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Yang C, Du Y, Zeng X, Ni G. Development and Testing of Species-Specific Primers for Detecting the Presence of the Northern Pacific Sea Star (Asterias amurensis) from Environmental DNA. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:215-222. [PMID: 38341825 DOI: 10.1007/s10126-024-10292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/25/2024] [Indexed: 02/13/2024]
Abstract
The starfish Asterias amurensis, a well-known predator of molluscan species in intertidal ecosystems, has caused substantial ecological and economic losses in North China such as offshore Qingdao. Effective monitoring and prevention measures are urged to minimize its negative impacts. Compared with traditional biomonitoring methods, environmental DNA technology has emerged as a powerful and cost-efficient tool for inferring species' presence and abundance. In this study, we developed a pair of species-specific primers (i.e., Ast-F and Ast-R) for the A. amurensis mitochondrial COI gene and tested its utility in amplifying and quantifying the DNA fragments from environmental samples under both laboratory and field conditions. The results of controlled water tank experiments demonstrated that the amount of eDNA released by A. amurensis was positively related to its biomass; after the removal of the starfish, the eDNA degraded significantly in 24 h and remained detectable for 8 days. The number of eDNA copies enriched tended to increase with smaller pore size of filter membrane and larger volume of filtered water. For field tests, we confirmed the validation of our approach in six locations in Qingdao by filtering 1000 ml water per sample with a 0.45-µm pore size filtration. All the amplification products generated a single and bright band via gel electrophoresis, and the quantitative PCR results unveiled significant differences in eDNA copies. This study provided an eDNA-based approach for investigating the distribution and biomass of A. amurensis, which may help to formulate early warning and management strategies in coastal Qingdao and other regions.
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Affiliation(s)
- Chenhu Yang
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China
| | - Yanzhen Du
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China
| | - Xiaoqi Zeng
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Gang Ni
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China.
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2
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Hong H, Deng A, Tang Y, Liu Z. How to identify biofouling species in marine and freshwater. BIOFOULING 2024; 40:130-152. [PMID: 38450626 DOI: 10.1080/08927014.2024.2324008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024]
Abstract
The identification and management of biofouling remain pressing challenges in marine and freshwater ecosystems, with significant implications for environmental sustainability and industrial operations. This comprehensive review synthesizes the current state-of-the-art in biofouling identification technologies, examining eight prominent methodologies: Microscopy Examination, Molecular Biology, Remote Sensing, Community Involvement, Ecological Methods, Artificial Intelligence, Chemical Analysis, and Macro Photography. Each method is evaluated for its respective advantages and disadvantages, considering factors such as precision, scalability, cost, and data quality. Furthermore, the review identifies current obstacles that inhibit the optimal utilization of these technologies, ranging from technical limitations and high operational costs to issues of data inconsistency and subjectivity. Finally, the review posits a future outlook, advocating for the development of integrated, standardized systems that amalgamate the strengths of individual approaches. Such advancement will pave the way for more effective and sustainable strategies for biofouling identification and management.
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Affiliation(s)
- Heting Hong
- Hubei Meteorological Bureau, Wuhan Regional Climate Center, Wuhan, China
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, China
| | - Aijuan Deng
- Hubei Meteorological Bureau, Wuhan Regional Climate Center, Wuhan, China
| | - Yang Tang
- Hubei Meteorological Bureau, Wuhan Regional Climate Center, Wuhan, China
| | - Zhixiong Liu
- Hubei Meteorological Bureau, Wuhan Regional Climate Center, Wuhan, China
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3
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Moutinho J, Carreira-Flores D, Gomes PT, Costa FO, Duarte S. Assessing the Seasonal and Spatial Dynamics of Zooplankton through DNA Metabarcoding in a Temperate Estuary. Animals (Basel) 2023; 13:3876. [PMID: 38136913 PMCID: PMC10740712 DOI: 10.3390/ani13243876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Zooplankton are key components of estuarine trophic networks. However, routine monitoring is hindered by the difficulty of morphology-based identification. DNA-based methods allow us to circumvent some of these hurdles, providing precise species identifications regardless of the taxonomic expertise of the investigator or the developmental stage of the specimens. However, the process is dependent on the completeness of the reference libraries. In this study, we sought to evaluate the potential of DNA metabarcoding to assess the seasonal (summer, autumn, and early spring) and spatial dynamics of zooplankton (four locations spanning ca. 6 km) in the Lima estuary (NW Portugal). Two genetic markers were used: the cytochrome c oxidase subunit I and the V4 hypervariable region of the ribosomal 18S rRNA genes. Overall, 327 species were recovered, and both markers displayed minute overlap (7% were detected with both markers). Species richness, composition, and taxonomic distinctness were majorly influenced by the season, with a declining tendency from summer (highest number of exclusive species, n = 74) to spring. Second to season, the taxa composition was influenced by spatial variation where the most downstream site displayed the highest number of exclusive species, n = 53. A total of 16 non-indigenous species were detected using metabarcoding, but only one (Austrominus modestus) has been documented out in the estuary. In conclusion, both the seasonal and spatial gradients influenced the recovered richness, composition, and taxonomic distinctness, confirming the great aptitude of DNA metabarcoding for providing higher density monitoring and shedding new light on the composition and dynamics of complex zooplankton communities.
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Affiliation(s)
- Jorge Moutinho
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Diego Carreira-Flores
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro T. Gomes
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET—Aquatic Research Network, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (D.C.-F.); (P.T.G.); (F.O.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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4
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Wang Y, Wang Y, Yang Y, Ni G, Li Y, Chen M. Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis. Sci Data 2023; 10:767. [PMID: 37925473 PMCID: PMC10625585 DOI: 10.1038/s41597-023-02688-w] [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: 07/06/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
Asterias amurensis has attracted widespread concern because of its population outbreaks, which has impacted fisheries and aquaculture, as well as disrupting local ecosystems. A high-quality reference genome is necessary to better investigate mechanisms of outbreak and adaptive changes. Combining PacBio HiFi and Hi-C sequencing data, we generated a chromosome-level A. amurensis genome with a size of 491.53 Mb. The contig N50 and scaffold N50 were 8.05 and 23.75 Mb, respectively. The result of BUSCO analysis revealed a completeness score of 98.85%. A total of 16,531 protein-coding genes were predicted in the genome, of which 94.63% were functionally annotated. The high-quality genome assembly resulting from this study will provide a valuable genetic resource for future research on the mechanism of population outbreaks and invasion ecology.
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Affiliation(s)
- Yanlin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yixin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Gang Ni
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yulong Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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Ni J, Pan J, Wang Y, Chen T, Feng X, Li Y, Lin T, Lynch M, Long H, Li W. An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:564-572. [PMID: 38045552 PMCID: PMC10689312 DOI: 10.1007/s42995-023-00182-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/02/2023] [Indexed: 12/05/2023]
Abstract
High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures, greatly promoting biological studies involving large amounts of complex samples, especially those involving environmental and pathogen-monitoring ones. Commercial library preparation kits for amplicon sequencing, which generally require multiple steps, including adapter ligation and indexing, are expensive and time-consuming, especially for applications at a large scale. To overcome these limitations, a "one-step PCR approach" has been previously proposed for constructions of amplicon libraries using long fusion primers. However, efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed. To tackle these, we present an integrative protocol for one-step PCR amplicon library construction (OSPALC). High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples. With this protocol, the amplicon library is constructed through one regular PCR with long primers, and the total cost per DNA/cDNA sample decreases to just 7% of the typical cost via the multi-step PCR approach. Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study. Tools to design primers targeting at any genomic regions are also presented. In principle, OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples, and will facilitate research in numerous fields. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00182-1.
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Affiliation(s)
- Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Tianhao Chen
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Xinshi Feng
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Yichen Li
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47401 USA
- Present Address: SLAC National Accelerator Laboratory, Stanford University, Stanford, 94305 USA
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6
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von Ammon U, Casanovas P, Pochon X, Zirngibl M, Leonard K, Smith A, Chetham J, Milner D, Zaiko A. Harnessing environmental DNA to reveal biogeographical patterns of non-indigenous species for improved co-governance of the marine environment in Aotearoa New Zealand. Sci Rep 2023; 13:17061. [PMID: 37816793 PMCID: PMC10564887 DOI: 10.1038/s41598-023-44258-5] [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: 06/12/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Aotearoa New Zealand's Northern region is a major gateway for the incursion and establishment of non-indigenous species (NIS) populations due to high numbers of recreational and commercial vessels. This region also holds a unique marine ecosystem, home to many taonga (treasured) species of cultural and economic importance. Regular surveillance, eradication plans and public information sharing are undertaken by local communities and governmental organizations to protect these ecosystems from the impact of NIS. Recently, considerable investments went into environmental DNA (eDNA) research, a promising approach for the early detection of NIS for complementing existing biosecurity systems. We applied eDNA metabarcoding for elucidating bioregional patterns of NIS distributions across a gradient from harbors (NIS hotspots) to open seas (spreading areas). Samples were collected during a research cruise sailing across three Aotearoa New Zealand harbors, Waitematā, Whangārei and Pēwhairangi (Bay of Islands), and their adjacent coastal waters. The small-ribosomal subunit (18S rRNA) and mitochondrial cytochrome c oxidase I (COI) genes were screened using the online Pest Alert Tool for automated detection of putative NIS sequences. Using a probabilistic modelling approach, location-dependent occupancies of NIS were investigated and related to the current information on species distribution from biosecurity surveillance programs. This study was collaboratively designed with Māori partners to initiate a model of co-governance within the existing science system.
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Affiliation(s)
| | | | - Xavier Pochon
- Cawthron Institute, Nelson, 7010, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, 6011, New Zealand
| | | | - Kaeden Leonard
- Northland Regional Council, Whangārei, 9021, New Zealand
| | - Aless Smith
- Northland Regional Council, Whangārei, 9021, New Zealand
| | - Juliane Chetham
- Patuharakeke Te Iwi Trust Board, Takahiwai, 0171, New Zealand
| | - Dave Milner
- Patuharakeke Te Iwi Trust Board, Takahiwai, 0171, New Zealand
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, 7010, New Zealand
- Sequench Ltd, Nelson, 7010, New Zealand
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7
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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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8
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DiBattista JD, Liu SYV, De Brauwer M, Wilkinson SP, West K, Koziol A, Bunce M. Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments. PeerJ 2023; 11:e16075. [PMID: 37790632 PMCID: PMC10542274 DOI: 10.7717/peerj.16075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/20/2023] [Indexed: 10/05/2023] Open
Abstract
In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.
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Affiliation(s)
- Joseph D. DiBattista
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Shang Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | | | - Shaun P. Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Katrina West
- CSIRO Australian National Fish Collection, CSIRO, Hobart, TAS, Australia
| | - Adam Koziol
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
- Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Michael Bunce
- Institute of Environmental Science and Research, Kenepuru, Porirua, New Zealand
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9
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Suzzi AL, Huggett MJ, Gaston TF, MacFarlane GR, Alam MR, Gibb J, Stat M. eDNA metabarcoding reveals shifts in sediment eukaryote communities in a metal contaminated estuary. MARINE POLLUTION BULLETIN 2023; 191:114896. [PMID: 37058833 DOI: 10.1016/j.marpolbul.2023.114896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023]
Abstract
Metal contamination is a global issue impacting biodiversity in urbanised estuaries. Traditional methods to assess biodiversity are time consuming, costly and often exclude small or cryptic organisms due to difficulties with morphological identification. Metabarcoding approaches have been increasingly recognised for their utility in monitoring, however studies have focused on freshwater and marine systems despite the ecological significance of estuaries. We targeted estuarine eukaryote communities within the sediments of Australia's largest urbanised estuary, where a history of industrial activity has resulted in a metal contamination gradient. We identified specific eukaryote families with significant correlations with bioavailable metal concentrations, indicating sensitivity or tolerance to specific metals. While polychaete families Terebellidae and Syllidae demonstrated tolerance to the contamination gradient, members of the meio- and microfaunal communities including diatoms, dinoflagellates and nematodes displayed sensitivities. These may have high value as indicators but are frequently missed in traditional surveys due to sampling limitations.
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Affiliation(s)
- Alessandra L Suzzi
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW 2258, Australia.
| | - Megan J Huggett
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Troy F Gaston
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Geoff R MacFarlane
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Md Rushna Alam
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW 2258, Australia; Department of Aquaculture, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh
| | - Jodie Gibb
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Michael Stat
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW 2258, Australia
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10
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Pujari L, Kan J, Xin Y, Zhang G, Noman MA, Nilajkar S, Sun J. Deciphering the diversity and distribution of chromophytic phytoplankton in the Bohai Sea and the Yellow Sea via RuBisCO genes (rbcL). MARINE POLLUTION BULLETIN 2022; 184:114193. [PMID: 36209535 DOI: 10.1016/j.marpolbul.2022.114193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Present study investigated composition and distribution of chromophytic phytoplankton in the Bohai Sea (BS) and the Yellow Sea (YS) by using rbcL genes. Bacillariophyceae, Haptophyceae and Pelagophyceae were the most abundant phytoplankton groups. Distinct phytoplankton communities were observed in the BS and the YS: offshore stations were dominated by bloom forming genera Thalassiosira and Skeletonema, while brown tide-forming species including Chrysochromulina spp. and Aureococcus anophagefferens were commonly found in the nearshore areas. Redundancy analysis showed that phosphate, temperature and silicic acid play key roles in structuring chromophytic phytoplankton, such as phytoplankton at nearshore stations were affected by nutrient runoff from adjacent rivers (Yellow River). Anthropogenic activities in the Bohai Sea and seasonal circulation of ocean currents may also contribute to shaping chromophytic phytoplankton communities. This study provides data support and foundational observations of chromophytic phytoplankton in the BS and the YS, and their responses to environmental gradients and human activities.
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Affiliation(s)
- Laxman Pujari
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China; Business Development Group, National Institute of Oceanography, Goa, India; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, PA, USA
| | - Yehong Xin
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Md Abu Noman
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Sujata Nilajkar
- Biological Oceanography Division, National Institute of Oceanography, Goa, India
| | - Jun Sun
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.
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11
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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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12
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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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13
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Sarkis CM, Hoenig BD, Seney EE, Gaspar SA, Forsman AM. Sea Snacks from DNA Tracks: Using DNA Metabarcoding to Characterize The Diet of Green Turtles (Chelonia Mydas). Integr Comp Biol 2022; 62:223-236. [PMID: 35679089 DOI: 10.1093/icb/icac080] [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: 03/16/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
The green turtle (Chelonia mydas) is a circumglobal species with a wide dietary breadth that varies among regions and life history stages. Comprehensive understanding of foraging ecology over space and time is critical to inform conservation and management of this species and its habitats. Here, we used DNA metabarcoding to test candidate primer sets with 39 gut content homogenates from stranded green turtles (FL, USA) to identify primer sets that maximize detection of food items and specificity of taxonomic classifications. We tested six existing universal primer sets to detect plants, animals, and eukaryotes more broadly (CO1, 18SV1-V3, 18SV4, rbcL, UPA, ITS). The CO1 and 18SV4 primer sets produced the greatest number of dietary amplicon sequence variants (ASVs) and unique taxonomic classifications, and they were the only primer sets to amplify taxa from all three kingdoms relevant to green turtle diet (Animalia, Chromista, and Plantae). Even though the majority of CO1-derived reads were of host origin (>90%), this primer set still produced the largest number of dietary ASVs classified to species among the six primer sets. However, because the CO1 primer set failed to detect both vascular plants and green algae, we do not recommend the use of this primer set on its own to characterize green turtle diet. Instead, our findings support previous research highlighting the utility of using multiple primer sets, specifically targeting CO1 and the V4 region of the 18S gene, as doing so will provide the most comprehensive understanding of green turtle diet. More generally, our results highlight the importance of primer and loci selection and the need to validate primer sets against the study system of interest. The addition of DNA metabarcoding with optimized primer sets to the sea turtle researcher's toolbox will both increase our understanding of foraging ecology and better inform science-based conservation and ecosystem management.
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Affiliation(s)
- Christine M Sarkis
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Brandon D Hoenig
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin E Seney
- Department of Biology, University of Central Florida, Orlando, Florida, USA.,Marine Turtle Research Group, Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Stephanie A Gaspar
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Anna M Forsman
- Department of Biology, University of Central Florida, Orlando, Florida, USA.,Genomics & Bioinformatics Cluster, University of Central Florida, Orlando, Florida, USA
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14
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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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15
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Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA. Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78128] [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
Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.
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16
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Fernandez S, Miller DL, Holman LE, Gittenberger A, Ardura A, Rius M, Mirimin L. Environmental DNA sampling protocols for the surveillance of marine non-indigenous species in Irish coastal waters. MARINE POLLUTION BULLETIN 2021; 172:112893. [PMID: 34464822 DOI: 10.1016/j.marpolbul.2021.112893] [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: 07/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Understanding the spread and distribution of Non-Indigenous Species (NIS) is key when implementing legislation to maintain good ecosystem health. Environmental DNA (eDNA) has shown great potential to detect aquatic organisms in a rapid and cost-effective way, however their applicability to new environments must be validated prior to their implementation. Here, we tested different field sampling methods in combination with eDNA metabarcoding to develop a tool to detect NIS. Large and small volumes of seawater were filtered, in addition to the collection of sediment and horizontal tow net samples at 12 locations across four distinct geographic areas in Ireland. The biggest dissimilarity in the species recovered was found between sediment and town net samples. Tow nets showed to be the most efficient. A total of 357 taxa were identified, including 16 NIS. Fine mesh tow nets were identified as the most cost-efficient for large-scale monitoring and surveillance of NIS.
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Affiliation(s)
- Sara Fernandez
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland.
| | - Dulaney L Miller
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
| | - Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom
| | - Arjan Gittenberger
- GiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, the Netherlands; Department of Marine Zoology, Naturalis Biodiversity Center, Pesthuislaan 7, 2333 BA Leiden, the Netherlands
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom; Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
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17
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Foster R, Peeler E, Bojko J, Clark PF, Morritt D, Roy HE, Stebbing P, Tidbury HJ, Wood LE, Bass D. Pathogens co-transported with invasive non-native aquatic species: implications for risk analysis and legislation. NEOBIOTA 2021. [DOI: 10.3897/neobiota..71358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Invasive Non-Native Species (INNS) can co-transport externally and internally other organisms including viruses, bacteria and other eukaryotes (including metazoan parasites), collectively referred to as the symbiome. These symbiotic organisms include pathogens, a small minority of which are subject to surveillance and regulatory control, but most of which are currently unscrutinized and/or unknown. These putatively pathogenetic symbionts can potentially pose diverse risks to other species, with implications for increased epidemiological risk to agriculture and aquaculture, wildlife/ecosystems, and human health (zoonotic diseases). The risks and impacts arising from co-transported known pathogens and other symbionts of unknown pathogenic virulence, remain largely unexplored, unlegislated, and difficult to identify and quantify. Here, we propose a workflow using PubMed and Google Scholar to systematically search existing literature to determine any known and potential pathogens of aquatic INNS. This workflow acts as a prerequisite for assessing the nature and risk posed by co-transported pathogens of INNS; of which a better understanding is necessary to inform policy and INNS risk assessments. Addressing this evidence gap will be instrumental to devise an appropriate set of statutory responsibilities with respect to these symbionts, and to underpin new and more effective legislative processes relating to the disease screening and risk assessment of INNS.
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18
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Foster R, Peeler E, Bojko J, Clark PF, Morritt D, Roy HE, Stebbing P, Tidbury HJ, Wood LE, Bass D. Pathogens co-transported with invasive non-native aquatic species: implications for risk analysis and legislation. NEOBIOTA 2021. [DOI: 10.3897/neobiota.69.71358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Invasive Non-Native Species (INNS) can co-transport externally and internally other organisms including viruses, bacteria and other eukaryotes (including metazoan parasites), collectively referred to as the symbiome. These symbiotic organisms include pathogens, a small minority of which are subject to surveillance and regulatory control, but most of which are currently unscrutinized and/or unknown. These putatively pathogenetic symbionts can potentially pose diverse risks to other species, with implications for increased epidemiological risk to agriculture and aquaculture, wildlife/ecosystems, and human health (zoonotic diseases). The risks and impacts arising from co-transported known pathogens and other symbionts of unknown pathogenic virulence, remain largely unexplored, unlegislated, and difficult to identify and quantify. Here, we propose a workflow using PubMed and Google Scholar to systematically search existing literature to determine any known and potential pathogens of aquatic INNS. This workflow acts as a prerequisite for assessing the nature and risk posed by co-transported pathogens of INNS; of which a better understanding is necessary to inform policy and INNS risk assessments. Addressing this evidence gap will be instrumental to devise an appropriate set of statutory responsibilities with respect to these symbionts, and to underpin new and more effective legislative processes relating to the disease screening and risk assessment of INNS.
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19
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Thomson-Laing G, Parai R, Kelly LT, Pochon X, Newnham R, Vandergoes MJ, Howarth JD, Wood SA. Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned ( Anguilla dieffenbachii) and short-finned ( Anguilla australis) eels in environmental samples. PeerJ 2021; 9:e12157. [PMID: 34692247 PMCID: PMC8483004 DOI: 10.7717/peerj.12157] [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: 05/19/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.
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Affiliation(s)
| | | | | | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | - Rewi Newnham
- Victoria University of Wellington, Wellington, New Zealand
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20
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Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species. Microorganisms 2021; 9:microorganisms9030510. [PMID: 33670984 PMCID: PMC7997176 DOI: 10.3390/microorganisms9030510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016–2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO2 levels.
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21
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Clusa L, Garcia-Vazquez E, Fernández S, Meyer A, Machado-Schiaffino G. Nuisance species in lake constance revealed through eDNA. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02462-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Hoffman JC, Meredith C, Pilgrim E, Trebitz A, Hatzenbuhler C, Kelly JR, Peterson G, Lietz J, Okum S, Martinson J. Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive Species Early Detection. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES. JOURNAL CANADIEN DES SCIENCES HALIEUTIQUES ET AQUATIQUES 2021; 78:752-764. [PMID: 35619733 PMCID: PMC9132201 DOI: 10.1139/cjfas-2020-0224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy, and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction 'hot-spot' in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.
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Affiliation(s)
- Joel Christopher Hoffman
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Christy Meredith
- Montana Department of Environmental Quality, 1520 E. 6th Avenue, Helena, Montana, 59601, USA
| | - Erik Pilgrim
- US Environmental Protection Agency Office of Research and Development, Watershed and Ecosystem Characterization Division, 26 West Martin Luther King Dr, Cincinnati, Ohio, 45268, USA
| | - Anett Trebitz
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Chelsea Hatzenbuhler
- Badger Technical Services c/o US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - John Russell Kelly
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Gregory Peterson
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Julie Lietz
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, Minnesota, 55804, USA
| | - Sara Okum
- US Environmental Protection Agency Office of Research and Development, Watershed and Ecosystem Characterization Division, 26 West Martin Luther King Dr, Cincinnati, Ohio, 45268, USA
| | - John Martinson
- US Environmental Protection Agency Office of Research and Development, Great Lakes Toxicology and Ecology Division, 26 West Martin Luther King Dr, Cincinnati, Ohio, 45268, USA
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23
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Duarte S, Vieira PE, Lavrador AS, Costa FO. Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141729. [PMID: 32889465 DOI: 10.1016/j.scitotenv.2020.141729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana S Lavrador
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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24
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Audrézet F, Zaiko A, Lear G, Wood SA, Tremblay LA, Pochon X. Biosecurity implications of drifting marine plastic debris: Current knowledge and future research. MARINE POLLUTION BULLETIN 2021; 162:111835. [PMID: 33220912 DOI: 10.1016/j.marpolbul.2020.111835] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
The introduction and spread of marine non-indigenous species (NIS) and pathogens into new habitats are a major threat to biodiversity, ecosystem services, human health, and can have substantial economic consequences. Shipping is considered the main vector for marine biological invasions; less well understood is the increased spread of marine NIS and pathogens rafting on marine plastic debris (MPD). Despite an increasing research interest and recent progress in characterizing the plastisphere, this manuscript highlights critical knowledge gaps and research priorities towards a better understanding of the biosecurity implications of MPD. We advocate for future research to (i) investigate plastisphere community succession and the factors influencing NIS propagules and pathogens recruitment through robust experimental investigations; (ii) combine microscopy and molecular approaches to effectively assess the presence of specific taxa; (iii) include additional genetic markers to thoroughly characterize the biodiversity associated with MPD and explore the presence of specific marine pests.
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Affiliation(s)
- François Audrézet
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand.
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Louis A Tremblay
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; School of Biological Sciences, University of Auckland, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
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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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26
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Aylagas E, Borja A, Pochon X, Zaiko A, Keeley N, Bruce K, Hong P, Ruiz GM, Stein ED, Theroux S, Geraldi N, Ortega A, Gajdzik L, Coker DJ, Katan Y, Hikmawan T, Saleem A, Alamer S, Jones BH, Duarte CM, Pearman J, Carvalho S. Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140780. [PMID: 32693276 DOI: 10.1016/j.scitotenv.2020.140780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology - the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.
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Affiliation(s)
- Eva Aylagas
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Angel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Nigel Keeley
- Benthic Resources and Processors Group, Institute of Marine Research, Postboks 6606 Langnes, 9296 Tromsø, Norway
| | - Kat Bruce
- Nature Metrics Ltd, CABI site, Bakeham Lane, Egham TW20 9TY, United Kingdom
| | - Peiying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA; Aquatic Bioinvasion Research and Policy Institute, Environmental Science and Management, Portland State University, Portland, OR 97201, USA
| | - Eric D Stein
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Susanna Theroux
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Nathan Geraldi
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Laura Gajdzik
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Darren J Coker
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yasser Katan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Tyas Hikmawan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Ammar Saleem
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Sultan Alamer
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Burton H Jones
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - John Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Antich A, Palacín C, Cebrian E, Golo R, Wangensteen OS, Turon X. Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Mol Ecol 2020; 30:3175-3188. [PMID: 32974967 DOI: 10.1111/mec.15641] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/06/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and Alveolata in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples and, of these, 180 (5.1%) were identified as benthic taxa that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex communities via metabarcoding.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, and Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Emma Cebrian
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Raül Golo
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
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28
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Metabarcoding of native and invasive species in stomach contents of Great Lakes fishes. PLoS One 2020; 15:e0236077. [PMID: 32780731 PMCID: PMC7419000 DOI: 10.1371/journal.pone.0236077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 06/30/2020] [Indexed: 11/19/2022] Open
Abstract
As aquatic invasive species (AIS) proliferate worldwide, a better understanding of their roles in invaded habitats is needed to inform management and introduction prevention strategies and priorities. Metabarcoding of stomach content DNA (scDNA) shows considerable promise in such regard. We thus metabarcoded scDNA from two non-native fish species (alewife (Alosa pseudoharengus) and rainbow smelt (Osmerus mordax)), and three native ones (bloater (Coregonus hoyi), ninespine stickleback (Pungitius pungitius), and slimy sculpin (Cottus cognatus)). Fishes (N = 376) were sampled in spring 2009 and 2010 from 73–128 m depths at three Lake Michigan sites. Four mitochondrial cytochrome oxidase 1 (CO1) primer sets designed to target five potential AIS prey, and a universal aquatic invertebrate CO1 primer set targeting both native and AIS prey were used. Quality controlled prey amplicons were matched to three AIS prey: Bythotrephes longimanus (mean percent frequency occurrence, all samples = 7%), Cercopagis pengoi (5%), and Dreissena rostriformis bugensis (11%). Neither invasive prey Dreissena polymorpha nor Hemimysis anomala were detected. Native prey Leptodiaptomus sicilis, Limnocalanus macrurus, and Mysis diluviana were relatively common in scDNA (respective mean percent occurrences, all samples: 48%, 25%, 42%). Analysis of variation in prey occurrences for sample site, predator species, sample year, sample depth, and predator total length (TL) indicated site and predator species were most important. However, B. longimanus occurrence in scDNA depended upon predator TL, perhaps indicative of its unique defensive spine limiting susceptibility to predation until fishes exceed species-specific gape-based limitations. Our analysis of native and invasive prey species indicated possible indirect AIS impacts such as native predators switching their diet due to AIS-driven losses of preferred native prey. Metabarcoding demonstrated that AIS are integrated components of the offshore Lake Michigan food web, with both native and non-native predators, and both invasive and native prey are affecting species interactions across multiple trophic levels.
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29
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Azevedo J, Antunes JT, Machado AM, Vasconcelos V, Leão PN, Froufe E. Monitoring of biofouling communities in a Portuguese port using a combined morphological and metabarcoding approach. Sci Rep 2020; 10:13461. [PMID: 32778680 PMCID: PMC7417558 DOI: 10.1038/s41598-020-70307-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/15/2020] [Indexed: 01/01/2023] Open
Abstract
Marine biofouling remains an unsolved problem with a serious economic impact on several marine associated industries and constitutes a major vector for the spread of non-indigenous species (NIS). The implementation of biofouling monitoring programs allows for better fouling management and also for the early identification of NIS. However, few monitoring studies have used recent methods, such as metabarcoding, that can significantly enhance the detection of those species. Here, we employed monthly monitoring of biofouling growth on stainless steel plates in the Atlantic Port of Leixões (Northern Portugal), over one year to test the effect of commercial anti-corrosion paint in the communities. Fouling organisms were identified by combining morpho-taxonomy identification with community DNA metabarcoding using multiple markers (16S rRNA, 18S rRNA, 23S rRNA, and COI genes). The dominant colonizers found at this location were hard foulers, namely barnacles and mussels, while other groups of organisms such as cnidarians, bryozoans, and ascidians were also abundant. Regarding the temporal dynamics of the fouling communities, there was a progressive increase in the colonization of cyanobacteria, green algae, and red algae during the sampled period with the replacement of less abundant groups. The tested anticorrosion paint demonstrated to have a significant prevention effect against the biofouling community resulting in a biomass reduction. Our study also reports, for the first time, 29 NIS in this port, substantiating the need for the implementation of recurring biofouling monitoring programs in ports and harbours.
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Affiliation(s)
- Joana Azevedo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
| | - Jorge T Antunes
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M Machado
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Matosinhos, Portugal
| | - Vitor Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro N Leão
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Matosinhos, Portugal.
| | - Elsa Froufe
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Matosinhos, Portugal.
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30
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DiBattista JD, Reimer JD, Stat M, Masucci GD, Biondi P, De Brauwer M, Wilkinson SP, Chariton AA, Bunce M. Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Sci Rep 2020; 10:8365. [PMID: 32433472 PMCID: PMC7239923 DOI: 10.1038/s41598-020-64858-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/23/2020] [Indexed: 01/29/2023] Open
Abstract
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.
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Affiliation(s)
- Joseph D DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia. .,Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW, 2010, Australia.
| | - James D Reimer
- Molecular Invertebrate and Systematics Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Giovanni D Masucci
- Molecular Invertebrate and Systematics Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Piera Biondi
- Molecular Invertebrate and Systematics Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Maarten De Brauwer
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.,School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Anthony A Chariton
- Department of Biological Sciences, Macquarie University, North Ryde, 2113, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.,Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011, New Zealand
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31
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Guibert I, Lecellier G, Torda G, Pochon X, Berteaux-Lecellier V. Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima. MICROBIOME 2020; 8:57. [PMID: 32317019 PMCID: PMC7175534 DOI: 10.1186/s40168-020-00835-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics. RESULTS Our results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima. CONCLUSIONS Altogether, our results suggest that at least three microbiotypes naturally exist in the studied clam populations, regardless of water temperature. These microbiotypes plausibly provide similar functions to the clam host via alternate molecular pathways as well as microbiotype-specific functions. This redundancy in functions among microbiotypes together with their specificities provides hope that giant clam populations can tolerate some levels of environmental variation such as increased temperature. Importantly, the composition of the benthic assemblage could make clams susceptible to infections by Vibrionaceae, especially when water temperature increases. Video abstract.
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Affiliation(s)
- Isis Guibert
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, SAR China
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
- USR3278 PSL CRIOBE CNRS-EPHE-UPVD, Papetoai, Moorea, French Polynesia
| | - Gael Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
- UVSQ, Université de Paris-Saclay, 45 Avenue des Etats-Unis, Versailles Cedex, France
| | - Gergely Torda
- ARC, Centre of Excellence for Coral Reef Studies, James Cook University, QLD, Townsville, 4811 Australia
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson, 7042 New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941 New Zealand
| | - Véronique Berteaux-Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
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32
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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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33
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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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Turon X, Antich A, Palacín C, Præbel K, Wangensteen OS. From metabarcoding to metaphylogeography: separating the wheat from the chaff. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02036. [PMID: 31709684 PMCID: PMC7078904 DOI: 10.1002/eap.2036] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 05/31/2023]
Abstract
Metabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α- and β-diversity estimates, that is, interspecies (or inter-MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information-mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.
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Affiliation(s)
- Xavier Turon
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Adrià Antich
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Institute of Biodiversity Research (IRBio)University of BarcelonaBarcelonaCataloniaSpain
| | - Kim Præbel
- Norwegian College of Fishery ScienceUiT the Arctic University of NorwayTromsøNorway
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35
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Rey A, Basurko OC, Rodriguez‐Ezpeleta N. Considerations for metabarcoding-based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments. Ecol Evol 2020; 10:2452-2465. [PMID: 32184993 PMCID: PMC7069299 DOI: 10.1002/ece3.6071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/10/2020] [Accepted: 01/15/2020] [Indexed: 01/13/2023] Open
Abstract
Monitoring introduction and spread of nonindigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability, and the time-consuming morphological approach used for taxonomic identification. Metabarcoding represents a promising alternative for rapid comprehensive port biological baseline surveys, but its application in this context requires further assessments.We applied metabarcoding (based on barcodes of the cytochrome c oxidase subunit I and of the 18S ribosomal RNA gene) to 192 port samples collected (a) from diverse habitats (water column-including environmental DNA and zooplankton, sediment, and fouling structures), (b) at different sites (from inner to outer estuary), and iii) during the four seasons of the year.By comparing the biodiversity metrics derived from each sample group, we show that each sampling method resulted in a distinct community profile and that environmental DNA alone cannot substitute for organismal sampling, and that, although sampling at different seasons and locations resulted in higher observed biodiversity, operational results can be obtained by sampling selected locations and seasons.By assessing the taxonomic composition of the samples, we show that metabarcoding data allowed the detection of previously recorded nonindigenous species as well as to reveal presence of new ones, even if in low abundance. Synthesis and application. Our comprehensive assessment of metabarcoding for port biological baseline surveys sets the basics for cost-effective, standardized, and comprehensive monitoring of nonindigenous species and for performing risk assessments in ports. This development will contribute to the implementation of the recently entered into force International Convention for the Control and Management of Ships' Ballast Water and Sediments.
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Affiliation(s)
- Anaïs Rey
- Marine Research DivisionAZTISukarrietaSpain
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36
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Ung L, Bispo PJM, Doan T, Van Gelder RN, Gilmore MS, Lietman T, Margolis TP, Zegans ME, Lee CS, Chodosh J. Clinical metagenomics for infectious corneal ulcers: Rags to riches? Ocul Surf 2020; 18:1-12. [PMID: 31669750 PMCID: PMC9837861 DOI: 10.1016/j.jtos.2019.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 01/17/2023]
Abstract
The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to diagnostic testing is set to fundamentally alter the way infectious diseases are detected. Long envisioned as the solution to the limitations of culture-based conventional microbiology, next generation sequencing methods will soon mature, and our attention will inevitably turn to how they can be applied to areas of medicine which need it most urgently. In ophthalmology, the demand for this technology is particularly pressing for the care of infectious corneal ulcers, where current diagnostic tests may fail to identify a causative organism in over half of cases. However, the optimism found in the budding discourse surrounding clinical metagenomics belies the reality that clinicians and scientists will soon be inundated by oppressive volumes of sequencing data, much of which will be foreign and unfamiliar. Therefore, our success in translating clinical metagenomics is likely to hinge on how we make sense of these data, and understanding its implications for the interpretation and implementation of sequencing into routine clinical care. In this consortium-led review, we provide an outline of these data-related issues and how they may be used to inform technical workflows, with the hope that we may edge closer to realizing the potential of clinical metagenomics for this important unmet need.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Paulo J M Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | | | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thomas Lietman
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Todd P Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in Saint Louis, Saint Louis, USA
| | - Michael E Zegans
- Department of Surgery (Ophthalmology), and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
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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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38
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Wood SA, Pochon X, Laroche O, Ammon U, Adamson J, Zaiko A. A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA. Mol Ecol Resour 2019; 19:1407-1419. [DOI: 10.1111/1755-0998.13055] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Susanna A. Wood
- Coastal and Freshwater Group Cawthron Institute Nelson New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group Cawthron Institute Nelson New Zealand
- Institute of Marine Science University of Auckland Auckland New Zealand
| | - Olivier Laroche
- Coastal and Freshwater Group Cawthron Institute Nelson New Zealand
- Department of Oceanography, School of Ocean and Earth Science and Technology University of Hawaii at Manoa Honolulu HI USA
| | - Ulla Ammon
- Coastal and Freshwater Group Cawthron Institute Nelson New Zealand
- Institute of Marine Science University of Auckland Auckland New Zealand
| | - Janet Adamson
- Coastal and Freshwater Group Cawthron Institute Nelson New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater Group Cawthron Institute Nelson New Zealand
- Institute of Marine Science University of Auckland Auckland New Zealand
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Pujari L, Wu C, Kan J, Li N, Wang X, Zhang G, Shang X, Wang M, Zhou C, Sun J. Diversity and Spatial Distribution of Chromophytic Phytoplankton in the Bay of Bengal Revealed by RuBisCO Genes ( rbcL). Front Microbiol 2019; 10:1501. [PMID: 31333613 PMCID: PMC6624743 DOI: 10.3389/fmicb.2019.01501] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/14/2019] [Indexed: 11/13/2022] Open
Abstract
Phytoplankton are the basis of primary production and play important roles in regulating energy export in marine ecosystems. Compared to other regions, chromophytic phytoplankton are considerably understudied in the Bay of Bengal (BOB). Here, we investigated community structure and spatial distribution of chromophytic phytoplankton in the BOB by using RuBisCO genes (Form ID rbcL). High throughput sequencing of rbcL genes revealed that diatoms, cyanobacteria (Cyanophyceae), Pelagophyceae, Haptophyceae, Chrysophyceae, Eustigamatophyceae, Xanthophyceae, Cryptophyceae, Dictyochophyceae, and Pinguiophyceae were the most abundant groups recovered in the BOB. Abundances and distribution of diatoms and Pelagophyceae were further verified using quantitative PCR analyses which showed the dominance of these groups near the Equator region (p < 0.01) where upwelling was likely the source of nutrients. Further, redundancy analysis demonstrated that temperature was an important environmental driver in structuring distributions of Cyanophyceae and dominant chromophytic phytoplankton. Morphological identification and quantification confirmed the dominance of diatoms, and also detected other cyanobacteria and dinoflagellates that were missing in our molecular characterizations. Pearson’s correlations of these morphologically identified phytoplankton with environmental gradients also indicated that nutrients and temperature were key variables shaping community structure. Combination of molecular characterization and morphological identification provided a comprehensive overview of chromophytic phytoplankton. This is the first molecular study of chromophytic phytoplankton accomplished in the BOB, and our results highlight a combination of molecular analysis targeting rbcL genes and microscopic detection in examining phytoplankton composition and diversity.
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Affiliation(s)
- Laxman Pujari
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Chao Wu
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, PA, United States
| | - Nan Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Nanning Normal University, Nanning, China
| | - Xingzhou Wang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Guicheng Zhang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaomei Shang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Min Wang
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Chun Zhou
- Key Laboratory of Physical Oceanography/CIMST, Ocean University of China, Qingdao, China
| | - Jun Sun
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
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40
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Li T, Unger ER, Rajeevan MS. Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection. BMC Genomics 2019; 20:231. [PMID: 30894118 PMCID: PMC6425667 DOI: 10.1186/s12864-019-5598-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 03/12/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND We recently described a method for unbiased detection of all known human papillomaviruses (HPV) types with the potential for the determination of their variant and integration from the resulting whole genome sequence data. Considering the complex workflow for target-enriched next generation sequencing (NGS), we focused on the reproducibility and limit of detection (LOD) of this new universal HPV typing assay in this study. RESULTS We evaluated the reproducibility and LOD for HPV genotyping based on our recently published method that used RNA-baits targeting whole genomes of 191 HPV types, Agilent SureSelect protocol for target enrichment and Illumina HiSeq 2500 for sequencing (eWGS, enriched whole genome sequencing). Two libraries, prepared from pooled plasmids representing 9 vaccine HPV types at varying input (1-625 copies/reaction), were sequenced twice giving four replicates for evaluating reproducibility and LOD. eWGS showed high correlation in the number of reads mapped to HPV reference genomes between the two flow-cell lanes within (R2 = 1) and between experiments (R2 = 0.99). The number of mapped reads was positively correlated to copy number (β = 13.9, p < 0.0001). The limit of blank (LOB) could be calculated based on mapped reads to HPV types not included in each sample. HPV genotyping was reproducible for all 9 types at 625 copies using multiple cut-off criteria but LOD was 25 copies based on number of reads above LOB even when multiple types were present. eWGS showed no bias for HPV genotyping under single or multiple infection (p = 0.16-0.99). CONCLUSIONS The universal eWGS method for HPV genotyping has sensitivity, competitive with widely used consensus PCR methods with reduced type competition, and with the potential for determination of variant and integration status. The protocol used in this study, using defined samples varying in complexity and copy number, analyzed in replicate and duplicate assays, is applicable to most WGS methods.
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Affiliation(s)
- Tengguo Li
- Division of High-Consequence Pathogens & Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Elizabeth R Unger
- Division of High-Consequence Pathogens & Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Mangalathu S Rajeevan
- Division of High-Consequence Pathogens & Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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Sow A, Brévault T, Benoit L, Chapuis MP, Galan M, Coeur d'acier A, Delvare G, Sembène M, Haran J. Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding. Sci Rep 2019; 9:3646. [PMID: 30842584 PMCID: PMC6403368 DOI: 10.1038/s41598-019-40243-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/12/2019] [Indexed: 12/26/2022] Open
Abstract
An accurate estimation of parasitism rates and diversity of parasitoids of crop insect pests is a prerequisite for exploring processes leading to efficient natural biocontrol. Traditional methods such as rearing have been often limited by taxonomic identification, insect mortality and intensive work, but the advent of high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is increasingly seen as a reliable and powerful alternative approach. Little has been done to explore the benefits of such an approach for estimating parasitism rates and parasitoid diversity in an agricultural context. In this study, we compared the composition of parasitoid species and parasitism rates between rearing and DNA metabarcoding of host eggs and larvae of the millet head miner, Heliocheilus albipunctella De Joannis (Lepidoptera, Noctuidae), collected from millet fields in Senegal. We first assessed the detection threshold for the main ten endoparasitoids, by sequencing PCR products obtained from artificial dilution gradients of the parasitoid DNAs in the host moth. We then assessed the potential of DNA metabarcoding for diagnosing parasitism rates in samples collected from the field. Under controlled conditions, our results showed that relatively small quantities of parasitoid DNA (0.07 ng) were successfully detected within an eight-fold larger quantity of host DNA. Parasitoid diversity and parasitism rate estimates were always higher for DNA metabarcoding than for host rearing. Furthermore, metabarcoding detected multi-parasitism, cryptic parasitoid species and differences in parasitism rates between two different sampling sites. Metabarcoding shows promise for gaining a clearer understanding of the importance and complexity of host-parasitoid interactions in agro-ecosystems, with a view to improving pest biocontrol strategies.
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Affiliation(s)
- Ahmadou Sow
- Département de Biologie Animale, FST-UCAD, Dakar, Senegal. .,BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal.
| | - Thierry Brévault
- BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal.,CIRAD, UPR AIDA, F-34398, Montpellier, France.,AIDA, University Montpellier, CIRAD, Montpellier, France
| | - Laure Benoit
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Marie-Pierre Chapuis
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Armelle Coeur d'acier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Gérard Delvare
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Mbacké Sembène
- Département de Biologie Animale, FST-UCAD, Dakar, Senegal.,BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal
| | - Julien Haran
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
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42
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Bessey C, Jarman SN, Stat M, Rohner CA, Bunce M, Koziol A, Power M, Rambahiniarison JM, Ponzo A, Richardson AJ, Berry O. DNA metabarcoding assays reveal a diverse prey assemblage for Mobula rays in the Bohol Sea, Philippines. Ecol Evol 2019; 9:2459-2474. [PMID: 30891193 PMCID: PMC6405500 DOI: 10.1002/ece3.4858] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/29/2022] Open
Abstract
Diet studies provide base understanding of trophic structure and are a valuable initial step for many fields of marine ecology, including conservation and fisheries biology. Considerable complexity in marine trophic structure can exist due to the presence of highly mobile species with long life spans. Mobula rays are highly mobile, large, planktivorous elasmobranchs that are frequently caught either directly or as bycatch in fisheries, which, combined with their conservative life history strategy, makes their populations susceptible to decline in intensely fished regions. Effective management of these iconic and vulnerable species requires an understanding of the diets that sustain them, which can be difficult to determine using conventional sampling methods. We use three DNA metabarcode assays to identify 44 distinct taxa from the stomachs (n = 101) of four sympatric Mobula ray species (Mobula birostris, Mobula tarapacana, Mobula japanica, and Mobula thurstoni) caught over 3 years (2013-2015) in a direct fishery off Bohol in the Philippines. The diversity and incidence of bony fishes observed in ray diets were unprecedented. Nevertheless, rays showed dietary overlap, with krill (Euphausia) dominating their diet. Our results provide a more detailed assessment of sympatric ray diets than was previously described and reveal the complexity that can exist in food webs at critical foraging habitats.
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Affiliation(s)
- Cindy Bessey
- Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research Organization, Oceans and AtmosphereCrawleyWestern AustraliaAustralia
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
- School of Plant Biology and the Oceans InstituteUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Environomics Future Science Platform, Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research OrganizationCrawleyWestern AustraliaAustralia
| | - Simon N. Jarman
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
- Environomics Future Science Platform, Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research OrganizationCrawleyWestern AustraliaAustralia
| | - Michael Stat
- Department of Biological SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | | | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Adam Koziol
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Matthew Power
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | | | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute PhilippinesBoholPhilippines
| | - Anthony J. Richardson
- Commonwealth Scientific and Industrial Research Organization, Oceans and AtmospheresBrisbaneQueenslandAustralia
- Centre for Applications in Natural Resource Mathematics, School of Mathematics and PhysicsUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research OrganizationCrawleyWestern AustraliaAustralia
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Differential effects of coral-giant clam assemblages on biofouling formation. Sci Rep 2019; 9:2675. [PMID: 30804382 PMCID: PMC6389951 DOI: 10.1038/s41598-019-39268-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/14/2019] [Indexed: 11/09/2022] Open
Abstract
To prevent the settlement and/or the growth of fouling organisms (i.e. bacteria, fungi or microalgae), benthic sessile species have developed various defense mechanisms among which the production of chemical molecules. While studies have mostly focused on the release of chemical compounds by single species, there exist limited data on multi-species assemblages. We used an integrative approach to explore the potential interactive effects of distinct assemblages of two corals species and one giant clam species on biofouling appearance and composition. Remarkably, we found distinct biofouling communities suggesting the importance of benthic sessile assemblages in biofouling control. Moreover, the assemblage of 3 species led to an inhibition of biofouling, likely through a complex of secondary metabolites. Our results highlight that through their different effect on their near environment, species assemblages might be of upmost importance for their survival and therefore, should now be taken into account for sustainable management of coral reefs.
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DiBattista JD, Reimer JD, Stat M, Masucci GD, Biondi P, De Brauwer M, Bunce M. Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ 2019; 7:e6379. [PMID: 30755831 PMCID: PMC6368839 DOI: 10.7717/peerj.6379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/24/2018] [Indexed: 11/20/2022] Open
Abstract
Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.
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Affiliation(s)
- Joseph D DiBattista
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - James D Reimer
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia.,Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Giovanni D Masucci
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, Japan
| | - Piera Biondi
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, Japan
| | - Maarten De Brauwer
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia
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Jeunen G, Knapp M, Spencer HG, Taylor HR, Lamare MD, Stat M, Bunce M, Gemmell NJ. Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecol Evol 2019; 9:1323-1335. [PMID: 30805162 PMCID: PMC6374651 DOI: 10.1002/ece3.4843] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/13/2018] [Accepted: 11/25/2018] [Indexed: 01/10/2023] Open
Abstract
DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding-based biodiversity studies is gaining popularity as a noninvasive, time-efficient, and cost-effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under-surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA-related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species-level assignment) and universal (broad taxonomic group with genus/family-level assignment) approaches obtained from replicates treated with the optimal and a low-performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false-negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol-chloroform-isoamyl for successful implementation of eDNA multi-marker metabarcoding surveys.
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Affiliation(s)
- Gert‐Jan Jeunen
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | - Miles D. Lamare
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
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46
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Tedersoo L, Drenkhan R, Anslan S, Morales‐Rodriguez C, Cleary M. High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations. Mol Ecol Resour 2019; 19:47-76. [PMID: 30358140 PMCID: PMC7379260 DOI: 10.1111/1755-0998.12959] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 12/26/2022]
Abstract
High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and Rural EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sten Anslan
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Michelle Cleary
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
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Koziol A, Stat M, Simpson T, Jarman S, DiBattista JD, Harvey ES, Marnane M, McDonald J, Bunce M. Environmental DNA metabarcoding studies are critically affected by substrate selection. Mol Ecol Resour 2018; 19:366-376. [DOI: 10.1111/1755-0998.12971] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Adam Koziol
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- School of Biological Sciences Macquarie University North Ryde New South Wales Australia
| | - Tiffany Simpson
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Simon Jarman
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- CSIRO Environomics Future Science Platform Indian Ocean Marine Research Centre The University of Western Australia Perth Western Australia Australia
| | - Joseph D. DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- Australian Museum Research Institute, Australian Museum Sydney New South Wales Australia
| | - Euan S. Harvey
- Fish Ecology Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Michael Marnane
- Chevron Energy Technology Company Perth Western Australia Australia
| | - Justin McDonald
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD) Hillarys Western Australia Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
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Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI. How quantitative is metabarcoding: A meta-analytical approach. Mol Ecol 2018; 28:420-430. [PMID: 30408260 PMCID: PMC7379500 DOI: 10.1111/mec.14920] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
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Affiliation(s)
- Philip D Lamb
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ewan Hunter
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - John K Pinnegar
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - Simon Creer
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Richard G Davies
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Forin-Wiart MA, Poulle ML, Piry S, Cosson JF, Larose C, Galan M. Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing. Sci Rep 2018; 8:17091. [PMID: 30459313 PMCID: PMC6244006 DOI: 10.1038/s41598-018-34430-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/18/2018] [Indexed: 01/01/2023] Open
Abstract
DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n = 41) and from free-ranging individuals (n = 326) were collected and analysed using a cytb mini-barcode in independent PCR replicates on the Ion PGM and the MiSeq platforms. Outputs from MiSeq were more sensitive and reproducible than those from Ion PGM due to a higher sequencing depth and sequence quality on MiSeq. DNA from intact prey taxa was detected more often (82% of the expected occurrences) than DNA from pet food (54%) and raw fish and meat (31%). We assumed that this variability was linked to different degree of DNA degradation: The Ion PGM detected significantly less human-linked food, birds, field voles, murids and shrews in the field-collected samples than the MiSeq platform. Pooling the replicates from both platforms and filtering the data allowed identification of at least one food item in 87.4% of the field-collected samples. Our DNA metabarcoding approach identified 29 prey taxa, of which 25 to species level (90% of items) including 9 rodents, 3 insectivores, 12 birds and 1 reptile and 33 human-related food taxa of which 23 were identified to genus level (75% of items). Our results demonstrate that using HTS platforms such as MiSeq, which provide reads of sufficiently high quantity and quality, with sufficient numbers of technical replicates, is a robust and non-invasive approach for further dietary studies on animals foraging on a wide range of food items in anthropogenic landscapes.
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Affiliation(s)
- Marie-Amélie Forin-Wiart
- Université de Reims Champagne-Ardenne, EA 7510 ESCAPE, UFR de Médecine, 51 rue Cognacq Jay, 51095, Reims Cedex, France.
- Université de Reims Champagne-Ardenne, Centre d'Etude et de Formation en Eco-Ethologie (CERFE), 5 rue de la Héronnière, 08240, Boult-aux-Bois, France.
- Université de Strasbourg, CNRS, IPHC, UMR 7178, Département Ecologie, Physiologie et Ethologie (DEPE), 67087, Strasbourg, France.
| | - Marie-Lazarine Poulle
- Université de Reims Champagne-Ardenne, EA 7510 ESCAPE, UFR de Médecine, 51 rue Cognacq Jay, 51095, Reims Cedex, France
- Université de Reims Champagne-Ardenne, Centre d'Etude et de Formation en Eco-Ethologie (CERFE), 5 rue de la Héronnière, 08240, Boult-aux-Bois, France
| | - Sylvain Piry
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 755 avenue du Campus Agropolis, CS 300 16, 34988, Montferrier-sur-Lez cedex, France
| | - Jean-François Cosson
- UMR BIPAR, Animal Health Laboratory, INRA, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Claire Larose
- DIANA PetFood Division, Z.A. du Gohélis, 56250, Elven, France
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 755 avenue du Campus Agropolis, CS 300 16, 34988, Montferrier-sur-Lez cedex, France
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