How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection
ABSTRACT Environmental DNA (eDNA) is a complex mixture of DNA, varying in particle sizes and distributed heterogeneously in aquatic systems. Optimizing eDNA sampling is crucial for maximizing species detection, particularly in high‐risk scenarios like invasive species management. In this study, we c...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-11-01
|
| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.70042 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832582972938649600 |
|---|---|
| author | Anish Kirtane Leif Howard Caitlin E. Beaver Margaret E. Hunter Gordon Luikart Kristy Deiner |
| author_facet | Anish Kirtane Leif Howard Caitlin E. Beaver Margaret E. Hunter Gordon Luikart Kristy Deiner |
| author_sort | Anish Kirtane |
| collection | DOAJ |
| description | ABSTRACT Environmental DNA (eDNA) is a complex mixture of DNA, varying in particle sizes and distributed heterogeneously in aquatic systems. Optimizing eDNA sampling is crucial for maximizing species detection, particularly in high‐risk scenarios like invasive species management. In this study, we compare two eDNA sampling methods ‐ namely tow net and grab sample, where the tow nets process large volumes of water (3500–7000 L) through a 64 μm pore size and the grab samples process 1 L sample at a single point through 0.45–1.2 μm pore size membranes. We compared these methods to ascertain what most influences (1) the detection of invasive species (Dreissena mussels and Burmese pythons) using qPCR or ddPCR and (2) total diversity monitoring of metazoan, protist, and fungi community using a COI marker and plant communities using the ITS marker. Sampling was conducted across a wide geography and diverse aquatic environments in Minnesota and Florida, USA, and Switzerland. The tow net samples had significantly higher eDNA yield compared to grab samples; however, they exhibited equal or lower alpha diversity of OTUs (Operational Taxonomic Units). The two sampling methods measured different beta diversity of communities detected with the COI marker across all three regions, highlighting the impact of the sampling method on the diversity of eDNA captured. In comparison, the beta diversity of plant eDNA was less impacted by the sampling method. We found no clear difference in detection for the invasive species targets based on the eDNA sampling method. These results underscore the need for pilot studies before conducting biodiversity inventory and monitoring, and a need for a greater understanding of not just how much, but also what, eDNA is captured depending on method choice, considering both spatial and particle size heterogeneity. |
| format | Article |
| id | doaj-art-bb4fe2474b07450a9d8d17893d3b1453 |
| institution | Kabale University |
| issn | 2637-4943 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj-art-bb4fe2474b07450a9d8d17893d3b14532025-01-29T05:11:50ZengWileyEnvironmental DNA2637-49432024-11-0166n/an/a10.1002/edn3.70042How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species DetectionAnish Kirtane0Leif Howard1Caitlin E. Beaver2Margaret E. Hunter3Gordon Luikart4Kristy Deiner5Institute of Biogeochemistry and Pollutant Dynamics Eidgenössische Technische Hochschule Zürich Zürich SwitzerlandDivision of Biological Sciences, Wildlife Biology Program University of Montana Missoula Montana USAU.S. Geological Survey Wetland and Aquatic Research Center Gainesville Florida USAU.S. Geological Survey Wetland and Aquatic Research Center Gainesville Florida USADivision of Biological Sciences, Wildlife Biology Program University of Montana Missoula Montana USAInstitute of Biogeochemistry and Pollutant Dynamics Eidgenössische Technische Hochschule Zürich Zürich SwitzerlandABSTRACT Environmental DNA (eDNA) is a complex mixture of DNA, varying in particle sizes and distributed heterogeneously in aquatic systems. Optimizing eDNA sampling is crucial for maximizing species detection, particularly in high‐risk scenarios like invasive species management. In this study, we compare two eDNA sampling methods ‐ namely tow net and grab sample, where the tow nets process large volumes of water (3500–7000 L) through a 64 μm pore size and the grab samples process 1 L sample at a single point through 0.45–1.2 μm pore size membranes. We compared these methods to ascertain what most influences (1) the detection of invasive species (Dreissena mussels and Burmese pythons) using qPCR or ddPCR and (2) total diversity monitoring of metazoan, protist, and fungi community using a COI marker and plant communities using the ITS marker. Sampling was conducted across a wide geography and diverse aquatic environments in Minnesota and Florida, USA, and Switzerland. The tow net samples had significantly higher eDNA yield compared to grab samples; however, they exhibited equal or lower alpha diversity of OTUs (Operational Taxonomic Units). The two sampling methods measured different beta diversity of communities detected with the COI marker across all three regions, highlighting the impact of the sampling method on the diversity of eDNA captured. In comparison, the beta diversity of plant eDNA was less impacted by the sampling method. We found no clear difference in detection for the invasive species targets based on the eDNA sampling method. These results underscore the need for pilot studies before conducting biodiversity inventory and monitoring, and a need for a greater understanding of not just how much, but also what, eDNA is captured depending on method choice, considering both spatial and particle size heterogeneity.https://doi.org/10.1002/edn3.70042biodiversity monitoringeDNAinvasive specieslarge‐volume samplingmetabarcodingqPCR |
| spellingShingle | Anish Kirtane Leif Howard Caitlin E. Beaver Margaret E. Hunter Gordon Luikart Kristy Deiner How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection Environmental DNA biodiversity monitoring eDNA invasive species large‐volume sampling metabarcoding qPCR |
| title | How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection |
| title_full | How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection |
| title_fullStr | How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection |
| title_full_unstemmed | How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection |
| title_short | How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection |
| title_sort | how what and where you sample environmental dna affects diversity estimates and species detection |
| topic | biodiversity monitoring eDNA invasive species large‐volume sampling metabarcoding qPCR |
| url | https://doi.org/10.1002/edn3.70042 |
| work_keys_str_mv | AT anishkirtane howwhatandwhereyousampleenvironmentaldnaaffectsdiversityestimatesandspeciesdetection AT leifhoward howwhatandwhereyousampleenvironmentaldnaaffectsdiversityestimatesandspeciesdetection AT caitlinebeaver howwhatandwhereyousampleenvironmentaldnaaffectsdiversityestimatesandspeciesdetection AT margaretehunter howwhatandwhereyousampleenvironmentaldnaaffectsdiversityestimatesandspeciesdetection AT gordonluikart howwhatandwhereyousampleenvironmentaldnaaffectsdiversityestimatesandspeciesdetection AT kristydeiner howwhatandwhereyousampleenvironmentaldnaaffectsdiversityestimatesandspeciesdetection |