Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve

Conserving aquatic ecosystems requires efficient tools to accurately assess the biodiversity of aquatic species. However, existing knowledge is insufficient in terms of the reliability and the comparability of methods measuring fish diversity. Environmental DNA (eDNA), as a promising method, was used to detect fish taxa in this study. We optimized the eDNA method in the laboratory, and applied the optimal eDNA method to survey fish diversity in a natural aquatic life reserve. We simulated necessary steps of the eDNA method in the lab to increase the confidence of the field survey. Specifically, we compared different eDNA sampling, extraction, and sequencing strategies for accurately capturing fish species of the target area. We found that 1L water samples were sufficient for sampling eDNA information of the majority taxa. The filtration was more effective than the centrifugal precipitation for the eDNA extraction. The cloning sequencing was better than the high-throughput sequencing. The field survey showed that the Shannon–Wiener diversity index of fish taxa was the highest in Huairou Reservoir. The diversity index also showed seasonal changes. The accuracy rate of detecting fish taxa was positively correlated with the eDNA concentration. This study provides a scientific reference for an application of the eDNA method in terms of surveying and estimating the biodiversity of aquatic species.

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Identifying spawning activity in aquatic species based on environmental DNA spikes

10.1101/2020.01.28.924167 ◽

2020 ◽

Author(s):

Satsuki Tsuji ◽

Naoki Shibata

Keyword(s):

Reproductive Biology ◽

Field Survey ◽

Aquatic Organisms ◽

Environmental Dna ◽

Reproductive Season ◽

Aquatic Species ◽

Spawning Activity ◽

Invasive Approach ◽

Non Invasive ◽

Management Actions

AbstractAn understanding of the reproductive biology of aquatic organisms is crucial for the efficient conservation and management of species and/or populations. Nevertheless, conventional spawning surveys such as visual- and capture-based monitoring generally require laborious, time-consuming work and are subject to monitoring biases such as observer bias, as well as miscounts due to false spawning. In addition, direct capture often damages eggs or individuals. Thus, an efficient non-invasive approach for monitoring spawning activity on aquatic species would be a valuable tool to understand their reproductive biology and conserving biodiversity. Here, we proposed an environmental DNA (eDNA)-based approach for monitoring and understanding spawning activity by observing spikes in eDNA concentration after spawning activity. We found in cross experiments using two medaka species (Oryzias latipes and O. sakaizumii, 1:1 individual per tank) that an eDNA spike occurred in only male species after spawning activity. In addition, the magnitude of the eDNA spike was dependent on the number of spawning activities with egg and sperm release. In the field survey during the reproductive season, eDNA concentration after spawning were 3–25 times higher than before spawning. On the other hand, there was no increase in eDNA concentration during the non-reproductive season. Therefore, our results demonstrated that spikes in the eDNA concentration are mainly caused by the release of sperm during spawning activity, and it can be used as evidence of spawning in field survey. The presented approach could be a practical tool for studying reproductive biology and provides an opportunity to design effective conservation and environmental management actions.

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Diversity, potentiality, and conservation status of fish fauna in the upper Mahakam’s tributaries, East Kalimantan

Jurnal Iktiologi Indonesia ◽

10.32491/jii.v19i3.471 ◽

2019 ◽

Vol 19 (3) ◽

pp. 391

Author(s):

Jusmaldi Jusmaldi ◽

Nova Hariani ◽

Norbeta Doq

Keyword(s):

Fish Species ◽

Diversity Index ◽

Conservation Status ◽

Fish Fauna ◽

Iucn Red List ◽

Fish Diversity ◽

East Kalimantan ◽

Wiener Diversity Index ◽

Data Deficient ◽

Almost All

Diversity, potentiality and conservation status of fish fauna in upper Mahakam’s tributaries of east Kalimantan is unknown. The purposes of this study were to analysis species diversity, determine potentiality and conservation status of fish fauna in upper Mahakam’s tributaries, east Kalimantan. Fish sampling with purposive method was conducted in four tributaries, i.e Tepai River, Pahangai River, Danum Parai River, and Meraseh River for one month. Fishes were collected by several gears type. The results of this research showed that the total number of fish caught was 820 individuals; consist of 26 species, 7 families, and 4 orders. The Cyprinidae was the most dominant family found in all tributaries. The Shannon-Wiener diversity index in four tributaries were varied and ranging from 1.749-2.087. The highest fish diversity was recorded at Maraseh River followed by Pahangai River, Danum Parai River, and Tepai River. The low fish diversity was discovered at Tepai River may be due to differences in substrate type, water velocity, and water depth as compared to the Maraseh River, Pahangai River, Danum Parai River. The fish species similarity coefficient between four tributaries ranged from 0.606-0.842 and the highest dissimilarity was found between Tepai River and Danum Parai River. Almost all fishes categorized as edible fish for local consumption. Syncrossus hymenophysa and Gastromyzon lepidogaster have potential as ornamental fish. Regarding IUCN red list status, six fish species were grouped into least concern status, two species as data deficient, one species as near threatened, one species as endangered species and 16 other species were not on the list.

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Investigation of Phytoplankton and Evaluation on Water Quality of Taizi River in Liaoyang Area

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.955-959.403 ◽

2014 ◽

Vol 955-959 ◽

pp. 403-406 ◽

Cited By ~ 1

Author(s):

Hong Wei Wang ◽

Qing Chao Xing ◽

Chun Long Zhao ◽

Hai Tao Zhao ◽

Liang Ma ◽

...

Keyword(s):

Water Pollution ◽

Water Quality ◽

Phytoplankton Community ◽

Diversity Index ◽

Species Diversity Index ◽

Wiener Diversity Index ◽

Evenness Index ◽

Taizi River ◽

Better Than

To evaluate water quality, an investigation of phytoplankton community was conducted in Taizi River of Liaoyang Area, June 2011. The results showed that 130 species of phytoplankton belong to 6 phyla and 63 genera existed. Chlorphyta has the richest species of algae, which accounted for 43.85% of the total number, followed by Bacillariophyta (32.41%). Water quality in upstream is better than downstream. Species and biomass of Cyanophyta and Euglenophyta which have tolerance of pollution increasing According to the integrative analysis result of Shannon-Wiener diversity index, Pielou Evenness index and Margalef Species diversity index, Taizi river is judged belong to low-polluted or oligo- polluted，but some sites belong to β -moderate polluted, effective managements should be taken in order to control the water pollution.

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The Effect of the Blue and Black Light Trap on the Diversity of the Trichoptera (Caddisfly Adult) and Other Insects in Lotic and Lentic Area of Mae Tam Reservoir, Thailand

Trends in Sciences ◽

10.48048/tis.2021.717 ◽

2021 ◽

Vol 18 (23) ◽

pp. 717

Author(s):

Arthit Nuntakwang ◽

Decha Thapanya ◽

Hakan Bozdoğan

Keyword(s):

Blue Light ◽

Diversity Index ◽

Light Trap ◽

Similarity Index ◽

Wiener Index ◽

Abundant Species ◽

Wiener Diversity Index ◽

Sampling Points ◽

Evenness Index ◽

Better Than

This study was conducted using two types of light traps to collect the insects at Mae Tam Reservoir from January to April 2018. The sampling area was divided into 4 points. Two points were located at the reservoir’s bank, and the others were located at the reservoir’s outlet. The study aimed to compare the efficiency of the fluorescent tube's blue and purple light, which had a different wavelength on insect’s attraction. To compare the diversity of Trichoptera in the different stream habitats, Sørensen similarity index, Shannon-Wiener index, and Evenness index were used. The result showed that purple light could attract insects better than blue light. Hymenoptera was attracted by purple light. Coleoptera and Hemiptera were attracted by blue light. The study on the diversity of Trichoptera showed that there were 2,534 individuals of 9 families 48 species were collected. Ecnomus puro was the most abundant species (1,120 individuals). The highest Shannon-Wiener diversity index was sampling points 4 (2.10). The highest Evenness index was sampling points 4 (0.62). Sørensen similarity index showed that sampling points 3 and 4 had the highest value (67.92 %) because they were adapted from a natural creek to concrete where boulder, gravel, cobble, sand, and woody material were deposited at the stream bottom. These provided various microhabitats for insect larva to live and develop. The riparian had affected the distribution and colonization of mature insects.

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eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake

10.1101/2020.10.20.347203 ◽

2020 ◽

Author(s):

Rebecca R Gehri ◽

Wesley A. Larson ◽

Kristen Gruenthal ◽

Nicholas Sard ◽

Yue Shi

Keyword(s):

Community Composition ◽

Lake Water ◽

Water Samples ◽

High Throughput Sequencing ◽

Environmental Dna ◽

Aquatic Systems ◽

Taxonomic Resolution ◽

Universal Primers ◽

Great Promise ◽

Fish Diversity

AbstractUnderstanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high-throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (137 ha) in Michigan, USA from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish-specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

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Ecosystem Health of Lake Tamrangabeel, Bongaigaon District, Assam, India with Special Reference to Aquatic Insect Assemblage

Current World Environment ◽

10.12944/cwe.10.2.15 ◽

2015 ◽

Vol 10 (2) ◽

pp. 500-508 ◽

Cited By ~ 1

Author(s):

R. R Bhagawati ◽

Susmita Gupta

Keyword(s):

Aquatic Insects ◽

Ecosystem Health ◽

Diversity Index ◽

Aquatic Insect ◽

Working Party ◽

Average Score ◽

Aquatic Life ◽

Wiener Diversity Index ◽

Signal Score ◽

Insect Assemblage

This study investigated the ecosystem health of a floodplain lake, Tamrangabeel of Bongaigaon district, Assam, India using aquatic insects as bioindicator. The aquatic community of Tamrangabeel was represented by 37 species belonging to 19 families and 5 orders. Shannon –Wiener diversity index (Shannon Hꞌ) values were recorded less than 1 in all the sites of the lake which indicated perturbed condition of the lake. Order Hemiptera was found to be the largest order with highest number of species. Eudominant species recorded in this lake were Micronecta siva (order Hemiptera) and Cloeon sp. (order Ephemeroptera). Biological Monitoring Working Party (BMWP) Score, Average Score per taxon (ASPT), and Stream Invertebrate Grade Number-Average Level (SIGNAL) Score reported from the study reflected good ecological potential as well as slightly impacted nature of the water body. The values of different environmental variables of water of all the sites of the lake were found conducive for aquatic life. This study provided an early warning of perturbation of the lake which is to be addressed before it is too late.

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Study on Soil Seed Bank in Urban Abandoned Land of Tianjin — Take Houtai Wetland for Example

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.448-453.978 ◽

2013 ◽

Vol 448-453 ◽

pp. 978-982

Author(s):

Meng Xuan He ◽

Hong Yuan Li ◽

Lan Lan Li ◽

Fang Wang

Keyword(s):

Seed Bank ◽

Coastal Wetlands ◽

Field Survey ◽

Diversity Index ◽

Glycine Soja ◽

Soil Seed Bank ◽

Similarity Index ◽

Simpson Index ◽

Germination Test ◽

Wiener Diversity Index

Urban abandoned lands play an important role to maintain urban biodiversity. In order to study the characteristics of soil seed bank (SSB) in Houtai Wetland, field survey and laboratory experiment were conducted. After germination test, the results show that the species richness is relatively low, only 12 kinds of species are contained, but the reserves of SSB are abundant. Its density reaches to7.27×105grains/m2, maintaining the same level with coastal wetlands. Glycine soja account for the vast majority of proportion, leading to uneven distribution within species.So the Shannon-Wiener Diversity Index, Simpson Index and Pielou Evenness Index are all lower than ground vegetation.The Sorensen Similarity Index is 0.330, its ability to reproduce ground plants is limited. The suggestions are that appropriate manners should be taken to protect native plants and soil seed bank.

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

Scientific Reports ◽

10.1038/s41598-021-83318-6 ◽

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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Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽

10.3390/w13111465 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1465

Author(s):

Chao Shen ◽

Liuyan Huang ◽

Guangwu Xie ◽

Yulai Wang ◽

Zongkai Ma ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Diversity Index ◽

Plastic Substrate ◽

Simpson Index ◽

Plastic Debris ◽

Plastic Substrates ◽

Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

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Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

Antarctic Science ◽

10.1017/s0954102021000274 ◽

2021 ◽

pp. 1-10

Author(s):

Micheline Carvalho-Silva ◽

Luiz Henrique Rosa ◽

Otávio H.B. Pinto ◽

Thamar Holanda Da Silva ◽

Diego Knop Henriques ◽

...

Keyword(s):

High Throughput Sequencing ◽

Crater Lake ◽

Environmental Dna ◽

Food Sources ◽

South Shetland Islands ◽

Deception Island ◽

Shetland Islands ◽

Operational Taxonomic Units ◽

First Time ◽

Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

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