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Meira A, Byers JE, Sousa R. A global synthesis of predation on bivalves. Biol Rev Camb Philos Soc 2024; 99:1015-1057. [PMID: 38294132 DOI: 10.1111/brv.13057] [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: 08/01/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Predation is a dominant structuring force in ecological communities. In aquatic environments, predation on bivalves has long been an important focal interaction for ecological study because bivalves have central roles as ecosystem engineers, basal components of food webs, and commercial commodities. Studies of bivalves are common, not only because of bivalves' central roles, but also due to the relative ease of studying predatory effects on this taxonomic group. To understand patterns in the interactions of bivalves and their predators we synthesised data from 52 years of peer-reviewed studies on bivalve predation. Using a systematic search, we compiled 1334 studies from 75 countries, comprising 61 bivalve families (N = 2259), dominated by Mytilidae (29% of bivalves), Veneridae (14%), Ostreidae (8%), Unionidae (7%), and Dreissenidae and Tellinidae (6% each). A total of 2036 predators were studied, with crustaceans the most studied predator group (34% of predators), followed by fishes (24%), molluscs (17%), echinoderms (10%) and birds (6%). The majority of studies (86%) were conducted in marine systems, in part driven by the high commercial value of marine bivalves. Studies in freshwater ecosystems were dominated by non-native bivalves and non-native predator species, which probably reflects the important role of biological invasions affecting freshwater biodiversity. In fact, while 81% of the studied marine bivalve species were native, only 50% of the freshwater species were native to the system. In terms of approach, most studies used predation trials, visual analysis of digested contents and exclusion experiments to assess the effects of predation. These studies reflect that many factors influence bivalve predation depending on the species studied, including (i) species traits (e.g. behaviour, morphology, defence mechanisms), (ii) other biotic interactions (e.g. presence of competitors, parasites or diseases), and (iii) environmental context (e.g. temperature, current velocity, beach exposure, habitat complexity). There is a lack of research on the effects of bivalve predation at the population and community and ecosystem levels (only 7% and 0.5% of studies respectively examined impacts at these levels). At the population level, the available studies demonstrate that predation can decrease bivalve density through consumption or the reduction of recruitment. At the community and ecosystem level, predation can trigger effects that cascade through trophic levels or effects that alter the ecological functions bivalves perform. Given the conservation and commercial importance of many bivalve species, studies of predation should be pursued in the context of global change, particularly climate change, acidification and biological invasions.
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Affiliation(s)
- Alexandra Meira
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
| | - James E Byers
- Odum School of Ecology, University of Georgia, 140 E. Green St, Athens, GA, 30602, USA
| | - Ronaldo Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
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2
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Green ME, Hardesty BD, Deagle BE, Wilcox C. Environmental DNA as a tool to reconstruct catch composition for longline fisheries vessels. Sci Rep 2024; 14:10188. [PMID: 38702492 PMCID: PMC11068744 DOI: 10.1038/s41598-024-60917-7] [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: 12/20/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Global wild-capture fisheries are a large and diverse sector requiring various tools for fisheries-dependant data collection and effective Monitoring, Control and Surveillance (MCS). Here we present a novel protocol to collect eDNA from brine tanks onboard commercial longline vessels to reconstruct catch composition. We collected samples from nine vessels operating out of the Eastern Tuna Billfish Fishery, Australia, validating eDNA results with reliable catch data consisting of seven target and bycatch species. Environmental DNA was highly effective for detecting species retained on vessels without contamination or false positives. For four vessels, logbook data and eDNA were consistent with detections of all species. The remaining vessels detected all species except for rare catches of short-billed spearfish (Tetrapturus angustirostris). Similarities between rank abundance distributions of catch and eDNA reads were observed with logbook data mirrored when eDNA sequences were organised into rank order abundance. The method was effective at identifying highly abundant taxa retained in brine tanks- tuna (Thunnus spp.), swordfish (Xiphias gladius), marlin (Kajijia audax), and Atlantic Pomfret (Brama brama). Further research is required to validate how eDNA and other molecular monitoring tools can be scaled and applied to provide solutions for monitoring challenges in the fisheries sector.
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Affiliation(s)
- M E Green
- Institute for Marine and Antactic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
| | - B D Hardesty
- CSIRO Environment, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - B E Deagle
- CSIRO Australian National Fish Collection, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - C Wilcox
- Wilco Analytics, 93 Carlton Beach Road, Dodges Ferry, TAS, 7173, Australia
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3
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Urquía DO, Anslan S, Asadobay P, Moreira‐Mendieta A, Vences M, Chaves JA, Páez‐Rosas D. DNA-metabarcoding supports trophic flexibility and reveals new prey species for the Galapagos sea lion. Ecol Evol 2024; 14:e10921. [PMID: 38435015 PMCID: PMC10905234 DOI: 10.1002/ece3.10921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Tropical ecosystems are challenging for pinnipeds due to fluctuating food availability. According to previous research, the Galapagos sea lion (GSL, Zalophus wollebaeki) adopts trophic flexibility to face such conditions. However, this hypothesis comes from studies using traditional methods (hard-parts analysis of scat and isotopic analysis from tissue). We studied the diet of five rookeries in the southeastern Galapagos bioregion (which harbors the highest GSL density), via DNA-metabarcoding of scat samples. The DNA-metabarcoding approach may identify consumed prey with a higher taxonomic resolution than isotopic analysis, while not depending on hard-parts remaining through digestion. Our study included five different rookeries to look for evidence of trophic flexibility at the bioregional level. We detected 98 prey OTUs (124 scats), mostly assigned to bony-fish taxa; we identified novel prey items, including a shark, rays, and several deep-sea fish. Our data supported the trophic flexibility of GSL throughout the studied bioregion since different individuals from the same rookery consumed prey coming from different habitats and trophic levels. Significant diet differentiations were found among rookeries, particularly between Punta Pitt and Santa Fe. Punta Pitt rookery, with a more pronounced bathymetry and lower productivity, was distinguished by a high trophic level and consumption of a high proportion of deep-sea prey; meanwhile, Santa Fe, located in more productive, shallow waters over the shelf, consumed a high proportion of epipelagic planktivorous fish. Geographic location and heterogeneous bathymetry of El Malecon, Española, and Floreana rookeries would allow the animals therein to access both, epipelagic prey over the shelf, and deep-sea prey out of the shelf; this would lead to a higher prey richness and diet variability there. These findings provide evidence of GSL adopting a trophic flexibility to tune their diets to different ecological contexts. This strategy would be crucial for this endangered species to overcome the challenges faced in a habitat with fluctuating foraging conditions.
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Affiliation(s)
- Diego O. Urquía
- Maestría en Ecología Tropical y Conservación, Universidad San Francisco de Quito USFQQuitoEcuador
- Galapagos Science Center, Universidad San Francisco de Quito USFQIslas GalápagosEcuador
| | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
- Deptartment of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Pacarina Asadobay
- Galapagos Science Center, Universidad San Francisco de Quito USFQIslas GalápagosEcuador
| | - Andrés Moreira‐Mendieta
- Maestría en Ecología Tropical y Conservación, Universidad San Francisco de Quito USFQQuitoEcuador
- Galapagos Science Center, Universidad San Francisco de Quito USFQIslas GalápagosEcuador
| | - Miguel Vences
- Zoological Institute, Technische Universität BraunschweigBraunschweigGermany
| | - Jaime A. Chaves
- Galapagos Science Center, Universidad San Francisco de Quito USFQIslas GalápagosEcuador
- Department of BiologySan Francisco State UniversitySan FranciscoCaliforniaUSA
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
| | - Diego Páez‐Rosas
- Galapagos Science Center, Universidad San Francisco de Quito USFQIslas GalápagosEcuador
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
- Dirección Parque Nacional Galápagos, Unidad Técnica Operativa San CristóbalIslas GalápagosEcuador
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Saenz-Agudelo P, Ramirez P, Beldade R, Campoy AN, Garmendia V, Search FV, Fernández M, Wieters EA, Navarrete SA, Landaeta MF, Pérez-Matus A. Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats. Ecol Evol 2024; 14:e10999. [PMID: 38390005 PMCID: PMC10881902 DOI: 10.1002/ece3.10999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.
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Affiliation(s)
- Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Paula Ramirez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Ricardo Beldade
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Ana N Campoy
- Center of Marine Sciences (CCMAR-CIMAR) University of the Algarve Faro Portugal
| | - Vladimir Garmendia
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Francesca V Search
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Miriam Fernández
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Evie A Wieters
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Sergio A Navarrete
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
- Center for Applied Ecology and Sustainability (CAPES) and Coastal Socio-Ecological Millennium Institute (SECOS) Pontificia Universidad Católica de Chile Santiago Chile
- Center for Oceanographic Research COASTAL-COASTAL Universidad de Concepción Concepción Chile
| | - Mauricio F Landaeta
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Laboratorio de Ictiología e Interacciones Biofísicas (LABITI) Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso Valparaíso Chile
| | - Alejandro Pérez-Matus
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
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Alexander JB, Marnane MJ, Elsdon TS, Bunce M, Sitaworawet P, Songploy S, Chaiyakul S, Harvey ES. Using environmental DNA to better inform decision making around decommissioning alternatives for offshore oil and gas infrastructure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165991. [PMID: 37536600 DOI: 10.1016/j.scitotenv.2023.165991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Artificial reefs are being utilised globally to aid in natural resource management, conservation, restoration or the creation of unique marine habitats. There is discussion around the optimal construction materials and designs for artificial reefs, the influences these have on biological communities, and the resulting ecological and social benefits. This discussion also includes the ecological value of repurposed marine infrastructure, such as decommissioned oil and gas platforms. Platforms often have an operational life spanning multiple decades, over which time they can develop extensive and unique community assemblages. The creation of artificial reefs by repurposing oil and gas platforms can have ecological, economic and sociological merit. However, with >12,000 platforms requiring decommissioning globally, there is the need for holistic assessment of biological communities associated with these platforms to inform the potential outcomes of different decommissioning options. We use environmental DNA metabarcoding (eDNA) of water, bio-foul and sediment samples to census broad eukaryotic diversity at eight platforms in the Gulf of Thailand (GoT) and five nearby soft sediment habitat locations. We sampled three target depths at sites (shallow, mid, deep) and detected 430 taxa at platforms, with higher diversity in shallow (near-surface) samples (313 taxa), compared to mid (30 m collection depth; 261 taxa) and deep (50 m; 273 taxa). Three percent of taxa were shared among all depths at platforms with distinct assembles at each depth. Introduced species are an ongoing risk for platforms, however the eDNA detected no known introduced species. While the eDNA data provide broad taxon coverage and significant assemblage patterns, ongoing sampling innovation, assay design and local reference material still require development to obtain the maximum benefit of the technique. This study highlights the versatility and scalability of eDNA metabarcoding to holistically census marine infrastructure and inform the management and potential conservation of extant communities.
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Affiliation(s)
- Jason B Alexander
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | | | - Travis S Elsdon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia; Chevron Technical Center, Perth, Western Australia, Australia
| | - Michael Bunce
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia; Department of Conservation, New Zealand
| | | | - Se Songploy
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Sarin Chaiyakul
- Chevron Thailand Exploration and Production, Bangkok, Thailand
| | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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6
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Papaioannou C, Geladakis G, Kommata V, Batargias C, Lagoumintzis G. Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding. TOXICS 2023; 11:903. [PMID: 37999555 PMCID: PMC10675236 DOI: 10.3390/toxics11110903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023]
Abstract
Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.
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Affiliation(s)
- Charikleia Papaioannou
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - George Geladakis
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Vasiliki Kommata
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Costas Batargias
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
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7
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Tang K, Wang Y, Wu M, Wang S, Fu C, Zhang Z, Fu Y. Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird. Curr Zool 2023; 69:501-513. [PMID: 37637316 PMCID: PMC10449430 DOI: 10.1093/cz/zoac071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/02/2022] [Indexed: 08/29/2023] Open
Abstract
Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management. The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China. Existing information on the diet of this species is biased and fragmented owing to traditional observation methods. Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year. In this study, a dietary analysis was performed on 60 fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across 3 critical periods of adult life history (breeding, postbreeding wandering, and overwintering). Preys from the dipteran order, followed by the lepidopteran and araneaen spp., were the predominant, animal-derived foods. Symplocos, Rubus, Celastrus, Holboellia, and Actinidia spp. supply a large abundance of fruits and seeds for this omnivorous bird. Substantial temporal dietary changes among the 3 periods and a general shift toward lower dietary diversity during the breeding season were observed, suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs. Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora (the plant taxa that can generate berries and seeds, such as Symplocos, Rubus, Celastrus, and Holboellia, which are likely of conservation interest) to achieve full life-cycle conservation.
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Affiliation(s)
- Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Yufeng Wang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Mengling Wu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Shufang Wang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Changkun Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yiqiang Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
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Hoban ML, Bunce M, Bowen BW. Plumbing the depths with environmental DNA (eDNA): Metabarcoding reveals biodiversity zonation at 45-60 m on mesophotic coral reefs. Mol Ecol 2023; 32:5590-5608. [PMID: 37728237 DOI: 10.1111/mec.17140] [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: 04/15/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023]
Abstract
Mesophotic coral ecosystems (MCEs) are tropical reefs found at depths of ~30-150 m, below the region most heavily impacted by heat stress and other disturbances. Hence, MCEs may serve as potential refugia for threatened shallow reefs, but they also harbour depth-endemic fauna distinct from shallow reefs. Previous studies have characterized biodiversity patterns along depth gradients, but focussed primarily on conspicuous taxa (fishes, corals, etc.). Environmental DNA (eDNA) metabarcoding offers a more holistic approach to assess biodiversity patterns across the tree of life. Here, we use three metabarcoding assays targeting fishes (16S rRNA), eukaryotes (18S rDNA) and metazoans (COI) to assess biodiversity change from the surface to ~90 m depth across 15-m intervals at three sites within the Hawaiian Archipelago. We observed significant community differences between most depth zones, with distinct zonation centred at 45-60 m for eukaryotes and metazoans, but not for fishes. This finding may be attributable to the higher mobility of reef fishes, although methodological limitations are likely a contributing factor. The possibility for MCEs to serve as refugia is not excluded for fishes, but invertebrate communities >45 m are distinct, indicating limited connectivity for the majority of reef fauna. This study provides a new approach for surveying biodiversity on MCEs, revealing patterns in a much broader context than the limited-taxon studies that comprise the bulk of our present knowledge.
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Affiliation(s)
- Mykle L Hoban
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
| | - Michael Bunce
- Department of Conservation, Wellington, New Zealand
- Trace and Environmental DNA Laboratory, Curtin University, Perth, Western Australia, Australia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
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Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162322. [PMID: 36801404 DOI: 10.1016/j.scitotenv.2023.162322] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
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Affiliation(s)
- Miwa Takahashi
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia.
| | - Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia.
| | - Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mieke van der Heyde
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew J Heydenrych
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Jarman Laboratory, Indian Ocean Marine Research Centre, School of Biological Sciences, University of Western Australia, Australia
| | - David J Juszkiewicz
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Kathryn L Dawkins
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Cindy Bessey
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Joshua P Newton
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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10
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Drake LE, Cuff JP, Bedmar S, McDonald R, Symondson WOC, Chadwick EA. Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters ( Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains. Ecol Evol 2023; 13:e10038. [PMID: 37181211 PMCID: PMC10170393 DOI: 10.1002/ece3.10038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space, therefore, provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled feces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analyses of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.
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Affiliation(s)
| | - Jordan P. Cuff
- School of BiosciencesCardiff UniversityCardiffUK
- School of Natural and Environmental SciencesNewcastle UniversityNewcastleUK
- Rothamsted Insect Survey, Rothamsted ResearchHarpendenUK
| | - Sergio Bedmar
- School of BiosciencesCardiff UniversityCardiffUK
- Department of Conservation BiologyDoñana Biological Station (EBD‐CSIC)SevillaSpain
| | - Robbie McDonald
- Environment and Sustainability InstituteUniversity of ExeterPenrynUK
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11
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Jeunen GJ, Cane JS, Ferreira S, Strano F, von Ammon U, Cross H, Day R, Hesseltine S, Ellis K, Urban L, Pearson N, Olmedo-Rojas P, Kardailsky A, Gemmell NJ, Lamare M. Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring. Mol Ecol Resour 2023; 23:771-786. [PMID: 36598115 DOI: 10.1111/1755-0998.13754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 11/06/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023]
Abstract
Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems are monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for active filtration are required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies to investigate the similarity between aquatic and filter-feeder eDNA signals are essential. Here, we investigated the differences among four eDNA sources (water; bivalve gill-tissue; sponges; and ethanol in which filter-feeding organisms were stored) along a vertically stratified transect in Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish and vertebrates. Combined, eDNA sources detected 59 vertebrates, while concurrent diver surveys observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was successfully extracted from the ethanol in which sponges were stored, although a reduced number of species were detected. Bivalve gill-tissue dissections, on the other hand, failed to reliably detect eDNA. Overall, our results show that vertebrate eDNA signals obtained from water samples and marine sponges are highly concordant. The strong similarity in eDNA signals demonstrates the potential of marine sponges as an additional tool for eDNA-based marine biodiversity surveys, by enabling the incorporation of larger sample numbers in eDNA surveys, reducing plastic waste, simplifying sample collection, and as a cost-efficient alternative. However, we note the importance to not detrimentally impact marine communities by, for example, nonlethal subsampling, specimen cloning, or using bycatch specimens.
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Affiliation(s)
- Gert-Jan Jeunen
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jasmine S Cane
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,ARC CoE for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Sara Ferreira
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, Kelburn, New Zealand
| | | | - Hugh Cross
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Robert Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sean Hesseltine
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | - Kaleb Ellis
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | - Lara Urban
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Niall Pearson
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | | | - Anya Kardailsky
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miles Lamare
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
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12
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Lee SK, Woo C, Lee EJ, Yamamoto N. Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison. Sci Rep 2022; 12:22271. [PMID: 36564425 PMCID: PMC9789119 DOI: 10.1038/s41598-022-26862-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The Korean water deer (Hydropotes inermis argyropus) is considered a vermin in Korea because it damages crops, but also listed as a vulnerable species on the IUCN's red list. Therefore, it is indispensable to manage them appropriately by understanding the ecology such as food habits. Here, we aimed to apply high-throughput sequencing (HTS), a sensitive and objective method, to investigate the dietary composition of the Korean water deer inhabiting the lowland and forest areas in summer and winter. We targeted the internal transcribed spacer 2 (ITS2) region for plant identification. From a total of 40 fecal samples analyzed, 63 plant genera were identified, with Morus being the most abundant, and some of the plant taxa identified by HTS were detected for the first time as the diets of Korean water deer. By type, woody plants (68.6%) were the most predominant, followed by forbs (7.0%) and graminoids (0.7%). We found that the deer in the forest area ate more woody plants (84.6%) than those in the lowland area (52.7%). It was also found that the type of woody plants that the deer ate changed by season. Overall, our results indicate that the Korean water deer is a browser that is seasonally adaptable and feeds on a wide variety of woody plants. We expect that the results and genetics methods reported here, by parallelly investigating their habitat range and reproductive behavior in the future, will help the management and conservation of the Korean water deer, which is in contradictory situations.
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Affiliation(s)
- Seung-Kyung Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Cheolwoon Woo
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea
| | - Eun Ju Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Naomichi Yamamoto
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Institute of Health and Environment, Seoul National University, Seoul, South Korea
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13
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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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14
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Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 2022; 10:e13790. [PMID: 35959477 PMCID: PMC9359134 DOI: 10.7717/peerj.13790] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.
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Affiliation(s)
- Mykle L. Hoban
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, Hawai‘i, United States of America
| | - Jonathan Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, Hawai‘i, United States of America
| | - Allen G. Collins
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine R. Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Abigail J. Reft
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine E. Bemis
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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15
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DiBattista JD, Fowler AM, Riley IJ, Reader S, Hay A, Parkinson K, Hobbs JPA. The use of environmental DNA to monitor impacted coastal estuaries. MARINE POLLUTION BULLETIN 2022; 181:113860. [PMID: 35779383 DOI: 10.1016/j.marpolbul.2022.113860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.
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Affiliation(s)
- Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia.
| | - Ashley M Fowler
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Indiana J Riley
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Sally Reader
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Amanda Hay
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Kerryn Parkinson
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Jean-Paul A Hobbs
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4069, Australia
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16
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Boyi JO, Heße E, Rohner S, Säurich J, Siebert U, Gilles A, Lehnert K. Deciphering Eurasian otter (
Lutra lutra
L.) and seal (
Phoca vitulina
L.;
Halichoerus grypus
F.) diet: metabarcoding tailored for fresh and saltwater fish species. Mol Ecol 2022; 31:5089-5106. [DOI: 10.1111/mec.16635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Joy Ometere Boyi
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Eileen Heße
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Simon Rohner
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Josefin Säurich
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation Hannover Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Anita Gilles
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Kristina Lehnert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
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17
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Alexander JB, Marnane MJ, Elsdon TS, Bunce M, Songploy S, Sitaworawet P, Harvey ES. Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation. MARINE ENVIRONMENTAL RESEARCH 2022; 179:105692. [PMID: 35785679 DOI: 10.1016/j.marenvres.2022.105692] [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: 12/06/2021] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of biodiversity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column samples, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.
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Affiliation(s)
- Jason B Alexander
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | | | - Travis S Elsdon
- Chevron Technical Center, Perth, Western Australia, Australia
| | - Michael Bunce
- Institute of Environmental Science and Research, New Zealand
| | - Se Songploy
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | | | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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18
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Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary. PLoS One 2022; 17:e0266720. [PMID: 35714082 PMCID: PMC9205523 DOI: 10.1371/journal.pone.0266720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 03/26/2022] [Indexed: 12/21/2022] Open
Abstract
Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.
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19
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Schultz JA, Hebert PDN. Do pseudogenes pose a problem for metabarcoding marine animal communities? Mol Ecol Resour 2022; 22:2897-2914. [PMID: 35700118 DOI: 10.1111/1755-0998.13667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Abstract
Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥ 150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 bp ± 200 bp. Among this total, 75 (24.3 %) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.
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Affiliation(s)
- Jessica A Schultz
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
| | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
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20
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Jeunen GJ, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ. Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.e68575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e. an ichthyological, hydrobiological and eDNA survey, whereby DNA was extracted from 500 ml surface water samples and amplified with two 16S rDNA primer assays targeting the fish and macroinvertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous benthic macroinvertebrates were detected by traditional surveys, while seven NISeDNA signals were picked up, including four fish, one aquatic and two benthic macroinvertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey might be attributed to: (i) preferential amplification of aquatic over benthic macroinvertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximise the probability of early detection of non-native organisms.
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21
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Bessey C, Gao Y, Truong YB, Miller H, Jarman SN, Berry O. Comparison of materials for rapid passive collection of environmental
DNA. Mol Ecol Resour 2022; 22:2559-2572. [PMID: 35570323 PMCID: PMC9544503 DOI: 10.1111/1755-0998.13640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/24/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive and efficient, and requires minimal equipment, making it suited to high‐density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3‐million‐litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibres and 1% chitosan, cotton fibres, hemp fibres, and sponge with either zeolite or active carbon) for intervals between 5 and 1080 min. We show that for most materials, with as little as 5 min of submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 and 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19–32). Using scanning electron microscopy, we visualized biological matter adhering to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. eDNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost‐ and time‐sensitive biological surveys, and where access to equipment is limited.
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Affiliation(s)
- Cindy Bessey
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, 64 Fairway Crawley WA Australia
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
| | - Yuan Gao
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Yen Bach Truong
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
| | - Simon Neil Jarman
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
- University of Western Australia School of Biological Sciences and the UWA Oceans Institute Crawley WA Australia
| | - Oliver Berry
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
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22
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Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour 2022; 22:1231-1246. [PMID: 34551203 PMCID: PMC9293284 DOI: 10.1111/1755-0998.13512] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.
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Affiliation(s)
- Kristine Bohmann
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Vasco Elbrecht
- Department of Environmental Systems ScienceETH ZurichZürichSwitzerland
| | - Christian Carøe
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Iliana Bista
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Tree of LifeWellcome Sanger InstituteHinxtonUK
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- School of Biological SciencesNorwich Research ParkUniversity of East AngliaNorwichUK
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming YunnanChina
| | - Mathew Seymour
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Simon Creer
- Molecular Ecology and Evolution GroupSchool of Natural SciencesBangor UniversityGwyneddUK
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23
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Günther B, Jourdain E, Rubincam L, Karoliussen R, Cox SL, Arnaud Haond S. Feces DNA analyses track the rehabilitation of a free-ranging beluga whale. Sci Rep 2022; 12:6412. [PMID: 35440734 PMCID: PMC9018719 DOI: 10.1038/s41598-022-09285-8] [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: 09/27/2021] [Accepted: 03/08/2022] [Indexed: 01/04/2023] Open
Abstract
Following the sudden appearance, and subsequent efforts to support the survival of a beluga whale (Delphinapterus leucas) speculated to have been previously trained off the coast of Norway, we investigate the animal's ability to readapt to life in the wild. Dietary DNA (dDNA) analysis was used to assess diet throughout this rehabilitation process, and during a return to unassisted foraging and self-feeding. Metabarcoding of feces collected throughout this process, confirmed the diversification of the beluga whale's diet to local prey. These findings are indicative of improved foraging behavior, and the ability of this individual to resume wild foraging following a period of dependency in managed care. New insight of digestion rates, and the time window during which prey detection through dDNA analysis is appropriate was also obtained. Beyond the case study presented here, we demonstrate the power of dDNA analysis as a non-intrusive tool to assess the diet of large mammals and track progress adapting to life in the wild following release from captivity and rehabilitation programs.
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Affiliation(s)
- Babett Günther
- ISEM (Institut des Sciences de l'Evolution), Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France. .,MARBEC (Marine Biodiversity Exploitation and Conservation), Univ Montpellier, CNRS, Ifremer, IRD, Sète, France.
| | | | | | | | - Sam L Cox
- MaREI Centre, Environmental Research Institute, University College Cork, Cork, Ireland.,School of Biological, Earth, and Environmental Sciences, University College Cork, Cork, Ireland
| | - Sophie Arnaud Haond
- MARBEC (Marine Biodiversity Exploitation and Conservation), Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
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24
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Mitchell G, Wilson PJ, Manseau M, Redquest B, Patterson BR, Rutledge LY. DNA metabarcoding of faecal pellets reveals high consumption of yew ( Taxus spp.) by caribou ( Rangifer tarandus) in a lichen-poor environment. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Woodland caribou ( Rangifer tarandus caribou) are threatened in Canada because of the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew ( Taxus spp.) based on relative read abundance (83.68%) with dogwood ( Cornus spp.; 9.67%) and maple ( Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.
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Affiliation(s)
- Greniqueca Mitchell
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Paul J. Wilson
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Micheline Manseau
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
- Landscape Science and Technology Division, Environment and Climate Change Canada, 1125 Colonel By Drive, Ottawa, ON K1S 5R1, Canada
| | - Bridgett Redquest
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources and Forestry, Trent University, DNA Building, Peterborough, ON K9L 1Z8, Canada
| | - Linda Y. Rutledge
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
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25
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Morrill A, Kaunisto KM, Mlynarek JJ, Sippola E, Vesterinen EJ, Forbes MR. Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets. PeerJ 2021; 9:e12634. [PMID: 35003931 PMCID: PMC8686731 DOI: 10.7717/peerj.12634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Sexes often differ in foraging and diet, which is associated with sex differences in size, trophic morphology, use of habitats, and/or life history tactics. Herein, strikingly similar diets were found for adult sexes of a dragonfly (Leucorrhinia intacta), based on comparing 141 dietary taxa identified from the metabarcoding of mitochondrial DNA archived in feces. Arthropods in > 5% of samples included five species of dipterans, two hemipterans, two spider species and one parasitic mite. The mite was not traditional prey as its presence was likely due to DNA contamination of samples arising through parasitism or possibly via accidental consumption during grooming, and therefore the mite was excluded from diet characterizations. Common prey species were found with statistically indistinguishable frequencies in male and female diets, with one exception of an aphid more often found in male diets, although this pattern was not robust to corrections for multiple statistical tests. While rare prey species were often found in diets of only one sex, instances of this were more frequent in the more oft-sampled females, suggesting sampling artefact. Sexes did not differ in the mean prey species richness in their diets. Overall, sexes showed statistically indistinguishable diets both on a prey species-by-species basis and in terms of multivariate characterizations of diet composition, derived from presence-absence data of prey species analyzed via PERMANOVA and accumulation curves. Males and females may have similar diets by being both opportunistic and generalist predators of arthropods, using the same foraging habitats and having similar sizes and flight agilities. Notably, similarities in diet between sexes occur alongside large interindividual differences in diet, within sexes. Researchers intending on explaining adaptive sex differences in diet should consider characteristics of species whose sexes show similar diets.
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Affiliation(s)
- André Morrill
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | | | | | - Ella Sippola
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Eero J. Vesterinen
- Department of Biology, University of Turku, Turku, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark R. Forbes
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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26
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Klunder L, van Bleijswijk JDL, Kleine Schaars L, van der Veer HW, Luttikhuizen PC, Bijleveld AI. Quantification of marine benthic communities with metabarcoding. Mol Ecol Resour 2021; 22:1043-1054. [PMID: 34687591 PMCID: PMC9298412 DOI: 10.1111/1755-0998.13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023]
Abstract
DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomass and abundance from molecular approaches with those from the traditional morphological approach. Abundance and biomass were quantified from 126 samples of benthic intertidal mudflat using traditional morphological approaches and compared with frequency of occurrence and relative read abundance estimates from a molecular approach. A relationship between biomass and relative read abundance was found for two widely dispersed annelid taxa (Pygospio and Scoloplos). None of the other taxons, however, showed such a relationship. We discuss how quantification of abundance and biomass using molecular approaches are hampered by the ecology of DNA i.e. all the processes that determine the amount of DNA in the environment, including the ecology of the benthic species as well as the compositional nature of sequencing data.
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Affiliation(s)
- Lise Klunder
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands.,Marine Evolution and Conservation, Groningen Institute of Life Sciences, University of Groningen, CC Groningen, The Netherlands
| | - Judith D L van Bleijswijk
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Loran Kleine Schaars
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Henk W van der Veer
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Pieternella C Luttikhuizen
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Allert I Bijleveld
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
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27
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Collins RA, Trauzzi G, Maltby KM, Gibson TI, Ratcliffe FC, Hallam J, Rainbird S, Maclaine J, Henderson PA, Sims DW, Mariani S, Genner MJ. Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes. JOURNAL OF FISH BIOLOGY 2021; 99:1446-1454. [PMID: 34269417 DOI: 10.1111/jfb.14852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib.
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Affiliation(s)
- Rupert A Collins
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Giulia Trauzzi
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Katherine M Maltby
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | - Thomas I Gibson
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University School of Natural Sciences, Environment Centre Wales, Bangor, UK
| | | | - Jane Hallam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sophie Rainbird
- Marine Biological Association of the United Kingdom, Plymouth, UK
| | - James Maclaine
- Department of Life Sciences, The Natural History Museum, London, UK
| | | | - David W Sims
- Marine Biological Association of the United Kingdom, Plymouth, UK
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton, UK
| | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, UK
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK
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28
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Lazic T, Pierri C, Corriero G, Balech B, Cardone F, Deflorio M, Fosso B, Gissi C, Marzano M, Nonnis Marzano F, Pesole G, Santamaria M, Gristina M. Evaluating the Efficiency of DNA Metabarcoding to Analyze the Diet of Hippocampus guttulatus (Teleostea: Syngnathidae). Life (Basel) 2021; 11:life11100998. [PMID: 34685370 PMCID: PMC8540156 DOI: 10.3390/life11100998] [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: 08/31/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022] Open
Abstract
Seahorses are considered a flagship species for conservation efforts and due to their conservation status, improving knowledge on their dietary composition while applying a non-invasive approach, could be useful. Using Hippocampus guttulatus as a case study, the present study represents pioneering research into investigating the diet of seahorses by NGS-based DNA metabarcoding of fecal samples. The study developed and tested the protocol for fecal DNA metabarcoding during the feeding trials where captive seahorses were fed on a diet of known composition; the process was subsequently applied on fecal samples collected from wild individuals. The analysis of samples collected during the feeding trials indicated the reliability of the applied molecular approach by allowing the characterization of the effectively ingested prey. In the field study, among detected prey species, results revealed that the majority of the seahorse samples contained taxa such as Amphipoda, Decapoda, Isopoda, and Calanoida, while less common prey taxa were Gastropoda and Polyplacophora. As only a small amount of starting fecal material is needed and the sampling procedure is neither invasive nor lethal. The present study indicates DNA metabarcoding as useful for investigating seahorse diet and could help define management and conservation actions.
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Affiliation(s)
- Tamara Lazic
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
| | - Cataldo Pierri
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
- Correspondence:
| | - Giuseppe Corriero
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
| | - Bachir Balech
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Frine Cardone
- Department of Integrated Marine Ecology, Zoological Station Anton Dohrn, 80127 Naples, Italy;
| | - Michele Deflorio
- Department of Veterinary Medicine, University of Bari, 70125 Bari, Italy;
| | - Bruno Fosso
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Carmela Gissi
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Marinella Marzano
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy;
| | - Graziano Pesole
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Monica Santamaria
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Michele Gristina
- Institute of Anthropic Impacts and Sustainability in Marine Environment (IAS), National Council of Research (CNR), 90100 Palermo, Italy;
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29
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Secondary predation constrains DNA-based diet reconstruction in two threatened shark species. Sci Rep 2021; 11:18350. [PMID: 34526519 PMCID: PMC8443726 DOI: 10.1038/s41598-021-96856-w] [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: 04/26/2021] [Accepted: 08/04/2021] [Indexed: 02/08/2023] Open
Abstract
Increasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards > 35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use and feeding ecologies is pivotal, especially among those species with wide-ranging distributions. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (Carcharhinus limbatus; globally classified as Near Threatened) and great hammerhead (Sphyrna mokarran; Critically Endangered). We opportunistically sampled the digestive tracts of these two species (and also any whole prey; termed the 'Russian-doll' approach), caught in bather-protection gillnets off northern New South Wales, to investigate the capacity for DNA metabarcoding to simultaneously determine predator and prey regional feeding ecologies. While sample sizes were small, S. mokkaran fed predominantly on stingrays and skates (Myliobatiformes and Rajiformes), but also teleosts, while C. limbatus mostly consumed teleosts. Metabarcoding assays showed extensive intermixing of taxa from the digestive tracts of predators and their whole prey, likely via the predator's stomach chyme, negating the opportunity to distinguish between primary and secondary predation. This Russian-doll effect requires further investigation in DNA metabarcoding studies focussing on dietary preferences and implies that any outcomes will need to be interpreted concomitant with traditional visual approaches.
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30
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de Melo AA, Nunes R, Telles MPDC. Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00507-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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31
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Liu Y, Xu C, Sun Y, Chen X, Dong W, Yang X, Zhou S. Method for quick DNA barcode reference library construction. Ecol Evol 2021; 11:11627-11638. [PMID: 34522329 PMCID: PMC8427591 DOI: 10.1002/ece3.7788] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
DNA barcoding has become one of the most important techniques in plant species identification. Successful application of this technology is dependent on the availability of reference database of high species coverage. Unfortunately, there are experimental and data processing challenges to construct such a library within a short time. Here, we present our solutions to these challenges. We sequenced six conventional DNA barcode fragments (ITS1, ITS2, matK1, matK2, rbcL1, and rbcL2) of 380 flowering plants on next-generation sequencing (NGS) platforms (Illumina Hiseq 2500 and Ion Torrent S5) and the Sanger sequencing platform. After comparing the sequencing depths, read lengths, base qualities, and base accuracies, we conclude that Illumina Hiseq2500 PE250 run is suitable for conventional DNA barcoding. We developed a new "Cotu" method to create consensus sequences from NGS reads for longer output sequences and more reliable bases than the other three methods. Step-by-step instructions to our method are provided. By using high-throughput machines (PCR and NGS), labeling PCR, and the Cotu method, it is possible to significantly reduce the cost and labor investments for DNA barcoding. A regional or even global DNA barcoding reference library with high species coverage is likely to be constructed in a few years.
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Affiliation(s)
- Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Yuzhe Sun
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xun Chen
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Landscape ArchitectureNortheast Forestry UniversityHarbinChina
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- Laboratory of Systematic Evolution and Biogeography of Woody PlantsSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Xueying Yang
- National Engineering Laboratory for Forensic ScienceKey Laboratory of Forensic GeneticsInstitute of Forensic ScienceMinistry of Public SecurityBeijingChina
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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32
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
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Appleyard SA, Maher S, Pogonoski JJ, Bent SJ, Chua XY, McGrath A. Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches. JOURNAL OF FISH BIOLOGY 2021; 98:1421-1432. [PMID: 33484178 DOI: 10.1111/jfb.14687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Natural history collections are repositories of biodiversity and are potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic and forensic purposes. Specimens in fish collections are preserved using a combination of methods with many fixed in formalin and then preserved in ethanol for long-term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared the DNA barcoding and identification success for frozen and formalin-fixed tissues obtained from specimens in the CSIRO Australian National Fish Collection. They studied 230 samples from fishes (consisting of >160 fish species). An optimized formalin-fixed, paraffin-embedded DNA extraction method resulted in usable DNA from degraded tissues. Four mini barcoding assays of the mitochondrial DNA (mtDNA) were characterized with Sanger and Illumina amplicon sequencing. In the good quality DNA (without exposure to formalin), up to 88% of the specimens were correctly matched at the species level using the cytochrome oxidase subunit 1 (COI) mini barcodes, whereas up to 58% of the specimens exposed to formalin for less than 8 weeks were correctly identified to species. In contrast, 16S primers provided higher amplification success with formalin-exposed tissues, although the COI gene was more successful for identification. Importantly, the authors found that DNA of a certain size and quality can be amplified and sequenced despite exposure to formalin, and Illumina sequencing provided them with greater power of resolution for taxa identification even when there was little DNA present. Overall, within parameter constraints, this study highlights the possibilities of recovering DNA barcodes for identification from formalin-fixed fish specimens, and the authors provide guidelines for when successful identification could be expected.
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Affiliation(s)
- Sharon A Appleyard
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Safia Maher
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - John J Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Stephen J Bent
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
| | - Xin-Yi Chua
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annette McGrath
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
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35
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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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36
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Bessey C, Neil Jarman S, Simpson T, Miller H, Stewart T, Kenneth Keesing J, Berry O. Passive eDNA collection enhances aquatic biodiversity analysis. Commun Biol 2021; 4:236. [PMID: 33619330 PMCID: PMC7900116 DOI: 10.1038/s42003-021-01760-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/25/2021] [Indexed: 01/28/2023] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more samples than can be practically collected with current filtration methods. Here we demonstrate how eDNA can be passively collected in both tropical and temperate marine systems by directly submerging filter membranes (positively charged nylon and non-charged cellulose ester) in the water column. Using a universal fish metabarcoding assay, we show that passive eDNA collection can detect fish as effectively as active eDNA filtration methods in temperate systems and can also provide similar estimates of total fish biodiversity. Furthermore, passive eDNA collection enables greater levels of biological sampling, which increases the range of ecological questions that eDNA metabarcoding can address. Bessey et al. present a method of passive eDNA collection from marine aquatic systems. This approach enables lower cost, high throughput sampling of aquatic environments and demonstrably collects high levels of eDNA for biodiversity studies.
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Affiliation(s)
- Cindy Bessey
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, WA, Australia. .,Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia. .,UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia.
| | - Simon Neil Jarman
- UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia.,School of Biological Sciences and the UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia
| | - Tiffany Simpson
- eDNA Frontiers, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
| | - Todd Stewart
- Bass Marine Pty Ltd, Port Denison, WA, Australia
| | - John Kenneth Keesing
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, WA, Australia.,UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia
| | - Oliver Berry
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
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37
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Traugott M, Thalinger B, Wallinger C, Sint D. Fish as predators and prey: DNA-based assessment of their role in food webs. JOURNAL OF FISH BIOLOGY 2021; 98:367-382. [PMID: 32441321 PMCID: PMC7891366 DOI: 10.1111/jfb.14400] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/26/2020] [Accepted: 05/20/2020] [Indexed: 05/04/2023]
Abstract
Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.
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Affiliation(s)
- Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Bettina Thalinger
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
- Centre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Corinna Wallinger
- Institute of Interdisciplinary Mountain Research, Austrian Academy of ScienceInnsbruckAustria
| | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
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38
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West K, Travers MJ, Stat M, Harvey ES, Richards ZT, DiBattista JD, Newman SJ, Harry A, Skepper CL, Heydenrych M, Bunce M. Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13228] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Katrina West
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Michael J. Travers
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Michael Stat
- School of Environmental and Life Sciences The University of Newcastle Callaghan NSW Australia
| | - Euan S. Harvey
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Joseph D. DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Australian Museum Australian Museum Research Institute Sydney NSW Australia
| | - Stephen J. Newman
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Alastair Harry
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Craig L. Skepper
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Matthew Heydenrych
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Environmental Protection Authority Wellington New Zealand
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39
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Ladin ZS, Ferrell B, Dums JT, Moore RM, Levia DF, Shriver WG, D'Amico V, Trammell TLE, Setubal JC, Wommack KE. Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems. Sci Rep 2021; 11:1629. [PMID: 33452291 PMCID: PMC7811025 DOI: 10.1038/s41598-020-80602-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.
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Affiliation(s)
- Zachary S Ladin
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA.
| | - Barbra Ferrell
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Jacob T Dums
- Biotechnology Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ryan M Moore
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Delphis F Levia
- Department of Entomology and Wildlife Ecology, University of Delaware, 250 Townsend Hall, Newark, DE, 19716, USA
| | - W Gregory Shriver
- Departments of Geography and Spatial Sciences and Plant and Soil Sciences, University of Delaware, 216C Pearson Hall, Newark, DE, 19716, USA
| | - Vincent D'Amico
- US Forest Service, Northern Research Station, Newark, DE, USA
| | - Tara L E Trammell
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
| | - João Carlos Setubal
- Instituto de Química, University of Sao Paulo, São Paulo, SP, 05508-000, Brazil
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
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40
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Tang K, Xie F, Liu H, Pu Y, Chen D, Qin B, Fu C, Wang Q, Chen S, Guo K. DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew ( Anourosorex squamipes) with potential implications for evaluating crop impacts. Ecol Evol 2021; 11:376-389. [PMID: 33437436 PMCID: PMC7790647 DOI: 10.1002/ece3.7055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/11/2020] [Accepted: 10/25/2020] [Indexed: 01/02/2023] Open
Abstract
Diet analysis of potential small mammals pest species is important for understanding feeding ecology and evaluating their impact on crops and stored foods. Chinese mole shrew (Anourosorex squamipes), distributed in Southwest China, has previously been reported as a farmland pest. Effective population management of this species requires a better understanding of its diet, which can be difficult to determine with high taxonomic resolution using conventional microhistological methods. In this study, we used two DNA metabarcoding assays to identify 38 animal species and 65 plant genera from shrew stomach contents, which suggest that A. squamipes is an omnivorous generalist. Earthworms are the most prevalent (>90%) and abundant (>80%) food items in the diverse diet of A. squamipes. Species of the Fabaceae (frequency of occurrence [FO]: 88%; such as peanuts) and Poaceae (FO: 71%; such as rice) families were the most common plant foods identified in the diet of A. squamipes. Additionally, we found a seasonal decrease in the diversity and abundance of invertebrate foods from spring and summer to winter. Chinese mole shrew has a diverse and flexible diet throughout the year to adapt to seasonal variations in food availability, contributing to its survival even when food resources are limited. This study provides a higher resolution identification of the diet of A. squamipes than has been previously described and is valuable for understanding shrew feeding ecology as well as evaluating possible species impacts on crops.
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Affiliation(s)
- Ke‐yi Tang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Fei Xie
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Hong‐yi Liu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Ying‐ting Pu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Dan Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Bo‐xin Qin
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Chang‐kun Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Qiong Wang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Shun‐de Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Ke‐ji Guo
- Central South Inventory and Planning Institute of National Forestry and Grassland AdministrationChangshaChina
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41
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Sigsgaard EE, Olsen K, Hansen MDD, Hansen OLP, Høye TT, Svenning JC, Thomsen PF. Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages. Mol Ecol 2020; 30:3374-3389. [PMID: 33205529 PMCID: PMC8359373 DOI: 10.1111/mec.15734] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 11/02/2020] [Indexed: 01/03/2023]
Abstract
Insects and other terrestrial invertebrates are declining in species richness and abundance. This includes the invertebrates associated with herbivore dung, which have been negatively affected by grazing abandonment and the progressive loss of large herbivores since the Late Pleistocene. Importantly, traditional monitoring of these invertebrates is time‐consuming and requires considerable taxonomic expertise, which is becoming increasingly scarce. In this study, we investigated the potential of environmental DNA (eDNA) metabarcoding of cow dung samples for biomonitoring of dung‐associated invertebrates. From eight cowpats we recovered eDNA from 12 orders, 29 families, and at least 54 species of invertebrates (mostly insects), representing several functional groups. Furthermore, species compositions differed between the three sampled habitats of dry grassland, meadow, and forest. These differences were in accordance with the species’ ecology; for instance, several species known to be associated with humid conditions or lower temperatures were found only in the forest habitat. We discuss potential caveats of the method, as well as directions for future study and perspectives for implementation in research and monitoring.
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Affiliation(s)
| | - Kent Olsen
- Natural History Museum Aarhus, Aarhus, Denmark
| | | | - Oskar Liset Pryds Hansen
- Department of Biology, Aarhus University, Aarhus, Denmark.,Natural History Museum Aarhus, Aarhus, Denmark
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42
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West KM, Richards ZT, Harvey ES, Susac R, Grealy A, Bunce M. Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia. Sci Rep 2020; 10:21479. [PMID: 33293686 PMCID: PMC7722930 DOI: 10.1038/s41598-020-78525-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.
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Affiliation(s)
- Katrina M West
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Euan S Harvey
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Robert Susac
- Western Australian Speleological Group, Nedlands, WA, 6909, Australia
| | - Alicia Grealy
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011, New Zealand
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43
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Harper LR, Watson HV, Donnelly R, Hampshire R, Sayer CD, Breithaupt T, Hänfling B. Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.56087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the UK, the native European otter (Lutra lutra) and invasive American mink (Neovison vison) have experienced concurrent declines and expansions. Currently, the otter is recovering from persecution and waterway pollution, whereas the mink is in decline due to population control and probable interspecific interaction with the otter. We explored the potential of DNA metabarcoding for investigating diet and niche partitioning between these mustelids. Otter spraints (n = 171) and mink scats (n = 19) collected from three sites (Malham Tarn, River Hull and River Glaven) in northern and eastern England were screened for vertebrates using high-throughput sequencing. Otter diet mainly comprised aquatic fishes (81.0%) and amphibians (12.7%), whereas mink diet predominantly consisted of terrestrial birds (55.9%) and mammals (39.6%). The mink used a lower proportion (20%) of available prey (n = 40 taxa) than the otter and low niche overlap (0.267) was observed between these mustelids. Prey taxon richness of mink scats was lower than otter spraints and beta diversity of prey communities was driven by taxon turnover (i.e. the otter and mink consumed different prey taxa). Considering otter diet only, prey taxon richness was higher in spraints from the River Hull catchment and beta diversity of prey communities was driven by taxon turnover (i.e. the otter consumed different prey taxa at each site). Studies using morphological faecal analysis may misidentify the predator as well as prey items. Faecal DNA metabarcoding can resolve these issues and provide more accurate and detailed dietary information. When scaled up across multiple habitat types, DNA metabarcoding should greatly improve future understanding of resource use and niche overlap between the otter and mink.
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44
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Havmøller RW, Jacobsen NS, Havmøller LW, Rovero F, Scharff N, Bohmann K. DNA metabarcoding reveals that African leopard diet varies between habitats. Afr J Ecol 2020. [DOI: 10.1111/aje.12817] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rasmus Worsøe Havmøller
- Section for Evolutionary Genomics Globe Institute University of Copenhagen Copenhagen K Denmark
- Department of Anthropology University of California Davis CA USA
- Center for Macroecology, Evolution and Climate Globe Institute University of Copenhagen Copenhagen K Denmark
- Natural History Museum of Denmark, Research and CollectionsUniversity of Copenhagen Copenhagen Denmark
| | - Nis Sand Jacobsen
- National Institute of Aquatic Resources Technical University of Denmark Lyngby Denmark
| | - Linnea Worsøe Havmøller
- Natural History Museum of Denmark, Research and CollectionsUniversity of Copenhagen Copenhagen Denmark
| | - Francesco Rovero
- Department of Biology University of Florence Sesto Fiorentino Italy
- Section for Tropical Biodiversity MUSE‐Museo delle Scienze Trento Italy
| | - Nikolaj Scharff
- Natural History Museum of Denmark, Research and CollectionsUniversity of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute University of Copenhagen Copenhagen K Denmark
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45
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Williams KM, Barkdull M, Fahmy M, Hekkala E, Siddall ME, Kvist S. Caught red handed: iDNA points to wild source for CITES-protected contraband leeches. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01419-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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46
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Uiterwaal SF, DeLong JP. Using patterns in prey DNA digestion rates to quantify predator diets. Mol Ecol Resour 2020; 20:1723-1732. [PMID: 32688451 DOI: 10.1111/1755-0998.13231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/01/2020] [Accepted: 07/10/2020] [Indexed: 11/26/2022]
Abstract
Dietary metabarcoding-the process of taxonomic identification of food species from DNA in consumer guts or faeces-has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi-quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives for some prey more often than for other prey, we cannot infer relative frequencies of prey in the diet. To correct for this, we can adjust detected prey frequencies using DNA detectability half-lives unique to each predator-prey combination. Because the feeding experiments required to deduce these half-lives are time- and resource-intensive, our ability to weight the frequency of observations using their detectability has thus far been limited to systems with just a few prey. Here, we present a meta-analysis of 24 spider prey DNA half-lives and show that these half-lives are predictable given predator and prey mass, predator family, digestion temperature and DNA amplicon length. We further provide a new technique for weighting observations with half-lives, which allows not just for the ranking of prey in the diet, but reveals the proportion of the diet each prey comprises. Lastly, we apply this method to published dietary metabarcoding data to calculate half-lives and proportion of the predator's diet for 35 prey families, demonstrating that this technique can generate improved understanding of diets in real, diverse systems.
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Affiliation(s)
- Stella F Uiterwaal
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - John P DeLong
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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Takahashi M, DiBattista JD, Jarman S, Newman SJ, Wakefield CB, Harvey ES, Bunce M. Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding. Sci Rep 2020; 10:4319. [PMID: 32152406 PMCID: PMC7062689 DOI: 10.1038/s41598-020-60779-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/17/2020] [Indexed: 01/23/2023] Open
Abstract
Lutjanus erythropterus and L. malabaricus are sympatric, sister taxa that are important to fisheries throughout the Indo-Pacific. Their juveniles are morphologically indistinguishable (i.e. cryptic). A DNA metabarcoding dietary study was undertaken to assess the diet composition and partitioning between the juvenile and adult life history stages of these two lutjanids. Major prey taxa were comprised of teleosts and crustaceans for all groups except adult L. erythropterus, which instead consumed soft bodied invertebrates (e.g. tunicates, comb jellies and medusae) as well as teleosts, with crustaceans being notably absent. Diet composition was significantly different among life history stages and species, which may be associated with niche habitat partitioning or differences in mouth morphology within adult life stages. This study provides the first evidence of diet partitioning between cryptic juveniles of overlapping lutjanid species, thus providing new insights into the ecological interactions, habitat associations, and the specialised adaptations required for the coexistence of closely related species. This study has improved our understanding of the differential contributions of the juvenile and adult diets of these sympatric species within food webs. The diet partitioning reported in this study was only revealed by the taxonomic resolution provided by the DNA metabarcoding approach and highlights the potential utility of this method to refine the dietary components of reef fishes more generally.
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Affiliation(s)
- Miwa Takahashi
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.
| | - Joseph D DiBattista
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.,Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia
| | - Simon Jarman
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.,School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia
| | - Corey B Wakefield
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia
| | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Michael Bunce
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.,Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011, New Zealand
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West KM, Stat M, Harvey ES, Skepper CL, DiBattista JD, Richards ZT, Travers MJ, Newman SJ, Bunce M. eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem. Mol Ecol 2020; 29:1069-1086. [PMID: 32045076 DOI: 10.1111/mec.15382] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 01/30/2020] [Accepted: 02/06/2020] [Indexed: 01/10/2023]
Abstract
Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.
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Affiliation(s)
- Katrina M West
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Euan S Harvey
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Craig L Skepper
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Joseph D DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michael J Travers
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Environmental Protection Authority, Wellington, New Zealand
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Huhn M, Madduppa HH, Khair M, Sabrian A, Irawati Y, Anggraini NP, Wilkinson SP, Simpson T, Iwasaki K, Setiamarga DHE, Dias PJ. Keeping up with introduced marine species at a remote biodiversity hotspot: awareness, training and collaboration across different sectors is key. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02126-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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