scholarly journals Environmental DNA methods for the analysis of macroorganismal populations

2021 ◽  
Vol 4 ◽  
Author(s):  
Hideyuki Doi
Keyword(s):  
Fish Species ◽  
Population Analysis ◽  
Species Distributions ◽  
Environmental Dna ◽  
Terrestrial Ecosystems ◽  
Measurement Methods ◽  
Natural Environments ◽  
New Methods ◽  
Dominant Fish ◽  
Last 300 Years

Environmental DNA (eDNA) methods have been widely used to investigate the distribution and abundance/biomass of macroorganisms. eDNA methods analyze DNA collected directly from the environment, such as from water, soil, and air. The techniques have been applied to many taxa inhabiting various aquatic and terrestrial ecosystems. The recent development of eDNA methods has revolutionized the way we assess macroorganisms in natural environments. In this talk, I will present current developments of eDNA methodology, especially with regard to population analysis using various DNA measurement methods. For example, 1) eDNA was used to assess fish species distributions and abundance/biomass (Takahara et al. 2012, Doi et al. 2017a), 2) quantitative PCR of sedimentary DNA was applied to sediment core samples to detect the DNA of three dominant fish species spanning the last 300 years (Kuwae et al. 2020), and 3) new methods for sampling eDNA from water (Doi et al. 2017b) and on-site measurement (Doi et al. 2020) will be presented. I end by addressing the need for standardized protocols for eDNA monitoring to enable broader uptake of eDNA technology (Minamoto et al. 2021).

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.

Temporo-spatial heterogeneity of dominant fish species in the Jiaozhou Bay community

2017 ◽  
Vol 24 (5) ◽  
pp. 1091
Author(s):  
Jia WO ◽  
Binduo XU ◽  
Ying XUE ◽  
Yiping REN ◽  
Chongliang ZHANG
Keyword(s):  
Spatial Heterogeneity ◽  
Fish Species ◽  
Jiaozhou Bay ◽  
Dominant Fish

scholarly journals Diversity of Bacteria and Fungi Associated with Freshwater Fishes from Mijawal River, Nasarawa, Nigeria

2020 ◽  
Vol 24 (6) ◽  
pp. 1085-2020
Author(s):  
K.M. Adamu ◽  
H. Muhammad ◽  
S.U. Ahmad ◽  
M.M. Ahmad ◽  
A.M. Yakubu
Keyword(s):  
Fish Species ◽  
Terrestrial Ecosystems ◽  
Freshwater Fishes ◽  
Frequency Of Occurrence ◽  
Salmonella Spp ◽  
Tilapia Zillii ◽  
Fish Samples ◽  
Bacteria And Fungi ◽  
Rhizopus Sp ◽  
Mormyrus Rume

Understudying the presence of bacteria and fungi population on freshwater fishes, provides the knowledge and understanding of their diversity and potential roles they may play in the health of the aquatic and terrestrial ecosystems. The present study was conducted to evaluate the diversity of bacteria and fungi species of identified fish samples from River Mijawal, Nasarawa State. The fishes were sampled from the only landing for three months (October to December, 2019) for this study. During the sampling periods, thirteen (13) different fish species were identified; they were  swabbed with sterilized swab stick from the skin surface for bacteria and fungi identification. The Dominant fish species were Tilapia zillii, Labeo senegalensis, Mormyrus rume and Mormyrus tapines. The total number of thirteen (13) bacterial and five (5) fungi species were isolated and  identified. Eight (8) of the bacteria isolates, were gram negative bacteria (Pseudomonas sp, Aeromonas sp, Serratia mercescenes, Proteus sp, Salmonella spp, Escherichia coli, Klebsiella sp, and Enterobacter sp.); whilst the other five (5) were gram positive bacteria (Bacillus sp, Micrococcus sp, Staphylococcus sp, Enterococcus sp and Listeria monocytogenes).The five isolated fungi species were Aspergillus niger, Rhizopus sp, Penicillium  sp, Trichoderma viridae and Geotrichum candidum. The frequency of occurrence of the isolated bacteria indicated that Staphylococcus sp had the highest frequency of occurrence (16.67%) while Serratia mercescens had the least occurrence (2.78%). The highest number of occurrence of the isolated fungi species was observed in Rhizopus sp while the least was recorded in Geotricum candidum. It was observed that Tilapia zillii and  Mormyrus rume had the most frequent bacteria and fungi isolates. It can therefore be deduced from the results that fish samples identified from River Mijawal has high bacteria and fungi diversity that may be pathogenic to man. The occurrence of these microbes may be attributed of human  and animal faeces in the River  Keywords: Freshwater fishes, Microbes, River Mijawal, Nasarawa  

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Meta Analysis ◽  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Promising Tool

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited because it is unclear whether eDNA concentrations actually represent species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influences of eDNA characteristics, including production source and state, and methodology, including collection and quantification strategy and abundance metrics, on the accuracy of eDNA-based abundance estimation were entirely overlooked. We conducted a meta-analysis using 56 previous eDNA literature and investigated the relationships between the accuracy (R2) of eDNA-based abundance estimation and eDNA characteristics and methodology. Our meta-regression analysis found that R2 values were significantly lower for crustaceans than fish, suggesting that less frequent eDNA production owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, R2 values were positively associated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Furthermore, R2 values were significantly lower for natural than laboratory conditions, while there was no difference in the estimation accuracy among natural environments. Our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

scholarly journals Zooplankton composition and trophic status of hydrobionts of the Laptev and East Siberian seas

2019 ◽  
Vol 59 (6) ◽  
pp. 987-997
Author(s):  
K. M. Gorbatenko ◽  
S. I. Kiyashko
Keyword(s):  
Fish Species ◽  
Trophic Status ◽  
Northwestern Part ◽  
Gut Content Analysis ◽  
Boreogadus Saida ◽  
Gut Content ◽  
Summer Period ◽  
East Siberian Sea ◽  
Dominant Fish ◽  
The Laptev Sea

Species composition, density, biomass and distribution of zooplankton on shelf and slope of northwestern part of the Laptev Sea and shallow-water shelf of the East Siberian Sea were studied in 2015 summer period. Using analysis of stable isotopes of carbon (13 С) and nitrogen (15N), trophic status of abundant zooplankton and fish species, and their positions in food webs of these two seas, were compared. Gut content analysis, as well stable isotope data, showed mutual changes in the trophic status of dominant fish species arctic cod, Boreogadus saida, with age.

scholarly journals Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood

Biology ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1132
Author(s):  
Hung-Tai Lee ◽  
Cheng-Hsin Liao ◽  
Te-Hua Hsu
Keyword(s):  
Species Diversity ◽  
Species Identification ◽  
Fish Species ◽  
Large Scale ◽  
Environmental Dna ◽  
Universal Primers ◽  
Similar Species ◽  
Operational Taxonomic Units ◽  
Fish Market ◽  
Fish Species Identification

Seafood, especially in traditional food Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, the species composition of seafood can be complicated. While a DNA-based approach has been routinely utilized for species identification, a large scale of seafood identification in fish markets and restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). In the present study, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using environmental DNA (eDNA) metabarcoding. Four eDNA samplings from a local fish market and nearby seafood restaurants were conducted using Sterivex cartridges. Nineteen universal primers previously validated for fish species identification were utilized to amplify the fragments of mitochondrial DNA (12S, COI, ND5) of species in eDNA samples and sequenced with NovaSeq 6000 sequencing. A total of 153 fish species have been identified based on 417 fish related operational taxonomic units (OTUs) generated from 50,534,995 reads. Principal Coordinate Analysis (PCoA) further showed the differences in fish species between the sampling times and sampling sites. Of these fish species, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were respectively associated with smoked sharks, braised moray eels, and grouper fish soups. To our best knowledge, this work represents the first study to demonstrate the feasibility of a large scale of seafood identification using eDNA metabarcoding approach. Our findings also imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources.

scholarly journals Monitoring spawning migrations of potamodromous fish species via eDNA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck
Keyword(s):  
Fish Species ◽  
Anthropogenic Impacts ◽  
Environmental Dna ◽  
Signal Strength ◽  
Digital Pcr ◽  
Freshwater Ecosystems ◽  
Non Invasive ◽  
River Stretch ◽  
Daily Discharge ◽  
Invasive Techniques

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

scholarly journals Improving herpetological surveys in eastern North America using the environmental DNA method

Genome ◽  
2016 ◽  
Vol 59 (11) ◽  
pp. 991-1007 ◽  
Author(s):  
Anaïs Lacoursière-Roussel ◽  
Yohann Dubois ◽  
Eric Normandeau ◽  
Louis Bernatchez
Keyword(s):  
Large Scale ◽  
Habitat Type ◽  
Environmental Dna ◽  
Conservation Strategies ◽  
Natural Environments ◽  
Detection Rates ◽  
Survey Tool ◽  
Declining Species ◽  
Species Specific ◽  
Wood Turtle

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

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