Using eDNA Metabarcoding to Monitor Changes in Fish Community Composition After Barrier Removal

Artificial instream barriers are a major cause of habitat fragmentation that reduce population connectivity and gene flow by limiting fish movements. To mitigate their impacts, obsolete barriers are increasingly been removed worldwide, but few barrier removal projects are monitored. We employed a powerful Before-After-Downstream-Upstream (BADU) approach using environmental DNA (eDNA) metabarcoding to examine the effects on fish community composition of removing a weir in the river Lugg (England) that had been suggested to have a detrimental effect on salmonid migration. We found no change in fish community diversity or relative abundance after the removal above or below the weir, but detected an important effect of sampling season, likely related to the species' life cycles. eDNA detected nine fish species that were also identified by electrofishing sampling and one additional species (Anguilla anguilla) that was missed by traditional surveys. Our results suggest that monitoring of barrier removal projects should be carried out to ensure that any ecological benefits are properly documented and that eDNA metabarcoding is a sensitive technique to monitor the effects of barrier removal.

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Environmental nucleic acids: a field-based comparison for monitoring freshwater habitats using eDNA and eRNA

10.1101/2021.12.01.469845 ◽

2021 ◽

Author(s):

Joanne E. Littlefair ◽

Michael D. Rennie ◽

Melania E. Cristescu

Keyword(s):

Nucleic Acids ◽

Community Composition ◽

Fish Community ◽

Environmental Dna ◽

True Positive Rate ◽

Molecular Monitoring ◽

Dna And Rna ◽

Monitoring Tools ◽

Fish Community Composition ◽

Biomonitoring Tool

AbstractNucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received attention recently, the potential of environmental RNA as a biomonitoring tool remains less explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect “metabolically active” parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra-organismal RNA will be important, but viability needs to be examined in a field-based setting. In this study we evaluate (a) whether extra-organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools.

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Fish-community composition in Mill Creek, Crooked Creek, and Tioga River in the vicinity of Tioga-Hammond Dams, Tioga County, Pennsylvania, 1998

Open-File Report ◽

10.3133/ofr99210 ◽

1999 ◽

Author(s):

Robin A. Brightbill ◽

Michael D. Bilger

Keyword(s):

Community Composition ◽

Fish Community ◽

Fish Community Composition

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Water level induced changes of habitat quality determine fish community composition in restored and modified riverbanks of a large alpine river

International Review of Hydrobiology ◽

10.1002/iroh.202002079 ◽

2021 ◽

Author(s):

Joachim Pander ◽

Christoffer Nagel ◽

Hannah Ingermann ◽

Juergen Geist

Keyword(s):

Water Level ◽

Community Composition ◽

Habitat Quality ◽

Fish Community ◽

Fish Community Composition ◽

Alpine River ◽

Induced Changes

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Environmental DNA metabarcoding provides enhanced detection of the European eel Anguilla anguilla and fish community structure in pumped river catchments

Journal of Fish Biology ◽

10.1111/jfb.14680 ◽

2021 ◽

Vol 98 (2) ◽

pp. 427-427

Keyword(s):

Community Structure ◽

Fish Community ◽

Anguilla Anguilla ◽

Environmental Dna ◽

European Eel ◽

Fish Community Structure ◽

Dna Metabarcoding ◽

River Catchments

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Assessing Historical Fish Community Composition Using Surveys, Historical Collection Data, and Species Distribution Models

PLoS ONE ◽

10.1371/journal.pone.0025145 ◽

2011 ◽

Vol 6 (9) ◽

pp. e25145 ◽

Cited By ~ 27

Author(s):

Ben Labay ◽

Adam E. Cohen ◽

Blake Sissel ◽

Dean A. Hendrickson ◽

F. Douglas Martin ◽

...

Keyword(s):

Community Composition ◽

Species Distribution ◽

Fish Community ◽

Species Distribution Models ◽

Distribution Models ◽

Fish Community Composition ◽

Collection Data

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Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

Frontiers in Microbiology ◽

10.3389/fmicb.2021.637811 ◽

2021 ◽

Vol 12 ◽

Author(s):

Larissa Frühe ◽

Verena Dully ◽

Dominik Forster ◽

Nigel B. Keeley ◽

Olivier Laroche ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Environmental Dna ◽

Community Diversity ◽

Rrna Gene ◽

Local Conditions ◽

Global Trends ◽

Bacterial Taxon ◽

Metabolic Properties

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

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