Traditional and emergent molecular techniques to characterize species biodiversity and ecosystem health (plus a bunch of other stuff)

Transcription

1 Traditional and emergent molecular techniques to characterize species biodiversity and ecosystem health (plus a bunch of other stuff) Heather Bracken Grissom Florida International University

2 Tracey Sutton, Kevin Boswell, April Cook, Sergio derada, David English, Ron Eytan, Danté Fenolio, Tamara Frank, Chuanmin Hu, Heather Judkins, Chad Lembke, Joseph Lopez, Jon Moore, Martha Nizinski, Brad Penta, Isabel Romero, Jay Rooker, Mahmood Shivji, Michael Vecchione, David Wells, Marsh Youngbluth

3 Mission Statement The DEEPEND consortium will characterize the oceanic ecosystem of the northern Gulf of Mexico to infer baseline conditions in the water column. This information will establish a time-series with which natural and anthropogenic changes can be detected.

4 Objective 1: How does oceanic biodiversity vary with space and time? Photos: Fenolio, Frank, Shale, Youngbluth, and Zankl

5 DEEPEND field sampling technology surface 200 m 600 m 1000 m 1200 m 1500 m R/V Point Sur 10-m 2 MOCNESS

6 Biodiversity and Community Structure Alpha taxonomy Tracey Sutton, Jon Moore, Ted Pietsch, Chris Kenaley, Dave Johnson, John Paxton DEEPEND Imaging Project: Danté Fenolio (SAZ)

7 Biodiversity and Community Structure Alpha taxonomy Tammy Frank (NSU), Martha Nizinski (NOAA), Heather Bracken-Grissom (FIU), Heather Judkins (USFSP), Mike Vecchione (NOAA), Marsh Youngbluth (HBOI-FAU)

8 Genetic Taxonomy Using DNA Barcoding Methods to document biodiversity and create species inventories Ron Eytan (TAMU), Mahmood Shivji (NSU), Joe Lopez (NSU), Heather Bracken-Grissom (FIU), Heather Judkins (USFSP)

9 DNA Barcoding Method used to identify organisms Much like assigning a numerical barcode to shopping item Sequence a ~600 base pair segment of DNA to reveal an organism barcode Organisms have unique DNA sequences for each species

10 DNA Barcoding Protocol Extracted DNA from muscle tissue PCR amplification DNA sequencing Selected genes with enough variation to detect species-level differences (COI, 16S) To date: 400 species fish, 100 species of crustaceans, 20 species of cephalopods

11 Why Barcode? Allows us to identify organisms based on DNA sequences and create species inventories Useful in discovery of new species OR when specimen is damaged, mutilated or identity is unknown/uncertain Allows us to make larval-adult linkages Useful when larval forms differs from adult counterpart Provides insights into the ecology and life history of the species Example = Cerataspis monstrosa (Bracken-Grissom et al. 2012) Larval form Adult

12 From Barcoding to Ecosystem Health, Recovery and Resilience

13 Objective 2: Are there longer-term consequences of DWHOS on the pelagic communities? ~ 1500 m Photos:Fenolio

14 Using genetic information, we are able to establish and measure proxies for health and resilience of an ecosystem.

15 Genetic Diversity (GD) is a proxy for ecosystem health Connectivity is a proxy for ecosystem resilience Spain Hughes et al., 2008 Mullus surmuletus, Felix-Hackradt et al Black lines = direct ecological consequences of GD Dotted lines = indirect ecological consequences of GD

16 How do we measure genetic diversity and connectivity? Comparisons will be made across populations within a species across time and space Extract DNA from ~20-30 individuals per population Recent advancements in DNA sequencing technology allows us to scan the entire genome Method called: Double Digest Restriction site associated DNA Sequencing or ddradseq

17 RADseq Protocol 1. Digest the genomic DNA with restriction enzymes 2. Attach a short barcode sequence that will allow you link the piece of DNA to an individual or species Do this multiple times throughout the genome and for many individuals (pool samples) 4. Sequence the DNA on a next-generation sequencing platform (ex. Illumina) Run an analysis that will allow you to compare all the same pieces of DNA. Identify DNA difference across the entire genome (1000s-10,000s basepairs) 5.

18 Genetic Diversity will be compared across temporal and spatial scales Total ( ): 235 sea-days, 1580 samples (Gulf of Mexico Offshore Nekton Sampling and Analysis Program) Total ( ): 78 sea-days, TBD samples (DEEPEND) NOAA FSV Pisces /V Meg Skansi 6 species of fish, 9 species of crustaceans and 3 species of cephalopods have been targeted Do we see evidence for changes in GD pre- and post spill? Document the natural variation in GD across temporal scales?

19 Connectivity studies are underway to study resilience and recovery of GoM Bear Seamount, N. Atlantic Gulf of Mexico FL Straits

20 Additional DEEPEND field sampling technology

21 DEEPEND field sampling Plankton M/V Blazing Seven Neuston/bongo nets

22 DEEPEND field sampling MOC10/Oceanography Cruise track Stations and watermasses DEEPEND cruise DP01 May fish spp. Astronesthes sp. nov.

23 Community Structure and Numerical Modelling Bio-acoustic Oceanography Kevin Boswell (FIU) Joe Warren (Stony Brook) Transducer Example of the mesopelagic layers that move between day and night. The highest density of animals is displayed in red and the lowest density is shown in dark blue. The microscopic view from the SONAR on the CTD shows the individuals that live in these migrating layers.

24 Community Structure and Numerical Modelling Meso-Scale Oceanography

25 Community Structure and Numerical Modelling Meso-Scale Oceanography Chuanmin Hu, Dave English, Chad Lembke (USF)

26 Please visit us at: Isistius plutodus, GoM THANK YOU!