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Gallego R, Arias MB, Corral-Lou A, Díez-Vives C, Neave EF, Wang C, Cárdenas P, Steffen K, Taboada S, Villamor A, Kenchington E, Mariani S, Riesgo A. North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA. Commun Biol 2024; 7:1015. [PMID: 39160260 DOI: 10.1038/s42003-024-06695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
The deep-sea remains the biggest challenge to biodiversity exploration, and anthropogenic disturbances extend well into this realm, calling for urgent management strategies. One of the most diverse, productive, and vulnerable ecosystems in the deep sea are sponge grounds. Currently, environmental DNA (eDNA) metabarcoding is revolutionising the field of biodiversity monitoring, yet complex deep-sea benthic ecosystems remain challenging to assess even with these novel technologies. Here, we evaluate the effectiveness of whole-community metabarcoding to characterise metazoan diversity in sponge grounds across the North Atlantic by leveraging the natural eDNA sampling properties of deep-sea sponges themselves. We sampled 97 sponge tissues from four species across four North-Atlantic biogeographic regions in the deep sea and screened them using the universal COI barcode region. We recovered unprecedented levels of taxonomic diversity per unit effort, especially across the phyla Chordata, Cnidaria, Echinodermata and Porifera, with at least 406 metazoan species found in our study area. These assemblages identify strong spatial patterns in relation to both latitude and depth, and detect emblematic species currently employed as indicators for these vulnerable habitats. The remarkable performance of this approach in different species of sponges, in different biogeographic regions and across the whole animal kingdom, illustrates the vast potential of natural samplers as high-resolution biomonitoring solutions for highly diverse and vulnerable deep-sea ecosystems.
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Affiliation(s)
- Ramón Gallego
- Department of Biology, Facultad de Ciencias, Universidad Autónoma de Madrid, Calle Darwin 2, Cantoblanco, 28049, Madrid, Spain
| | - María Belén Arias
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London, SW7 5BD, UK
| | - Andrea Corral-Lou
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Cristina Díez-Vives
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London, SW7 5BD, UK
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Calle Darwin 3, 28049, Madrid, Spain
| | - Erika F Neave
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Cai Wang
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Paco Cárdenas
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36, Uppsala, Sweden
| | - Karin Steffen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Sergio Taboada
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Adriana Villamor
- International Council for the Exploration of the Sea (ICES), H. C. Andersens Boulevard 44-46, DK, 1553, Copenhagen V, Denmark
| | - Ellen Kenchington
- Ocean and Ecosystem Sciences Division, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Ana Riesgo
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London, SW7 5BD, UK.
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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Zarcero J, Antich A, Rius M, Wangensteen OS, Turon X. A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species. iScience 2024; 27:108588. [PMID: 38111684 PMCID: PMC10726295 DOI: 10.1016/j.isci.2023.108588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/04/2023] [Accepted: 11/23/2023] [Indexed: 12/20/2023] Open
Abstract
Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.
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Affiliation(s)
- Jesús Zarcero
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
| | - Marc Rius
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park Johannesburg 2006, South Africa
| | - Owen S. Wangensteen
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
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Aglieri G, Quattrocchi F, Mariani S, Baillie C, Spatafora D, Di Franco A, Turco G, Tolone M, Di Gerlando R, Milazzo M. Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea. MARINE POLLUTION BULLETIN 2023; 189:114792. [PMID: 36921451 DOI: 10.1016/j.marpolbul.2023.114792] [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: 11/10/2022] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Gathering comprehensive marine biodiversity data can be difficult, costly and time consuming, preventing adequate knowledge of diversity patterns in many areas worldwide. We propose fishing ports as "natural" sinks of biodiversity information collected by fishing vessels probing disparate habitats, depths, and environments. By combining rapid environmental DNA metabarcoding (eDNA) surveys and data from public registers and Automatic Identification Systems, we show significant positive relationships between fishing fleet activities (i.e. fishing effort and characteristics of the fishing grounds) and the taxonomic fish assemblage composition in eleven Mediterranean fishing ports. Overall, we identified 160 fish and 123 invertebrate OTUs, including at least seven non-indigenous species, in some instances well beyond their known distribution areas. Our findings suggest that eDNA assessments of fishing harbours' waters might offer a rapid way to monitor marine biodiversity in unknown or under-sampled areas, as well as to reconstruct fishing catches, often underreported in several regions.
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Affiliation(s)
- Giorgio Aglieri
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Palermo, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy.
| | - Federico Quattrocchi
- NBFC, National Biodiversity Future Center, Palermo, Italy; University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy; Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Mazara del Vallo, Italy
| | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | | | - Davide Spatafora
- University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy
| | - Antonio Di Franco
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Palermo, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Gabriele Turco
- University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy
| | - Marco Tolone
- University of Palermo, Department of Agricultural Food and Forest Sciences, Palermo, Italy
| | - Rosalia Di Gerlando
- University of Palermo, Department of Agricultural Food and Forest Sciences, Palermo, Italy
| | - Marco Milazzo
- NBFC, National Biodiversity Future Center, Palermo, Italy; University of Palermo, Department of Earth and Marine Sciences (DiSTeM), Palermo, Italy
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4
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Coppo G, Pais FS, Ferreira TO, Halanych KM, Donnelly K, Mazzuco AC, Bernardino AF. Transition of an estuarine benthic meiofauna assemblage 1.7 and 2.8 years after a mining disaster. PeerJ 2023; 11:e14992. [PMID: 36935931 PMCID: PMC10022502 DOI: 10.7717/peerj.14992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/12/2023] [Indexed: 03/15/2023] Open
Abstract
Background Estuaries are transitional coastal ecosystems that are threatened by multiple sources of human pollution. In 2015, mining tailings from an upstream dam failure caused massive metal contamination that impacted benthic assemblages on the Brazilian Rio Doce estuary. Methods In this study, we investigate and compare meiofaunal assemblages with eDNA metabarcoding 1.7 years (2017) and 2.8 years (2018) after the initial contamination by mine tailings in order to evaluate the continued impact of sediment mine tailing contaminants on the structure of benthic assemblages after the disaster. Results The community was dominated by Arthropoda and Nematoda 1.7 yr after the impacts (42 and 29% of meiofaunal sequence reads, respectively) but after 2.8 years Arthropoda (64.8% of meiofaunal sequence reads) and Rotifera (11.8%) were the most common taxa. This continued impact on meiofaunal assemblage revealed a lower phylogenetic diversity (7.8-fold) in 2018, despite overall decrease in metal concentration (Al, Ba, Cr, As, Fe, Zn, Mn, Pb, Cd, Co) in sediments. Our data suggests that differences in benthic assemblages and loss of diversity may be influenced by contaminants in sediments of this estuary, and indicate that broad eDNA assessments are greatly useful to understand the full range of biodiversity changes in dynamic estuarine ecosystems.
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Affiliation(s)
- Gabriel Coppo
- Grupo de Ecologia Bentônica, Department of Oceanography, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Fabiano S. Pais
- Plataforma de Bioinformática, Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago O. Ferreira
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Ken M. Halanych
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, NC, United States of America
| | - Kyle Donnelly
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, NC, United States of America
| | - Ana Carolina Mazzuco
- Grupo de Ecologia Bentônica, Department of Oceanography, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Angelo F. Bernardino
- Grupo de Ecologia Bentônica, Department of Oceanography, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
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Turon M, Nygaard M, Guri G, Wangensteen OS, Præbel K. Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding. Front Genet 2022; 13:957251. [PMID: 36092881 PMCID: PMC9458982 DOI: 10.3389/fgene.2022.957251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
Aquaculture impacts on marine benthic ecosystems are widely recognized and monitored. However, little is known about the community changes occurring in the water masses surrounding aquaculture sites. In the present study, we studied the eukaryotic communities inside and outside salmonid aquaculture cages through time to assess the community changes in the neighbouring waters of the farm. Water samples were taken biweekly over five months during the production phase from inside the cages and from nearby points located North and South of the salmon farm. Eukaryotic communities were analyzed by eDNA metabarcoding of the partial COI Leray-XT fragment. The results showed that eukaryotic communities inside the cages were significantly different from those in the outside environment, with communities inside the cages having higher diversity values and more indicator species associated with them. This is likely explained by the appearance of fouling species that colonize the artificial structures, but also by other species that are attracted to the cages by other means. Moreover, these effects were highly localized inside the cages, as the communities identified outside the cages, both North and South, had very similar eukaryotic composition at each point in time. Overall, the eukaryotic communities, both inside and outside the cages, showed similar temporal fluctuations through the summer months, with diversity peaks occurring at the end of July, beginning of September, and in the beginning of November, with the latter showing the highest Shannon diversity and richness values. Hence, our study suggests that seasonality, together with salmonid aquaculture, are the main drivers of eukaryotic community structure in surface waters surrounding the farm.
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Affiliation(s)
- Marta Turon
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Magnus Nygaard
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Gledis Guri
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian Institute of Marine Research, Tromsø, Norway
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Kim Præbel,
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Durso AM, Kieran TJ, Glenn TC, Mullin SJ. Comparison of Three Methods for Measuring Dietary Composition of Plains Hog-nosed Snakes. HERPETOLOGICA 2022. [DOI: 10.1655/herpetologica-d-21-00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Andrew M. Durso
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Stephen J. Mullin
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
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7
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Domènech M, Wangensteen OS, Enguídanos A, Malumbres‐Olarte J, Arnedo MA. For all audiences: Incorporating immature stages into standardised spider inventories has a major impact on the assessment of biodiversity patterns. Mol Ecol Resour 2022; 22:2319-2332. [DOI: 10.1111/1755-0998.13625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/19/2022] [Accepted: 04/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Marc Domènech
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio) Universitat de Barcelona Av. Diagonal 643 E‐08028 Barcelona Spain
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science University of Tromsø The Arctic University of Norway Norway
| | - Alba Enguídanos
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio) Universitat de Barcelona Av. Diagonal 643 E‐08028 Barcelona Spain
| | - Jagoba Malumbres‐Olarte
- Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Faculty of Agrarian and Environmental Sciences Rua Capitão João d’Ávila 9700‐042 Terceira Açores Portugal
- Finnish Museum of Natural History University of Helsinki P.O.Box 17 Pohjoinen Rautatiekatu 13) 00014 Helsinki Finland
| | - Miquel A. Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio) Universitat de Barcelona Av. Diagonal 643 E‐08028 Barcelona Spain
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Urban P, Praebel K, Bhat S, Dierking J, Wangensteen OS. DNA-metabarcoding reveals the importance of gelatinous zooplankton in the diet of Pandalus borealis, a keystone species in the Arctic. Mol Ecol 2021; 31:1562-1576. [PMID: 34936153 DOI: 10.1111/mec.16332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly molecular approaches such as DNA-metabarcoding are used in studying trophic relations, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA-metabarcoding with universal primers for cytochrome c oxidase I (COI), to study the diet composition of the Northern shrimp (Pandalus borealis), an Arctic keystone species with large socio-economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40-60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on SCA. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underscores the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs.
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Affiliation(s)
- Paulina Urban
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway.,GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Kim Praebel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway.,Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, Elverum, Norway
| | - Shripathi Bhat
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
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9
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Zhao B, van Bodegom PM, Trimbos K. The particle size distribution of environmental DNA varies with species and degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149175. [PMID: 34303977 DOI: 10.1016/j.scitotenv.2021.149175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) analysis is frequently used as a non-invasive method to investigate species and biodiversity in ecosystems. However, such eDNA may represent both organisms currently present as well as species that released their DNA some point in the past, thereby representing a mix of current and historic biodiversity. This may lead to a false-positive detection of organisms' presence. As the eDNA particle size distribution (PSD) changes along with the decay process, it may facilitate solving the above problem. Here, we set up tank experiments with snails, zebrafish and daphnids, respectively, to monitor the change in eDNA PSD and eDNA degradation through time after removing organisms. We found that zebrafish eDNA decays more slowly for larger particle sizes. Across all species tested, the percentage of large size ranges tended to increase over time while the smaller sizes showed relatively fast decay rates. As a result, PSD changed consistently with eDNA decay, although initial PSD varied between species. In combination, we propose that eDNA PSD can be used to assess the current prevalence of organisms at an eDNA sampling location while avoiding false-positives on the presence of species. Our findings expand the applicability of eDNA for monitoring target species in freshwater ecosystems.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands.
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
| | - Krijn Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
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10
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Ríos-Castro R, Romero A, Aranguren R, Pallavicini A, Banchi E, Novoa B, Figueras A. High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem. Front Vet Sci 2021; 8:765606. [PMID: 34805343 PMCID: PMC8595318 DOI: 10.3389/fvets.2021.765606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 12/04/2022] Open
Abstract
The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.
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Affiliation(s)
- Raquel Ríos-Castro
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alejandro Romero
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Raquel Aranguren
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Elisa Banchi
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Beatriz Novoa
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Antonio Figueras
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
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11
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Antich A, Palacin C, Wangensteen OS, Turon X. To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics 2021; 22:177. [PMID: 33820526 PMCID: PMC8020537 DOI: 10.1186/s12859-021-04115-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. RESULTS Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. CONCLUSIONS We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain
| | - Creu Palacin
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona and Research Institute of Biodiversity (IRBIO), Barcelona, Catalonia, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsö, Norway.
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain.
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12
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Wang X, Li H, Zhan X, Ma M, Yuan D, Hu Q, Gong Y. Development and application of quantitative real-time PCR based on the mitochondrial cytochrome oxidase subunit I gene for early detection of the grazer Poterioochromonas malhamensis contaminating Chlorella culture. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Compson ZG, McClenaghan B, Singer GAC, Fahner NA, Hajibabaei M. Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.581835] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.
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Aglieri G, Baillie C, Mariani S, Cattano C, Calò A, Turco G, Spatafora D, Di Franco A, Di Lorenzo M, Guidetti P, Milazzo M. Environmental DNA effectively captures functional diversity of coastal fish communities. Mol Ecol 2020; 30:3127-3139. [PMID: 33078500 DOI: 10.1111/mec.15661] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 01/04/2023]
Abstract
Robust assessments of taxonomic and functional diversity are essential components of research programmes aimed at understanding current biodiversity patterns and forecasting trajectories of ecological changes. Yet, evaluating marine biodiversity along its dimensions is challenging and dependent on the power and accuracy of the available data collection methods. Here we combine three traditional survey methodologies (underwater visual census strip transects [UVCt], baited underwater videos [BUV] and small-scale fishery catches [SSFc]), and one novel molecular technique (environmental DNA metabarcoding [eDNA]-12S rRNA and cytochrome oxidase subunit 1 [COI]) to investigate their efficiency and complementarity in assessing fish diversity. We analysed 1,716 multimethod replicates at a basin scale to measure the taxonomic and functional diversity of Mediterranean fish assemblages. Taxonomic identities were investigated at species, genus and family levels. Functional identities were assessed using combinations of morphological, behavioural and trophic traits. We show that: (a) SSFc provided the higher taxonomic diversity estimates followed by eDNA, and then UVCt and BUV; (b) eDNA was the only method able to gather the whole spectrum of considered functional traits, showing the most functionally diversified and least redundant fish assemblages; and (c) the effectiveness of eDNA in describing functional structure reflected its lack of selectivity towards any considered functional trait. Our findings suggest that the reach of eDNA analysis stretches beyond taxon detection efficiency and provides new insights into the potential of metabarcoding in ecological studies.
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Affiliation(s)
- Giorgio Aglieri
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Stefano Mariani
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Carlo Cattano
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,Department of Integrative Marine Ecology, Sicily, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo (complesso Roosevelt), Palermo, Italy
| | - Antonio Calò
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,UMR 7035 ECOSEAS, CNRS, Université Côte d'Azur, Nice, France
| | - Gabriele Turco
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Davide Spatafora
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Antonio Di Franco
- Department of Integrative Marine Ecology, Sicily, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo (complesso Roosevelt), Palermo, Italy.,UMR 7035 ECOSEAS, CNRS, Université Côte d'Azur, Nice, France
| | - Manfredi Di Lorenzo
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Mazara del Vallo, Italy
| | - Paolo Guidetti
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,UMR 7035 ECOSEAS, CNRS, Université Côte d'Azur, Nice, France.,Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marco Milazzo
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
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15
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Antich A, Palacín C, Cebrian E, Golo R, Wangensteen OS, Turon X. Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Mol Ecol 2020; 30:3175-3188. [PMID: 32974967 DOI: 10.1111/mec.15641] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/06/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and Alveolata in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples and, of these, 180 (5.1%) were identified as benthic taxa that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex communities via metabarcoding.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, and Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Emma Cebrian
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Raül Golo
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
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16
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Suter L, Polanowski AM, Clarke LJ, Kitchener JA, Deagle BE. Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder. Mol Ecol 2020; 30:3140-3157. [PMID: 32767849 DOI: 10.1111/mec.15587] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/24/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship-based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan-targeted cytochrome c oxidase I (COI) marker was used to characterize species-level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non-metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote-targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity.
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Affiliation(s)
- Leonie Suter
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Andrea Maree Polanowski
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Laurence John Clarke
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia.,Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
| | - John Andrew Kitchener
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Bruce Emerson Deagle
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia.,Commonwealth Scientific and Industrial Research Organisation, Battery Point, Tas., Australia
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17
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Nguyen BN, Shen EW, Seemann J, Correa AMS, O'Donnell JL, Altieri AH, Knowlton N, Crandall KA, Egan SP, McMillan WO, Leray M. Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape. Sci Rep 2020; 10:6729. [PMID: 32317664 PMCID: PMC7174284 DOI: 10.1038/s41598-020-63565-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/16/2020] [Indexed: 01/08/2023] Open
Abstract
Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.
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Affiliation(s)
- Bryan N Nguyen
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Elaine W Shen
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
- Department of Biosciences, Rice University, Houston, Texas, USA.
| | - Janina Seemann
- Smithsonian Tropical Research Institute, Smithsonian Institution, Balboa, Ancon, Panama
| | | | - James L O'Donnell
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, USA
| | - Andrew H Altieri
- Smithsonian Tropical Research Institute, Smithsonian Institution, Balboa, Ancon, Panama
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biostatistics & Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Scott P Egan
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Smithsonian Institution, Balboa, Ancon, Panama
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Balboa, Ancon, Panama
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18
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DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040123] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900–1750 m) at two seasons, and used a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a metabarcoding marker. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing MOTU richness and diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, which was significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs and in the most diverse taxa. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, the broad spatio-temporal patterns elucidated from both datasets coincided, with both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high-resolution method to detect ecological shifts. We also highlight that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.
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