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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1368-1384. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Dan ME, Portner EJ, Bowman JS, Semmens BX, Owens SM, Greenwald SM, Choy CA. Using low volume eDNA methods to sample pelagic marine animal assemblages. PLoS One 2024; 19:e0303263. [PMID: 38748719 PMCID: PMC11095688 DOI: 10.1371/journal.pone.0303263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.
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Affiliation(s)
- Michelle E. Dan
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Elan J. Portner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Brice X. Semmens
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sarah M. Owens
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Stephanie M. Greenwald
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - C. Anela Choy
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
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Ye L, Peng S, Ma Y, Zhang W, Wang L, Sun X, Zhang C, Yeasmin M, Zhao J, Dong Z. Biodiversity and distribution patterns of blooming jellyfish in the Bohai Sea revealed by eDNA metabarcoding. BMC Ecol Evol 2024; 24:37. [PMID: 38500049 PMCID: PMC10946145 DOI: 10.1186/s12862-024-02224-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The mass occurrence of scyphozoan jellyfish severely affects marine ecosystems and coastal economies, and the study of blooming jellyfish population dynamics has emerged in response. However, traditional ecological survey methods required for such research have difficulties in detecting cryptic life stages and surveying population dynamics owing to high spatiotemporal variations in their occurrence. The environmental DNA (eDNA) technique is an effective tool for overcoming these limitations. RESULTS In this study, we investigated the biodiversity and spatial distribution characteristics of blooming jellyfish in the Bohai Sea of China using an eDNA metabarcoding approach, which covered the surface, middle, and bottom seawater layers, and sediments. Six jellyfish taxa were identified, of which Aurelia coerulea, Nemopilema nomurai, and Cyanea nozakii were the most dominant. These three blooming jellyfish presented a marked vertical distribution pattern in the offshore regions. A. coerulea was mainly distributed in the surface layer, whereas C. nozakii and N. nomurai showed a upper-middle and middle-bottom aggregation, respectively. Horizontally, A. coerulea and C. nozakii were more abundant in the inshore regions, whereas N. nomurai was mainly distributed offshore. Spearman's correlation analysis revealed a strong correlation between the eDNA of the three dominant blooming jellyfish species and temperature, salinity, and nutrients. CONCLUSIONS Our study confirms the applicability of the eDNA approach to both biodiverstiy evaluation of blooming jellyfish and investigating their spatial distribution, and it can be used as a supplementary tool to traditional survey methods.
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Affiliation(s)
- Lijing Ye
- Yantai University, 264005, Yantai, Shandong, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
| | - Saijun Peng
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, 264006, Yantai, Shandong, China
| | - Wenjing Zhang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lei Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiyan Sun
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chen Zhang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Munjira Yeasmin
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jianmin Zhao
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhijun Dong
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Blanluet A, Game ET, Dunn DC, Everett JD, Lombard AT, Richardson AJ. Evaluating ecological benefits of oceanic protected areas. Trends Ecol Evol 2024; 39:175-187. [PMID: 37778906 DOI: 10.1016/j.tree.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
Oceans beyond the continental shelf represent the largest yet least protected environments. The new agreement to increase protection targets to 30% by 2030 and the recent United Nations (UN) High Seas Treaty try to address this gap, and an increase in the declaration of oceanic Marine Protected Areas (oMPAs) in waters beyond 200 m in depth is likely. Here we find that there is contradictory evidence concerning the benefits of oMPAs in terms of protecting pelagic habitats, providing refuge for highly mobile species, and potential fisheries benefits. We discover a mismatch between oMPA management objectives focusing on protection of pelagic habitats and biodiversity, and scientific research focusing on fisheries benefits. We suggest that the solution is to harness emerging technologies to monitor inside and outside oMPAs.
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Affiliation(s)
- Arthur Blanluet
- School of the Environment, The University of Queensland, St Lucia, QLD, 4072, Australia; The Nature Conservancy, South Brisbane, Queensland 4101, Australia.
| | - Edward T Game
- The Nature Conservancy, South Brisbane, Queensland 4101, Australia
| | - Daniel C Dunn
- School of the Environment, The University of Queensland, St Lucia, QLD, 4072, Australia; Centre for Biodiversity and Conservation Science (CBCS), The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Jason D Everett
- School of the Environment, The University of Queensland, St Lucia, QLD, 4072, Australia; Commonwealth Scientific and Industrial Research Organization (CSIRO) Environment, Queensland Biosciences Precinct (QBP), St Lucia, QLD 4067, Australia; Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW, Australia
| | - Amanda T Lombard
- Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha, South Africa
| | - Anthony J Richardson
- School of the Environment, The University of Queensland, St Lucia, QLD, 4072, Australia; Centre for Biodiversity and Conservation Science (CBCS), The University of Queensland, St Lucia, 4072, QLD, Australia; Commonwealth Scientific and Industrial Research Organization (CSIRO) Environment, Queensland Biosciences Precinct (QBP), St Lucia, QLD 4067, Australia
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5
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Canals O, Corell J, Villarino E, Chust G, Aylagas E, Mendibil I, Michell CT, González-Gordillo JI, Irigoien X, Rodríguez-Ezpeleta N. Global mesozooplankton communities show lower connectivity in deep oceanic layers. Mol Ecol 2024:e17286. [PMID: 38287749 DOI: 10.1111/mec.17286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 01/31/2024]
Abstract
Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution and connectivity at global scale is still fragmented. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across the Atlantic, Indian and Pacific oceans from the surface to bathypelagic depths. We highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the oceanic regions with the highest proportion of hidden diversity. We report no consistent alpha-diversity patterns for mesozooplankton at a global scale, neither across vertical nor horizontal gradients. However, beta-diversity analysis suggests horizontal and vertical structuring of mesozooplankton communities mostly attributed to turnover and reveals an increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers. Additionally, we identify a water mass type-mediated structuring of mesozooplankton bathypelagic communities instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types, thus reinforcing the importance of oceanic currents and barriers to dispersal in shaping global plankton communities.
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Affiliation(s)
- Oriol Canals
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Jon Corell
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Ernesto Villarino
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Guillem Chust
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Eva Aylagas
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Iñaki Mendibil
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Craig T Michell
- Biological and Environmental Science and Engineering Division, Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Juan Ignacio González-Gordillo
- Área de Ecología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Campus de Excelencia Internacional del Mar, Puerto Real, Spain
| | - Xabier Irigoien
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Naiara Rodríguez-Ezpeleta
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
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O'Brien TD, Blanco-Bercial L, Questel JM, Batta-Lona PG, Bucklin A. MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems. Methods Mol Biol 2024; 2744:475-489. [PMID: 38683336 DOI: 10.1007/978-1-0716-3581-0_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/ ) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases ( https://metazoogene.org ).
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Affiliation(s)
- Todd D O'Brien
- NOAA Fisheries, Office of Science & Technology, Silver Spring, MD, USA
| | | | - Jennifer M Questel
- College of Fisheries & Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Paola G Batta-Lona
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
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Peng S, Wang L, Ma Y, Ye L, Hou C, Liu Y, Li Y, Sun T, Zhao J, Dong Z. Application of environmental DNA metabarcoding and quantitative PCR to detect blooming jellyfish in a temperate bay of northern China. Ecol Evol 2023; 13:e10669. [PMID: 37915801 PMCID: PMC10616739 DOI: 10.1002/ece3.10669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Frequently occurring jellyfish blooms have severe impacts on the socioeconomics of coastal areas, which stress the importance of early detection and assessments of blooming jellyfish taxa. Environmental DNA (eDNA) techniques (quantitative PCR and eDNA metabarcoding) have the advantage of high sensitivity and are an emerging powerful tool for investigations of target species. However, a comprehensive analysis of the biodiversity and biomass of jellyfish taxa in the target area by combining the two eDNA techniques is still lacking. Here, we developed eDNA metabarcoding and quantitative PCR for the detection and assessment of jellyfish taxa in the temperate Yantai Sishili Bay (YSB) and estimated the spatial distribution of Aurelia coerulea. Species-specific quantitative PCR assays targeting the mitochondrial cytochrome c oxidase subunit I gene of A. coerulea were developed. Additionally, eDNA metabarcoding based on the mitochondrial 16S rDNA sequences identified six jellyfish species in YSB. Moreover, our results indicate that A. coerulea aggregations were more likely to occur in the inner part of the bay than in the outer part, and they gathered in the bottom layer of seawater rather than in the surface layer. Our results demonstrate the potential of two eDNA techniques in jellyfish biomass investigation and jellyfish taxa detection. These eDNA techniques may contribute to the discovery of jellyfish aggregation so as to achieve early warning of large-scale jellyfish blooms in coastal areas.
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Affiliation(s)
- Saijun Peng
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Wang
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological RestorationShandong Marine Resource and Environment Research InstituteYantaiShandongChina
| | - Lijing Ye
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
| | - Chaowei Hou
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yongliang Liu
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yongxue Li
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tingting Sun
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jianmin Zhao
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhijun Dong
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
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Duhamet A, Albouy C, Marques V, Manel S, Mouillot D. The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding. Ecol Evol 2023; 13:e9672. [PMID: 36699576 PMCID: PMC9846838 DOI: 10.1002/ece3.9672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 01/19/2023] Open
Abstract
The bathymetric and geographical distribution of marine species represent a key information in biodiversity conservation. Yet, deep-sea ecosystems are among the least explored on Earth and are increasingly impacted by human activities. Environmental DNA (eDNA) metabarcoding has emerged as a promising method to study fish biodiversity but applications to the deep-sea are still scarce. A major limitation in the application of eDNA metabarcoding is the incompleteness of species sequences available in public genetic databases which reduces the extent of detected species. This incompleteness by depth is still unknown. Here, we built the global bathymetric and geographical distribution of 10,826 actinopterygian and 960 chondrichthyan fish species. We assessed their genetic coverage by depth and by ocean for three main metabarcoding markers used in the literature: teleo and MiFish-U/E. We also estimated the number of primer mismatches per species amplified by in silico polymerase chain reaction which influence the probability of species detection. Actinopterygians show a stronger decrease in species richness with depth than Chondrichthyans. These richness gradients are accompanied by a continuous species turnover between depths. Fish species coverage with the MiFish-U/E markers is higher than with teleo while threatened species are more sequenced than the others. "Deep-endemic" species, those not ascending to the shallow depth layer, are less sequenced than not threatened species. The number of primer mismatches is not higher for deep-sea species than for shallower ones. eDNA metabarcoding is promising for species detection in the deep-sea to better account for the 3-dimensional structure of the ocean in marine biodiversity monitoring and conservation. However, we argue that sequencing efforts on "deep-endemic" species are needed.
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Affiliation(s)
- Agnès Duhamet
- MARBECUniv Montpellier, CNRS, IRD, IfremerMontpellierFrance,CEFEUniv Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
| | - Camille Albouy
- Ecosystem and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland,Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Virginie Marques
- Ecosystem and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland,Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Stephanie Manel
- CEFEUniv Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
| | - David Mouillot
- MARBECUniv Montpellier, CNRS, IRD, IfremerMontpellierFrance,Institut Universitaire de FranceParisFrance
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Rangaswamy B, Ji CW, Kim WS, Park JW, Kim YJ, Kwak IS. Profiling Analysis of Filter Feeder Polypedilum (Chironomidae) Gut Contents Using eDNA Metabarcoding Following Contrasting Habitat Types-Weir and Stream. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10945. [PMID: 36078662 PMCID: PMC9517803 DOI: 10.3390/ijerph191710945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
We analyzed the dietary composition of Polypedilum larvae among two contrasting habitats (river and weir). Our approach was (i) to apply eDNA-based sampling to reveal the gut content of the chironomid larvae, (ii) the diversity of gut contents in the two aquatic habitats, and (iii) assessment of habitat sediment condition with the food sources in the gut. The most abundant food was Chlorophyta in the gut of the river (20%) and weir (39%) chironomids. The average ratio of fungi, protozoa, and zooplankton in river chironomids gut was 5.9%, 7.2%, and 3.8%, while it was found decreased to 1.2%, 2.5%, and 0.1% in weir chironomids. Aerobic fungi in river midge guts were 3.6% and 10.34% in SC and IS, while they were in the range of 0.34-2.58% in weir midges. The hierarchical clustering analysis showed a relationship of environmental factors with food contents. Abiotic factors (e.g., pH) in the river and weir habitats correlated the clustered pattern with phytoplankton and minor groups of fungi. This study could help understand the food source diversity in the chironomid and habitat environmental conditions by using eDNA metabarcoding as an effective tool to determine dietary composition.
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Affiliation(s)
- Boobal Rangaswamy
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
| | - Chang Woo Ji
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
| | - Won-Seok Kim
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Jae-Won Park
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Yong Jun Kim
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Ihn-Sil Kwak
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
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10
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Zhang J, Ding R, Wang Y, Wen J. Experimental study on the response relationship between environmental DNA concentration and biomass of Schizothorax prenanti in still water. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.972680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The superiority of the environmental DNA (eDNA) method for estimating the biomass of aquatic species has been demonstrated. However, the relationship between eDNA concentration and biomass is difficult to clarify under the influence of complex water flow and habitat conditions. It seriously restricts the popularization and application of the eDNA method in estimating aquatic biomass. In this paper, a typical fish species of rivers in southwest China, Schizothorax prenanti, was selected as the target species. Under standardized laboratory hydrostatic conditions, two environmental factors, water pH and water temperature were firstly determined through pre-experiments. Then we investigated the correlation between eDNA concentration and biomass under different body sizes and different body size compositions. The experimental results showed that water pH and the water temperature had a great influence on eDNA concentration. Therefore, the effects of these environmental factors need to be considered simultaneously when using eDNA concentration to estimate biomass. Under the premise of consistent environmental conditions, the biomass of Schizothorax prenanti was positively correlated with the eDNA concentration when the individual body size was the same. For each 1% increase in biomass of the fish, the eDNA concentration of adult (larger size) fish increased by 0.98%, while the eDNA concentration of juvenile (smaller size) fish increased by 1.38%. The smaller the size of individual fish, the greater the increase of eDNA concentration with biomass, and the increase of juvenile fish was about 1.4 times that the adult fish. When the biomass was the same but the body size composition was different, the higher the proportion of small body size individuals in the population, the higher the eDNA concentration. Special attention needs to be paid to the body size composition of the population to avoid the biomass estimation being lower than the actual value when the smaller size fish are dominant. The experimental results provide a strong basis for a more accurate estimation of aquatic biomass in reservoirs, lakes, and other still water areas by using the eDNA method.
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11
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McCartin LJ, Vohsen SA, Ambrose SW, Layden M, McFadden CS, Cordes EE, McDermott JM, Herrera S. Temperature Controls eDNA Persistence across Physicochemical Conditions in Seawater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8629-8639. [PMID: 35658125 PMCID: PMC9231374 DOI: 10.1021/acs.est.2c01672] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 05/20/2023]
Abstract
Environmental DNA (eDNA) quantification and sequencing are emerging techniques for assessing biodiversity in marine ecosystems. Environmental DNA can be transported by ocean currents and may remain at detectable concentrations far from its source depending on how long it persist. Thus, predicting the persistence time of eDNA is crucial to defining the spatial context of the information derived from it. To investigate the physicochemical controls of eDNA persistence, we performed degradation experiments at temperature, pH, and oxygen conditions relevant to the open ocean and the deep sea. The eDNA degradation process was best explained by a model with two phases with different decay rate constants. During the initial phase, eDNA degraded rapidly, and the rate was independent of physicochemical factors. During the second phase, eDNA degraded slowly, and the rate was strongly controlled by temperature, weakly controlled by pH, and not controlled by dissolved oxygen concentration. We demonstrate that marine eDNA can persist at quantifiable concentrations for over 2 weeks at low temperatures (≤10 °C) but for a week or less at ≥20 °C. The relationship between temperature and eDNA persistence is independent of the source species. We propose a general temperature-dependent model to predict the maximum persistence time of eDNA detectable through single-species eDNA quantification methods.
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Affiliation(s)
- Luke J. McCartin
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Samuel A. Vohsen
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Susan W. Ambrose
- Department
of Earth and Environmental Sciences, Lehigh
University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Michael Layden
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Catherine S. McFadden
- Department
of Biology, Harvey Mudd College, Claremont, California 91711, United States
| | - Erik E. Cordes
- Department
of Biology, Temple University, Philadelphia, Pennsylvania 19122-6008, United States
| | - Jill M. McDermott
- Department
of Earth and Environmental Sciences, Lehigh
University, Bethlehem, Pennsylvania 18015-3027, United States
| | - Santiago Herrera
- Department
of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-3027, United States
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Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
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13
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Allan EA, DiBenedetto MH, Lavery AC, Govindarajan AF, Zhang WG. Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean. Sci Rep 2021; 11:21273. [PMID: 34711868 PMCID: PMC8553870 DOI: 10.1038/s41598-021-00288-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022] Open
Abstract
Increasingly, researchers are using innovative methods to census marine life, including identification of environmental DNA (eDNA) left behind by organisms in the water column. However, little is understood about how eDNA is distributed in the ocean, given that organisms are mobile and that physical and biological processes can transport eDNA after release from a host. Particularly in the vast mesopelagic ocean where many species vertically migrate hundreds of meters diurnally, it is important to link the location at which eDNA was shed by a host organism to the location at which eDNA was collected in a water sample. Here, we present a one-dimensional mechanistic model to simulate the eDNA vertical distribution after its release and to compare the impact of key biological and physical parameters on the eDNA vertical and temporal distribution. The modeled vertical eDNA profiles allow us to quantify spatial and temporal variability in eDNA concentration and to identify the most important parameters to consider when interpreting eDNA signals. We find that the vertical displacement by advection, dispersion, and settling has limited influence on the eDNA distribution, and the depth at which eDNA is found is generally within tens of meters of the depth at which the eDNA was originally shed from the organism. Thus, using information about representative vertical migration patterns, eDNA concentration variability can be used to answer ecological questions about migrating organisms such as what depths species can be found in the daytime and nighttime and what percentage of individuals within a species diurnally migrate. These findings are critical both to advance the understanding of the vertical distribution of eDNA in the water column and to link eDNA detection to organism presence in the mesopelagic ocean as well as other aquatic environments.
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Affiliation(s)
- Elizabeth Andruszkiewicz Allan
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, USA.
| | - Michelle H DiBenedetto
- Department of Physical Oceanography, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Andone C Lavery
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | - Weifeng G Zhang
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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14
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Ogata M, Masuda R, Harino H, Sakata MK, Hatakeyama M, Yokoyama K, Yamashita Y, Minamoto T. Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Sci Rep 2021; 11:16830. [PMID: 34417484 PMCID: PMC8379222 DOI: 10.1038/s41598-021-94286-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.
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Affiliation(s)
- Mizuki Ogata
- grid.258799.80000 0004 0372 2033Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086 Japan ,Benesse Corporation, 3-7-17 Minamigata, Kitaku, Okayama 700-8686 Japan
| | - Reiji Masuda
- grid.258799.80000 0004 0372 2033Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086 Japan
| | - Hiroya Harino
- grid.444507.60000 0001 0424 8271Department of Human Sciences, Kobe College, 4-1 Okadayama, Nishinomiya, Hyogo 662-8508 Japan
| | - Masayuki K. Sakata
- grid.31432.370000 0001 1092 3077Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, Hyogo 657-8501 Japan
| | - Makoto Hatakeyama
- Non-Profit Organization Mori-Umi, Nishi-Moune, Karakuwa, Kesennuma, Miyagi 988-0527 Japan
| | - Katsuhide Yokoyama
- grid.265074.20000 0001 1090 2030Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 092-0397 Japan
| | - Yoh Yamashita
- grid.258799.80000 0004 0372 2033Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto 625-0086 Japan
| | - Toshifumi Minamoto
- grid.31432.370000 0001 1092 3077Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, Hyogo 657-8501 Japan
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