scholarly journals Lateral and longitudinal fish environmental DNA distribution in dynamic riverine habitats

2020 ◽  
Author(s):  
Bettina Thalinger ◽  
Dominik Kirschner ◽  
Yannick Pütz ◽  
Christian Moritz ◽  
Richard Schwarzenberger ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Dna Distribution ◽  
Riverine Habitats

scholarly journals A non-invasive eDNA tool for detecting sea lamprey larvae in river sediments: analytical validation and field testing in a low abundance ecosystem

2020 ◽  
Author(s):  
Miguel Baltazar-Soares ◽  
Adrian C. Pinder ◽  
Andrew J. Harrison ◽  
Will Oliver ◽  
Jessica Picken ◽  
...  
Keyword(s):  
Anthropogenic Activities ◽  
River Sediments ◽  
Environmental Dna ◽  
Field Testing ◽  
Sea Lamprey ◽  
Larval Stages ◽  
Non Invasive ◽  
Census Techniques ◽  
Burrowing Activity ◽  
Riverine Habitats

AbstractAnthropogenic activities are increasingly threatening aquatic biodiversity, especially anadromous species. Monitoring and conservation measures are thus required to protect, maintain, and restore imperilled populations. While many species can be surveyed using traditional capture and visual census techniques, species that use riverine habitats in a less conspicuous manner, such as sea lamprey Petromyzon marinus, can be more challenging to monitor. Sea lamprey larvae (ammocoetes) can spend several years in freshwater burrowed within soft sediments, inhibiting their detection and assessment. Here we present an environmental DNA (eDNA) assay to detect ammocoetes burrowed in the sediment. We performed a battery of tests that ensured both species-specificity of the assay as well as the capacity to detect ammocoetes when abundances are low. Experiments on burrowing activity suggested that most of the DNA released into the sediment occurs during burrowing. Overall, we demonstrated this new molecular-based tool is an efficient and effective complement to traditional monitoring activities targeting larval stages of sea lampreys.

The application of environmental DNA in the monitoring of the Yangtze finless porpoise, Neophocaena phocaenoides asaeorientalis

2019 ◽  
Vol 26 (1) ◽  
pp. 124
Author(s):  
Yunsheng WU ◽  
Yongkai TANG ◽  
Jianlin LI ◽  
Kai LIU ◽  
Hongxia LI ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Finless Porpoise ◽  
Yangtze Finless Porpoise ◽  
Neophocaena Phocaenoides

RELATIONSHIPS BETWEEN DISTRIBUTION PATTERNS OF Plecoglossus altivelis altivelis ESTIMATED BY ENVIRONMENTAL DNA ANALYSIS AND STREAM TEMPARATURE

2018 ◽  
Vol 74 (7) ◽  
pp. III_457-III_462
Author(s):  
Takanori KONO ◽  
Yoshihisa AKAMATSU ◽  
Ryutei INUI ◽  
Masuji GOTO ◽  
Kohei YAMAGUCHI
Keyword(s):  
Dna Analysis ◽  
Environmental Dna ◽  
Distribution Patterns ◽  
Plecoglossus Altivelis

SPAWNING HABITAT POTENTIAL EVALUATION FOR AYU BASED ON AN ENVIRONMENTAL DNA ANALYSIS AND FIELD WORKS OF PHYSICAL ENVIRONMENT FACTORS IN THE LOWER ASAHI RIVER

2019 ◽  
Vol 75 (2) ◽  
pp. I_529-I_534
Author(s):  
Keisuke YOSHIDA ◽  
Ryuutei INUI ◽  
Ryohei UDAGAWA ◽  
Shiro MAENO ◽  
Yoshihisa AKAMATSU ◽  
...  
Keyword(s):  
Physical Environment ◽  
Dna Analysis ◽  
Environmental Dna ◽  
Spawning Habitat ◽  
Environment Factors ◽  
Potential Evaluation ◽  
Field Works

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.

Estimating native and invasive crayfish distributions in relation to culvert barriers with environmental DNA

2019 ◽  
Vol 38 (3) ◽  
pp. 629-641 ◽  
Author(s):  
Kousuke Ikeda ◽  
Hideyuki Doi ◽  
Shigeharu Terui ◽  
Atsuko Kato ◽  
Takashi Mitsuzuka ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Invasive Crayfish

scholarly journals Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy

2020 ◽  
Vol 9 (1) ◽  
pp. 62
Author(s):  
Aysha Kamran ◽  
Kathrin Sauter ◽  
Andreas Reimer ◽  
Theresa Wacker ◽  
Joachim Reitner ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Environmental Dna ◽  
Cyanobacterial Mats ◽  
Cyanobacterial Community ◽  
Mineral Precipitation ◽  
Community Based ◽  
Specific Adaptation ◽  
Carbonate Buildups ◽  
Generation Sequencing

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

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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