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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1368-1384. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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2
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Chen X, Li S, Zhao J, Yao M. Passive eDNA sampling facilitates biodiversity monitoring and rare species detection. ENVIRONMENT INTERNATIONAL 2024; 187:108706. [PMID: 38696978 DOI: 10.1016/j.envint.2024.108706] [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: 10/31/2023] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.
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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, China 100871
| | - Sheng Li
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871.
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3
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Müller ND, Kirtane A, Schefer RB, Mitrano DM. eDNA Adsorption onto Microplastics: Impacts of Water Chemistry and Polymer Physiochemical Properties. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7588-7599. [PMID: 38624040 DOI: 10.1021/acs.est.3c10825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Adsorption of biomacromolecules onto polymer surfaces, including microplastics (MPs), occurs in multiple environmental compartments, forming an ecocorona. Environmental DNA (eDNA), genetic material shed from organisms, can adsorb onto MPs which can potentially either (1) promote long-range transport of antibiotic resistant genes or (2) serve to gain insights into the transport pathways and origins of MPs by analyzing DNA sequences on MPs. However, little is known about the capacity of MPs to adsorb eDNA or the factors that influence sorption, such as polymer and water chemistries. Here we investigated the adsorption of extracellular linear DNA onto a variety of model MP fragments composed of three of the most environmentally prevalent polymers (polyethylene, polyethylene terephthalate, and polystyrene) in their pristine and photochemically weathered states. Batch adsorption experiments in a variety of water chemistries were complemented with nonlinear modeling to quantify the rate and extent of eDNA sorption. Ionic strength was shown to strongly impact DNA adsorption by reducing or inhibiting electrostatic repulsion. Polyethylene terephthalate exhibited the highest adsorption capacity when normalizing for MP specific surface area, likely due to the presence of ester groups. Kinetics experiments showed fast adsorption (majority adsorbed under 30 min) before eventually reaching equilibrium after 1-2 h. Overall, we demonstrated that DNA quickly binds to MPs, with pseudo-first- and -second-order models describing adsorption kinetics and the Freundlich model describing adsorption isotherms most accurately. These insights into DNA sorption onto MPs show that there is potential for MPs to act as vectors for genetic material of interest, especially considering that particle-bound DNA typically persists longer in the environment than dissolved DNA.
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Affiliation(s)
- Nicolas D Müller
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Anish Kirtane
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Roman B Schefer
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Denise M Mitrano
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
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Zhang L, Zhou W, Jiao M, Xie T, Xie M, Li H, Suo A, Yue W, Ding D, He W. Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168298. [PMID: 37939943 DOI: 10.1016/j.scitotenv.2023.168298] [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: 04/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.
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Affiliation(s)
- Li Zhang
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiguo Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Mengyu Jiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mujiao Xie
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Hanying Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anning Suo
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Weizhong Yue
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Dewen Ding
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 51145, China
| | - Weihong He
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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Zhang Y, Zhang X, Li F, Altermatt F. Fishing eDNA in One of the World's Largest Rivers: A Case Study of Cross-Sectional and Depth Profile Sampling in the Yangtze. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21691-21703. [PMID: 37878726 DOI: 10.1021/acs.est.3c03890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
The world's largest rivers are home to diverse, endemic, and threatened fish species. However, their sheer sizes make large-scale biomonitoring challenging. While environmental DNA (eDNA) metabarcoding has become an established monitoring approach in smaller freshwater ecosystems, its suitability for large rivers may be challenged by the sheer extent of their cross sections (>1 km wide and tens of meters deep). Here, we sampled fish eDNA from multiple vertical layers and horizontal locations from two cross sections of the lower reach of the Yangtze River in China. Over half of the ASVs (amplicon sequence variants) were detected in only a single combination of the vertical layers and horizontal locations, with ∼7% across all combinations. We estimated the need to sample >100 L of water across the cross-sectional profiles to achieve ASV richness saturation, which translates to ∼60 L of water at the species level. No consistent pattern emerged for prioritizing certain depth and horizontal samples, yet we underline the importance of sampling and integrating different layers and locations simultaneously. Our study highlights the significance of spatially stratified sampling and sampling volumes when using eDNA approaches. Specifically, we developed and tested a scalable and broadly applicable strategy that advances the monitoring and conservation of large rivers.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich 8006, Switzerland
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich 8006, Switzerland
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Brandão-Dias PFP, Tank JL, Snyder ED, Mahl UH, Peters B, Bolster D, Shogren AJ, Lamberti GA, Bibby K, Egan SP. Suspended Materials Affect Particle Size Distribution and Removal of Environmental DNA in Flowing Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13161-13171. [PMID: 37610829 DOI: 10.1021/acs.est.3c02638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Environmental DNA (eDNA) in aquatic systems is a complex mixture that includes dissolved DNA, intracellular DNA, and particle-adsorbed DNA. Information about the various components of eDNA and their relative proportions could be used to discern target organism abundance and location. However, a limited knowledge of eDNA adsorption dynamics and interactions with other materials hinders these applications. To address this gap, we used recirculating stream mesocosms to investigate the impact of suspended materials (fine particulate organic matter, plankton, clay, and titanium dioxide) on the eDNA concentration and particle size distribution (PSD) from two fish species in flowing water. Our findings revealed that eDNA rapidly adsorbs to other materials in the water column, affecting its concentration and PSD. Nonetheless, only particulate organic matter affected eDNA removal rate after 30 h. Moreover, we observed that the removal of larger eDNA components (≥10 μm) was more strongly influenced by physical processes, whereas the removal of smaller eDNA components was driven by biological degradation. This disparity in removal mechanisms between larger and smaller eDNA components could explain changes in eDNA composition over time and space, which have implications for modeling the spatial distribution and abundance of target species and optimizing eDNA detection in high turbidity systems.
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Affiliation(s)
| | - Jennifer L Tank
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elise D Snyder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ursula H Mahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Brett Peters
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Diogo Bolster
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Arial J Shogren
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35401, United States
| | - Gary A Lamberti
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle Bibby
- Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [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: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162322. [PMID: 36801404 DOI: 10.1016/j.scitotenv.2023.162322] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
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Affiliation(s)
- Miwa Takahashi
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia.
| | - Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia.
| | - Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mieke van der Heyde
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew J Heydenrych
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Jarman Laboratory, Indian Ocean Marine Research Centre, School of Biological Sciences, University of Western Australia, Australia
| | - David J Juszkiewicz
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Kathryn L Dawkins
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Cindy Bessey
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Joshua P Newton
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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Jeunen GJ, Cane JS, Ferreira S, Strano F, von Ammon U, Cross H, Day R, Hesseltine S, Ellis K, Urban L, Pearson N, Olmedo-Rojas P, Kardailsky A, Gemmell NJ, Lamare M. Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring. Mol Ecol Resour 2023; 23:771-786. [PMID: 36598115 DOI: 10.1111/1755-0998.13754] [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: 04/08/2022] [Revised: 11/06/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023]
Abstract
Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems are monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for active filtration are required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies to investigate the similarity between aquatic and filter-feeder eDNA signals are essential. Here, we investigated the differences among four eDNA sources (water; bivalve gill-tissue; sponges; and ethanol in which filter-feeding organisms were stored) along a vertically stratified transect in Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish and vertebrates. Combined, eDNA sources detected 59 vertebrates, while concurrent diver surveys observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was successfully extracted from the ethanol in which sponges were stored, although a reduced number of species were detected. Bivalve gill-tissue dissections, on the other hand, failed to reliably detect eDNA. Overall, our results show that vertebrate eDNA signals obtained from water samples and marine sponges are highly concordant. The strong similarity in eDNA signals demonstrates the potential of marine sponges as an additional tool for eDNA-based marine biodiversity surveys, by enabling the incorporation of larger sample numbers in eDNA surveys, reducing plastic waste, simplifying sample collection, and as a cost-efficient alternative. However, we note the importance to not detrimentally impact marine communities by, for example, nonlethal subsampling, specimen cloning, or using bycatch specimens.
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Affiliation(s)
- Gert-Jan Jeunen
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jasmine S Cane
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,ARC CoE for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Sara Ferreira
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, Kelburn, New Zealand
| | | | - Hugh Cross
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Robert Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sean Hesseltine
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | - Kaleb Ellis
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | - Lara Urban
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Niall Pearson
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | | | - Anya Kardailsky
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miles Lamare
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
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10
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Picard MH, Zaiko A, Tidy AM, Kelly DJ, Thomson-Laing G, Wilkinson SP, Pochon X, Vandergoes MJ, Hawes I, Wood SA. Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA. PeerJ 2023; 11:e15210. [PMID: 37151294 PMCID: PMC10162041 DOI: 10.7717/peerj.15210] [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: 06/23/2022] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research.
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Affiliation(s)
- Maïlys H.V. Picard
- School of Biological Sciences, Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | | | - David J. Kelly
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | | | | | - Xavier Pochon
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | | | - Ian Hawes
- School of Biological Sciences, Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
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11
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Bairoliya S, Goel A, Mukherjee M, Koh Zhi Xiang J, Cao B. Monochloramine Induces Release of DNA and RNA from Bacterial Cells: Quantification, Sequencing Analyses, and Implications. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15791-15804. [PMID: 36215406 DOI: 10.1021/acs.est.2c06632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Monochloramine (MCA) is a widely used secondary disinfectant to suppress microbial growth in drinking water distribution systems. In monochloraminated drinking water, a significant amount of extracellular DNA (eDNA) has been reported, which has many implications ranging from obscuring DNA-based drinking water microbiome analyses to posing potential health concerns. To address this, it is imperative for us to know the origin of the eDNA in drinking water. Using Pseudomonas aeruginosa as a model organism, we report for the first time that MCA induces the release of nucleic acids from both biofilms and planktonic cells. Upon exposure to 2 mg/L MCA, massive release of DNA from suspended cells in both MilliQ water and 0.9% NaCl was directly visualized using live cell imaging in a CellASIC ONIX2 microfluidic system. Exposing established biofilms to MCA also resulted in DNA release from the biofilms, which was confirmed by increased detection of eDNA in the effluent. Intriguingly, massive release of RNA was also observed, and the extracellular RNA (eRNA) was also found to persist in water for days. Sequencing analyses of the eDNA revealed that it could be used to assemble the whole genome of the model organism, while in the water, certain fragments of the genome were more persistent than others. RNA sequencing showed that the eRNA contains non-coding RNA and mRNA, implying its role as a possible signaling molecule in environmental systems and a snapshot of the past metabolic state of the bacterial cells.
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Affiliation(s)
- Sakcham Bairoliya
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
| | - Apoorva Goel
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
| | - Jonas Koh Zhi Xiang
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
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12
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Cai W, Harper LR, Neave EF, Shum P, Craggs J, Arias MB, Riesgo A, Mariani S. Environmental DNA persistence and fish detection in captive sponges. Mol Ecol Resour 2022; 22:2956-2966. [PMID: 35751617 PMCID: PMC9796769 DOI: 10.1111/1755-0998.13677] [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: 03/24/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 01/07/2023]
Abstract
Large and hyperdiverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as "natural samplers" of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the dynamics of eDNA particles in sponge tissue, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA captured by three encrusting sponge species and compare the sponge's eDNA capturing ability with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the "chosen" natural samplers in certain habitats and regions.
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Affiliation(s)
- Wang Cai
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Lynsey R. Harper
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK,NatureMetrics LtdGuildfordUK
| | - Erika F. Neave
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK,Department of Life SciencesNatural History MuseumLondonUK
| | - Peter Shum
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | | | - María Belén Arias
- Department of Life SciencesNatural History MuseumLondonUK,School of Life SciencesUniversity of EssexColchesterUK
| | - Ana Riesgo
- Department of Life SciencesNatural History MuseumLondonUK,Departamento de Biodiversidad y Biología EvolutivaMuseo Nacional de Ciencias Naturales (CSIC)MadridSpain
| | - Stefano Mariani
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
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13
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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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14
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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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15
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Nordstrom B, Mitchell N, Byrne M, Jarman S. A review of applications of environmental DNA for reptile conservation and management. Ecol Evol 2022; 12:e8995. [PMID: 35784065 PMCID: PMC9168342 DOI: 10.1002/ece3.8995] [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: 02/02/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 11/28/2022] Open
Abstract
Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.
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Affiliation(s)
- Bethany Nordstrom
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
| | - Nicola Mitchell
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
| | - Margaret Byrne
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Perth Western Australia Australia
| | - Simon Jarman
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
- UWA Oceans Institute The University of Western Australia Crawley Western Australia Australia
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16
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Bessey C, Gao Y, Truong YB, Miller H, Jarman SN, Berry O. Comparison of materials for rapid passive collection of environmental
DNA. Mol Ecol Resour 2022; 22:2559-2572. [PMID: 35570323 PMCID: PMC9544503 DOI: 10.1111/1755-0998.13640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/24/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive and efficient, and requires minimal equipment, making it suited to high‐density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3‐million‐litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibres and 1% chitosan, cotton fibres, hemp fibres, and sponge with either zeolite or active carbon) for intervals between 5 and 1080 min. We show that for most materials, with as little as 5 min of submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 and 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19–32). Using scanning electron microscopy, we visualized biological matter adhering to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. eDNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost‐ and time‐sensitive biological surveys, and where access to equipment is limited.
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Affiliation(s)
- Cindy Bessey
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, 64 Fairway Crawley WA Australia
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
| | - Yuan Gao
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Yen Bach Truong
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
| | - Simon Neil Jarman
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
- University of Western Australia School of Biological Sciences and the UWA Oceans Institute Crawley WA Australia
| | - Oliver Berry
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
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17
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Verdier H, Konecny-Dupre L, Marquette C, Reveron H, Tadier S, Grémillard L, Barthès A, Datry T, Bouchez A, Lefébure T. Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers. Mol Ecol Resour 2022; 22:2158-2170. [PMID: 35218316 DOI: 10.1111/1755-0998.13604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as water filtration and DNA precipitation are time consuming, require difficult-to-handle equipment and partially integrate eDNA signals. To overcome these limitations, we created the first proof of concept of a passive, 3D-printed and easy-to-use eDNA sampler. We designed the samplers from hydroxyapatite (HAp samplers), a natural mineral with a high DNA adsorption capacity. The porous structure and shape of the samplers were designed to optimise DNA adsorption and facilitate their handling in the laboratory and in the field. Here we show that HAp samplers can efficiently collect genomic DNA in controlled set-ups, but can also collect animal eDNA under controlled and natural conditions with yields similar to conventional methods. However, we also observed large variations in the amount of DNA collected even under controlled conditions. A better understanding of the DNA-hydroxyapatite interactions on the surface of the samplers is now necessary to optimise the eDNA adsorption and to allow the development of a reliable, easy-to-use and reusable eDNA sampling tool.
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Affiliation(s)
- Héloïse Verdier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France.,Eurofins Hydrobiologie France, Rue Lucien Cuenot, 54521, Maxéville, France.,INRAE, UR-Riverly, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, VILLEURBANNE Cedex, France
| | - Lara Konecny-Dupre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Christophe Marquette
- 3d.FAB, Univ Lyon, Université Lyon1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, 43, Bd du 11 novembre 1918, 69622, Villeurbanne cedex, France
| | - Helen Reveron
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Solène Tadier
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Laurent Grémillard
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Amélie Barthès
- Eurofins Hydrobiologie France, Rue Lucien Cuenot, 54521, Maxéville, France
| | - Thibault Datry
- INRAE, UR-Riverly, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, VILLEURBANNE Cedex, France
| | - Agnès Bouchez
- INRAE, USMB, UMR CARRTEL, 75bis av. de Corzent, 742000, Thonon les Bains, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
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18
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Delafosse D, Reinert L, Azaïs P, Fontvieille D, Soneda Y, Morand P, Duclaux L. Potentialities of a mesoporous activated carbon as virus detection probe in aquatic systems. J Virol Methods 2022; 303:114496. [PMID: 35181346 DOI: 10.1016/j.jviromet.2022.114496] [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: 01/03/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/30/2022]
Abstract
Enteric viruses are widely spread in water environments, some being harmful for human communities. Regular epidemics highlight the usefulness of analysing such viruses in wastewaters as a tool for epidemiologists to monitor the extent of their dissemination among populations. In this context, CNovel™ Powdered Activated Carbon (PAC) was chosen for its high porosity and high adsorption capacity to investigate sorbent ability to be used as part of of virus detection probes. Self-supported PAC Foils (PAC-F), PAC coated Brushes (PAC-B) and PAC Sampler (PAC-S) were used to prospect PAC efficacy in virus adsorption and above all, the feasibility of virus retrieval from them, allowing to further analysis such as molecular analysis quantification. Aiming at the development of a field-operational tool, PAC saturation and reusability were also investigated, as well as PAC-polarisation effect on its adsorption capacity. Our results pointed out that sorbent-based probes exhibited a high adsorption efficacy of spiked Murine Norovirus (MNV-1) in bare 0.1 M NaCl solution (>90 % for PAC-B and >86 % for PAC-F at ≈107 genome unit virus concentration), with no saturation within our experimental framework. On the other hand, polarisation assays using PAC-F as electrode, did not demonstrate any adsorption improvement. Experiments on PAC probes reusability suggested that they should be used three times at the most for a maximum efficiency. Values of virus retrieval were low (up to 11 % with PAC-B and up to 14 % with PAC-F in 0.1 M NaCl virus suspensions), illustrating the need for the techniques to be improved. A preliminary field assay using PAC-S, demonstrated that our catch-and-retrieve protocol yielded to the detection of autochthonous human Norovirus Genogroup I (NoV GI) and Adenovirus (AdV), in wastewaters suggesting its promising application as virus detection tool in such high loaded and complex waters.
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Affiliation(s)
- Doriane Delafosse
- Laboratoire Abiolab-Asposan, Montbonnot-Saint-Martin, France; Université Grenoble Alpes, CNRS, CEA, Institut de biologie structurale (IBS), Grenoble, France.
| | | | | | | | - Yasushi Soneda
- National Institute of Advanced Industrial Science and Technology (AIST), Energy Process Research Institute, Tsukuba, Ibaraki, 305-8569, Japan
| | - Patrice Morand
- Université Grenoble Alpes, CNRS, CEA, Institut de biologie structurale (IBS), Grenoble, France
| | - Laurent Duclaux
- Université Savoie Mont Blanc, EDYTEM, F-73000, Chambéry, France
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19
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Wang H, Liu C, Teng X, Liang Z, Zhu L, Xu G, Chen C, Ma K, Liu R, Zhou L, Yan B. A TbPO 4-based capturer for environmental extracellular antibiotic genes by interrogating lanthanide phosphates nanoneedles. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127139. [PMID: 34537653 DOI: 10.1016/j.jhazmat.2021.127139] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Accurate determination of antibiotic resistance genes (ARGs) in environmental DNA molecules (eDNA) is challenging owing to its low abundance in the aquatic environment. Here we report a facile and cost-efficient approach to extract trace amount of eDNAs in the aquatic environment using LnPO4 nanomaterials. Among the nanomaterials, less crystalline TbPO4 nanoneedles was identified as the most prominent candidate for long stranded DNA and short stranded DNA with adsorption efficiency above 97%. The adsorbed DNA was washed off from TbPO4 nanoneedles by optimized eluant (85% PBS, 15% EtOH, 4 g/L glycine, pH 10.0) with an optimal DNA recovery of 78.83%. Our approach showed a comparable or better eDNA extraction efficiency than a commercial extraction method for different environmental samples, but 89% less cost. The high purity of the extracted eDNA was demonstrated by a high A260/280 ratio. Using qPCR experiment, the occurrence of six common ARGs in the eDNA were detected with abundance ranging from 4.06 × 103 to 3.51 × 109 copies/L in river samples. This specific DNA capturer is valuable for the evaluation of spatial and temporal dynamic of ARGs pollution to provide insight into the potential risk with regard to the human health.
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Affiliation(s)
- Haiqing Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chao Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xuepeng Teng
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, China
| | - Zhenda Liang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lishan Zhu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Gang Xu
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Chaoxiang Chen
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Kunyu Ma
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Rongrong Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Li Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Bing Yan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
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20
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Redwan AM, Millerick K. Anaerobic bacterial responses to carbonaceous materials and implications for contaminant transformation: Cellular, metabolic, and community level findings. BIORESOURCE TECHNOLOGY 2021; 341:125738. [PMID: 34474238 DOI: 10.1016/j.biortech.2021.125738] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Carbonaceous materials (CM) enhance the abundance and activity of bacteria capable of persistent organic (micro)pollutant (POP) degradation. This review synthesizes anaerobic bacterial responses to minimally modified CM in non-fuel cell bioremediation applications at three stages: attachment, metabolism, and biofilm genetic composition. Established relationships between biological behavior and CM surface properties are identified, but temporal relationships are not well understood, making it difficult to connect substratum properties and "pioneer" bacteria with mature microorganism-CM systems. Stark differences in laboratory methodology at each temporal stage results in observational, but not causative, linkages as system complexity increases. This review is the first to critically examine relationships between material and cellular properties with respect to time. The work highlights critical knowledge gaps that must be addressed to accurately predict microorganism-CM behavior and to tailor CM properties for optimized microbial activity, critical frontiers in establishing this approach as an effective bioremediation strategy.
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Affiliation(s)
- Asef Mohammad Redwan
- Department of Civil, Environmental & Construction Engineering, Texas Tech University, TX, United States
| | - Kayleigh Millerick
- Department of Civil, Environmental & Construction Engineering, Texas Tech University, TX, United States.
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21
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Wilcox TM, Caragiulo A, Dysthe JC, Franklin TW, Mason DH, McKelvey KS, Zarn KE, Schwartz MK. Detection of Jaguar (Panthera onca) From Genetic Material in Drinking Water. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Jaguar (Panthera onca) are of conservation concern and occur at very low densities in the northern portion of their range in northern Mexico and the southwestern United States. Environmental DNA sampling to detect genetic material from drinking water may be an effective approach for jaguar detection in these arid landscapes. Here we develop a qPCR assay for the detection of jaguar mitochondrial DNA, show that large quantities of DNA (mean 66,820 copies/L) can be found in the drinking water of captive animals, and observe detectable levels of DNA (80 copies/L) in a wild habitat with known jaguar populations. We suggest that environmental DNA sampling may represent a useful, complementary sampling tool for detection of rare jaguars, although effective application would require careful consideration of DNA persistence time in the environment.
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22
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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance. WATER 2021. [DOI: 10.3390/w13081113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.
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23
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Bessey C, Neil Jarman S, Simpson T, Miller H, Stewart T, Kenneth Keesing J, Berry O. Passive eDNA collection enhances aquatic biodiversity analysis. Commun Biol 2021; 4:236. [PMID: 33619330 PMCID: PMC7900116 DOI: 10.1038/s42003-021-01760-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/25/2021] [Indexed: 01/28/2023] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more samples than can be practically collected with current filtration methods. Here we demonstrate how eDNA can be passively collected in both tropical and temperate marine systems by directly submerging filter membranes (positively charged nylon and non-charged cellulose ester) in the water column. Using a universal fish metabarcoding assay, we show that passive eDNA collection can detect fish as effectively as active eDNA filtration methods in temperate systems and can also provide similar estimates of total fish biodiversity. Furthermore, passive eDNA collection enables greater levels of biological sampling, which increases the range of ecological questions that eDNA metabarcoding can address. Bessey et al. present a method of passive eDNA collection from marine aquatic systems. This approach enables lower cost, high throughput sampling of aquatic environments and demonstrably collects high levels of eDNA for biodiversity studies.
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Affiliation(s)
- Cindy Bessey
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, WA, Australia. .,Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia. .,UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia.
| | - Simon Neil Jarman
- UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia.,School of Biological Sciences and the UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia
| | - Tiffany Simpson
- eDNA Frontiers, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
| | - Todd Stewart
- Bass Marine Pty Ltd, Port Denison, WA, Australia
| | - John Kenneth Keesing
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, WA, Australia.,UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia
| | - Oliver Berry
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
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