scholarly journals Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

2021 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne M. Gleeson ◽  
Elise Furlan ◽  
Tim Haeusler ◽  
Jonas Bylemans
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Native Fish ◽  
Dna Metabarcoding

scholarly journals Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Masaaki Sato ◽  
Nariaki Inoue ◽  
Ryogen Nambu ◽  
Naoki Furuichi ◽  
Tomohito Imaizumi ◽  
...  
Keyword(s):  
Fish Species ◽  
Internal Standard ◽  
Environmental Dna ◽  
Artificial Reefs ◽  
Sampling Station ◽  
Biodiversity Monitoring ◽  
Dna Metabarcoding ◽  
Positive Correlations ◽  
Multiple Species ◽  
Echo Sounder

AbstractSince the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.

scholarly journals Evaluation of biodiversity in estuaries using environmental DNA metabarcoding

2020 ◽  
Author(s):  
Hyojin Ahn ◽  
Manabu Kume ◽  
Yuki Terashima ◽  
Feng Ye ◽  
Satoshi Kameyama ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Conditions ◽  
Environmental Dna ◽  
Aquatic Biodiversity ◽  
Non Invasive ◽  
Dna Metabarcoding ◽  
And Migration ◽  
Low Degrees ◽  
River Mouths ◽  
Rare Fishes

AbstractBiodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river, suggesting the potential of eDNA for non-invasive assessment of aquatic biodiversity.

scholarly journals Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout

2020 ◽  
Vol 8 ◽  
Author(s):  
Akio Imamura ◽  
Kana Hayami ◽  
Masayuki Sakata ◽  
Toshifumi Minamoto
Keyword(s):  
Invasive Species ◽  
Species Richness ◽  
Rainbow Trout ◽  
Fish Species ◽  
Seasonal Changes ◽  
Fish Community ◽  
Environmental Dna ◽  
Native Fish ◽  
Native Salmonids ◽  
Hokkaido Island

In freshwater ecosystems, invasive salmonid fishes can have a significant impact on native fish species. Detecting the invasion and its negative effects is critical for the conservation of native fish communities. We examined the species composition and seasonal changes in the freshwater fish community, including salmonids, on the Kamikawa Plain, Hokkaido Island, Japan, using environmental DNA (eDNA) metabarcoding. We detected 23 fish species in 176 samples collected from 16 sites over 12 months (October 2018 – August 2019). Between 11 and 20 species were detected at each site, including five native salmonids (Oncorhynchus masou, Oncorhynchus keta, Parahucho perryi, Salvelinus leucomaenis leucomaenis and Salvelinus malma krascheninnikova). The invasive alien rainbow trout Oncorhynchus mykiss was detected at all 16 sites and it was the most commonly detected salmonid. Although we found no obvious competitive exclusion of native salmonids by rainbow trout in the study area, the invasive species occurred more often and at more sites than any of the natives. We also determined the occurrence and seasonal changes in the fish community, classified as native salmonids, invasive rainbow trout, Cypriniformes and other benthic fishes. There were fewer species overall in winter, but the sites with higher species richness in winter were on the lower reaches of the river. In addition, we detected domestic invaders, such as the topmouth gudgeon, Pseudorasbora parva, although they were less prevalent than rainbow trout. These results show the effectiveness of eDNA metabarcoding, which can be used for surveying species richness at an ecosystem scale. In particular, the detection of the early stages of establishment and spread of invasive species can be achieved by eDNA monitoring.

scholarly journals Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

2020 ◽  
Vol 8 ◽  
Author(s):  
Mary E. McElroy ◽  
Terra L. Dressler ◽  
Georgia C. Titcomb ◽  
Emily A. Wilson ◽  
Kristy Deiner ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Species ◽  
Environmental Dna ◽  
Dna Metabarcoding

Revealing an Invasion Risk of Fish Species in Qingdao Underwater World by Environmental DNA Metabarcoding

2021 ◽  
Vol 20 (1) ◽  
pp. 124-136
Author(s):  
Jianwei Chen ◽  
Zhi Chen ◽  
Shanshan Liu ◽  
Wenjie Guo ◽  
Di Li ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Invasion Risk ◽  
Dna Metabarcoding

COMPARATIVE STUDY BETWEEN FISH COLLECTION BY NATIONAL CENSUS ON RIVER ENVIRONMENT AND ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (5) ◽  
pp. I_415-I_420 ◽  
Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  
Keyword(s):  
Comparative Study ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Fish Collection

Environmental DNA for functional diversity

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Functional Groups ◽  
Functional Diversity ◽  
Environmental Dna ◽  
Soil Organisms ◽  
Meaningful Information ◽  
Dna Metabarcoding ◽  
Pros And Cons ◽  
Target Community

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

Environmental DNA

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Graduate Students ◽  
Feeding Habits ◽  
Environmental Dna ◽  
Research Field ◽  
Background Information ◽  
Ecological Processes ◽  
Biodiversity Research ◽  
Dna Metabarcoding ◽  
Standard Information

Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

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