Using Environmental DNA as a Tool for Biomonitoring

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Loss & Dynamics".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 10491

Special Issue Editor


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Guest Editor
Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
Interests: community ecology; metacommunity dynamics; dispersal; spatio-temporal analysis; meta-analysis; computational ecology; molecular identification

Special Issue Information

Dear Colleagues,

The Diversity journal is launching a Special Issue dedicated to using eDNA as a tool for biomonitoring. Biomonitoring, or determining the consequences of pollution on ecosystem health through the presence of tolerant or the absence of sensitive species, is an important tool to quantify and minimize anthropogenic impacts on the natural environment. Past and current regulatory practices rely mainly on traditional sampling techniques and morphological identification to determine those sensitive or tolerant species. However, developments in molecular identification techniques are slowly catching up. Their promise of species-specific, fast, cheap, and continuous monitoring techniques has kept track with the development and explosion of sequencing techniques, from single-specimen barcoding to tissue metabarcoding of bulk samples to eDNA metabarcoding of short sequences from environmental samples. eDNA especially promises to detect cryptic taxa or life stages with greater sensitivity and is not hindered by specimen damage issues. However, there is still a need to compare, for instance, biotic indices obtained from conventional sampling to eDNA, whether this is dependent on the type of environment sampled, the origin and fate of sequences in the environment, methodological and bioinformatic standardizations. In this Special Issue, we invite submissions of research that address these and other issues related to the application of eDNA techniques to biomonitoring studies.

Prof. Dr. Karl Cottenie
Guest Editor

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Keywords

  • Biomonitoring 
  • eDNA 
  • Bioinformatics 
  • Molecular identification 
  • Conservation 
  • Species richness

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Published Papers (2 papers)

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Research

15 pages, 18876 KiB  
Article
Digital Droplet PCR-Based Environmental DNA Tool for Monitoring Cryptocaryon irritans in a Marine Fish Farm from Hong Kong
by Hin Hung Tsang, Jose A. Domingos, Jacob A. F. Westaway, Maximilian H. Y. Kam, Roger Huerlimann and Giana Bastos Gomes
Diversity 2021, 13(8), 350; https://doi.org/10.3390/d13080350 - 29 Jul 2021
Cited by 11 | Viewed by 4300
Abstract
The adoption of new investigative strategies based on environmental DNA (eDNA) can be used to monitor parasites, associated bacterial microbiomes, and physical-chemical parameters in fish farms. In this study, we used the economically important and globally distributed fish ciliate parasite Cryptocaryon irritans as [...] Read more.
The adoption of new investigative strategies based on environmental DNA (eDNA) can be used to monitor parasites, associated bacterial microbiomes, and physical-chemical parameters in fish farms. In this study, we used the economically important and globally distributed fish ciliate parasite Cryptocaryon irritans as a model to understand the parasite abundance and potential drivers of its presence in marine fish farms. Environmental (rainfall) and physical-chemical (temperature, oxygen, salinity, pH) data collected from a marine fish farm in Hong Kong were analyzed together with the eDNA approach targeting C. irritans abundance based on digital droplet PCR and 16S metagenomics to determine associations and triggers between parasites and specific bacterial groups. Rainfall and temperature demonstrated positive associations with high abundance of C. irritans (eDNA) at the studied marine fish cage farm. However, rainfall was the only parameter tested that demonstrated a significant association with parasite eDNA, indicating that the raining season is a risky period for fish farmers in Hong Kong. Coraliomargarita was the bacterial genus with the most significant relationship with low abundance of C. irritans in water. Understanding the environmental triggers of ciliate parasites propagation and associated bacterial microbiome could elucidate new insights into environmental control, microbial management, and promote the reduction of chemical use in marine fish farms. Full article
(This article belongs to the Special Issue Using Environmental DNA as a Tool for Biomonitoring)
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15 pages, 6307 KiB  
Article
Ethanol eDNA Reveals Unique Community Composition of Aquatic Macroinvertebrates Compared to Bulk Tissue Metabarcoding in a Biomonitoring Sampling Scheme
by Sadhna Fiona Persaud, Karl Cottenie and Jennifer Erin Gleason
Diversity 2021, 13(1), 34; https://doi.org/10.3390/d13010034 - 17 Jan 2021
Cited by 12 | Viewed by 4866
Abstract
Freshwater ecosystems provide essential ecosystem services and support biodiversity; however, their water quality and biological communities are influenced by adjacent agricultural land use. Aquatic macroinvertebrates are commonly used as bioindicators of stream conditions in freshwater biomonitoring programs. Sorting benthic samples for molecular identification [...] Read more.
Freshwater ecosystems provide essential ecosystem services and support biodiversity; however, their water quality and biological communities are influenced by adjacent agricultural land use. Aquatic macroinvertebrates are commonly used as bioindicators of stream conditions in freshwater biomonitoring programs. Sorting benthic samples for molecular identification is a time-consuming process, and this study investigates the potential of ethanol-collected environmental DNA (eDNA) for metabarcoding macroinvertebrates, especially for common bioindicator groups. The objective of this study was to compare macroinvertebrate composition between paired bulk tissue and ethanol eDNA samples, as eDNA could provide a less time-consuming and non-destructive method of sampling macroinvertebrates. We collected benthic samples from streams in Ontario, Canada, and found that community composition varied greatly between sampling methods and that few taxa were shared between paired tissue and ethanol samples, suggesting that ethanol eDNA is not an acceptable substitute. It is unclear why we did not detect all the organisms that were preserved in the ethanol, or the origin of the DNA we did detect. Furthermore, we also detected no difference in community composition for bioindicator taxa due to surrounding land use or water chemistry, suggesting sites were similar in ecological condition. Full article
(This article belongs to the Special Issue Using Environmental DNA as a Tool for Biomonitoring)
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