Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication
Abstract Biodiversity monitoring in conservation projects is essential to understand environmental health, complexity, and recovery. However, traditional field surveys can be expensive, time‐consuming, biased toward visual detection, and/or only measure a limited set of taxa. Environmental DNA (eDNA...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-01-01
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| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.445 |
| _version_ | 1827329475689316352 |
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| author | Kimberly M. Ballare Anna Worth Tyler Goodearly Dannise V. Ruiz‐Ramos Eric Beraut Hailey Nava Colin Fairbairn Robert K. Wayne Beth Shapiro Ginny Short Rachel S. Meyer |
| author_facet | Kimberly M. Ballare Anna Worth Tyler Goodearly Dannise V. Ruiz‐Ramos Eric Beraut Hailey Nava Colin Fairbairn Robert K. Wayne Beth Shapiro Ginny Short Rachel S. Meyer |
| author_sort | Kimberly M. Ballare |
| collection | DOAJ |
| description | Abstract Biodiversity monitoring in conservation projects is essential to understand environmental health, complexity, and recovery. However, traditional field surveys can be expensive, time‐consuming, biased toward visual detection, and/or only measure a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has the potential to sample a taxonomically broader set of organisms with a similar effort, but many of these approaches are still in the early stages of development and testing. Here, we used multi‐locus eDNA metabarcoding to understand how the removal of invasive red swamp crayfish using cypermethrin pesticide impacts local biodiversity of a desert oasis ecosystem, as well as to detect crayfish both directly and indirectly. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish directly in either control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes, similar to previous studies which have shown variable levels of success in detecting crayfish from environmental samples. However, we were successful in discerning a suite of 90 crayfish‐associated taxa to serve as candidate bioindicators of invasive presence using 16S and fungal ITS2 metabarcoding. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish associations in the literature, we support nine taxa to be high ranking, and suggest they be prioritized in future biomonitoring. Biodiversity analyses from five metabarcode loci including plants, animals, and both prokaryotic and eukaryotic microbes showed that communities differed but that species richness remained relatively similar between oases through time. Our results reveal that, while there are limitations of eDNA approaches to detect crayfish and other invasive species, microbial bioindicators offer a largely untapped biomonitoring opportunity for invasive species management, adding a valuable resource to a conservation manager's toolkit. |
| first_indexed | 2024-03-07T15:37:21Z |
| format | Article |
| id | doaj.art-1943f0d00b5249509ef88e6d79b1a870 |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-03-07T15:37:21Z |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-1943f0d00b5249509ef88e6d79b1a8702024-03-05T09:32:37ZengWileyEnvironmental DNA2637-49432024-01-0161n/an/a10.1002/edn3.445Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradicationKimberly M. Ballare0Anna Worth1Tyler Goodearly2Dannise V. Ruiz‐Ramos3Eric Beraut4Hailey Nava5Colin Fairbairn6Robert K. Wayne7Beth Shapiro8Ginny Short9Rachel S. Meyer10Department of Ecology and Evolutionary Biology University of California Santa Cruz California USADepartment of Ecology and Evolutionary Biology University of California Santa Cruz California USACenter for Natural Lands Management Temecula California USADepartment of Life and Environmental Sciences University of California Merced California USADepartment of Ecology and Evolutionary Biology University of California Los Angeles California USADepartment of Ecology and Evolutionary Biology University of California Santa Cruz California USADepartment of Ecology and Evolutionary Biology University of California Santa Cruz California USADepartment of Ecology and Evolutionary Biology University of California Los Angeles California USADepartment of Ecology and Evolutionary Biology University of California Santa Cruz California USACenter for Natural Lands Management Temecula California USADepartment of Ecology and Evolutionary Biology University of California Santa Cruz California USAAbstract Biodiversity monitoring in conservation projects is essential to understand environmental health, complexity, and recovery. However, traditional field surveys can be expensive, time‐consuming, biased toward visual detection, and/or only measure a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has the potential to sample a taxonomically broader set of organisms with a similar effort, but many of these approaches are still in the early stages of development and testing. Here, we used multi‐locus eDNA metabarcoding to understand how the removal of invasive red swamp crayfish using cypermethrin pesticide impacts local biodiversity of a desert oasis ecosystem, as well as to detect crayfish both directly and indirectly. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish directly in either control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes, similar to previous studies which have shown variable levels of success in detecting crayfish from environmental samples. However, we were successful in discerning a suite of 90 crayfish‐associated taxa to serve as candidate bioindicators of invasive presence using 16S and fungal ITS2 metabarcoding. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish associations in the literature, we support nine taxa to be high ranking, and suggest they be prioritized in future biomonitoring. Biodiversity analyses from five metabarcode loci including plants, animals, and both prokaryotic and eukaryotic microbes showed that communities differed but that species richness remained relatively similar between oases through time. Our results reveal that, while there are limitations of eDNA approaches to detect crayfish and other invasive species, microbial bioindicators offer a largely untapped biomonitoring opportunity for invasive species management, adding a valuable resource to a conservation manager's toolkit.https://doi.org/10.1002/edn3.445bioindicatorsconservation managementeDNAholobiomeProcambarus clarkiirestoration |
| spellingShingle | Kimberly M. Ballare Anna Worth Tyler Goodearly Dannise V. Ruiz‐Ramos Eric Beraut Hailey Nava Colin Fairbairn Robert K. Wayne Beth Shapiro Ginny Short Rachel S. Meyer Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication Environmental DNA bioindicators conservation management eDNA holobiome Procambarus clarkii restoration |
| title | Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication |
| title_full | Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication |
| title_fullStr | Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication |
| title_full_unstemmed | Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication |
| title_short | Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication |
| title_sort | environmental dna reveals invasive crayfish microbial associates and ecosystem wide biodiversity before and after eradication |
| topic | bioindicators conservation management eDNA holobiome Procambarus clarkii restoration |
| url | https://doi.org/10.1002/edn3.445 |
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