Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools
Abstract Vernal pools are temporary wetlands that can form during a rainy season, often in Mediterranean climates, and serve as ideal testing grounds to understand species detection using eDNA and how biological communities may shift across time and spatial and environmental heterogeneity. Most vern...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-01-01
|
| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.360 |
| _version_ | 1797946761148366848 |
|---|---|
| author | Dannise V. Ruiz‐Ramos Rachel S. Meyer Daniel Toews Molly Stephens Monique K. Kolster Jason P. Sexton |
| author_facet | Dannise V. Ruiz‐Ramos Rachel S. Meyer Daniel Toews Molly Stephens Monique K. Kolster Jason P. Sexton |
| author_sort | Dannise V. Ruiz‐Ramos |
| collection | DOAJ |
| description | Abstract Vernal pools are temporary wetlands that can form during a rainy season, often in Mediterranean climates, and serve as ideal testing grounds to understand species detection using eDNA and how biological communities may shift across time and spatial and environmental heterogeneity. Most vernal pools exhibit high plant and animal diversity and endemism, but due to their ephemeral nature, they are understudied, especially their microorganisms. Habitat destruction and fragmentation creates an urgent need to monitor their biodiversity, but traditional species surveys require time and taxonomic expertise. We conducted a community science‐enabled examination of soil environmental DNA (eDNA) in California's Great Central Valley and assessed the capacity of eDNA to aid biomonitoring. We used metabarcoding of 16S, ITS1, CO1, 18S, and ITS2 marker regions to quantify and compare differences in pool communities across two sampling periods (during years with disparate precipitation) and to estimate variation among pools and inundation zones (vernal pool bottom, transitional edge, and grassland upland). We found differences in beta diversity among sampling periods, pools, and inundation zones; alpha diversity was mainly affected by sampling period and zone, but this differed by marker. Numerous taxonomic families varied in abundance and composition among samples, yet vernal pool communities remained distinct from upland grass communities, even between sampling periods differing by 1 year. Turnover in ecologically co‐occurring taxon pairs varied by over 90% between sampling periods in all metabarcodes but plants, which were more stable. Finally, we confirmed substantial concordance between eDNA and traditional inventories of the reserve's plants and presented a case in which we detected one endangered plant species, Colusa grass (Neostapfia colusana), in advance of its emergence. This initial study adds hundreds of new taxon records for California vernal pools and discusses benefits and challenges of using eDNA for biomonitoring within stressful, temporary, or otherwise challenging ecosystems. |
| first_indexed | 2024-04-10T21:16:08Z |
| format | Article |
| id | doaj.art-36c6a045118f4ca581a316bd8556f65b |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-04-10T21:16:08Z |
| publishDate | 2023-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-36c6a045118f4ca581a316bd8556f65b2023-01-20T12:18:11ZengWileyEnvironmental DNA2637-49432023-01-01518510110.1002/edn3.360Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal poolsDannise V. Ruiz‐Ramos0Rachel S. Meyer1Daniel Toews2Molly Stephens3Monique K. Kolster4Jason P. Sexton5Department of Life and Environmental Sciences University of California Merced California USAUniversity of California Los Angeles California USADepartment of Life and Environmental Sciences University of California Merced California USADepartment of Life and Environmental Sciences University of California Merced California USAMerced Vernal Pools & Grassland Reserve University of California Merced California USADepartment of Life and Environmental Sciences University of California Merced California USAAbstract Vernal pools are temporary wetlands that can form during a rainy season, often in Mediterranean climates, and serve as ideal testing grounds to understand species detection using eDNA and how biological communities may shift across time and spatial and environmental heterogeneity. Most vernal pools exhibit high plant and animal diversity and endemism, but due to their ephemeral nature, they are understudied, especially their microorganisms. Habitat destruction and fragmentation creates an urgent need to monitor their biodiversity, but traditional species surveys require time and taxonomic expertise. We conducted a community science‐enabled examination of soil environmental DNA (eDNA) in California's Great Central Valley and assessed the capacity of eDNA to aid biomonitoring. We used metabarcoding of 16S, ITS1, CO1, 18S, and ITS2 marker regions to quantify and compare differences in pool communities across two sampling periods (during years with disparate precipitation) and to estimate variation among pools and inundation zones (vernal pool bottom, transitional edge, and grassland upland). We found differences in beta diversity among sampling periods, pools, and inundation zones; alpha diversity was mainly affected by sampling period and zone, but this differed by marker. Numerous taxonomic families varied in abundance and composition among samples, yet vernal pool communities remained distinct from upland grass communities, even between sampling periods differing by 1 year. Turnover in ecologically co‐occurring taxon pairs varied by over 90% between sampling periods in all metabarcodes but plants, which were more stable. Finally, we confirmed substantial concordance between eDNA and traditional inventories of the reserve's plants and presented a case in which we detected one endangered plant species, Colusa grass (Neostapfia colusana), in advance of its emergence. This initial study adds hundreds of new taxon records for California vernal pools and discusses benefits and challenges of using eDNA for biomonitoring within stressful, temporary, or otherwise challenging ecosystems.https://doi.org/10.1002/edn3.360biodiversitybiotic interactionsCaliforniaCentral Valleyenvironmental DNAmetabarcoding |
| spellingShingle | Dannise V. Ruiz‐Ramos Rachel S. Meyer Daniel Toews Molly Stephens Monique K. Kolster Jason P. Sexton Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools Environmental DNA biodiversity biotic interactions California Central Valley environmental DNA metabarcoding |
| title | Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools |
| title_full | Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools |
| title_fullStr | Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools |
| title_full_unstemmed | Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools |
| title_short | Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools |
| title_sort | environmental dna edna detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems a case study in vernal pools |
| topic | biodiversity biotic interactions California Central Valley environmental DNA metabarcoding |
| url | https://doi.org/10.1002/edn3.360 |
| work_keys_str_mv | AT dannisevruizramos environmentaldnaednadetectstemporalandhabitateffectsoncommunitycompositionandendangeredspeciesinephemeralecosystemsacasestudyinvernalpools AT rachelsmeyer environmentaldnaednadetectstemporalandhabitateffectsoncommunitycompositionandendangeredspeciesinephemeralecosystemsacasestudyinvernalpools AT danieltoews environmentaldnaednadetectstemporalandhabitateffectsoncommunitycompositionandendangeredspeciesinephemeralecosystemsacasestudyinvernalpools AT mollystephens environmentaldnaednadetectstemporalandhabitateffectsoncommunitycompositionandendangeredspeciesinephemeralecosystemsacasestudyinvernalpools AT moniquekkolster environmentaldnaednadetectstemporalandhabitateffectsoncommunitycompositionandendangeredspeciesinephemeralecosystemsacasestudyinvernalpools AT jasonpsexton environmentaldnaednadetectstemporalandhabitateffectsoncommunitycompositionandendangeredspeciesinephemeralecosystemsacasestudyinvernalpools |