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Downie AT, Bennett WW, Wilkinson S, de Bruyn M, DiBattista JD. From land to sea: Environmental DNA is correlated with long-term water quality indicators in an urbanized estuary. MARINE POLLUTION BULLETIN 2024; 207:116887. [PMID: 39217873 DOI: 10.1016/j.marpolbul.2024.116887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Estuaries provide critical ecosystem services, and yet are increasingly under threat from urbanization. Non-invasive approaches to monitor biodiversity resident to or migrating through estuaries is critical to evaluate the holistic health of these ecosystems, often based entirely on water quality. In this study we compared tree of life metabarcoding (ToL-metabarcoding) biodiversity detections with measurements of physico-chemical variables (chlorophyll a, turbidity, total nitrogen, total phosphorous, dissolved oxygen) at eight sites of varying degrees of water quality in the Gold Coast Broadwater Estuary (Queensland, Australia). These sites were ranked according to an adapted Water Quality Index (WQI) score. Here, we detected 787 unique taxa, adding 137 new biodiversity records to the region, mostly micro-organisms such as bacteria, ciliates, diatoms, dinoflagellates, and cryptomonads. Sites with the lowest WQI were characterised by higher turbidity, lower dissolved oxygen, as well as higher total nitrogen and phosphorous, which correlated with an increased diversity of bacteria, ciliates, and green algae. Similarly, the composition of taxa was significantly different between sites with variable WQI values for most taxa but was less apparent for larger vertebrate groups. These findings suggest that rapid ToL-metabarcoding biodiversity detections, particularly for lower order taxonomic groups, can serve as valuable indicators of flora and fauna across the tree of life associated with dynamically shifting estuarine health along urbanized coastlines.
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Affiliation(s)
- Adam T Downie
- School of the Environment, The University of Queensland, St. Lucia, Queensland, Australia.
| | - William W Bennett
- School of Environment and Science, Griffith University, Southport, Queensland, Australia.
| | - Shaun Wilkinson
- Wilderlab NZ Ltd., Wellington, New Zealand; School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | - Mark de Bruyn
- School of Environment and Science, Griffith University, Southport, Queensland, Australia.
| | - Joseph D DiBattista
- School of Environment and Science, Griffith University, Southport, Queensland, Australia; Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
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2
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DiBattista JD, Fowler AM, Shalders TC, Williams RJ, Wilkinson S. Tree of life metabarcoding can serve as a biotic benchmark for shifting baselines in urbanized estuaries. ENVIRONMENTAL RESEARCH 2024; 258:119454. [PMID: 38906450 DOI: 10.1016/j.envres.2024.119454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.
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Affiliation(s)
- Joseph D DiBattista
- School of Environment and Science, Griffith University, Southport, QLD, 4222, Australia; 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.
| | - Tanika C Shalders
- Faculty of Science and Engineering, National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, 2450, Australia.
| | - Robert J Williams
- New South Wales Department of Primary Industries, Fisheries (retired), Australia.
| | - Shaun Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6012, New Zealand.
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Saenz-Agudelo P, Ramirez P, Beldade R, Campoy AN, Garmendia V, Search FV, Fernández M, Wieters EA, Navarrete SA, Landaeta MF, Pérez-Matus A. Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats. Ecol Evol 2024; 14:e10999. [PMID: 38390005 PMCID: PMC10881902 DOI: 10.1002/ece3.10999] [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: 09/27/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.
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Affiliation(s)
- Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Paula Ramirez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Ricardo Beldade
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Ana N Campoy
- Center of Marine Sciences (CCMAR-CIMAR) University of the Algarve Faro Portugal
| | - Vladimir Garmendia
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Francesca V Search
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Miriam Fernández
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Evie A Wieters
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Sergio A Navarrete
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
- Center for Applied Ecology and Sustainability (CAPES) and Coastal Socio-Ecological Millennium Institute (SECOS) Pontificia Universidad Católica de Chile Santiago Chile
- Center for Oceanographic Research COASTAL-COASTAL Universidad de Concepción Concepción Chile
| | - Mauricio F Landaeta
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Laboratorio de Ictiología e Interacciones Biofísicas (LABITI) Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso Valparaíso Chile
| | - Alejandro Pérez-Matus
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
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Marques V, Loot G, Blanchet S, Miaud C, Planes S, Peyran C, Arnal V, Calvet C, Pioch S, Manel S. Optimizing detectability of the endangered fan mussel using eDNA and ddPCR. Ecol Evol 2024; 14:e10807. [PMID: 38288365 PMCID: PMC10822771 DOI: 10.1002/ece3.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 01/31/2024] Open
Abstract
Spatial and temporal monitoring of species threatened with extinction is of critical importance for conservation and ecosystem management. In the Mediterranean coast, the fan mussel (Pinna nobilis) is listed as critically endangered after suffering from a mass mortality event since 2016, leading to 100% mortality in most marine populations. Conventional monitoring for this macroinvertebrate is done using scuba, which is challenging in dense meadows or with low visibility. Here we developed an environmental DNA assay targeting the fan mussel and assessed the influence of several environmental parameters on the species detectability in situ. We developed and tested an eDNA molecular marker and collected 48 water samples in two sites at the Thau lagoon (France) with distinct fan mussel density, depths and during two seasons (summer and autumn). Our marker can amplify fan mussel DNA but lacks specificity since it also amplifies a conspecific species (Pinna rudis). We successfully amplified fan mussel DNA from in situ samples with 46 positive samples (out of 48) using ddPCR, although the DNA concentrations measured were low over almost all samples. Deeper sampling depth slightly increased DNA concentrations, but no seasonal effect was found. We highlight a putative spawning event on a single summer day with much higher DNA concentration compared to all other samples. We present an eDNA molecular assay able to detect the endangered fan mussel and provide guidelines to optimize the sampling protocol to maximize detectability. Effective and non-invasive monitoring tools for endangered species are promising to monitor remaining populations and have the potential of ecological restoration or habitat recolonization following a mass mortality event.
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Affiliation(s)
- Virginie Marques
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental System ScienceETH ZürichZürichSwitzerland
- Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Géraldine Loot
- EDB, Laboratoire Ecologie et Evolution (UMR 5174)Université de Toulouse, UPS, CNRS, IRDToulouseFrance
| | - Simon Blanchet
- SETE, Station d'Écologie Théorique et Expérimentale (UAR2029), Centre National pour la Recherche ScientifiqueMoulisFrance
| | - Claude Miaud
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Serge Planes
- PSL Research University: EPHE – UPVD – CNRS, UAR 3278 CRIOBEPerpignanFrance
| | - Claire Peyran
- PSL Research University: EPHE – UPVD – CNRS, UAR 3278 CRIOBEPerpignanFrance
| | - Véronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Coralie Calvet
- AgroParisTechParisFrance
- Montpellier Research in Management (MRM)Univ Montpellier, Univ Paul Valéry Montpellier 3, Univ Perpignan Via DomitiaMontpellierFrance
| | - Sylvain Pioch
- AgroParisTechParisFrance
- Montpellier Research in Management (MRM)Univ Montpellier, Univ Paul Valéry Montpellier 3, Univ Perpignan Via DomitiaMontpellierFrance
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
- Institut Universitaire de FranceParisFrance
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Rieseberg L, Warschefsky E, Burton J, Huang K, Sibbett B. Editorial 2024. Mol Ecol 2024; 33:e17239. [PMID: 38146175 DOI: 10.1111/mec.17239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Affiliation(s)
- Loren Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Emily Warschefsky
- William L. Brown Center, Missouri Botanical Garden, Saint Louis, MO, USA
| | - Jade Burton
- John Wiley & Sons, Atrium Southern Gate, Chichester, West Sussex, UK
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Benjamin Sibbett
- John Wiley & Sons, Atrium Southern Gate, Chichester, West Sussex, UK
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6
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Gillespie RG, Bik HM, Hickerson MJ, Krehenwinkel H, Overcast I, Rominger AJ. Insights into Ecological & Evolutionary Processes via community metabarcoding. Mol Ecol 2023; 32:6083-6092. [PMID: 37999451 DOI: 10.1111/mec.17208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/05/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023]
Affiliation(s)
- Rosemary G Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Holly M Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Michael J Hickerson
- Graduate Center of the City University of New York, New York City, New York, USA
- Biology Department, City College of New York, New York City, New York, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA
| | | | - Isaac Overcast
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
- Department of Vertebrate Zoology, Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA
- California Academy of Sciences, San Francisco, California, USA
| | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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7
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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: 29] [Impact Index Per Article: 29.0] [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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