Exploring the ecological relevance of edna in freshwater ecosystems

Transcription

1 Molecular Ecology and Fisheries Genetics Laboratory Exploring the ecological relevance of edna in freshwater ecosystems Si

2 Types of environmentally derived DNA Community DNA - DNA that comes from many individuals representing several species, and is isolated from actual sampled organisms edna - Free DNA molecules are ubiquitous, released from skin, mucous, saliva, sperm, secretions, eggs, faeces, urine, blood, root, leaves, fruit, pollen, and rotting bodies, and are collectively referred to as environmental DNA (edna) Creer et al Methods in Ecology and Evolution

3 Barnes and Turner Conservation Genetics

4 edna fate/persistence Artificial trials suggest that edna persists for days to weeks

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6 Understanding the ecological relevance of community freshwater edna in a natural lake ecosystem Iliana Bista edna Community DNA: Exuviae Annual cycle

7 Understanding the ecological relevance of community freshwater edna in a natural lake ecosystem n=38 Iliana Bista n=31 n=32 Bista et al. Nat. Comms. 2017

8 Understanding the ecological relevance of community freshwater edna in a natural lake ecosystem Iliana Bista Bista et al. Nat. Comms. 2017

9 Understanding the ecological relevance of community freshwater edna in a natural lake ecosystem Summer Iliana Bista COIF Winter Spring COIS Summer Spring-Winter Animalia Bista et al. Nat. Comms. 2017

10 Understanding the ecological relevance of community freshwater edna in a natural lake ecosystem Iliana Bista Bista et al. Nature Comms 2017

11 Barnes and Turner Conservation Genetics

12 Figure 3. Observed and predicted detection of edna along river transect. Deiner K, Altermatt F (2014) Transport Distance of Invertebrate Environmental DNA in a Natural River. PLoS ONE 9(2): e doi: /journal.pone

13 Molecular genetic solutions NERC Highlight Topic Grant ( 1.25M): Understanding the ecological relevance of edna in freshwater lotic ecosystems edna:lofresh To understand the spatial, temporal and ecological relevance of temperate lotic edna in relation to functional community biodiversity and explore linkages to freshwater ecosystem function.

14 Aims: To understand the spatial, temporal and ecological relevance of temperate lotic edna in relation to functional community biodiversity. Work packages WP1. Quantify the persistence and loss of lotic community edna and controlling factors (e.g. ph and dissolved organic carbon). Bangor Creer, DeBruyn, Carvalho, Seymour Co-ordination; edna wet lab All WPs CEH - Cosby, Edwards Ecology, Conwy and national field support, statistics WP1,2,3,5 Cardiff Durance, Ormerod Ecology, Llyn Brianne support WP1, WP5 Birmingham, Riverside Colbourne, Bik PDRA2 Sequencing; informatics WP4

15 Molecular genetic solutions Quantitative PCR (qpcr) - represents the gold standard in both the qualitative and quantitative assessment of cells/biomass Metabarcoding - high throughput DNA-based identification of multiple species from a.. complex mixture Mitochondrial genome shotgun environmental sequencing

16 Aims: To understand the spatial, temporal and ecological relevance of temperate lotic edna in relation to functional community biodiversity. Work packages WP2.(a.) Test experimentally derived estimates of edna persistence at the catchment scale; and (b.) Assess and quantify the linkages between edna profiles and the functional biodiversity in natural streams experiencing different land use pressures. Bangor Creer, DeBruyn, Carvalho, Seymour Co-ordination; edna wet lab All WPs CEH - Cosby, Edwards Ecology, Conwy and national field support, statistics WP1,2,3,5 Cardiff Durance, Ormerod Ecology, Llyn Brianne support WP1, WP5 Birmingham, Riverside Colbourne, Bik PDRA2 Sequencing; informatics WP4

17 Aims: To understand the spatial, temporal and ecological relevance of temperate lotic edna in relation to functional community biodiversity. Work packages WP3. Explore linkages between edna profiles, land use, physicochemical/environmental parameters and functional biodiversity at the landscape scale and explore predictive power at the national scale. Bangor Creer, DeBruyn, Carvalho, Seymour Co-ordination; edna wet lab All WPs CEH - Cosby, Edwards Ecology, Conwy and national field support, statistics WP1,2,3,5 Cardiff Durance, Ormerod Ecology, Llyn Brianne support WP1, WP5 Birmingham, Riverside Colbourne, Bik PDRA2 Sequencing; informatics WP4

18 Aims: To understand the spatial, temporal and ecological relevance of temperate lotic edna in relation to functional community biodiversity. Work packages WP4. Develop ecologically and phylogenetically informed novel workflows to delimit species level information from metabarcoding and metagenomic edna analyses. Bangor Creer, DeBruyn, Carvalho, Seymour Co-ordination; edna wet lab All WPs CEH - Cosby, Edwards Ecology, Conwy and national field support, statistics WP1,2,3,5 Caitlin Potter Cardiff Durance, Ormerod Ecology, Llyn Brianne support WP1, WP5 Birmingham, Riverside Colbourne, Bik PDRA2 Sequencing; informatics WP4 In revision PeerJ

19 Aims: To understand the spatial, temporal and ecological relevance of temperate lotic edna in relation to functional community biodiversity. Work packages WP5. Experimentally test the linkages between land use pressures and edna signals in relation to freshwater decomposition, a primary lotic ecosystem function. Bangor Creer, DeBruyn, Carvalho, Seymour Co-ordination; edna wet lab All WPs CEH - Cosby, Edwards Ecology, Conwy and national field support, statistics WP1,2,3,5 Cardiff Durance, Ormerod Ecology, Llyn Brianne support WP1, WP5 Birmingham, Riverside Colbourne, Bik PDRA2 Sequencing; informatics WP4

20 Molecular Ecology and Fisheries Genetics Laboratory

21 Synthesis Freshwater lentic edna analysis provides ecologically tractable data of ecosystem level community biodiversity at the annual timescale Taxonomy Extant community Appropriate temporal scales Future investigations into lotic edna will complement existing findings wrt fate and transport

22 Universities Gov Orgs UK edna network Ecological Consultancies NGOs

23 Molecular Ecology and Fisheries Genetics Laboratory Collaborators and contributors Mat Seymour Iliana Bista Vera Fonseca Delphine Lallias Kelley Thomas John Gaspar Gary Carvalho Kerry Walsh Martin Christmas Mehrdad Hajibabaei Tristan Hatton-Ellis Matt Morgan Cuong Tang

24 LOFRESH systems and multi-omic tools Kristy Deiner Llyn Brianne (DURESS) experimental streams

25 Understanding the ecological relevance of community freshwater edna in a natural lake ecosystem Iliana Bista The FBA Gilson Le Cren Memorial Award 2014; NBAF grant

26 Bista et al. Nat. Comms. Final tech revisions n=73

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28 Zhou Beijing Genomics Institute, China Morgan CSIRO, Australia Bangor Creer, DeBruyn, Carvalho, Seymour Co-ordination; edna wet lab All WPs CEH - Cosby, Edwards Ecology, Conwy and national field support, statistics WP1,2,3,5 Lodge, Pfrender Cornell, Notre Dame Cardiff Birmingham, Riverside Tang NHM, London Durance, Ormerod Ecology, Llyn Brianne support WP1, WP5 Colbourne, Bik PDRA2 Sequencing; informatics WP4 Deiner Cornell Taberlet, Valentini CNRS Laboratoire d'ecologie Alpine, SPYGEN