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Sbrana A, Maiello G, Gravina MF, Cicala D, Galli S, Stefani M, Russo T. Environmental DNA metabarcoding reveals the effects of seafloor litter and trawling on marine biodiversity. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106415. [PMID: 38395681 DOI: 10.1016/j.marenvres.2024.106415] [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: 11/10/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Environmental DNA (eDNA) techniques are emerging as promising tools for monitoring marine communities. However, they have not been applied to study the integrated effects of anthropogenic pressures on marine biodiversity. This study examined the relationships between demersal community species composition, key environmental features, and anthropogenic impacts such as fishing effort and seafloor litter using eDNA data in the central Tyrrhenian Sea. The results indicated that both fishing effort and seafloor litter influenced species composition and diversity. The adaptive traits of marine species played a critical role in their response to debris accumulation and fishing. Mobile species appeared to use relocation strategies, while sessile species showed flexibility in the face of disturbance. Epibiotic species relied on passive transport. The use of eDNA-based methods is a valuable resource for monitoring anthropogenic impacts during scientific surveys, enhancing our ability to monitor marine ecosystems and more effectively assess the effects of pollution.
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Affiliation(s)
- Alice Sbrana
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; PhD program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy.
| | - Giulia Maiello
- School of Biological and Environmental Sciences, Liverpool John Moores University, L33AF, Liverpool, UK
| | - Maria Flavia Gravina
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Rome, Italy
| | - Davide Cicala
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy
| | - Simone Galli
- CoNISMa, Piazzale Flaminio 9, 00196, Rome, Italy
| | - Matteo Stefani
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; PhD program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Tommaso Russo
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Rome, Italy
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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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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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Kim K, Joo GJ, Jeong KS, Gim JS, Lee Y, Hong D, Jo H. Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary. BIOLOGY 2023; 12:1245. [PMID: 37759644 PMCID: PMC10525425 DOI: 10.3390/biology12091245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.
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Affiliation(s)
- Kanghui Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Gea-Jae Joo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Kwang-Seuk Jeong
- Department of Nursing Science, Busan Health University, Busan 49318, Republic of Korea;
| | - Jeong-Soo Gim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Yerim Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Donghyun Hong
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Hyunbin Jo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
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Neave EF, Cai W, Arias MB, Harper LR, Riesgo A, Mariani S. Trapped DNA fragments in marine sponge specimens unveil North Atlantic deep-sea fish diversity. Proc Biol Sci 2023; 290:20230771. [PMID: 37644836 PMCID: PMC10465980 DOI: 10.1098/rspb.2023.0771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023] Open
Abstract
Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80-1600 m), and even the level of protection in place. Given the cost associated with ocean biodiversity surveys, we argue that targeted and opportunistic sponge samples - as well as the specimens already stored in museums and other research collections - represent an invaluable trove of biodiversity information that can significantly extend the reach of ocean monitoring.
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Affiliation(s)
- Erika F. Neave
- School of Biological & Environmental Sciences, Liverpool John Moores University, Byrom St, Liverpool L3 3AF, UK
- Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - Wang Cai
- School of Biological & Environmental Sciences, Liverpool John Moores University, Byrom St, Liverpool L3 3AF, UK
| | - Maria Belén Arias
- Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - Lynsey R. Harper
- School of Biological & Environmental Sciences, Liverpool John Moores University, Byrom St, Liverpool L3 3AF, UK
- The Freshwater Biological Association, The Hedley Wing, YMCA North Campus, Lakeside, Newby Bridge, Cumbria LA12 8BD, UK
| | - Ana Riesgo
- Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales de Madrid, Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Byrom St, Liverpool L3 3AF, UK
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Cuff JP, Kitson JJN, Hemprich‐Bennett D, Tercel MPTG, Browett SS, Evans DM. The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth? Mol Ecol Resour 2023; 23:41-51. [PMID: 36017818 PMCID: PMC10087656 DOI: 10.1111/1755-0998.13705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022]
Abstract
Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed "the predator problem". We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multipredator-taxon studies. We suggest that multiprimer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multitaxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way.
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Affiliation(s)
- Jordan P. Cuff
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | - James J. N. Kitson
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | | | - Maximillian P. T. G. Tercel
- School of BiosciencesCardiff UniversityCardiffUK
- Durrell Wildlife Conservation Trust, Les Augrès Manor, La Profonde RueTrinityJersey
| | - Samuel S. Browett
- Ecosystems and Environment Research Centre, School of Science, Engineering and EnvironmentUniversity of SalfordSalfordUK
| | - Darren M. Evans
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
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Zainal Abidin DH, Mohd Nor SA, Lavoué S, A Rahim M, Mohammed Akib NA. Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding. Sci Rep 2022; 12:16346. [PMID: 36175455 PMCID: PMC9523059 DOI: 10.1038/s41598-022-19954-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
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Affiliation(s)
- Danial Hariz Zainal Abidin
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | | | - Noor Adelyna Mohammed Akib
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia. .,School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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Rangaswamy B, Ji CW, Kim WS, Park JW, Kim YJ, Kwak IS. Profiling Analysis of Filter Feeder Polypedilum (Chironomidae) Gut Contents Using eDNA Metabarcoding Following Contrasting Habitat Types-Weir and Stream. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10945. [PMID: 36078662 PMCID: PMC9517803 DOI: 10.3390/ijerph191710945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
We analyzed the dietary composition of Polypedilum larvae among two contrasting habitats (river and weir). Our approach was (i) to apply eDNA-based sampling to reveal the gut content of the chironomid larvae, (ii) the diversity of gut contents in the two aquatic habitats, and (iii) assessment of habitat sediment condition with the food sources in the gut. The most abundant food was Chlorophyta in the gut of the river (20%) and weir (39%) chironomids. The average ratio of fungi, protozoa, and zooplankton in river chironomids gut was 5.9%, 7.2%, and 3.8%, while it was found decreased to 1.2%, 2.5%, and 0.1% in weir chironomids. Aerobic fungi in river midge guts were 3.6% and 10.34% in SC and IS, while they were in the range of 0.34-2.58% in weir midges. The hierarchical clustering analysis showed a relationship of environmental factors with food contents. Abiotic factors (e.g., pH) in the river and weir habitats correlated the clustered pattern with phytoplankton and minor groups of fungi. This study could help understand the food source diversity in the chironomid and habitat environmental conditions by using eDNA metabarcoding as an effective tool to determine dietary composition.
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Affiliation(s)
- Boobal Rangaswamy
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
| | - Chang Woo Ji
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
| | - Won-Seok Kim
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Jae-Won Park
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Yong Jun Kim
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Ihn-Sil Kwak
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
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Riccioni G, Stagioni M, Manfredi C, Tinti F, Piccinetti C, Libralato S. DNA metabarcoding suggests dietary niche partitioning in the Adriatic European hake. Sci Rep 2022; 12:1343. [PMID: 35079081 PMCID: PMC8789918 DOI: 10.1038/s41598-022-05346-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
The Northern Adriatic Sea (FAO Geographical Sub-Area 17) is one of the most productive fishing areas of the Mediterranean Sea and it includes a broad diversity of habitats. In the Northern Adriatic basin, the Pomo Pit (200-273 m of depth) is one of the most important areas of aggregation for some demersal stocks shared in the Adriatic Sea and it is an important spawning/nursery area of the European hake (Merluccius merluccius). Through a metabarcoding approach we investigated the feeding habits of European hake, both inside and outside the Pomo Pit, and their temporal variability comparing samples collected in 2016 and 2014. Our analyses proved the presence of an ontogenetic shift from a diet based mainly on crustaceans in juveniles to a more piscivorous feeding behaviour in adult hakes and suggested the presence of a specific niche partitioning and food preferences between hakes living inside and outside the Pomo Pit. The main differences among adult hakes refer to the presence of molluscs in the stomachs of hakes collected within the Pomo Pit and the presence of high depth prey species (i.e., Micromesistius poutassou). Metabarcoding revealed the relevant ecological role played by the Pomo Pit in M. merluccius feeding behaviour and ontogenetic development, promoting a careful ecosystem-based management of fisheries in this area through focused conservation measures.
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Affiliation(s)
- Giulia Riccioni
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy.
- BioDNA - Centro di Ricerca sulla Biodiversità e DNA Antico, Facoltà di scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, via Emilia Parmense n. 84, 29122, Piacenza, Italy.
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy
- Co.N.I.S.Ma- URL Fano, Laboratory of Marine Biology and Fisheries, viale Adriatico 1/n, 61032, Fano, Italy
| | - Chiara Manfredi
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy
- Co.N.I.S.Ma- URL Fano, Laboratory of Marine Biology and Fisheries, viale Adriatico 1/n, 61032, Fano, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Sant'Alberto 163, 48123, Ravenna, Italy
| | - Corrado Piccinetti
- Department of Biological, Geological and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, viale Adriatico 1/n, 61032, Fano, Italy
| | - Simone Libralato
- National Institute of Oceanography and Applied Geophysics - OGS, Via Beirut 2/4 (Ex-Sissa building), 34151, Trieste, Italy
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King AC, Krieg R, Weston A, Zenker AK. Using eDNA to simultaneously detect the distribution of native and invasive crayfish within an entire country. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:113929. [PMID: 34688048 DOI: 10.1016/j.jenvman.2021.113929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/03/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
The introduction of invasive crayfish has led to a decline of many European native species of crayfish across their range. In this study, novel duplex assays for all crayfish occurring in Switzerland were developed. We aimed to identify the distribution of the seven species using a traditional trap surveillance method as well by collecting water samples to detect eDNA by species-specific quantitative real-time PCR. We reveal our overall experience in finding optimal field and laboratory techniques to discover the distribution and abundance of native and invasive species in order to enhance knowledge of early invasive species invasion and highlight important pockets of populations where native species remain, for implementation of conservation strategies. Using eDNA, important populations of native noble and white-clawed crayfish were revealed in multiple waters across various cantons. The successful identification of native and invasive crayfish species in Switzerland using eDNA can be applied to future nationwide projects. This method which has the ability to detect all species simultaneously across an entire country, will allow an improvement in freshwater crayfish conservation management.
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Affiliation(s)
- Alex C King
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
| | - Raphael Krieg
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
| | - Anna Weston
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
| | - Armin K Zenker
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland.
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11
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Ankley PJ, Xie Y, Black TA, DeBofsky A, Perry M, Paterson MJ, Hanson M, Higgins S, Giesy JP, Palace V. Using zooplankton metabarcoding to assess the efficacy of different techniques to clean-up an oil-spill in a boreal lake. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 236:105847. [PMID: 34015755 DOI: 10.1016/j.aquatox.2021.105847] [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: 12/22/2020] [Revised: 04/14/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Regulators require adequate information to select best practices with less ecosystem impacts for remediation of freshwater ecosystems after oil spills. Zooplankton are valuable indicators of aquatic ecosystem health as they play pivotal roles in biochemical cycles while stabilizing food webs. Compared with morphological identification, metabarcoding holds promise for cost-effective, high-throughput, and benchmarkable biomonitoring of zooplankton communities. The objective of this study was to apply DNA and RNA metabarcoding of zooplankton for ecotoxicological assessment and compare it with traditional morphological identification in experimental shoreline enclosures in a boreal lake. These identification methods were also applied in context of assessing response of the zooplankton community exposed to simulated spills of diluted bitumen (dilbit), with experimental remediation practices (enhanced monitored natural recovery and shoreline cleaner application). Metabarcoding detected boreal zooplankton taxa up to the genus level, with a total of 24 shared genera, and while metabarcoding-based relative abundance served as an acceptable proxy for biomass inferred by morphological identification (ρ ≥ 0.52). Morphological identification determined zooplankton community composition changes due to treatments at 11 days post-spill (PERMANOVA, p = 0.0143) while metabarcoding methods indicated changes in zooplankton richness and communities at 38 days post-spill (T-test, p < 0.05; PERMANOVA, p ≤ 0.0429). Shoreline cleaner application overall seemed to have the largest impact on zooplankton communities relative to enhanced monitored natural recovery, regardless of zooplankton identification method. Both metabarcoding and morphological identification were able to discern the differences between the two experimental remediation practices. Metabarcoding of zooplankton could provide informative results for ecotoxicological assessment of the remediation practices of dilbit, advancing our knowledge of best practices for remediating oil-impacted aquatic ecosystems while serving to accelerate the assessment of at-risk freshwater ecosystems.
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Affiliation(s)
- Phillip J Ankley
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Tyler A Black
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Abigail DeBofsky
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - McKenzie Perry
- Department of Environment and Geography, University of Manitoba, Winnipeg, MB, Canada
| | - Michael J Paterson
- International Institute for Sustainable Development - Experimental Lakes Area, Kenora, ON, Canada
| | - Mark Hanson
- Department of Environment and Geography, University of Manitoba, Winnipeg, MB, Canada
| | - Scott Higgins
- International Institute for Sustainable Development - Experimental Lakes Area, Kenora, ON, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, Texas, USA
| | - Vince Palace
- International Institute for Sustainable Development - Experimental Lakes Area, Kenora, ON, Canada
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12
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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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13
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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Sci Rep 2021; 11:6820. [PMID: 33767219 PMCID: PMC7994446 DOI: 10.1038/s41598-021-85488-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
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14
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Browett SS, Curran TG, O’Meara DB, Harrington AP, Sales NG, Antwis RE, O’Neill D, McDevitt AD. Primer biases in the molecular assessment of diet in multiple insectivorous mammals. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00115-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractOur understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing between species that occupy an identical niche type. Here, we apply DNA metabarcoding to empirically compare the prey detection capabilities of two widely used primer sets when assessing the diets of a flying (lesser horseshoe bat; Rhinolophus hipposideros) and two ground-dwelling insectivores (greater white-toothed shrew; Crocidura russula and pygmy shrew; Sorex minutus). Although R. hipposideros primarily rely on two prey orders (Lepidoptera and Diptera), the unique taxa detected by each primer shows that a combination of primers may be the best approach to fully describe bat trophic ecology. However, random forest classifier analysis suggests that one highly degenerate primer set detected the majority of both shrews’ diet despite higher levels of host amplification. The wide range of prey consumed by ground-dwelling insectivores can therefore be accurately documented from using a single broad-range primer set, which can decrease cost and labour. The results presented here show that dietary inferences will differ depending on the primer or primer combination used for insectivores occupying different niches (i.e., hunting in the air or ground) and demonstrate the importance of performing empirical pilot studies for novel study systems.
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15
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Qu C, Stewart KA, Clemente-Carvalho R, Zheng J, Wang Y, Gong C, Ma L, Zhao J, Lougheed SC. Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding. Sci Rep 2020; 10:16715. [PMID: 33028872 PMCID: PMC7542144 DOI: 10.1038/s41598-020-73648-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 09/09/2020] [Indexed: 12/16/2022] Open
Abstract
Using environmental DNA (eDNA) metabarcoding, we compared fish diversity in two distinct water bodies within the Yangtze River Basin with known populations of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis; YFP): the Tian-e-Zhou Reserve and Poyang Lake. We aimed to create a fish surveying tool for use in the Yangtze River Basin, while also gaining a better understanding of the prey distribution and diversity within two of the remaining strongholds of YFP. 16S rRNA universal primers were developed to amplify fish eDNA. After high-throughput sequencing and stringent data filtering, we identified a total of 75 fish species (6 orders, 9 families, 57 genera) across seasons and regions. Nine of the 75 fish species were among the 28 known YFP prey species, three of which were detected in all water samples. Our eDNA metabarcoding identified many species that had been previously captured using traditional netting practices, but also numerous species not previously collected in these water bodies. Fish diversity was higher in Poyang Lake than in Tian-e-Zhou Reserve, as well as higher in the spring than in summer. These methods provide a broadly applicable tool to quantify fish diversity and distributions throughout the Yangtze River Basin, and to inform conservation strategies of YFP.
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Affiliation(s)
- Chanjuan Qu
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China.,Department of Biology, Queen's University, Kingston, ON, Canada
| | - Kathryn A Stewart
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Jinsong Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yuxiang Wang
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Cheng Gong
- Administrative Office of Hubei Yangtze Tian'eZhou Baiji National Natural Reserve, Shishou, Hubei, China
| | - Limin Ma
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Jianfu Zhao
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
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16
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Bakker J, Wangensteen OS, Baillie C, Buddo D, Chapman DD, Gallagher AJ, Guttridge TL, Hertler H, Mariani S. Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding. Ecol Evol 2019; 9:14341-14355. [PMID: 31938523 PMCID: PMC6953649 DOI: 10.1002/ece3.5871] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 01/12/2023] Open
Abstract
Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic "protists," with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.
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Affiliation(s)
- Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- School of Engineering & Environment University of Salford Salford UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Charles Baillie
- School of Engineering & Environment University of Salford Salford UK
| | - Dayne Buddo
- Discovery Bay Marine Laboratory and Field Station University of the West Indies St. Ann Jamaica
| | - Demian D Chapman
- Department of Biological Sciences Florida International University Miami FL USA
| | | | | | - Heidi Hertler
- The School for Field Studies Centre for Marine Resource Studies South Caicos Turks and Caicos Islands
| | - Stefano Mariani
- School of Engineering & Environment University of Salford Salford UK
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17
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Shum P, Barney BT, O'Leary JK, Palumbi SR. Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems. Mol Ecol Resour 2019; 19:1470-1485. [PMID: 31436907 DOI: 10.1111/1755-0998.13067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/05/2019] [Accepted: 07/17/2019] [Indexed: 01/04/2023]
Abstract
Kelp forest ecosystems dominate 150,000 km of global temperate coastline, rivalling the coastal occurrence of coral reefs. Despite the astounding biological diversity and productive ecological communities associated with kelp forests, patterns of species richness and composition are difficult to monitor and compare. Crustose coralline algae are a critically important substrate for propagule settlement for a range of kelp forest species. Coralline-covered cobbles are home to hundreds of species of benthic animals and algae and form a replicable unit for ecological assays. Here, we use DNA metabarcoding of bulk DNA extracts sampled from cobbles to explore patterns of species diversity in kelp forests of the central California coast. The data from 97 cobbles within kelp forest ecosystems at three sites in Central California show the presence of 752 molecular operational taxonomic units (MOTUs) and 53 MOTUs assigned up to the species level with >95% similarity to current databases. We are able to detect spatial patterns of important management targets such as abalone recruits, and localized abundance of sea stars in 2012. Comparison of classic ecological surveys of these sites reveals large differences in species targets for these two approaches. In order to make such comparisons more quantitative, we use Presence/Absence Metabarcoding, using the fraction of replicate cobbles showing a species as a measure of its local abundance. This approach provides a fast and repeatable survey method that can be applied for biodiversity assessments across systems to shed light on the impact of different ecological disturbances and the role played by marine protected areas.
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Affiliation(s)
- Peter Shum
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - Bryan T Barney
- Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Jennifer K O'Leary
- The Nature Conservancy, Tanzania Marine Parks Unit, Kenya Wildlife Service, & Seychelles National Parks Authority, Mombasa, Kenya
- California Sea Grant, 1 Grand Ave, San Luis Obispo, USA
- California Polytechnic State University, 1 Frand Ave, San Luis Obispo, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
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18
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Mariani S, Baillie C, Colosimo G, Riesgo A. Sponges as natural environmental DNA samplers. Curr Biol 2019; 29:R401-R402. [DOI: 10.1016/j.cub.2019.04.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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Singer GAC, Fahner NA, Barnes JG, McCarthy A, Hajibabaei M. Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater. Sci Rep 2019; 9:5991. [PMID: 30979963 PMCID: PMC6461652 DOI: 10.1038/s41598-019-42455-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/01/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.
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Affiliation(s)
- G A C Singer
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - N A Fahner
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - J G Barnes
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - A McCarthy
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - M Hajibabaei
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada.
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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20
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Barbato M, Kovacs T, Coleman MA, Broadhurst MK, de Bruyn M. Metabarcoding for stomach-content analyses of Pygmy devil ray ( Mobula kuhlii cf. eregoodootenkee): Comparing tissue and ethanol preservative-derived DNA. Ecol Evol 2019; 9:2678-2687. [PMID: 30891208 PMCID: PMC6405894 DOI: 10.1002/ece3.4934] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/22/2018] [Accepted: 12/28/2018] [Indexed: 01/05/2023] Open
Abstract
The application of high-throughput sequencing to retrieve multi-taxon DNA from different substrates such as water, soil, and stomach contents has enabled species identification without prior knowledge of taxon compositions. Here we used three minibarcodes designed to target mitochondrial COI in plankton, 16S in fish, and 16S in crustaceans, to compare ethanol- and tissue-derived DNA extraction methodologies for metabarcoding. The stomach contents of pygmy devilrays (Mobula kuhlii cf. eregoodootenkee) were used to test whether ethanol-derived DNA would provide a suitable substrate for metabarcoding. The DNA barcoding assays indicated that tissue-derived operational taxonomic units (OTUs) were greater compared to those from extractions performed directly on the ethanol preservative. Tissue-derived DNA extraction is therefore recommended for broader taxonomic coverage. Metabarcoding applications should consider including the following: (i) multiple barcodes, both taxon specific (e.g., 12S or 16S) and more universal (e.g., COI or 18S) to overcome bias and taxon misidentification and (ii) PCR inhibitor removal steps that will likely enhance amplification yields. However, where tissue is limited or no longer available, but the ethanol-preservative medium is still available, metabarcoding directly from ethanol does recover the majority of common OTUs, suggesting the ethanol-retrieval method could be applicable for dietary studies. Metabarcoding directly from preservative ethanol may also be useful where tissue samples are limited or highly valued; bulk samples are collected, such as for rapid species inventories; or mixed-voucher sampling is conducted (e.g., for plankton, insects, and crustaceans).
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Affiliation(s)
- Matteo Barbato
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Toby Kovacs
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Melinda A. Coleman
- National Marine Science CentreNSW Department of Primary IndustriesCoffs HarbourNew South WalesAustralia
| | - Matt K. Broadhurst
- Fisheries Conservation Technology UnitNSW Department of Primary Industries, National Marine Science CentreCoffs HarbourNew South WalesAustralia
| | - Mark de Bruyn
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
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21
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Siegenthaler A, Wangensteen OS, Soto AZ, Benvenuto C, Corrigan L, Mariani S. Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring. Mol Ecol Resour 2018; 19:206-220. [PMID: 30358106 PMCID: PMC7379652 DOI: 10.1111/1755-0998.12956] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 11/30/2022]
Abstract
Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high‐throughput DNA‐based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey‐based techniques, we show that the DNA‐assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost‐effective tool for large‐scale, routine estuarine biodiversity monitoring.
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Affiliation(s)
- Andjin Siegenthaler
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Ana Z Soto
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Chiara Benvenuto
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Laura Corrigan
- Environment Agency, Tyneside House, Newcastle upon Tyne, UK
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
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