Enhanced DNA Sampling in the Far South Bay The Dumbarton South Region (Region 4) is one of the highest priority tidal areas for protecting current and future SBSP sites, but it is also one of the most difficult to access and presents significant Spartina identification challenges. High tidal amplitude, large amounts of freshwater input, and the large volume of nutrient-rich wastewater runoff from San Jose all cause S. foliosa to grow very tall and robust and to resemble hybrid S. alterniflora. Additionally, the continuing multi-year drought further complicates matters by causing some hybrid S. alterniflora stands to senesce early, contributing to incomplete or sub-optimal treatment. The ISP s Spartina Assessment Planning Team is developing a focused genetic sampling plan for 2015 that will improve understanding of the morphological characteristics of both S. foliosa and hybrid S. alterniflora in the far South Bay. Based on the success of 2014 early season genetic sampling in informing important inventory and treatment decisions (as described in Section 3.4), the ISP will again conduct early-season DNA sampling in The 2015 sampling will encompass larger stretches of marsh where data from previous years indicate a high degree of introgression/backcrossing between native and non-native Spartina. The goal will be to use DNA to identify cryptic hybrid S. alterniflora forms that have not yet matured to the point of easy field identification. This will be accomplished by sampling along transects in three marshes found to be most problematic in 2014: the outboard marsh of Knapp Tract, the mainland of Coyote Creek upstream of the confluence with Alviso Slough, and Ogilvie Island (all three are portions of 15a.4, Alviso Slough). This information can then once again be used to better interpret the more mature Spartina plants later during inventory and treatment. The details of this new sampling technique are being developed by the SAPT for implementation in mid-july Invasive Spartina Project Monitoring and Treatment Report

78 5. Summary of 2014 Inventory Monitoring and Treatment The ISP conducted mapping and treatment throughout 60,000 acres of potential Spartina habitat in the San Francisco Estuary. The project inventoried a total of 28.9 acres of hybrid S. alterniflora baywide, which marks a decline of 96.4% since the peak infestation of 805 acres in This success was realized despite a number of additional adverse factors, such as accelerated senescence due to stressors from the multi-year drought, limited tide windows that were even more restrictive than usual during the core season, and many access challenges due to a limited number of available airboats, which are now necessary to work safely and efficiently at a number of sites. While the infestation of hybrid S. alterniflora continues to be reduced, the 1.8-acre increase (8%) since 2013 in the 11 sub-areas with treatment prohibitions and restrictions resulted in a net reduction of only 12% bay-wide. The 22.7 acres of hybrid S. alterniflora present in restricted sub-areas accounts for almost 80% of the 2014 bay-wide total. The footprint at these restricted sites continues to expand, and there is an urgent need to resume full treatment of all sub-areas in order to prevent risk to this major investment, and to ensure the success of large-scale restoration. No current tidal marsh restoration efforts are safe from infestation if complete eradication of invasive Spartina is not achieved. Inventory and treatment efficiency increased in 2014 as a result of technological advancements in ISP s data sharing capabilities. Biologists now have the ability to conduct two way synchronization of data in the field, enabling real-time viewing of where others have completed inventory and which plants have been treated, and they are better able to identify areas that have not received adequate survey and/or plants that have been missed during treatment. Successful eradication can be achieved by incorporating these types of technical innovations, close cooperation amongst ISP s local, state and regional partners, and continued persistence in pursuing the strategies that have been developed. Invasive Spartina Project Monitoring and Treatment Report

79 6. References Ayres, D. R., E. Grotkopp, et al. (2008). "Hybridization between invasive Spartina densiflora (Poaceae) and native S-foliosa in San Francisco Bay, California, USA." American Journal of Botany 95(6): Ayres, D. R., D. R. Strong, et al. (2003). "Spartina foliosa - a common species on the road to rarity?" Madrono 50: Ayres, D. R., K. Zaremba, et al. (2004). "Extinction of a common native species by hybridization with an invasive congener." Weed Technology 18: Daehler, C. C. and D. R. Strong (1996). "Status, prediction and prevention of introduced cordgrass Spartina spp invasions in Pacific estuaries, USA." Biological Conservation 78(1-2): Elrod, M., J. Wood, et al. (2014) California Ridgway's Rail Survey Report, Point Blue Conservation Science: 18. Goals (1999). Baylands Ecosystem Habitat Goals. A report of habitat recommendations prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project. P. Olofson, U.S. Environmental Protection Agency, San Francisco, CA / San Francisco Bay Regional Water Quality Board, Oakland, CA. McBroom, J. T. (2014). California Ridgway's Rail Surveys for the San Francisco Estuary Invasive Spartina Project., Olofson Environmental Inc.: 99. Pritchard, J. K., M. Stephens, et al. (2000). "Inference of population structure using multilocus genotype data." Genetics 155(2): Rohmer, T., D. Kerr, et al. (2014). San Francisco Estuary Invasive Spartina Project 2012 ISP monitoring and treatment report. Oakland, ISP: 86. State Coastal Conservancy (2003). Final Programmatic Environmental Impact Statement/Environmental Impact Report, San Francisco Estuary Invasive Spartina Project: Spartina Control Program. Oakland, CA. Volume 1: Final Programmatic Environmental Impact Statement/Environmental Impact Report. Invasive Spartina Project Monitoring and Treatment Report

80 APPENDIX 1: Target Plant Species Descriptions

81

82 APPENDIX 1 ISP Target Species Descriptions There are one native and four non-native species of cordgrass in the San Francisco Estuary. The native species, Pacific cordgrass (Spartina foliosa), is avoided during treatment and is conserved by controlling the invasive species that can displace or genetically assimilate it. Key aspects of the cordgrass species found in the Estuary are contrasted below. All species and hybrids are perennial, salt-tolerant grasses that spread both sexually and asexually. The roles these species play in their native habitats give ecologists an indication of their potential to alter the salt marsh ecosystem of San Francisco Bay. NATIVE: PACIFIC CORDGRASS (SPARTINA FOLIOSA) California s only native cordgrass, S. foliosa, grows in a narrow range of the tidal spectrum due to its relatively short stature and intolerance for drought. Spartina foliosa is a vital component of the salt marsh plant community, occurring at the lowest intertidal elevation of any native macrophyte. This lower tidal marsh zone occurs at the upper elevation of the mudflat and along channel banks and benches. Native cordgrass is also found scattered throughout the next zone in the elevational gradient, the middle tidal marsh zone, or pickleweed (Salicornia virginica) marsh plain. Spartina foliosa s slender leafy shoots seldom exceed five feet in height including seed heads, with most shoots ranging from approximately one to three feet tall. Cordgrass height correlates with its tolerance of submersion, and as such S. foliosa can occupy only a limited range in the lower and middle tidal marsh zones (Cain and Harvey 1983). Its leaves and stems wither in fall and are shed in winter, as the clones die back to the mud substrate. Spartina foliosa is particularly valued as habitat for the endangered California clapper rail (Rallus longirostris obsoletus), which spends most of its time foraging for food within, or close to, the protective canopy of cordgrass. California clapper rails can move within S. foliosa stands, and they spend most of their time under cover of the cordgrass foliar canopy, usually selecting prey items such as benthic and aquatic invertebrates inhabiting the cordgrass stands and their edges. The benthic invertebrate community found in the substrate at the base of S. foliosa is also an important food source to a variety of other consumers including both resident and migratory shorebirds. While it was widely recognized that hybrid S. alterniflora (discussed in the next section) could potentially threaten the existence of native S. foliosa, control of the hybrids began sufficiently early that S. foliosa still anchors thousands of acres of tidal marsh throughout the Estuary. Most of the North Bay was relatively unimpacted by hybrid S. alterniflora, and more than 99% of the cordgrass in the remnant marshes throughout the Estuary is still intact S. foliosa. However, S. foliosa was assimilated into the hybrid swarm, and even locally extirpated, in some of the largest infestations around South San Francisco Bay, including the Alameda Flood Control Channel (Site 1) and Eden Landing (Site 13). These sites are the focus of an extensive reintroduction effort by the Conservancy that began in 2010, to establish stands of S. foliosa that will begin to disperse seeds throughout these sites, leveraging the investment in direct planting. San Francisco Invasive Spartina Project 1 Target Species Desciriptions

83 ATLANTIC SMOOTH CORDGRASS (SPARTINA ALTERNIFLORA) AND ITS HYBRIDS Atlantic smooth cordgrass is unique among the world s cordgrass species in terms of its growth potential and ecological breadth. Spartina alterniflora is genetically very similar to S. foliosa, but the two species have significant differences. In size, growth rate, pollen and seed production, culm (stem) density and ecological tolerances, S. alterniflora is more robust than S. foliosa (Smart and Barko 1978; Boyer, Callaway et al. 2000). The San Francisco Estuary population of S. alterniflora was introduced from seed collected in Maryland in the early-1970s to aid in a dredge spoils stabilization and marsh restoration experiment (Faber 2000). Genetic similarity to S. foliosa allowed multiple hybridization and eventual backcrossing events that produced the hybrid swarm that has posed the most widespread and intrusive threat to the Estuary (Daehler and Strong 1997). Pollen production, higher fertility, greater tolerance for both inundation and drought, and increased timeframe for flowering make these hybrids a prominent threat to native cordgrass through outcompetition, pollen swamping, and hybrid assimilation (Rhymer and Simberloff 1996; Ayres, Garcia-Rossi et al. 1999; Anttila, King et al. 2000; Levin, Neira et al. 2006). APPENDIX 1 Hybrid S. alterniflora was well established and widely distributed in the Central and South Bay at the start of the ISP Control Program, but it was detected early and controlled by ISP in the North Bay. Although a small population established on the shoreline of Southampton Marsh (Site 11) in Benicia State Recreation Area, hybrid S. alterniflora has not yet been detected further into Suisun Bay, despite intensive surveys. Over the years, outlier populations have been detected on the Petaluma River (Site 24), Sonoma Creek (26c), and Mare Island (26b), and single clones were found at both China Camp State Park (23o) and Sonoma Baylands (26d). Pioneering hybrid S. alterniflora populations have also been detected and managed at Drakes Estero, Limantour Estero, and Bolinas Lagoon on the Point Reyes peninsula (Site 25). The abundance of hybrid S. alterniflora remains greatest in San Leandro Bay (Oakland), Robert s Landing in San Leandro, and outer Bair Island Ecological Reserve (Redwood City), but has been reduced by 95% bay-wide, down to 38 net acres 1 since its peak of 805 net acres in When stands of S. foliosa are displaced by hybrid S. alterniflora, not only does the biomass of the benthic invertebrates decline by more than 70%, the benthic community also shifts from surface feeders to belowground feeders that are inaccessible to foraging birds (Levin et. al. 2006). 1 The ISP uses the terms net area and treatment area to define the extent of non-native Spartina. Net area refers to the size of the infestation if the space between stems were subtracted from the overall footprint of the plant or clump of plants. Net area is the metric typically used in botanical surveys. Treatment area describes the area that will be directly affected by treatment. Treatment area is a separate measurement used for planning, and it is general 2 to 3 times greater than the net area of given instance of invasive Spartina. San Francisco Invasive Spartina Project 2 Target Species Desciriptions

84 CHILEAN CORDGRASS (SPARTINA DENSIFLORA) AND ITS HYBRID WITH PACIFIC CORDGRASS (S. FOLIOSA) Chilean cordgrass (also called dense-flowered cordgrass) is a distinctive cordgrass species native to South America that grows as a bunchgrass in the middle marsh plain, eventually forming tussocks and meadows (Spicher and Josselyn 1985; Kittelson and Boyd 1997). Spartina densiflora was introduced to California in Humboldt Bay by dry ship ballast containing propagules from South American ports that traded lumber (Spicher and Josselyn 1985). Thought for most of the 20 th century to be a form of Pacific cordgrass, S. densiflora was deliberately transplanted to a salt marsh restoration project at Creekside Park (4g) along Corte Madera Creek in Marin County in the 1970s. Within the salt marshes fringing Corte Madera Creek, it became a locallydominant component of the middle and high salt marsh vegetation, displacing even robust pickleweed. APPENDIX 1 While the bulk of the S. densiflora invasion has been contained within Marin around the Corte Madera Creek watershed, other populations have been detected and largely eliminated in Redwood City (19s), Point Pinole Regional Shoreline (Site 10), Burlingame (19k & 19l), Tom s Point (25a) in Tomales Bay, and the shoreline of San Pablo Bay National Wildlife Refuge (26b). Most of the novel population establishments appear to have been the result of active planting by anonymous parties. When established in close proximity to S. foliosa, S. densiflora has produced infertile hybrids with the native cordgrass that spread solely via vegetative growth (Ayres, Zaremba et al. 2008). By 2014, the population of S. densiflora had been reduced to 24 m 2 Estuary-wide, and 17 m 2 of the hybrid between S. foliosa and S. densiflora remained; both are reductions of more than 95% since the peak years for each. These successful reductions have been achieved through dedicated implementation of an adaptive Integrated Vegetation Management (IVM) strategy that includes multiple treatment methods. Because of the unique biology of this form of Spartina, any single-tool approach would have been ineffective. The efficacy of herbicide treatment (using imazapyr) varies widely between large plants and small plants, as well as between pioneering individuals and established stands. The seed bank viability of S. densiflora is estimated at 3 to 5 years (as compared to 1 to 1.5 years for S. alterniflora), which increases the time required for full eradication, even after an infestation is effectively reduced to just a few individuals. With these additional challenges, it is fortunate that S. densiflora appears to be somewhat limited in its ability to disperse around the San Francisco Bay ecosystem, and that the infestation has never approached the scale of hybrid S. alterniflora, which both consistently responds well to imazapyr treatment and has shorter seed viability. ENGLISH CORDGRASS (SPARTINA ANGLICA) English cordgrass is an aggressive invader of mudflats and salt marshes in Britain, New Zealand, Australia, and the Pacific Northwest, and thrives in cool temperate climates. It originated in Britain as a fertile hybrid derived from introduced Atlantic smooth cordgrass and common cordgrass (S. maritima). It was introduced to the San Francisco Estuary at Creekside Park (4g) along Corte Madera Creek in Marin San Francisco Invasive Spartina Project 3 Target Species Desciriptions

85 County, along with Chilean cordgrass (S. densiflora), in Unlike Atlantic smooth cordgrass and Chilean cordgrass, this species failed to disperse from its point of introduction to expand the infestation beyond Creekside Park. It may be at or near its southern climatic limit on the Pacific Coast in the Estuary. APPENDIX 1 Spartina anglica is nearly eradicated from San Francisco Bay, and it is not known to occur in any other location in California. The ISP mapped just 5.6 m 2 of S. anglica in There are several factors that contributed to this infestation lingering longer than might be expected given its relatively small size and presence at only a single ISP site. Spartina anglica flowers and sets seed in early summer, slightly later than S. densiflora but far ahead of hybrid S. alterniflora. This phenology did not allow for treatment ahead of seed dispersal prior to 2008, when ISP was first permitted to enter the sites before California clapper rail breeding season ends on September 1. In addition, there were several other years where either delayed permits (2011 and 2012 Biological Opinions) or political concerns (delays with Marin County finalizing its revised IPM Policy in 2009) caused the implementing ISP partner, Friends of Corte Madera Creek Watershed, to miss the optimal treatment window for that year. Finally, the remaining S. anglica at Creekside Park is often found growing as a short understory to the native S. foliosa that lines the main channel, which limited the full detection of the target plants, and the desire to preserve as much of the native cordgrass as possible further complicated the matter. SALT-MEADOW CORDGRASS (SPARTINA PATENS) In its native range on the Atlantic coast, salt-meadow cordgrass is naturally restricted to the well-drained high salt marsh and relatively moist sandy depressions at or above tidal influence. However, in the San Francisco Estuary, it has thrived along channel banks and on the pickleweed plain. Spartina patens arrived in the Estuary by the early 1960s in Southampton Marsh (Site 11; Benicia State Recreation Area), as evidenced by a sample present in the California Academy of Science s collection from circa At the initiation of treatment by ISP and the California Department of Parks and Recreation (State Parks), 0.65 net acre of salt-meadow cordgrass was present in large, discrete patches at Southampton Marsh. In 2014, the net cover was only 75 m 2, and treatment has been reinitiated after three years of hiatus due to complications related to the presence of three special status species. Spartina patens has spread into an area of Southampton Marsh that supports a population of an endangered annual hemi-parasitic plant, soft bird's-beak (Chloropyron molle ssp. molle, formerly Cordylanthus mollis ssp. mollis). The treatment approach initially approved and used in this area of the marsh was to treat the S. patens stands with herbicide in the late fall, after the soft bird s beak had produced seed and senesced, so that the treatment would not negatively affect the soft bird s beak population. However, S. patens itself flowers in San Francisco Invasive Spartina Project 4 Target Species Desciriptions

86 APPENDIX 1 May at that location, and by the time herbicide was applied in October, the S. patens plants had also already produced seed and begun senescing. When a plant senesces it is no longer able to uptake and translocate the herbicide, processes that are necessary to kill the plant. It soon was clear that no additional headway was being made toward eradication of S. patens. In 2011, the ISP worked with rare plant researcher Brenda Grewell (USDA-ARS) and State Parks to develop a new eradication plan to address the shortcomings of the earlier plan. The new plan would permit limited, temporary impacts to C. molle ssp. molle e so that the S. patens could be treated effectively, and may include collecting and banking seed from the hemi-parasite to sow once S. patens has been eradicated and native host plants reestablished. However, implementation of the new plan was postponed because of the reappearance of California Ridgway s rail in Southampton Marsh in 2011, after years of absence at the site. In an effort to nurture the potential new Ridgway s rail population, State Parks set up extensive marsh exclusion zones, including areas of S. patens populations, and again restricted entry for treatment until after October 1. As of 2014, no Ridgway s rails have been detected for three consecutive breeding seasons, and the eradication plan that was first conceived of in 2011 was finally implemented with resumed treatment. REFERENCES Anttila, C. K., R. A. King, et al. (2000). "Reciprocal hybrid formation of Spartina in San Francisco Bay." Molecular Ecology 9(6): Ayres, D. R., D. Garcia-Rossi, et al. (1999). "Extent and degree of hybridization between exotic (Spartina alterniflora) and native (S-foliosa) cordgrass (Poaceae) in California, USA determined by random amplified polymorphic DNA (RAPDs)." Molecular Ecology 8(7): Ayres, D. R., K. Zaremba, et al. (2008). "Sexual reproduction of cordgrass hybrids (Spartina foliosa x alterniflora) invading tidal marshes in San Francisco Bay." Diversity and Distributions 14(2): Boyer, K. E., J. C. Callaway, et al. (2000). "Evaluating the progress of restored cordgrass (Spartina foliosa) marshes: belowground biomass and tissue nitrogen." Estuaries 23: Cain, D. and H. Harvey (1983). "Evidence of salinity-induced ecophenic variation in cordgrass(spartina foliosa Trin.)." Madrono 30(1): Daehler, C. C. and D. R. Strong (1997). "Hybridization between introduced smooth cordgrass (Spartina alterniflora; Poaceae) and native California cordgrass (S-foliosa) in San Francisco Bay, California, USA." American Journal of Botany 84(5): Faber, P. (2000). "Grass Wars-- Good Intentions Gone Awry. Why would anyone Bring an Alien Cordgrass into S. F. Bay?" California Coast & Ocean 16(2): Kittelson, P. M. and M. J. Boyd (1997). "Mechanisms of expansion for an introduced species of cordgrass, Spartina densiflora, in Humboldt Bay, California." Estuaries 20(4): Levin, L. A., C. Neira, et al. (2006). "Invasive cordgrass modifies wetland trophic function." Ecology 87(2): Rhymer, J. M. and D. Simberloff (1996). "Extinction by hybridization and introgression." Annual Review of Ecological Systems 27: San Francisco Invasive Spartina Project 5 Target Species Desciriptions

87 APPENDIX 1 Smart, R. M. and J. W. Barko (1978). "Influence of sediment salinity and nutrients on the physiological ecology of selected salt marsh plants.." Estuarine and Coastal Marine Science 7: Spicher, D. and M. Josselyn (1985). "Spartina(Gramineae) in northern California: Distribution and taxonomic notes." Madrono 32(3): San Francisco Invasive Spartina Project 6 Target Species Desciriptions

88 APPENDIX 2: ISP Program Areas

89

90 APPENDIX 2 Invasive Spartina Project Programs The ISP is comprised of three broad programs treatment, monitoring, and restoration, which coordinate closely to achieve the ISP goals. Monitoring is comprised of several programs including Spartina inventory monitoring, treatment monitoring, California Ridgway s (formerly clapper ) rail monitoring, and water quality monitoring. Important tools within the monitoring programs are genetic sampling and analysis of Spartina, and photo point monitoring. The many programs work together to assure and document an effective regional treatment effort, while protecting water quality, wildlife, and the ecosystem structure. The status of each of the program areas is provided below. TREATMENT PROGRAM The Treatment Program coordinates a multitude of contractors, agencies, landowners, and staff to plan and conduct annual treatment of the various non-native Spartina species found throughout the Estuary. Pilot efforts to test herbicide methods and coordination mechanisms began in 2004, when the total known footprint of non-native Spartina was at that time 758 acres. In 2005, the ISP partners began coordinated, Estuary-wide treatment. Treatment initially focused on large infestations and areas where partners were most ready to begin work, and expanded to include the total of sites in 2006 and Aerial broadcast treatment by helicopter at several of the large hybrid Spartina monocultures of the central and south bay soon effectively reversed the spread of hybrid Spartina and established control over the infestations. Once continuous meadows of hybrid Spartina at sites like Alameda Flood Control Channel (Site 1), Eden Landing Ecological Reserve (Site 13) in Union City, and Seal Slough (19p) in San Mateo, were reduced to a patchy distribution of plants across each site, the herbicide methods were shifted away from broadcast spray to use of amphibious tracked vehicles on the mudflats and marsh plain, and hauling hose from trucks staged on surrounding levees to accessible marshes. Smaller infestations were treated by applicators with backpack sprayers walking through the marsh, as well as by manual removal of isolated seedlings. Spartina densiflora, a species that grows in a bunchgrass form and doesn t spread significantly by rhizome, was effectively controlled by a strategic combination of herbicide application and digging (see Chilean Cordgrass description in Appendix 1 of the 2014 ISP Monitoring and Treatment Report). After several years of regionally coordinated control work, the character of the infestations had changed. Very large meadows of non-native Spartina were rare, replaced by sparse infestations spread over larger areas that were more difficult to locate and access. New outlier populations were being discovered in more remote areas of the Estuary. By 2008, the ISP began to experiment with utilizing airboats on the open mud to allow treatment during low tide, thus maximizing herbicide dry time. The airboats were also used to deploy personnel with backpacks onto the marsh plain of islands and other sites San Francisco Invasive Spartina Project 1. ISP Programs

91 APPENDIX 2 that were inaccessible by land. By 2009, this approach was employed for treatment throughout Don Edwards San Francisco Bay National Wildlife Refuge (DENWR), and by 2012 there were as many as four airboats on a given day working on hybrid Spartina treatment around the Estuary. While the use of airboats in this way is essential for accessing difficult areas at this stage, the vast majority of herbicide treatment is conducted by trained personnel walking through the marsh with backpack herbicide sprayers. Similarly, there have been shifts in methodology for S. densiflora treatment. By 2012, all sites were using manual removal as the primary technique, with only two sites still requiring an early season application of herbicide to stop seed production until digging could be implemented after California Ridgway s rail breeding season. Mowing was also an important technique used early on in combination with other treatment methods at sites with meadows of S. densiflora, but the reductions achieved through the successful implementation of the adaptive IPM strategies allowed Friends of Corte Madera Creek to discontinue mowing in Control methods used in 2014 are listed by sub-area in each of the Reporting Region tables in the accompanying report. MONITORING PROGRAM Inventory Monitoring The ISP began Estuary-wide inventory monitoring of invasive Spartina in 2000, with annual monitoring of all known infestation sites beginning in The original geographic scope of inventory monitoring was limited to the bayward side of most major highways (Hogle 2008). Since 2006, all potential invasive Spartina habitat identified within the San Francisco Estuary and tidal tributaries, Bolinas Lagoon, Point Reyes National Seashore, and Tomales Bay has been surveyed by ISP biologists or its partners. This includes annual surveys over 50,000 acres of tidal marsh and mudflat throughout the Estuary and Outer Coast areas. The inventory area is shown in Section 2.1 of the 2014 Monitoring and Treatment Report. While the area inventoried covers some large remnant marshes as well as many fringe marshes, it also includes miles of flood control channels and many small fragmented marshes, channels and drainage ditches in a matrix of highly urbanized land use. Inventory monitoring is conducted for two purposes: to track change in the extent and net cover of the infestation over time for analyzing and reporting, and to locate and map patches of invasive Spartina to inform management and coordination of Treatment Program operations. The ISP typically completes inventory of sites prior to treatment (generally from May through October) to allow for the most efficient use of time and personnel during limited treatment windows. Minimizing time in the marsh during treatment also serves to minimize potential disturbance to marsh plants and animals. Data is collected using global positioning system (GPS) and managed using a Geographic Information System (GIS). Since 2008, all monitoring has been conducted on the ground or by helicopter for select large and remote sites where large patches of infestation persist. Ground mapping is done mostly on foot, but also by kayak and motorized boats when surveying islands, extensive shorelines, and lengthy waterways was the last year that ISP conducted monitoring by helicopter due to its inherent decrease in precision as compared to ground mapping. As of 2013, all sites previously monitored by helicopter have been reduced to a lower status of infestation level and warrant more detailed ground mapping. A history of the evolution of the ISP Monitoring Program between 2000 and 2012 (Zaremba and Hogle, in progress) is also available on the ISP website ( San Francisco Invasive Spartina Project 2. ISP Programs

92 Genetic Sampling and Analysis APPENDIX 2 Genetic analysis is a necessary tool for all of the ISP programs. Spartina leaf samples are collected and genetically analyzed to distinguish plants with native vs. non-native ancestry. Staff collect leaf samples from S. foliosa and hybrid S. alterniflora to verify identification of select plants, guide treatment practices, and keep an eye on new or changing plant morphologies. A genetic sampling plan is developed internally each season to address questions posed by the Treatment and Restoration programs and assure efficient use of limited laboratory resources. Samples are shipped to a commercial laboratory for extraction, and then sent to the UCLA Human Genomics Laboratory, where they are analyzed using Simple Sequence Repeats (SSRs; aka microsatellites ) and scored. The laboratory used fifteen SSR loci during the 2014 monitoring season. The ISP analyzes the data from UCLA using the software package Structure (Pritchard Lab, Stanford University) to determine, for every sampled plant, the likelihood of it being descended from S. alterniflora ancestry. The ISP incorporates these results into the program s GIS layers for further analysis and for reference in the field during future treatment and inventory events. Over 3,500 plants have been collected and analyzed in this manner since 2010, allowing the identification and treatment of many otherwise morphologically indistinct hybrid S. alterniflora plants throughout the Estuary. More information regarding the genetic sampling program is available in the Monitoring Program Quality Assurance Document ( and the ISP Spartina Monitoring Program Approach report referenced above. Photo Point Monitoring Another tool used by the Treatment and Monitoring Programs is photo point monitoring. The ISP established and has maintained 93 permanent locations within 51 sub-areas from which staff take consistent photos twice annually to qualitatively monitor marsh changes between seasons and years. Photo points are used to inform the extent of the next treatment effort and to visually document the changes in vegetation occurring at the sites. Visible changes often include rapid disappearance of large areas of nonnative Spartina within one to three seasons of treatment, passive (and frequently rapid) establishment of native vegetation, and expansion or rebounding of hybrid Spartina populations when treatment is missed or restricted for one or more seasons. The intra- and inter-annual visual comparisons of marsh composition are useful to the ISP for monitoring treatment efficacy and for presenting local trends to outside parties. These photos are especially useful to illustrate different marsh trajectories when comparing sites with continuous full treatment with those where treatment was absent or incomplete, as has happened since 2011 in 11 sub-areas a result of permit restrictions. An example of photo point data is provided on the next page. Also, all ISP Photo Point photos are available on the web, through Google Maps and Picasa Web Albums, at 82daadf691d97&t=h&z=10. Treatment Monitoring The ISP began monitoring all treatment events in Treatment monitoring involves pairing ISP personnel with the agency or private contractor treatment crews to accomplish the following important objectives: (1) assure protection of California Ridgway s rails and other sensitive species during treatment activities; (2) enhance conservation of native S. foliosa that may be present by delimiting it in no-treatment areas for the crew; (3) substantially improve the ability for crews to locate and target plants for treatment by leading them to less obvious plants requiring treatment; and (4) document completed San Francisco Invasive Spartina Project 3. ISP Programs

93 treatment in real time at the patch level. As previously mapped Spartina locations are revisited, ISP staff update the map features using GPS data loggers to reflect the day s treatment action (e.g. treated, not treated, sub-optimally treated etc.). This data is uploaded daily to the ISP s ArcGIS geodatabase for use in the field the next day. Accompanying treatment crews also allows ISP staff to identify, mapping, and concurrently record treatment of patches of invasive Spartina that had not been detected during initial inventory monitoring. Treatment monitoring is perhaps the most important of the ISP s new programmatic initiatives, allowing ISP partners to gain ground on the remaining substantial infestations in the West Bay, and greatly accelerating the rate at which eradication may be achieved at all sites. APPENDIX 2 Since the timing of inventory and treatment overlap from mid-july through November, the ISP hires additional staff (interns) to conduct treatment monitoring at suitable sites that is, at sites where native Spartina is not present, where hybrid Spartina has been recently mapped by more experienced staff, or where native and hybrid morphologies are sufficiently distinct to allow the interns to make consistently correct determinations. More experienced biologists are thus reserved to inventory and monitor treatment at more complex sites. The ISP employed three interns for the 2014 monitoring season to conduct treatment surveys and assist with inventory. California Ridgway s Rail Monitoring An example of photo point monitoring data showing habitat transition over several years. Implementation of Spartina control measures requires annual breeding season surveys of the endangered California Ridgway s rail (Rallus obsoletus obsoletus) in marshes affected by the invasion and management of non-native Spartina. Annual breeding season surveys provide a standardized measure of San Francisco Invasive Spartina Project 4. ISP Programs