151
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Aucone E, Kirchgeorg S, Valentini A, Pellissier L, Deiner K, Mintchev S. Drone-assisted collection of environmental DNA from tree branches for biodiversity monitoring. Sci Robot 2023; 8:eadd5762. [PMID: 36652506 DOI: 10.1126/scirobotics.add5762] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The protection and restoration of the biosphere is crucial for human resilience and well-being, but the scarcity of data on the status and distribution of biodiversity puts these efforts at risk. DNA released into the environment by organisms, i.e., environmental DNA (eDNA), can be used to monitor biodiversity in a scalable manner if equipped with the appropriate tool. However, the collection of eDNA in terrestrial environments remains a challenge because of the many potential surfaces and sources that need to be surveyed and their limited accessibility. Here, we propose to survey biodiversity by sampling eDNA on the outer branches of tree canopies with an aerial robot. The drone combines a force-sensing cage with a haptic-based control strategy to establish and maintain contact with the upper surface of the branches. Surface eDNA is then collected using an adhesive surface integrated in the cage of the drone. We show that the drone can autonomously land on a variety of branches with stiffnesses between 1 and 103 newton/meter without prior knowledge of their structural stiffness and with robustness to linear and angular misalignments. Validation in the natural environment demonstrates that our method is successful in detecting animal species, including arthropods and vertebrates. Combining robotics with eDNA sampling from a variety of unreachable aboveground substrates can offer a solution for broad-scale monitoring of biodiversity.
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Affiliation(s)
- Emanuele Aucone
- Environmental Robotics Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland
| | - Steffen Kirchgeorg
- Environmental Robotics Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland
| | | | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland.,Ecosystems and Landscape Evolution Group, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Kristy Deiner
- Environmental DNA Group, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Stefano Mintchev
- Environmental Robotics Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland
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152
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Setsuko S, Yoshimura K, Ueno S, Worth JRP, Ujino-Ihara T, Katsuki T, Noshiro S, Fujii T, Arai T, Yoshimaru H. A DNA barcode reference library for the native woody seed plants of Japan. Mol Ecol Resour 2023; 23:855-871. [PMID: 36694075 DOI: 10.1111/1755-0998.13748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/25/2022] [Accepted: 12/08/2022] [Indexed: 01/26/2023]
Abstract
DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL & trnH-psbA, rbcL & matK and trnH-psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.
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Affiliation(s)
- Suzuki Setsuko
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Kensuke Yoshimura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - James Raymond Peter Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Toshio Katsuki
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tokyo, Japan
| | - Shuichi Noshiro
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tomoyuki Fujii
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Takahisa Arai
- Tohoku University Botanical Gardens, Tohoku University, Miyagi, Japan
| | - Hiroshi Yoshimaru
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
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153
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Klimova A, Rodríguez‐Estrella R, Meng G, Gutiérrez‐Rivera JN, Jimenez‐Jimenez ML, Liu S. Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula, Mexico. DIVERS DISTRIB 2023. [DOI: 10.1111/ddi.13672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Anastasia Klimova
- Centro de Investigaciones Biológicas del Noroeste S.C. La Paz Mexico
| | | | - Guanliang Meng
- Zoological Research Museum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change Bonn Germany
| | | | | | - Shanlin Liu
- Department of Entomology, College of Plant Protection China Agricultural University Beijing China
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154
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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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155
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Prager M, Lundin D, Ronquist F, Andersson AF. ASV portal: an interface to DNA-based biodiversity data in the Living Atlas. BMC Bioinformatics 2023; 24:6. [PMID: 36604610 PMCID: PMC9817246 DOI: 10.1186/s12859-022-05120-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas. RESULTS The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. CONCLUSION The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.
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Affiliation(s)
- Maria Prager
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden ,grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Daniel Lundin
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, 391 82 Kalmar, Sweden
| | - Fredrik Ronquist
- grid.425591.e0000 0004 0605 2864Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden
| | - Anders F. Andersson
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 21 Stockholm, Sweden
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156
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Shea MM, Kuppermann J, Rogers MP, Smith DS, Edwards P, Boehm AB. Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility. PeerJ 2023; 11:e14993. [PMID: 36992947 PMCID: PMC10042160 DOI: 10.7717/peerj.14993] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/12/2023] [Indexed: 03/31/2023] Open
Abstract
The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and reusable-despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.
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Affiliation(s)
- Meghan M. Shea
- Emmett Interdisciplinary Program in Environment & Resources (E-IPER), Stanford University, Stanford, CA, United States of America
| | - Jacob Kuppermann
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Megan P. Rogers
- Program in Human Biology, Stanford University, Stanford, CA, United States of America
| | - Dustin Summer Smith
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Paul Edwards
- Program in Science, Technology and Society, Stanford University, Stanford, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
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157
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Gold Z, Shelton AO, Casendino HR, Duprey J, Gallego R, Van Cise A, Fisher M, Jensen AJ, D'Agnese E, Andruszkiewicz Allan E, Ramón-Laca A, Garber-Yonts M, Labare M, Parsons KM, Kelly RP. Signal and noise in metabarcoding data. PLoS One 2023; 18:e0285674. [PMID: 37167310 PMCID: PMC10174484 DOI: 10.1371/journal.pone.0285674] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from a single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates of underlying biological communities from metabarcoding is critical for enhancing the utility of such approaches for health and conservation. Recent work has demonstrated that correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data stems from non-detections across technical PCR replicates where one replicate fails to detect a species observed in other replicates. Such non-detections are a special case of variability among technical replicates in metabarcoding data. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) suggest how non-detections may arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show with both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing-both of which we can model-but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.
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Affiliation(s)
- Zachary Gold
- Cooperative Institute for Climate, Ocean, & Ecosystem Studies, UW, Seattle, Washington, United States of America
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Andrew Olaf Shelton
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Helen R Casendino
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Joe Duprey
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Ramón Gallego
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Amy Van Cise
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Mary Fisher
- School of Aquatic Fisheries Science, UW, Seattle, Washington, United States of America
| | - Alexander J Jensen
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Erin D'Agnese
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | | | - Ana Ramón-Laca
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Maya Garber-Yonts
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Michaela Labare
- Scripps Institution of Oceanography, UCSD, La Jolla, California, United States of America
| | - Kim M Parsons
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
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158
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Zhao B, van Bodegom PM, Trimbos KB. Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA. Mol Ecol Resour 2023; 23:81-91. [PMID: 35899418 PMCID: PMC10087510 DOI: 10.1111/1755-0998.13691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
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159
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Mahon AR, Grey EK, Jerde CL. Integrating invasive species risk assessment into environmental DNA metabarcoding reference libraries. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2730. [PMID: 36054696 PMCID: PMC10078450 DOI: 10.1002/eap.2730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/12/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) metabarcoding has shown promise as a tool for estimating biodiversity and early detection of invasive species. In aquatic systems, advantages of this method include the ability to concurrently monitor biodiversity and detect incipient invasions simply through the collection and analysis of water samples. However, depending on the molecular markers chosen for a given study, reference libraries containing target sequences from present species may limit the usefulness of eDNA metabarcoding. To explore the extent of this issue and how it may be resolved to aid biodiversity and invasive species early detection goals, we focus on fishes in the well-studied Laurentian Great Lakes region. First, we provide a synthesis of species currently known from the region and of non-indigenous species identified as threats by international, national, regional, and introduction pathway-specific fish risk assessments. With these species lists, we then evaluate 23 primer pairs commonly used in fish eDNA metabarcoding with available databases of sequence coverage and species specificity. Finally, we identify established and potentially invasive non-indigenous fish that should be prioritized for genetic sequencing to ensure robust eDNA metabarcoding for the region. Our results should increase confidence in using eDNA metabarcoding for fisheries conservation and management in the Great Lakes region and help prioritize reference sequencing efforts. The ultimate utility of eDNA metabarcoding approaches will come when conservation management of existing fish communities is integrated with early detection efforts for invasive species surveillance to assess total fish biodiversity.
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Affiliation(s)
- Andrew R. Mahon
- Department of BiologyCentral Michigan UniversityMount PleasantMichiganUSA
| | - Erin K. Grey
- School of Biology and Ecology and Maine Center for Genetics in the EnvironmentUniversity of MaineOronoMaineUSA
| | - Christopher L. Jerde
- Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
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160
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Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish. DIVERSITY 2022. [DOI: 10.3390/d14121139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cubozoan jellyfish pose a risk of envenomation to humans and a threat to many businesses, yet crucial gaps exist in determining threats to stakeholders and understanding their ecology. Environmental DNA (eDNA) provides a cost-effective method for detection that is less labour intensive and provides a higher probability of detection. The objective of this study was to develop, optimise and trial the use of eDNA to detect the Australian box jellyfish, Chironex fleckeri. This species was the focus of this study as it is known to have the strongest venom of any cubozoan; it is responsible for more than 200 recorded deaths in the Indo-Pacific region. Further, its ecology is poorly known. Herein, a specific and sensitive probe-based assay, multiplexed with an endogenous control assay, was developed, and successfully utilised to detect the deadly jellyfish species and differentiate them from closely related taxa. A rapid eDNA decay rate of greater than 99% within 27 h was found with no detectable influence from temperature. The robustness of the technique indicates that it will be of high utility for detection and to address knowledge gaps in the ecology of C. fleckeri; further, it has broad applicability to other types of zooplankton.
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161
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Tsuji S, Inui R, Nakao R, Miyazono S, Saito M, Kono T, Akamatsu Y. Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community. Sci Rep 2022; 12:21524. [PMID: 36513686 PMCID: PMC9747787 DOI: 10.1038/s41598-022-25274-3] [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: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between the eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity.
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Affiliation(s)
- Satsuki Tsuji
- grid.258799.80000 0004 0372 2033Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, 606–8502 Japan ,grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
| | - Ryutei Inui
- grid.418051.90000 0000 8774 3245Faculty of Socio-Environmental Studies, Fukuoka Institute of Technology, Wajiro-Higashi, Higashi-Ku, Fukuoka, 811–0295 Japan
| | - Ryohei Nakao
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
| | - Seiji Miyazono
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
| | - Minoru Saito
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan ,grid.452611.50000 0001 2107 8171Fisheries Division, Japan International Research Center for Agricultural Sciences, 1-1, Ohwashi, Tsukuba, Ibaraki 305–8686 Japan
| | - Takanori Kono
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan ,grid.472015.50000 0000 9513 8387Aqua Restoration Research Center, Public Works Research Institute, National Research and Development Agency, Kawashima, Kasada-Machi, Kakamigahara, Gifu, 501–6021 Japan
| | - Yoshihisa Akamatsu
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
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162
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Sun H, Chen Q, Chen W, Qu C, Mo J, Song J, Guo J, Tian Y. Assessment of biological community in riparian zone contaminated by PAHs: Linking source apportionment to biodiversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158121. [PMID: 35988620 DOI: 10.1016/j.scitotenv.2022.158121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The distribution of multiple communities in riparian groundwater was investigated by environmental DNA metabarcoding, including 16S rRNA, 18S rRNA, and COI gene sequencing for bacteria, microbial eukaryotes (including algae, fungi, and protozoa), and metazoan, respectively, followed by correlation analysis between multiple communities and PAH contamination levels. The concentration of PAHs in the Beiluo River ranged largely from 35.32 to 728.59 ng/L. Here, the Shannon's diversity index of bacteria (Firmicutes) decreased possibly due to the occurrence of Pyrene, which mainly derives from coal and biomass combustion. Furthermore, the reduced richness of fungi (Ascomycota, Basidiomycota) and algae (Chlorophyta, Chrysophyceae) can be attributed to the presence of medium molecular weight (MMW) PAHs (Pyrene, Benz(a)anthracene, Chrysene), and low molecular weight (LMW) PAHs (Naphthalene, Fluorene, Phenanthrene). The richness and Shannon's diversity index of metazoan (Arthropoda) were promoted owing to MMW PAHs (Chrysene, Fluoranthene) generated from coal and biomass combustion and traffic emission. The ecological risk of PAHs in the groundwater environment of the Beiluo River was characterized as low to medium, where LMW and MMW PAHs posed higher risk than the high molecular weight (HMW) compounds. Overall, this study provides insights into the structures of riparian multi-biological communities altered by PAHs.
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Affiliation(s)
- Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Qiqi Chen
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Wenwu Chen
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Chengkai Qu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jiezhang Mo
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Jinxi Song
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
| | - Yulu Tian
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
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163
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Fungal and fungal-like diversity in marine sediments from the maritime Antarctic assessed using DNA metabarcoding. Sci Rep 2022; 12:21044. [PMID: 36473886 PMCID: PMC9726857 DOI: 10.1038/s41598-022-25310-2] [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: 09/11/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
We assessed the fungal and fungal-like sequence diversity present in marine sediments obtained in the vicinity of the South Shetland Islands (Southern Ocean) using DNA metabarcoding through high-throughput sequencing (HTS). A total of 193,436 DNA reads were detected in sediment obtained from three locations: Walker Bay (Livingston Island) at 52 m depth (48,112 reads), Whalers Bay (Deception Island) at 151 m (104,704) and English Strait at 404 m (40,620). The DNA sequence reads were assigned to 133 distinct fungal amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Glomeromycota, Monoblepharomycota, Mucoromycota and Rozellomycota and the fungal-like Straminopila. Thelebolus balaustiformis, Pseudogymnoascus sp., Fungi sp. 1, Ciliophora sp., Agaricomycetes sp. and Chaetoceros sp. were the dominant assigned taxa. Thirty-eight fungal ASVs could only be assigned to higher taxonomic levels, and may represent taxa not currently included in the available databases or represent new taxa and/or new records for Antarctica. The total fungal community displayed high indices of diversity, richness and moderate to low dominance. However, diversity and taxa distribution varied across the three sampling sites. In Walker Bay, unidentified fungi were dominant in the sequence assemblage. Whalers Bay sediment was dominated by Antarctic endemic and cold-adapted taxa. Sediment from English Strait was dominated by Ciliophora sp. and Chaetoceros sp. These fungal assemblages were dominated by saprotrophic, plant and animal pathogenic and symbiotic taxa. The detection of an apparently rich and diverse fungal community in these marine sediments reinforces the need for further studies to characterize their richness, functional ecology and potential biotechnological applications.
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164
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Huang S, Yoshitake K, Watabe S, Asakawa S. Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116310. [PMID: 36261997 DOI: 10.1016/j.jenvman.2022.116310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Environmental DNA (eDNA) is organismal DNA that can be detected in the environment and is derived from cellular material of organisms shed into aquatic or terrestrial environments. It can be sampled and monitored using molecular methods, which is important for the early detection of invasive and native species as well as the discovery of rare and cryptic species. While few reviews have summarized the latest findings on eDNA for most aquatic animal categories in the aquatic ecosystem, especially for aquatic eDNA processing and application. In the present review, we first performed a bibliometric network analysis of eDNA studies on aquatic animals. Subsequently, we summarized the abiotic and biotic factors affecting aquatic eDNA occurrence. We also systematically discussed the relevant experiments and analyses of aquatic eDNA from various aquatic organisms, including fish, molluscans, crustaceans, amphibians, and reptiles. Subsequently, we discussed the major achievements of eDNA application in studies on the aquatic ecosystem and environment. The application of eDNA will provide an entirely new paradigm for biodiversity conservation, environment monitoring, and aquatic species management at a global scale.
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Affiliation(s)
- Songqian Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 200120, China; Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, 252-0313, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
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165
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Didaskalou EA, Trimbos KB, Stewart KA. Environmental DNA. Curr Biol 2022; 32:R1250-R1252. [PMID: 36413963 DOI: 10.1016/j.cub.2022.09.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Emilie Didaskalou and colleagues introduce the analysis of DNA form environmental samples.
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Affiliation(s)
- Emilie A Didaskalou
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Netherlands.
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | - Kathryn A Stewart
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
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166
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Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment. Sci Rep 2022; 12:19828. [PMID: 36400924 PMCID: PMC9674700 DOI: 10.1038/s41598-022-23888-1] [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: 04/28/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is widely used for species analysis, while the use of environmental RNA (eRNA) metabarcoding is more limited. We conducted comparative eDNA/eRNA metabarcoding of the algae and arthropods (aquatic insects) in water samples from Naka River, Japan, to evaluate their potential for biological monitoring and water quality assessment. Both methods detected various algae and arthropod species; however, their compositions were remarkably different from those in traditional field surveys (TFSs), indicating low sensitivity. For algae, the species composition derived from eDNA and eRNA metabarcoding was equivalent. While TFSs focus on attached algae, metabarcoding analysis theoretically detects both planktonic and attached algae. A recently expanded genomic database for aquatic insects significantly contributed to the sensitivity and positive predictivity for arthropods. While the sensitivity of eRNA was lower than that of eDNA, the positive predictivity of eRNA was higher. The eRNA of terrestrial arthropods indicated extremely high or low read numbers when compared with eDNA, suggesting that eRNA could be an effective indicator of false positives. Arthropod and algae eDNA/eRNA metabarcoding analysis enabled water quality estimates from TFSs. The eRNA of algae and arthropods could thus be used to evaluate biodiversity and water quality and provide insights from ecological surveys.
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167
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Willassen E, Westgaard JI, Kongsrud JA, Hanebrekke T, Buhl-Mortensen P, Holte B. Benthic invertebrates in Svalbard fjords-when metabarcoding does not outperform traditional biodiversity assessment. PeerJ 2022; 10:e14321. [PMID: 36415859 PMCID: PMC9676020 DOI: 10.7717/peerj.14321] [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: 06/02/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
To protect and restore ecosystems and biodiversity is one of the 10 challenges identified by the United Nations's Decade of the Ocean Science. In this study we used eDNA from sediments collected in two fjords of the Svalbard archipelago and compared the taxonomic composition with traditional methods through metabarcoding, targeting mitochondrial CO1, to survey benthos. Clustering of 21.6 mill sequence reads with a d value of 13 in swarm, returned about 25 K OTU reads. An identification search with the BOLD database returned 12,000 taxonomy annotated sequences spanning a similarity range of 50% to 100%. Using an acceptance filter of minimum 90% similarity to the CO1 reference sequence, we found that 74% of the ca 100 taxon identified sequence reads were Polychaeta and 22% Nematoda. Relatively few other benthic invertebrate species were detected. Many of the identified sequence reads were extra-organismal DNA from terrestrial, planktonic, and photic zone sources. For the species rich Polychaeta, we found that, on average, only 20.6% of the species identified from morphology were also detected with DNA. This discrepancy was not due to missing reference sequences in the search database, because 90-100% (mean 96.7%) of the visually identified species at each station were represented with barcodes in Boldsystems. The volume of DNA samples is small compared with the volume searched in visual sorting, and the replicate DNA-samples in sum covered only about 2% of the surface area of a grab. This may considerably reduce the detection rate of species that are not uniformly distributed in the sediments. Along with PCR amplification bias and primer mismatch, this may be an important reason for the limited congruence of species identified with the two approaches. However, metabarcoding also identified 69 additional species that are usually overlooked in visual sample sorting, demonstrating how metabarcoding can complement traditional methodology by detecting additional, less conspicuous groups of organisms.
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Affiliation(s)
- Endre Willassen
- Department of Natural History, University of Bergen, Bergen, Norway
| | - Jon-Ivar Westgaard
- Department of Population Genetics, Institute of Marine Research, Tromsø, Troms, Norway
| | | | - Tanja Hanebrekke
- Department of Population Genetics, Institute of Marine Research, Tromsø, Troms, Norway
| | - Pål Buhl-Mortensen
- Department of Bentic Communities, Institute of Marine Research, Bergen, Norway
| | - Børge Holte
- Department of Bentic Communities, Institute of Marine Research, Tromsø, Troms, Norway
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168
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Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ 2022; 10:e14071. [PMID: 36405018 PMCID: PMC9673773 DOI: 10.7717/peerj.14071] [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: 06/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Adam R. Wall
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Teia M. Schweizer
- Department of Fish and Wildlife Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
| | - N. Dean Pentcheff
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Emily E. Curd
- Department of Natural Sciences, Landmark College, Putney, VT, United States of America
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Kevin Stolzenbach
- Wood Environment and Infrastructure, Inc., San Diego, CA, United States of America
| | - Kat Prickett
- Port of Los Angeles, Los Angeles, CA, United States of America
| | - Justin Luedy
- Port of Long Beach, Long Beach, CA, United States of America
| | - Regina Wetzer
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
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169
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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170
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Garcés-Pastor S, Coissac E, Lavergne S, Schwörer C, Theurillat JP, Heintzman PD, Wangensteen OS, Tinner W, Rey F, Heer M, Rutzer A, Walsh K, Lammers Y, Brown AG, Goslar T, Rijal DP, Karger DN, Pellissier L, Heiri O, Alsos IG. High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change. Nat Commun 2022; 13:6559. [PMID: 36333301 PMCID: PMC9636257 DOI: 10.1038/s41467-022-34010-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.
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Affiliation(s)
- Sandra Garcés-Pastor
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Eric Coissac
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Sébastien Lavergne
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Christoph Schwörer
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Jean-Paul Theurillat
- grid.8591.50000 0001 2322 4988Fondation Aubert, 1938 Champex-Lac, Switzerland, Department of Plant Sciences, University of Geneva, 1292 Chambésy, Switzerland
| | - Peter D. Heintzman
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Owen S. Wangensteen
- grid.10919.300000000122595234Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway ,grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Catalonia Spain
| | - Willy Tinner
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Fabian Rey
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Martina Heer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Astrid Rutzer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Kevin Walsh
- grid.5685.e0000 0004 1936 9668Department of Archaeology, University of York, York, 11 YO1 7EP UK
| | - Youri Lammers
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Antony G. Brown
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Tomasz Goslar
- grid.5633.30000 0001 2097 3545Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, 61-680 Poznań, Poland
| | - Dilli P. Rijal
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Dirk N. Karger
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute for Forest, Snow, and Landscape Research (WSL), Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Loïc Pellissier
- grid.5801.c0000 0001 2156 2780Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zurich, Zürich, Switzerland ,grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Oliver Heiri
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Inger Greve Alsos
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
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171
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Wanniarachchi S, Swan M, Nevil P, York A. Using eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem. Ecol Evol 2022; 12:e9457. [PMID: 36381390 PMCID: PMC9643072 DOI: 10.1002/ece3.9457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022] Open
Abstract
Food acquisition is a fundamental process that drives animal distribution and abundance, influencing how species respond to changing environments. Disturbances such as fire create significant shifts in available dietary resources, yet, for many species, we lack basic information about what they eat, let alone how they respond to a changing resource base. In order to create effective management strategies, faunal conservation in flammable landscapes requires a greater understanding of what animals eat and how this change following a fire. What animals eat in postfire environments has received little attention due to the time-consuming methodologies and low-resolution identification of food taxa. Recently, molecular techniques have been developed to identify food DNA in scats, making it possible to identify animal diets with enhanced resolution. The primary aim of this study was to utilize eDNA metabarcoding to obtain an improved understanding of the diet of three native Australian small mammal species: yellow-footed antechinus (Antechinus flavipes), heath mouse (Pseudomys shortridgei), and bush rat (Rattus fuscipes). Specifically, we sought to understand the difference in the overall diet of the three species and how diet changed over time after fire. Yellow-footed antechinus diets mostly consisted of moths, and plants belonging to myrtles and legume families while bush rats consumed legumes, myrtles, rushes, and beetles. Heath mouse diet was dominated by rushes. All three species shifted their diets over time after fire, with most pronounced shifts in the bush rats and least for heath mice. Identifying critical food resources for native animals will allow conservation managers to consider the effect of fire management actions on these resources and help conserve the species that use them.
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Affiliation(s)
- Saumya Wanniarachchi
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Matthew Swan
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Paul Nevil
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Alan York
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
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172
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Littlefair JE, Rennie MD, Cristescu ME. Environmental nucleic acids: A field-based comparison for monitoring freshwater habitats using eDNA and eRNA. Mol Ecol Resour 2022; 22:2928-2940. [PMID: 35730338 PMCID: PMC9796649 DOI: 10.1111/1755-0998.13671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 01/01/2023]
Abstract
Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received much attention, the potential of environmental RNA as a biomonitoring tool remains under-explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect "metabolically active" parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra-organismal RNA will be important, but viability needs to be examined in a field-based setting. In this study we evaluate (a) whether extra-organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools.
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Affiliation(s)
- Joanne E. Littlefair
- Department of BiologyMcGill UniversityMontréalQuebecCanada,Queen Mary University of LondonLondonUK
| | - Michael D. Rennie
- IISD Experimental Lakes AreaWinnipegManitobaCanada,Department of BiologyLakehead UniversityThunder BayOntarioCanada
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173
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Environmental DNA in human and veterinary parasitology - Current applications and future prospects for monitoring and control. Food Waterborne Parasitol 2022; 29:e00183. [DOI: 10.1016/j.fawpar.2022.e00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022] Open
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174
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Fox G, Vellaniparambil LR, Ros L, Sammy J, Preziosi RF, Rowntree JK. Complex urban environments provide Apis mellifera with a richer plant forage than suburban and more rural landscapes. Ecol Evol 2022; 12:e9490. [PMID: 36381392 PMCID: PMC9643131 DOI: 10.1002/ece3.9490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/11/2022] Open
Abstract
Growth in the global development of cities, and increasing public interest in beekeeping, has led to increase in the numbers of urban apiaries. Towns and cities can provide an excellent diet for managed bees, with a diverse range of nectar and pollen available throughout a long flowering season, and are often more ecologically diverse than the surrounding rural environments. Accessible urban honeybee hives are a valuable research resource to gain insights into the diet and ecology of wild pollinators in urban settings. We used DNA metabarcoding of the rbcL and ITS2 gene regions to characterize the pollen community in Apis mellifera honey, inferring the floral diet, from 14 hives across an urban gradient around Greater Manchester, UK. We found that the proportion of urban land around a hive is significantly associated with an increase in the diversity of plants foraged and that invasive and non-native plants appear to play a critical role in the sustenance of urban bees, alongside native plant species. The proportion of improved grassland, typical of suburban lawns and livestock farms, is significantly associated with decreases in the diversity of plant pollen found in honey samples. These findings are relevant to urban landscape developers motivated to encourage biodiversity and bee persistence, in line with global bio-food security agendas.
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Affiliation(s)
- Graeme Fox
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Latha R. Vellaniparambil
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Loreto Ros
- Faculty of Life SciencesThe University of ManchesterManchesterUK
| | - Joshua Sammy
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Richard F. Preziosi
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
- Present address:
School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
| | - Jennifer K. Rowntree
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
- Present address:
School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
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175
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Pratomo A, Bengen DG, Zamani NP, Lane C, Humphries AT, Borbee E, Subhan B, Madduppa H. Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding. PeerJ 2022; 10:e14006. [PMID: 36312748 PMCID: PMC9610659 DOI: 10.7717/peerj.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/14/2022] [Indexed: 01/19/2023] Open
Abstract
Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA). Methods Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4-12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction). Results Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species. Conclusions eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral-algal mutualisms.
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Affiliation(s)
- Arief Pratomo
- Raja Ali Haji Maritime University, Tanjungpinang, Indonesia,Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Dietriech G. Bengen
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Neviaty P. Zamani
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Christopher Lane
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Austin T. Humphries
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Erin Borbee
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia,Oceanogen Research Center, Bogor, Indonesia
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176
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Holmes V, Aman J, York G, Kinnison MT. Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax). BMC Ecol Evol 2022; 22:121. [PMID: 36280813 PMCID: PMC9594880 DOI: 10.1186/s12862-022-02073-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anadromous rainbow smelt (Osmerus mordax) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecological, cultural, and commercial relevance. Defining the remnant range of anadromous smelt is more difficult than for many declining fish species because adults are only ephemerally present while spawning in small coastal streams at night during spring runoff periods when traditional assessments can be unreliable or even hazardous. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat, but that detection could also face challenges from adult eDNA quickly flushing out of these small stream systems. We combined daytime eDNA sampling with nighttime fyke netting to ascertain a potential window of eDNA detection before conducting eDNA surveys in four streams of varying abundance. Hierarchical occupancy modeling was in turn employed to estimate eDNA encounter probabilities relative to numbers of sampling events (date), samples within events, and qPCR replicates within samples. RESULTS Results from the combined eDNA and fyke net study indicated eDNA was detectable over an extended period, culminating approximately 8-13 days following peak spawning, suggesting developing smelt larvae might be the primary source of eDNA. Subsequently, smelt eDNA was readily detected in eDNA surveys of four streams, particularly following remediation of PCR inhibitors. Hierarchical occupancy modeling confirmed our surveys had high empirical detection for most sites, and that future surveys employing at least three sampling events, three samples per event, and six qPCR replicates can afford greater than 90% combined detection capability in low abundance systems. CONCLUSIONS These results demonstrate that relatively modest eDNA sampling effort has high capacity to detect this ephemerally present species of concern at low to moderate abundances. As such, smelt eDNA detection could improve range mapping by providing longer survey windows, safer sampling conditions, and lower field effort in low density systems, than afforded by existing visual and netting approaches.
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Affiliation(s)
- Vaughn Holmes
- grid.21106.340000000121820794Center for Genetics in the Environment and School of Biology and Ecology, University of Maine, Orono, USA
| | - Jacob Aman
- grid.448608.60000 0000 9349 2745Wells National Estuarine Research Reserve, Wells, USA
| | - Geneva York
- grid.21106.340000000121820794University of Maine Environmental DNA CORE Laboratory, Orono, USA
| | - Michael T. Kinnison
- grid.21106.340000000121820794Center for Genetics in the Environment and School of Biology and Ecology, University of Maine, Orono, USA ,grid.21106.340000000121820794University of Maine Environmental DNA CORE Laboratory, Orono, USA
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177
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Giroux MS, Reichman JR, Langknecht T, Burgess RM, Ho KT. Environmental RNA as a Tool for Marine Community Biodiversity Assessments. Sci Rep 2022; 12:17782. [PMID: 36273070 PMCID: PMC9588027 DOI: 10.1038/s41598-022-22198-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/11/2022] [Indexed: 01/19/2023] Open
Abstract
Microscopic organisms are often overlooked in traditional diversity assessments due to the difficulty of identifying them based on morphology. Metabarcoding is a method for rapidly identifying organisms where Environmental DNA (eDNA) is used as a template. However, legacy DNA is problematically detected from organisms no longer in the environment during sampling. Environmental RNA (eRNA), which is only produced by living organisms, can also be collected from environmental samples and used for metabarcoding. The aim of this study was to determine differences in community composition and diversity between eRNA and eDNA templates for metabarcoding. Using mesocosms containing field-collected communities from an estuary, RNA and DNA were co-extracted from sediment, libraries were prepared for two loci (18S and COI), and sequenced using an Illumina MiSeq. Results show a higher number of unique sequences detected from eRNA in both markers and higher α-diversity compared to eDNA. Significant differences between eRNA and eDNA for all β-diversity metrics were also detected. This study is the first to demonstrate community differences detected with eRNA compared to eDNA from an estuarine system and illustrates the broad applications of eRNA as a tool for assessing benthic community diversity, particularly for environmental conservation and management applications.
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Affiliation(s)
- Marissa S Giroux
- ORISE C/O US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, USA.
| | - Jay R Reichman
- Pacific Ecological Systems Division, US Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment, Corvallis, OR, USA
| | - Troy Langknecht
- ORISE C/O US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, USA
| | - Robert M Burgess
- Atlantic Coastal Environmental Sciences Division, US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Narragansett, RI, USA
| | - Kay T Ho
- Atlantic Coastal Environmental Sciences Division, US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Narragansett, RI, USA
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178
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Wang Y, Korneliussen TS, Holman LE, Manica A, Pedersen MW.
ngs
LCA
—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yucheng Wang
- Department of Zoology University of Cambridge Cambridge UK
- Lundbeck Foundation GeoGenetics Centre, Globe Institute University of Copenhagen Copenhagen K Denmark
- ALPHA, State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER) Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences (CAS) Beijing China
- BGI BGI‐Shenzhen Shanghai China
| | | | - Luke E. Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Andrea Manica
- Department of Zoology University of Cambridge Cambridge UK
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute University of Copenhagen Copenhagen K Denmark
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179
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Naumova NB, Kabilov MR. About the Biodiversity of the Air Microbiome. Acta Naturae 2022; 14:50-56. [PMID: 36694900 PMCID: PMC9844089 DOI: 10.32607/actanaturae.11671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 10/27/2022] [Indexed: 01/22/2023] Open
Abstract
This brief review focuses on the properties of bioaerosols, presenting some recent results of metagenomic studies of the air microbiome performed using next-generation sequencing. The taxonomic composition and structure of the bioaerosol microbiome may display diurnal and seasonal dynamics and be dependent on meteorological events such as dust storms, showers, fogs, etc., as well as air pollution. The Proteobacteria and Ascomycota members are common dominants in bioaerosols in different troposphere layers. The microbiological composition of the lower troposphere air affects the composition and diversity of the indoor bioaerosol microbiome, and information about the latter is very important, especially during exacerbated epidemiological situations. Few studies focusing on the bioaerosol microbiome of the air above Russia urge intensification of such research.
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Affiliation(s)
- N. B. Naumova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
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180
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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181
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Nagler M, Podmirseg SM, Ascher‐Jenull J, Sint D, Traugott M. Why eDNA fractions need consideration in biomonitoring. Mol Ecol Resour 2022; 22:2458-2470. [PMID: 35652762 PMCID: PMC9545497 DOI: 10.1111/1755-0998.13658] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/12/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022]
Abstract
The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA-based biodiversity data. Finally, future avenues of research towards eDNA fraction-specific analyses are outlined to unravel the full potential of eDNA-based studies targeting micro- and macro-organisms.
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Affiliation(s)
| | | | | | - Daniela Sint
- Department of ZoologyUniversität InnsbruckInnsbruckAustria
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182
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Good E, Holman LE, Pusceddu A, Russo T, Rius M, Iacono CL. Detection of community-wide impacts of bottom trawl fishing on deep-sea assemblages using environmental DNA metabarcoding. MARINE POLLUTION BULLETIN 2022; 183:114062. [PMID: 36075115 DOI: 10.1016/j.marpolbul.2022.114062] [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: 04/04/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Although considerable research progress on the effects of anthropogenic disturbance in the deep sea has been made in recent years, our understanding of these impacts at community level remains limited. Here, we studied deep-sea assemblages of Sicily (Mediterranean Sea) subject to different intensities of benthic trawling using environmental DNA (eDNA) metabarcoding and taxonomic identification of meiofauna communities. Firstly, eDNA metabarcoding data did not detect trawling impacts using alpha diversity whereas meiofauna data detected a significant effect of trawling. Secondly, both eDNA and meiofauna data detected significantly different communities across distinct levels of trawling intensity when we examined beta diversity. Taxonomic assignment of the eDNA data revealed that Bryozoa was present only at untrawled sites, highlighting their vulnerability to trawling. Our results provide evidence for community-wide impacts of trawling, with different trawling intensities leading to distinct deep-sea communities. Finally, we highlight the need for further studies to unravel understudied deep-sea biodiversity.
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Affiliation(s)
- Edward Good
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom.
| | - Luke E Holman
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Section for Molecular Ecology and Evolution, Faculty of Health and Medical Sciences, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Pusceddu
- Department of Life and Environmental Sciences, University of Cagliari, Via T. Fiorelli, 1, 09126 Cagliari, Italy
| | - Tommaso Russo
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marc Rius
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Centre for Advanced Studies of Blanes - Spanish National Research Council (CEAB-CSIC), Accés a la Cala Sant Francesc 14, 17300 Blanes (Girona), Spain; Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
| | - Claudio Lo Iacono
- Marine Sciences Institute - Spanish National Research Council (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
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183
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Xing Z, Gao H, Wang D, Shang Y, Tuliebieke T, Jiang J, Li C, Wang H, Li Z, Jia L, Wu Y, Wang D, Yang W, Chang Y, Zhang X, Xu L, Jiang C, Huang L, Tian X. A novel biological sources consistency evaluation method reveals high level of biodiversity within wild natural medicine: A case study of Amynthas earthworms as “Guang Dilong”. Acta Pharm Sin B 2022; 13:1755-1770. [PMID: 37139429 PMCID: PMC10150161 DOI: 10.1016/j.apsb.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022] Open
Abstract
For wild natural medicine, unanticipated biodiversity as species or varieties with similar morphological characteristics and sympatric distribution may co-exist in a single batch of medical materials, which affects the efficacy and safety of clinical medication. DNA barcoding as an effective species identification tool is limited by its low sample throughput nature. In this study, combining DNA mini-barcode, DNA metabarcoding and species delimitation method, a novel biological sources consistency evaluation strategy was proposed, and high level of interspecific and intraspecific variations were observed and validated among 5376 Amynthas samples from 19 sampling points regarded as "Guang Dilong" and 25 batches of proprietary Chinese medicines. Besides Amynthas aspergillum as the authentic source, 8 other Molecular Operational Taxonomic Units (MOTUs) were elucidated. Significantly, even the subgroups within A. aspergillum revealed here differ significantly on chemical compositions and biological activity. Fortunately, this biodiversity could be controlled when the collection was limited to designated areas, as proved by 2796 "decoction pieces" samples. This batch biological identification method should be introduced as a novel concept regarding natural medicine quality control, and to offer guidelines for in-situ conservation and breeding bases construction of wild natural medicine.
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Affiliation(s)
- Zhimei Xing
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Han Gao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Dan Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Ye Shang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Tenukeguli Tuliebieke
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Jibao Jiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunxiao Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Hong Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhenguo Li
- Mudanjiang YouBo Pharmaceutical Co. Ltd., Mudanjiang 157000, China
| | - Lifu Jia
- Guizhou Ruihe Pharmaceutical Co. Ltd., Guizhou 550000, China
| | - Yongsheng Wu
- Mudanjiang YouBo Pharmaceutical Co. Ltd., Mudanjiang 157000, China
| | - Dandan Wang
- Mudanjiang YouBo Pharmaceutical Co. Ltd., Mudanjiang 157000, China
| | - Wenzhi Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Yanxu Chang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Liuwei Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Chao Jiang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100010, China
- Corresponding authors.
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100010, China
- Corresponding authors.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
- Corresponding authors.
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184
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Zainal Abidin DH, Mohd Nor SA, Lavoué S, A Rahim M, Mohammed Akib NA. Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding. Sci Rep 2022; 12:16346. [PMID: 36175455 PMCID: PMC9523059 DOI: 10.1038/s41598-022-19954-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
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Affiliation(s)
- Danial Hariz Zainal Abidin
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | | | - Noor Adelyna Mohammed Akib
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia. .,School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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185
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Wong YS, Osborne NJ. Biodiversity Effects on Human Mental Health via Microbiota Alterations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11882. [PMID: 36231182 PMCID: PMC9565733 DOI: 10.3390/ijerph191911882] [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: 08/11/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The biodiversity hypothesis postulates that the natural environment positively affects human physical and mental health. We evaluate the latest evidence and propose new tools to examine the halobiont environment. We chose to target our review at neuropsychiatric disorders, including depression, anxiety, autism, dementia, multiple sclerosis, etc. because a green prescription (exposure to green spaces) was shown to benefit patients with neuropsychiatric disorders. Specifically, our review consists of three mini reviews on the associations exploring: (1) ecological biodiversity and human microbiota; (2) human microbiota and neuropsychiatric disorders; (3) ecological biodiversity and neuropsychiatric disorders. We conclude that the environment could directly transfer microbes to humans and that human studies support the gut microbiota as part of the pathophysiology of neuropsychiatric disorders. Overall, the results from the three mini reviews consistently support the biodiversity hypothesis. These findings demonstrated the plausibility of biodiversity exerting mental health effects through biophysiological mechanisms instead of psychological mechanisms alone. The idea can be further tested with novel biodiversity measurements and research on the effects of a green prescription.
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Affiliation(s)
- Yee Sang Wong
- School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Nicholas John Osborne
- School of Public Health, The University of Queensland, Herston, QLD 4006, Australia
- School of Population Health, University of New South Wales, Sydney, NSW 2052, Australia
- European Centre for Environment and Human Health (ECEHH), University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro TR1 3HD, Cornwall, UK
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186
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Banchi E, Manna V, Fonti V, Fabbro C, Celussi M. Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67466-67482. [PMID: 36056283 PMCID: PMC9492620 DOI: 10.1007/s11356-022-22752-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Cinzia Fabbro
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
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187
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Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. BIOLOGY 2022; 11:biology11091297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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188
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Khan G, Hegge A, Gemeinholzer B. Development and Testing of the A1 Volumetric Air Sampler, an Automatic Pollen Trap Suitable for Long-Term Monitoring of eDNA Pollen Diversity. SENSORS (BASEL, SWITZERLAND) 2022; 22:6512. [PMID: 36080967 PMCID: PMC9460460 DOI: 10.3390/s22176512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Airborne pollen surveys provide information on various aspects of biodiversity and human health monitoring. Such surveys are typically conducted using the Burkard Multi-Vial Cyclone Sampler, but have to be technically optimized for eDNA barcoding. We here developed and tested a new airborne pollen trap, especially suitable for autonomous eDNA-metabarcoding analyses, called the A1 volumetric air sampler. The trap can sample pollen in 24 different tubes with flexible intervals, allowing it to operate independently in the field for a certain amount of time. We compared the efficiency of the new A1 volumetric air sampler with another automated volumetric spore trap, the Burkard Multi-Vial Cyclone Sampler, which features shorter and fewer sampling intervals to evaluate the comparability of ambient pollen concentrations. In a sterile laboratory environment, we compared trap performances between the automated volumetric air samplers by using pure dry pollen of three species-Fagus sylvatica, Helianthus annuus and Zea mays-which differ both by exine ornamentation and pollen size. The traps had a standard suction flow rate of 16.5 L/min, and we counted the inhaled pollen microscopically after a predefined time interval. Our results showed that though we put three different pollen types in the same container, both the traps inhaled all the pollens in a statistically significant manner irrespective of their size. We found that, on average, both traps inhaled equal an number of pollens for each species. We did not detect any cross-contamination between tubes. We concluded that the A1 volumetric air sampler has the potential to be used for longer and more flexible sampling intervals in the wild, suitable for autonomous monitoring of eDNA pollen diversity.
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Affiliation(s)
- Gulzar Khan
- AG Botanik, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Albrecht Hegge
- A1 Productdesign, Reindl + Partner GmbH, Bahnhofstraße 13, 50999 Cologne, Germany
| | - Birgit Gemeinholzer
- AG Botanik, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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189
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Woodcock BA, Oliver AE, Newbold LK, Soon Gweon H, Read DS, Sayed U, Savage J, Bacon J, Upcott E, Howell K, Turvey K, Roy DB, Gloria Pereira M, Sleep D, Greenop A, Pywell RF. Citizen science monitoring reveals links between honeybee health, pesticide exposure and seasonal availability of floral resources. Sci Rep 2022; 12:14331. [PMID: 35995928 PMCID: PMC9395358 DOI: 10.1038/s41598-022-18672-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/17/2022] [Indexed: 11/23/2022] Open
Abstract
We use a national citizen science monitoring scheme to quantify how agricultural intensification affects honeybee diet breadth (number of plant species). To do this we used DNA metabarcoding to identify the plants present in 527 honey samples collected in 2019 across Great Britain. The species richness of forage plants was negatively correlated with arable cropping area, although this was only found early in the year when the abundance of flowering plants was more limited. Within intensively farmed areas, honeybee diets were dominated by Brassica crops (including oilseed rape). We demonstrate how the structure and complexity of honeybee foraging relationships with plants is negatively affected by the area of arable crops surrounding hives. Using information collected from the beekeepers on the incidence of an economically damaging bee disease (Deformed Wing Virus) we found that the occurrence of this disease increased where bees foraged in agricultural land where there was a high use of foliar insecticides. Understanding impacts of land use on resource availability is fundamental to assessing long-term viability of pollinator populations. These findings highlight the importance of supporting temporally timed resources as mitigation strategies to support wider pollinator population viability.
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Affiliation(s)
- Ben A Woodcock
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK.
| | - Anna E Oliver
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - Lindsay K Newbold
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - H Soon Gweon
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - Ujala Sayed
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - Joanna Savage
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - Jim Bacon
- UK Centre for Ecology & Hydrology (UKCEH), Lancaster Environment Centre, Library Ave., Bailrigg, Lancaster, LA1 4AP, UK
| | - Emily Upcott
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - Katherine Howell
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - Katharine Turvey
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - David B Roy
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - M Gloria Pereira
- UK Centre for Ecology & Hydrology (UKCEH), Lancaster Environment Centre, Library Ave., Bailrigg, Lancaster, LA1 4AP, UK
| | - Darren Sleep
- UK Centre for Ecology & Hydrology (UKCEH), Lancaster Environment Centre, Library Ave., Bailrigg, Lancaster, LA1 4AP, UK
| | - Arran Greenop
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
| | - Richard F Pywell
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire, OX10 8BB, UK
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190
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Hempel CA, Wright N, Harvie J, Hleap JS, Adamowicz S, Steinke D. Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments. Nucleic Acids Res 2022; 50:9279-9293. [PMID: 35979944 PMCID: PMC9458450 DOI: 10.1093/nar/gkac689] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.
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Affiliation(s)
- Christopher A Hempel
- To whom correspondence should be addressed. Tel: +1 519 824 4120; Fax: +1 519 824 5703;
| | - Natalie Wright
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Julia Harvie
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jose S Hleap
- SHARCNET, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
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191
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Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates. Sci Rep 2022; 12:13987. [PMID: 35977991 PMCID: PMC9385848 DOI: 10.1038/s41598-022-17937-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/03/2022] [Indexed: 11/14/2022] Open
Abstract
Biological invasions drive environmental change, potentially threatening native biodiversity, human health, and global economies. Population genomics is an increasingly popular tool in invasion biology, improving accuracy and providing new insights into the genetic factors that underpin invasion success compared to research based on a small number of genetic loci. We examine the extent to which population genomic resources, including reference genomes, have been used or are available for invasive species research. We find that 82% of species on the International Union for Conservation of Nature “100 Worst Invasive Alien Species” list have been studied using some form of population genetic data, but just 32% of these species have been studied using population genomic data. Further, 55% of the list’s species lack a reference genome. With incursion rates escalating globally, understanding how genome-driven processes facilitate invasion is critical, but despite a promising trend of increasing uptake, “invasion genomics” is still in its infancy. We discuss how population genomic data can enhance our understanding of biological invasion and inform proactive detection and management of invasive species, and we call for more research that specifically targets this area.
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192
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Salmaso N, Vasselon V, Rimet F, Vautier M, Elersek T, Boscaini A, Donati C, Moretto M, Pindo M, Riccioni G, Stefani E, Capelli C, Lepori F, Kurmayer R, Mischke U, Klemenčič AK, Novak K, Greco C, Franzini G, Fusato G, Giacomazzi F, Lea A, Menegon S, Zampieri C, Macor A, Virgilio D, Zanut E, Zorza R, Buzzi F, Domaizon I. DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155175. [PMID: 35421505 DOI: 10.1016/j.scitotenv.2022.155175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Valentin Vasselon
- OFB, Pôle R&D ECLA, Site INRAE CARRTEL, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Frédéric Rimet
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Marine Vautier
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Tina Elersek
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Marco Moretto
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Giulia Riccioni
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Erika Stefani
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Camilla Capelli
- Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Flora Ruchat-Roncati 15, 6850 Mendrisio, Switzerland.
| | - Fabio Lepori
- Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Flora Ruchat-Roncati 15, 6850 Mendrisio, Switzerland.
| | - Rainer Kurmayer
- Research Department for Limnology, University of Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria.
| | - Ute Mischke
- Bavarian Environment Agency, Ref. 83, Wielenbach, Germany.
| | | | - Katarina Novak
- Slovenian Environment Agency, Vojkova 1b, 1000 Ljubljana, Slovenia.
| | - Claudia Greco
- Italian National Institute for Environmental Protection and Research (ISPRA), Ozzano, Italy.
| | - Giorgio Franzini
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Giampaolo Fusato
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Federica Giacomazzi
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Alessia Lea
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via Ospedale Civile 24, 35121 Padova, Italy.
| | - Silvia Menegon
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via Santa Barbara 5/a, 31100 Treviso, Italy.
| | - Chiara Zampieri
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Arianna Macor
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Damiano Virgilio
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Elisa Zanut
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Raffaella Zorza
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Fabio Buzzi
- ARPA Lombardia, Sede di Lecco, U.O. Laghi e Monitoraggio Biologico Fiumi, Italy.
| | - Isabelle Domaizon
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
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193
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Sakata MK, Sato M, Sato MO, Watanabe T, Mitsuishi H, Hikitsuchi T, Kobayashi J, Minamoto T. Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens. PLoS One 2022; 17:e0272653. [PMID: 35947597 PMCID: PMC9365122 DOI: 10.1371/journal.pone.0272653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 07/24/2022] [Indexed: 11/18/2022] Open
Abstract
Preventing mosquito-borne infectious diseases requires that vector mosquitoes are monitored and controlled. Targeting immature mosquitoes (eggs, larvae, and pupae), which have less mobility than adults, is an effective management approach. However, conducting these surveys is often difficult due to the limitations of morphological classification and survey costs. The application of environmental DNA (eDNA) analysis can solve these issues because it allows easy estimation of species distribution and morphology-independent species identification. Although a few previous studies have reported mosquito eDNA detection, there is a gap in knowledge regarding the dynamics related to the persistence of immature mosquito eDNA. We used Culex pipiens pallens, a vector of West Nile fever, as a model species. First, we developed a species-specific detection assay and confirmed its specificity using in silico and in vitro tests. Next, we conducted laboratory experiments using breeding tanks. Water samples were collected at each developmental stage. In addition, water samples were collected daily until the seventh day after emergence from the pupae. We quantified eDNA using real-time PCR with the developed assay to investigate the dynamics of mosquito eDNA. The specificity of the developed assay was confirmed by in silico and in vitro tests. Mosquito eDNA was detected at all developmental stages and detected up to seven days after emergence of pupae. In particular, high concentrations of eDNA were detected immediately after hatching from eggs and after emergence from pupae. Highly frequent positive eDNA signals were continuously detected between egg hatching and pupa hatching. Mosquito eDNA was detected immediately after the eggs were introduced, and eDNA-positive detections continued until pupae emergence, suggesting that eDNA analysis is useful for monitoring mosquito larvae. In the future, monitoring immature mosquitoes using eDNA analysis will contribute to prevent mosquito-borne infectious diseases.
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Affiliation(s)
- Masayuki K. Sakata
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Japan
- Kobe University Innovation, Co., Ltd, Kobe City, Japan
- * E-mail:
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, Niigata, Japan
| | - Marcello Otake Sato
- Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Tomoe Watanabe
- Dainihon Jochugiku Co., Ltd Research & Development Laboratory Biological Research Section 1–11, Osaka, Japan
| | - Honami Mitsuishi
- Dainihon Jochugiku Co., Ltd Research & Development Laboratory Biological Research Section 1–11, Osaka, Japan
| | - Tomoyuki Hikitsuchi
- Dainihon Jochugiku Co., Ltd Research & Development Laboratory Biological Research Section 1–11, Osaka, Japan
| | - Jun Kobayashi
- Graduate School of Health Sciences, University of the Ryukyus, Okinawa, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Japan
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194
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Kirse A, Bourlat SJ, Langen K, Zapke B, Zizka VMA. Comparison of destructive and non-destructive DNA extraction methods for the metabarcoding of arthropod bulk samples. Mol Ecol Resour 2022; 23:92-105. [PMID: 35932285 DOI: 10.1111/1755-0998.13694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/07/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
DNA metabarcoding is routinely used for biodiversity assessment, especially targeting highly diverse groups for which limited taxonomic expertise is available. Various protocols are currently in use, although standardization is key to its application in large-scale monitoring. DNA metabarcoding of arthropod bulk samples can be either conducted destructively from sample tissue, or non-destructively from sample fixative or lysis buffer. Non-destructive methods are highly desirable for the preservation of sample integrity but have yet to be experimentally evaluated in detail. Here, we compare diversity estimates from 14 size sorted Malaise trap samples processed consecutively with three non-destructive approaches (one using fixative ethanol and two using lysis buffers) and one destructive approach (using homogenized tissue). Extraction from commercial lysis buffer yielded comparable species richness and high overlap in species composition to the ground tissue extracts. A significantly divergent community was detected from preservative ethanol-based DNA extraction. No consistent trend in species richness was found with increasing incubation time in lysis buffer. These results indicate that non-destructive DNA extraction from incubation in lysis buffer could provide a comparable alternative to destructive approaches with the added advantage of preserving the specimens for post-metabarcoding taxonomic work but at a higher cost per sample.
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Affiliation(s)
- Ameli Kirse
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Sarah J Bourlat
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Kathrin Langen
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Björn Zapke
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Vera M A Zizka
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
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195
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Chen X, Kong Y, Zhang S, Zhao J, Li S, Yao M. Comparative Evaluation of Common Materials as Passive Samplers of Environmental DNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10798-10807. [PMID: 35856738 DOI: 10.1021/acs.est.2c02506] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) technology has revolutionized biomonitoring in recent years; however, eDNA collection from aquatic environments generally relies on the time-consuming and equipment-dependent process of water filtration. Passive eDNA sampling deploys sorbent materials to capture eDNA from water, circumventing many problems associated with active filtration; yet, very few candidate materials have been systematically evaluated for this purpose. Here, we evaluated the ability of 12 different types of common loose sorbents and filter membranes to capture eDNA in laboratory and field experiments compared with conventional water filtration. Glass fiber filters (GF) outperformed all other materials in laboratory experiments with respect to their quantitative capacity to recover amphibian eDNA, with the eDNA yield increasing linearly with submersion time up to 72 h. Furthermore, GF rapidly (within 0.5 h) captured the eDNA of up to 71% of the total fish species in a lake, in addition to detecting the entire fish community by 8 h, as assessed by metabarcoding analysis. Our results demonstrate that GF could passively capture aqueous eDNA with a similar or greater efficiency than conventional methods, thus paving the way for convenient, effective, and eco-friendly eDNA sampling in aquatic environments.
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Affiliation(s)
- Xiaoyu Chen
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yueqiao Kong
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shan Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Sheng Li
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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196
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AOB PLANTS 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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197
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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198
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DiBattista JD, Fowler AM, Riley IJ, Reader S, Hay A, Parkinson K, Hobbs JPA. The use of environmental DNA to monitor impacted coastal estuaries. MARINE POLLUTION BULLETIN 2022; 181:113860. [PMID: 35779383 DOI: 10.1016/j.marpolbul.2022.113860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.
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Affiliation(s)
- Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia.
| | - Ashley M Fowler
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Indiana J Riley
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Sally Reader
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Amanda Hay
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Kerryn Parkinson
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Jean-Paul A Hobbs
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4069, Australia
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199
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Diversity and ecology of fungal assemblages present in lake sediments at Clearwater Mesa, James Ross Island, Antarctica, assessed using metabarcoding of environmental DNA. Fungal Biol 2022; 126:640-647. [DOI: 10.1016/j.funbio.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/23/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022]
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200
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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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