1
|
Correia E, Granadeiro JP, Santos B, Mata VA, Dias E, Regalla A, Catry T. Diet of the critically endangered blackchin guitarfish Glaucostegus cemiculus revealed using DNA metabarcoding. JOURNAL OF FISH BIOLOGY 2024; 104:324-328. [PMID: 37787164 DOI: 10.1111/jfb.15574] [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: 07/10/2023] [Revised: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 10/04/2023]
Abstract
We present the first assessment of the diet of the blackchin guitarfish Glaucostegus cemiculus (Geoffroy Saint-Hilaire, 1817) for West Africa using DNA metabarcoding on stomach contents of individuals captured in the Bijagós Archipelago, Guinea-Bissau. The diet was dominated by crustaceans, particularly caramote prawn Penaeus kerathurus (frequency of occurrence [FO] = 74%, numerical frequency [NF] = 54%) and fiddler crab Afruca tangeri (FO = 74%, NF = 12%). Bony fishes were present in 30% of the stomachs. We highlight the importance of conservation action for intertidal habitats and their associated benthic invertebrates for the survival of the critically endangered blackchin guitarfish.
Collapse
Affiliation(s)
- Edna Correia
- Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - José Pedro Granadeiro
- Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Bárbara Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Vanessa A Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Emanuel Dias
- Instituto da Biodiversidade e das Áreas Protegidas, Dr. Alfredo Simão da Silva (IBAP), Bissau, Guinea-Bissau
| | - Aissa Regalla
- Instituto da Biodiversidade e das Áreas Protegidas, Dr. Alfredo Simão da Silva (IBAP), Bissau, Guinea-Bissau
| | - Teresa Catry
- Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
2
|
Rosa FDAS, Gasalla MA, de Queiroz AKO, Ribas TFA, Mauvisseau Q, de Boer HJ, Thorbek BLG, Oliveira RRM, Laux M, Postuma FA, Ready JS. Molecular analyses of carangid fish diets reveal inter-predation, dietary overlap, and the importance of early life stages in trophic ecology. Ecol Evol 2024; 14:e10817. [PMID: 38187922 PMCID: PMC10766566 DOI: 10.1002/ece3.10817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Carangid fishes are commercially important in fisheries and aquaculture. They are distributed worldwide in both tropical and subtropical marine ecosystems. Their role in food webs is often unclear since their diet cannot be easily identified by traditional gut content analysis. They are suspected to prey on pelagic and benthic species, with clupeiform fishes being important dietary items for some species, though it is unknown whether carangids share food resources or show trophic segregation. Here, we used metabarcoding to overcome traditional challenges of taxonomic approaches to analyze the diet of seven carangid species caught as bycatch in the Brazilian southwest Atlantic sardine fishery. Stomach contents were processed from the following species: Caranx crysos, Caranx latus, Chloroscombrus chrysurus, Hemicaranx amblyrhynchus, Oligoplites saliens, Selene setapinnis, and Trachinotus carolinus. Identified diets were dominated by teleost fishes. The C. latus diet was the most distinct among the seven species, preferentially consuming Engraulis anchoita, but H. amblyrhynchus, O. saliens, and S. setapinnis also showed a trend of predominantly consuming small pelagic fishes. Finally, we found evidence of inter-predation in carangids, especially strong between S. setapinnis and C. crysos, suggesting that consumption of early life stages may result in indirect competition through reduced recruitment in these fishes. These findings provide unprecedented insights into the biodiversity in marine ecosystems, especially the poorly known diet of carangid fishes.
Collapse
Affiliation(s)
- Fabricio dos Anjos Santa Rosa
- Group for Integrated Biological Investigation, Center for Advanced Studies of BiodiversityFederal University of ParáBelémBrazil
| | - Maria A. Gasalla
- Fisheries Ecosystems Laboratory, Oceanographic InstituteUniversity of São PauloSão PauloBrazil
| | - Anna Karolina Oliveira de Queiroz
- Group for Integrated Biological Investigation, Center for Advanced Studies of BiodiversityFederal University of ParáBelémBrazil
- Natural History MuseumUniversity of OsloOsloNorway
| | - Talita Fernanda Augusto Ribas
- Group for Integrated Biological Investigation, Center for Advanced Studies of BiodiversityFederal University of ParáBelémBrazil
| | | | | | | | - Renato Renison Moreira Oliveira
- Instituto Tecnológico ValeBelémBrazil
- Postgraduate Program in BioinformaticsFederal University of Minas GeraisBelo HorizonteBrazil
| | - Marcele Laux
- Ecology DepartmentFederal University of Minas GeraisBelo HorizonteBrazil
| | - Felippe A. Postuma
- Fisheries Ecosystems Laboratory, Oceanographic InstituteUniversity of São PauloSão PauloBrazil
| | - Jonathan Stuart Ready
- Group for Integrated Biological Investigation, Center for Advanced Studies of BiodiversityFederal University of ParáBelémBrazil
| |
Collapse
|
3
|
Clerissi C, Huot C, Portet A, Gourbal B, Toulza E. Covariation between microeukaryotes and bacteria associated with Planorbidae snails. PeerJ 2023; 11:e16639. [PMID: 38144201 PMCID: PMC10740603 DOI: 10.7717/peerj.16639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/19/2023] [Indexed: 12/26/2023] Open
Abstract
Background Microbial communities associated with macroorganisms might affect host physiology and homeostasis. Bacteria are well studied in this context, but the diversity of microeukaryotes, as well as covariations with bacterial communities, remains almost unknown. Methods To study microeukaryotic communities associated with Planorbidae snails, we developed a blocking primer to reduce amplification of host DNA during metabarcoding analyses. Analyses of alpha and beta diversities were computed to describe microeukaryotes and bacteria using metabarcoding of 18S and 16S rRNA genes, respectively. Results Only three phyla (Amoebozoa, Opisthokonta and Alveolata) were dominant for microeukaryotes. Bacteria were more diverse with five dominant phyla (Proteobacteria, Bacteroidetes, Tenericutes, Planctomycetes and Actinobacteria). The composition of microeukaryotes and bacteria were correlated for the Biomphalaria glabrata species, but not for Planorbarius metidjensis. Network analysis highlighted clusters of covarying taxa. Among them, several links might reflect top-down control of bacterial populations by microeukaryotes, but also possible competition between microeukaryotes having opposite distributions (Lobosa and Ichthyosporea). The role of these taxa remains unknown, but we believe that the blocking primer developed herein offers new possibilities to study the hidden diversity of microeukaryotes within snail microbiota, and to shed light on their underestimated interactions with bacteria and hosts.
Collapse
Affiliation(s)
- Camille Clerissi
- Current Affiliation: PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Camille Huot
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Anaïs Portet
- Current Affiliation: MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Benjamin Gourbal
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| |
Collapse
|
4
|
Kim K, Joo GJ, Jeong KS, Gim JS, Lee Y, Hong D, Jo H. Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary. BIOLOGY 2023; 12:1245. [PMID: 37759644 PMCID: PMC10525425 DOI: 10.3390/biology12091245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.
Collapse
Affiliation(s)
- Kanghui Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Gea-Jae Joo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Kwang-Seuk Jeong
- Department of Nursing Science, Busan Health University, Busan 49318, Republic of Korea;
| | - Jeong-Soo Gim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Yerim Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Donghyun Hong
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| | - Hyunbin Jo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (K.K.); (G.-J.J.); (J.-S.G.); (Y.L.); (D.H.)
| |
Collapse
|
5
|
Rijal DP, Hanebrekke T, Arneberg P, Johansen T, Sint D, Traugott M, Skern‐Mauritzen M, Westgaard J. Contaminants reach everywhere: Fish dietary samples should be surface decontaminated prior to molecular diet analysis. Ecol Evol 2023; 13:e10187. [PMID: 37342457 PMCID: PMC10277604 DOI: 10.1002/ece3.10187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Knowledge of trophic interaction is necessary to understand the dynamics of ecosystems and develop ecosystem-based management. The key data to measure these interactions should come from large-scale diet analyses with good taxonomic resolution. To that end, molecular methods that analyze prey DNA from guts and feces provide high-resolution dietary taxonomic data. However, molecular diet analysis may also produce unreliable results if the samples are contaminated by external sources of DNA. Employing the freshwater European whitefish (Coregonus lavaretus) as a tracer for sample contamination, we studied the possible route of whitefish in beaked redfish (Sebastes mentella) guts sampled in the Barents Sea. We used whitefish-specific COI primers for diagnostic analysis, and fish-specific 12S and metazoa-specific COI primers for metabarcoding analyses of intestine and stomach contents of fish samples that were either not cleaned, water cleaned, or bleach cleaned after being in contact with whitefish. Both the diagnostic and COI metabarcoding revealed clear positive effects of cleaning samples as whitefish were detected in significantly higher numbers of uncleaned samples compared to water or bleach-cleaned samples. Stomachs were more susceptible to contamination than intestines and bleach cleaning reduced the frequency of whitefish contamination. Also, the metabarcoding approach detected significantly more reads of whitefish in the stomach than in intestine samples. The diagnostic analysis and COI metabarcoding detected contaminants in a higher and comparable number of gut samples than the 12S-based approach. Our study underlines thus the importance of surface decontamination of aquatic samples to obtain reliable diet information from molecular data.
Collapse
Affiliation(s)
| | | | | | | | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | | | | |
Collapse
|
6
|
Mondino A, Crovadore J, Lefort F, Ursenbacher S. Impact of invading species on biodiversity: Diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
7
|
Homma C, Inokuchi D, Nakamura Y, Uy WH, Ohnishi K, Yamaguchi H, Adachi M. Effectiveness of blocking primers and a peptide nucleic acid (PNA) clamp for 18S metabarcoding dietary analysis of herbivorous fish. PLoS One 2022; 17:e0266268. [PMID: 35442965 PMCID: PMC9020718 DOI: 10.1371/journal.pone.0266268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/17/2022] [Indexed: 11/18/2022] Open
Abstract
The structure of food webs and carbon flow in aquatic ecosystems can be better understood by studying contributing factors such as the diets of herbivorous fish. Metabarcoding using a high-throughput sequencer has recently been used to clarify prey organisms of various fish except herbivorous fish. Since sequences of predator fish have dominated in sequences obtained by metabarcoding, we investigated a method for suppressing the amplification of fish DNA by using a blocking primer or peptide nucleic acid (PNA) clamp to determine the prey organisms of herbivorous fish. We designed three blocking primers and one PNA clamp that anneal to fish-specific sequences and examined how efficient they were in suppressing DNA amplification in various herbivorous fish. The results showed that the PNA clamp completely suppressed fish DNA amplification, and one of the blocking primers suppressed fish DNA amplification but less efficiently than the PNA clamp. Finally, we conducted metabarcoding using mock community samples as templates to determine whether the blocking primer or the PNA clamp was effective in suppressing fish DNA amplification. The results showed that the PNA clamp suppressed 99.3%-99.9% of fish DNA amplification, whereas the blocking primer suppressed 3.3%-32.9%. Therefore, we propose the application of the PNA clamp for clarifying the prey organisms and food preferences of various herbivorous fish.
Collapse
Affiliation(s)
- Chiho Homma
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan
| | - Daiki Inokuchi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Yohei Nakamura
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Wilfredo H. Uy
- Institute of Fisheries Research and Development, Mindanao State University at Naawan, Naawan, Misamis Oriental, Philippines
| | - Kouhei Ohnishi
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Haruo Yamaguchi
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Masao Adachi
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
- * E-mail:
| |
Collapse
|
8
|
Scheifler M, Magnanou E, Sanchez-Brosseau S, Desdevises Y. Host specificity of monogenean ectoparasites on fish skin and gills assessed by a metabarcoding approach. Int J Parasitol 2022; 52:559-567. [DOI: 10.1016/j.ijpara.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 11/05/2022]
|
9
|
Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
Collapse
|
10
|
Zhong KX, Cho A, Deeg CM, Chan AM, Suttle CA. Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS). MICROBIOME 2021; 9:230. [PMID: 34823604 PMCID: PMC8620255 DOI: 10.1186/s40168-021-01180-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The microbiome affects the health of plants and animals, including humans, and has many biological, ecological, and evolutionary consequences. Microbiome studies typically rely on sequencing ribosomal 16S RNA gene fragments, which serve as taxonomic markers for prokaryotic communities; however, for eukaryotic microbes this approach is compromised, because 18S rRNA gene sequences from microbial eukaryotes are swamped by contaminating host rRNA gene sequences. RESULTS To overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rRNA gene sequences of the host, while leaving protistan and fungal sequences intact. We validated the specificity of the sgRNA on ten model organisms and an artificially constructed (mock) community of nine protistan and fungal pathogens. The results showed that > 96.5% of host rRNA gene amplicons were cleaved, while 18S rRNA gene sequences from protists and fungi were unaffected. When used to assess the eukaryotic microbiome of oyster spat from a hatchery, CCSAS revealed a diverse community of eukaryotic microbes, typically with much less contamination from oyster 18S rRNA gene sequences than other methods using non-metazoan or blocking primers. However, each method revealed taxonomic groups that were not detected using the other methods, showing that a single approach is unlikely to uncover the entire eukaryotic microbiome in complex communities. To facilitate the application of CCSAS, we designed taxon-specific sgRNA for ~16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected. CONCLUSION CCSAS provides a high-through-put and cost-effective approach for resolving the eukaryotic microbiome of metazoa and plants with minimal contamination from host 18S rRNA gene sequences. Video Abstract.
Collapse
Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Anna Cho
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christoph M Deeg
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy M Chan
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Botany, The University of British Columbia, Vancouver, British Columbia, Canada.
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
11
|
Secondary predation constrains DNA-based diet reconstruction in two threatened shark species. Sci Rep 2021; 11:18350. [PMID: 34526519 PMCID: PMC8443726 DOI: 10.1038/s41598-021-96856-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/04/2021] [Indexed: 02/08/2023] Open
Abstract
Increasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards > 35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use and feeding ecologies is pivotal, especially among those species with wide-ranging distributions. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (Carcharhinus limbatus; globally classified as Near Threatened) and great hammerhead (Sphyrna mokarran; Critically Endangered). We opportunistically sampled the digestive tracts of these two species (and also any whole prey; termed the 'Russian-doll' approach), caught in bather-protection gillnets off northern New South Wales, to investigate the capacity for DNA metabarcoding to simultaneously determine predator and prey regional feeding ecologies. While sample sizes were small, S. mokkaran fed predominantly on stingrays and skates (Myliobatiformes and Rajiformes), but also teleosts, while C. limbatus mostly consumed teleosts. Metabarcoding assays showed extensive intermixing of taxa from the digestive tracts of predators and their whole prey, likely via the predator's stomach chyme, negating the opportunity to distinguish between primary and secondary predation. This Russian-doll effect requires further investigation in DNA metabarcoding studies focussing on dietary preferences and implies that any outcomes will need to be interpreted concomitant with traditional visual approaches.
Collapse
|
12
|
Günther B, Fromentin JM, Metral L, Arnaud-Haond S. Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey. PeerJ 2021; 9:e11757. [PMID: 34447617 PMCID: PMC8366523 DOI: 10.7717/peerj.11757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Studies of the diet, feeding habits and trophic activity of top marine predators are essential for understanding their trophodynamics. The main direct method used for such studies thus far has been morphological inventories of stomach contents. This approach presents limitations such as missing gelatinous prey, which are usually digested too quickly to be detectable. Here, we analysed the stomachs of 48 Atlantic bluefin tuna (Thunnus thynnus, approximately 15 to 60 kg, including juveniles and adult fishes) collected from the Mediterranean Sea through the metabarcoding of two gene regions (cytochrome c oxidase subunit I (COI) and the ribosomal 18S-V1V2 region). The identified prey taxa and their relative read abundances (RRAs) estimated using COI results were in line with the findings of morphologically based inventories simultaneously performed on the same set of tuna samples. In both cases (and with the same rankings), the prey taxa included anchovy (Engraulis encrasicolus, here detected in more than 80% of samples, RRA = 43%), sardine (Sardina pilchardus, also approximately 80%, RRA = 30%), sprat (Sprattus sprattus, approximately 66%, RRA = 8%), mackerel (Scomber colias, approximately 44%, RRA = 7%) and cephalopods (approximately 15%, RRA = 1.4%). Another striking result was the detection, based on 18S (with which vertebrates were detected as the most abundant group, RRA = 61.6%), of a high prevalence and diversity of gelatinous organisms (RRA = 27.1%), including cnidarians (6.7%), salps (11.7%), and ctenophores (8.7%), the latter increasing with the size of the predator. These results thus support the hypothesis of the role of gelatinous prey in the diet of Atlantic bluefin tuna, suggesting that this species is even more generalist and opportunistic than previously thought. This study further confirms that DNA metabarcoding can be a powerful tool for assessing the diet and trophodynamics of top marine predators.
Collapse
Affiliation(s)
- Babett Günther
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | | | - Luisa Metral
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | | |
Collapse
|
13
|
Evans HK, Bunch AJ, Schmitt JD, Hoogakker FJ, Carlson KB. High-throughput sequencing outperforms traditional morphological methods in Blue Catfish diet analysis and reveals novel insights into diet ecology. Ecol Evol 2021; 11:5584-5597. [PMID: 34026031 PMCID: PMC8131796 DOI: 10.1002/ece3.7460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
Blue Catfish Ictalurus furcatus are an invasive, yet economically important species in the Chesapeake Bay. However, their impact on the trophic ecology of this system is not well understood. In order to provide in-depth analysis of predation by Blue Catfish, we identified prey items using high-throughput DNA sequencing (HTS) of entire gastrointestinal tracts from 134 samples using two genetic markers, mitochondrial cytochrome c oxidase I (COI) and the nuclear 18S ribosomal RNA gene. We compared our HTS results to a more traditional "hybrid" approach that coupled morphological identification with DNA barcoding. The hybrid study was conducted on additional Blue Catfish samples (n = 617 stomachs) collected from the same location and season in the previous year. Taxonomic representation with HTS vastly surpassed that achieved with the hybrid methodology in Blue Catfish. Significantly, our HTS study identified several instances of at-risk and invasive species consumption not identified using the hybrid method, supporting the hypothesis that previous studies using morphological methods may greatly underestimate consumption of critical species. Finally, we report the novel finding that Blue Catfish diet diversity inversely correlates to daily flow rates, perhaps due to higher mobility and prey-seeking behaviors exhibited during lower flow.
Collapse
Affiliation(s)
- Heather K. Evans
- Genomics and Microbiology LaboratoryNorth Carolina Museum of Natural SciencesRaleighNCUSA
- North Carolina Wildlife Resources CommissionRaleighNCUSA
| | - Aaron J. Bunch
- Virginia Department of Wildlife ResourcesCharles CityVAUSA
- Department of Forestry and Environmental ConservationClemson UniversityClemsonSCUSA
| | - Joseph D. Schmitt
- Virginia Polytechnic Institute and State UniversityBlacksburgVAUSA
- U.S. Geological SurveyGreat Lakes Science CenterSanduskyOHUSA
| | - Frederick J. Hoogakker
- Virginia Department of Wildlife ResourcesCharles CityVAUSA
- Tennessee Cooperative Fishery Research UnitTennessee Tech UniversityCookevilleTNUSA
| | - Kara B. Carlson
- Genomics and Microbiology LaboratoryNorth Carolina Museum of Natural SciencesRaleighNCUSA
- Department of GeneticsNorth Carolina State UniversityRaleighNCUSA
| |
Collapse
|
14
|
Traugott M, Thalinger B, Wallinger C, Sint D. Fish as predators and prey: DNA-based assessment of their role in food webs. JOURNAL OF FISH BIOLOGY 2021; 98:367-382. [PMID: 32441321 PMCID: PMC7891366 DOI: 10.1111/jfb.14400] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/26/2020] [Accepted: 05/20/2020] [Indexed: 05/04/2023]
Abstract
Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.
Collapse
Affiliation(s)
- Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Bettina Thalinger
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
- Centre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Corinna Wallinger
- Institute of Interdisciplinary Mountain Research, Austrian Academy of ScienceInnsbruckAustria
| | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| |
Collapse
|
15
|
Lefèvre E, Gardner CM, Gunsch CK. A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization. FEMS Microbiol Ecol 2020; 96:5850752. [PMID: 32490528 DOI: 10.1093/femsec/fiaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.
Collapse
Affiliation(s)
- Emilie Lefèvre
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane street, Sloan 101, Box 642910, Pullman, WA 99164, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
| |
Collapse
|
16
|
Ducotterd C, Crovadore J, Lefort F, Rubin JF, Ursenbacher S. A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758). Mol Ecol Resour 2020; 21:433-447. [PMID: 33047508 PMCID: PMC7821331 DOI: 10.1111/1755-0998.13277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 08/31/2020] [Accepted: 10/01/2020] [Indexed: 01/16/2023]
Abstract
High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.
Collapse
Affiliation(s)
- Charlotte Ducotterd
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Centre Emys, Association de Protection et Récupération des Tortues, Chavornay, Switzerland.,La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Julien Crovadore
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - François Lefort
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Jean-François Rubin
- La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, Basel, Switzerland.,info fauna - Centre Suisse de Cartographie de la Faune (CSCF) and Centre de coordination pour les reptiles et les amphibiens de Suisse (Karch), Neuchâtel, Switzerland
| |
Collapse
|
17
|
Nishitani G, Shiromoto M, Sato-Okoshi W, Ishikawa A. Molecular approach for analysis of in situ feeding by the dinoflagellate Noctiluca scintillans. HARMFUL ALGAE 2020; 99:101928. [PMID: 33218450 DOI: 10.1016/j.hal.2020.101928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/01/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
The red tide forming heterotrophic dinoflagellate Noctiluca scintillans is common in temperate to tropical waters around the world. Understanding the in situ prey of N. scintillans is essential for elucidating its role in marine microbial food webs. In this study, we applied two polymerase chain reaction (PCR)-based cloning techniques, a predator-specific restriction enzyme, and a blocking primer. The PCR of nuclear 18S rDNA was performed on single N. scintillans cells that were collected from Ishinomaki Bay, Japan, in May 2018. The maximum detection rates of non-Noctiluca sequences were 56% using the restriction enzyme method and 87% with the blocking primer method, representing a broad taxonomic range of organisms, including diatom, dinoflagellate, bolidophyte, haptophyte, euglenophyte, green algae, golden algae, ciliate, heliozoa, copepod, brown seaweed, sponge, bivalve, and polychaete. The diverse DNA was probably ingested by N. scintillans directly or indirectly through secondary predation or ingestion of marine snow or detritus containing many organisms. The application of molecular approaches to various species may reveal undiscovered interactions within the phytoplankton community, including prey-predator, or symbiotic relationships.
Collapse
Affiliation(s)
- Goh Nishitani
- Graduate School of Agricultural Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai 980-0845, Japan.
| | - Masaomi Shiromoto
- Graduate School of Agricultural Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai 980-0845, Japan
| | - Waka Sato-Okoshi
- Graduate School of Agricultural Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai 980-0845, Japan.
| | - Akira Ishikawa
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
| |
Collapse
|
18
|
Clerissi C, Guillou L, Escoubas JM, Toulza E. Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers. BMC Microbiol 2020; 20:193. [PMID: 32620152 PMCID: PMC7333408 DOI: 10.1186/s12866-020-01860-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. RESULTS To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples. CONCLUSIONS Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.
Collapse
Affiliation(s)
- Camille Clerissi
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France. .,PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, Roscoff, France
| | - Jean-Michel Escoubas
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Montpellier, France
| | - Eve Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| |
Collapse
|
19
|
Huggins LG, Koehler AV, Schunack B, Inpankaew T, Traub RJ. A Host-Specific Blocking Primer Combined with Optimal DNA Extraction Improves the Detection Capability of a Metabarcoding Protocol for Canine Vector-Borne Bacteria. Pathogens 2020; 9:E258. [PMID: 32244645 PMCID: PMC7238069 DOI: 10.3390/pathogens9040258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Bacterial canine vector-borne diseases are responsible for some of the most life-threatening conditions of dogs in the tropics and are typically poorly researched with some presenting a zoonotic risk to cohabiting people. Next-generation sequencing based methodologies have been demonstrated to accurately characterise a diverse range of vector-borne bacteria in dogs, whilst also proving to be more sensitive than conventional PCR techniques. We report two improvements to a previously developed metabarcoding tool that increased the sensitivity and diversity of vector-borne bacteria detected from canine blood. Firstly, we developed and tested a canine-specific blocking primer that prevents cross-reactivity of bacterial primer amplification on abundant canine mitochondrial sequences. Use of our blocking primer increased the number of canine vector-borne infections detected (five more Ehrlichia canis and three more Anaplasma platys infections) and increased the diversity of bacterial sequences found. Secondly, the DNA extraction kit employed can have a significant effect on the bacterial community characterised. Therefore, we compared four different DNA extraction kits finding the Qiagen DNeasy Blood and Tissue Kit to be superior for detection of blood-borne bacteria, identifying nine more A. platys, two more E. canis, one more Mycoplasma haemocanis infection and more putative bacterial pathogens than the lowest performing kit.
Collapse
Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | | | - Tawin Inpankaew
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| |
Collapse
|
20
|
French BJ, Lim YW, Zgliczynski BJ, Edwards RA, Rohwer F, Sandin SA. Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents. Ecol Evol 2020; 10:3413-3423. [PMID: 32273998 PMCID: PMC7141070 DOI: 10.1002/ece3.6138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/22/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022] Open
Abstract
AIM Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo-Malay-Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next-generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence. LOCATION Flint Island, Southern Line Islands, Republic of Kiribati. METHODS A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four "arc-eye" hawkfish species in the Paracirrhites species complex and a potential hybrid. Fish from four Paracirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species. RESULTS Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of P. bicolor with P. arcatus and P. xanthus with P. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches. MAIN CONCLUSIONS Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus, P. xanthus, and P. bicolor) cluster separately from the more broadly distributed P. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.
Collapse
Affiliation(s)
- Beverly J. French
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| | - Yan Wei Lim
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Brian J. Zgliczynski
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| | - Robert A. Edwards
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
- Department of Computer ScienceSan Diego State UniversitySan DiegoCAUSA
| | - Forest Rohwer
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Stuart A. Sandin
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| |
Collapse
|
21
|
Casey JM, Meyer CP, Morat F, Brandl SJ, Planes S, Parravicini V. Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13206] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jordan M. Casey
- PSL Université Paris: EPHE‐UPVD‐CNRS, USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
- Department of Invertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington District of Columbia USA
| | - Christopher P. Meyer
- Department of Invertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington District of Columbia USA
| | - Fabien Morat
- PSL Université Paris: EPHE‐UPVD‐CNRS, USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
| | - Simon J. Brandl
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
| | - Serge Planes
- PSL Université Paris: EPHE‐UPVD‐CNRS, USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
| | - Valeriano Parravicini
- PSL Université Paris: EPHE‐UPVD‐CNRS, USR 3278 CRIOBE Université de Perpignan Perpignan France
- Laboratoire d'Excellence “CORAIL” Perpignan France
| |
Collapse
|
22
|
Leray M, Alldredge AL, Yang JY, Meyer CP, Holbrook SJ, Schmitt RJ, Knowlton N, Brooks AJ. Dietary partitioning promotes the coexistence of planktivorous species on coral reefs. Mol Ecol 2019; 28:2694-2710. [PMID: 30933383 PMCID: PMC6852152 DOI: 10.1111/mec.15090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 11/29/2022]
Abstract
Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co‐occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In particular, the extent to which food partitioning contributes to species coexistence in hyperdiverse tropical ecosystems remains unresolved. Here, we use a molecular approach to investigate inter‐ and intraspecific dietary partitioning between two species of damselfish (Dascyllus flavicaudus, Chromis viridis) that commonly co‐occur in branching corals. Species‐level identification of their diverse zooplankton prey revealed significant differences in diet composition between species despite their seemingly similar feeding strategies. Dascyllus exhibited a more diverse diet than Chromis, whereas Chromis tended to select larger prey items. A large calanoid copepod, Labidocera sp., found in low density and higher in the water column during the day, explained more than 19% of the variation in dietary composition between Dascyllus and Chromis. Dascyllus did not significantly shift its diet in the presence of Chromis, which suggests intrinsic differences in feeding behaviour. Finally, prey composition significantly shifted during the ontogeny of both fish species. Our findings show that levels of dietary specialization among coral reef associated species have likely been underestimated, and they underscore the importance of characterizing trophic webs in tropical ecosystems at higher levels of taxonomic resolution. They also suggest that niche redundancy may not be as common as previously thought.
Collapse
Affiliation(s)
- Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Balboa, Ancon, Panama
| | - Alice L Alldredge
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California
| | - Joy Y Yang
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher P Meyer
- National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Sally J Holbrook
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California.,Coastal Research Center, Marine Science Institute, University of California Santa Barbara, Santa Barbara, California
| | - Russell J Schmitt
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California.,Coastal Research Center, Marine Science Institute, University of California Santa Barbara, Santa Barbara, California
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Andrew J Brooks
- Coastal Research Center, Marine Science Institute, University of California Santa Barbara, Santa Barbara, California
| |
Collapse
|
23
|
Sawaya NA, Djurhuus A, Closek CJ, Hepner M, Olesin E, Visser L, Kelble C, Hubbard K, Breitbart M. Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding. Ecol Evol 2019; 9:1029-1040. [PMID: 30805138 PMCID: PMC6374654 DOI: 10.1002/ece3.4742] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 01/09/2023] Open
Abstract
Environmental DNA (eDNA) is the DNA suspended in the environment (e.g., water column), which includes cells, gametes, and other material derived from but not limited to shedding of tissue, scales, mucus, and fecal matter. Amplifying and sequencing marker genes (i.e., metabarcoding) from eDNA can reveal the wide range of taxa present in an ecosystem through analysis of a single water sample. Metabarcoding of eDNA provides higher resolution data than visual surveys, aiding in assessments of ecosystem health. This study conducted eDNA metabarcoding of two molecular markers (cytochrome c oxidase I (COI) and 18S ribosomal RNA (rRNA) genes) to survey eukaryotic diversity across multiple trophic levels in surface water samples collected at three sites along the coral reef tract within the Florida Keys National Marine Sanctuary (FKNMS) during four research cruises in 2015. The 18S rRNA gene sequences recovered 785 genera while the COI gene sequences recovered 115 genera, with only 33 genera shared between the two datasets, emphasizing the complementarity of these marker genes. Community composition for both genetic markers clustered by month of sample collection, suggesting that temporal variation has a larger effect on biodiversity than spatial variability in the FKNMS surface waters. Sequences from both marker genes were dominated by copepods, but each marker recovered distinct phytoplankton groups, with 18S rRNA gene sequences dominated by dinoflagellates and COI sequences dominated by coccolithophores. Although eDNA samples were collected from surface waters, many benthic species such as sponges, crustaceans, and corals were identified. These results show the utility of eDNA metabarcoding for cataloging biodiversity to establish an ecosystem baseline against which future samples can be compared in order to monitor community changes.
Collapse
Affiliation(s)
- Natalie A. Sawaya
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
| | - Anni Djurhuus
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
| | - Collin J. Closek
- Stanford Center for Ocean SolutionsStanford UniversityStanfordCalifornia
- Department of Civil and Environmental EngineeringStanford UniversityStanfordCalifornia
| | - Megan Hepner
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
| | - Emily Olesin
- Florida Fish and Wildlife Conservation Commission‐Fish and Wildlife Research InstituteSaint PetersburgFlorida
| | - Lindsey Visser
- Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
- NOAA Atlantic Oceanographic and Meteorological LaboratoryMiamiFlorida
| | | | - Katherine Hubbard
- Florida Fish and Wildlife Conservation Commission‐Fish and Wildlife Research InstituteSaint PetersburgFlorida
| | - Mya Breitbart
- College of Marine ScienceUniversity of South FloridaSaint PetersburgFlorida
| |
Collapse
|
24
|
Hyperdiverse Macrofauna Communities Associated with a Common Sponge, Stylissa carteri, Shift across Ecological Gradients in the Central Red Sea. DIVERSITY 2019. [DOI: 10.3390/d11020018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sponges act as important microhabitats in the marine environment and promote biodiversity by harboring a wide variety of macrofauna, but little is known about the magnitude and patterns of diversity of sponge-associated communities. This study uses DNA barcoding to examine the macrofaunal communities associated with Stylissa carteri in the central Saudi Arabian Red Sea, an understudied ecosystem with high biodiversity and endemism. In total, 146 operational taxonomic units (OTUs) were distinguished from 938 successfully-sequenced macrofauna individuals from 99 sponges. A significant difference was found in the macrofaunal community composition of S. carteri along a cross-shelf gradient using OTU abundance (Bray–Curtis dissimilarity index), with more amphipods associated with offshore sponges and more brittle stars and fishes associated with inshore sponges. The abundance of S. carteri also showed a gradient, increasing with proximity to shore. However, no significant differences in macrofaunal community composition or total macrofauna abundance were observed between exposed and sheltered sides of the reefs and there was no significant change in total macrofauna abundance along the inshore–offshore gradient. As climate change and ocean acidification continue to impact coral reef ecosystems, understanding the ecology of sponges and their role as microhabitats may become more important for understanding their full ramifications for biodiversity.
Collapse
|
25
|
Fotedar S, Lukehurst S, Jackson G, Snow M. Molecular tools for identification of shark species involved in depredation incidents in Western Australian fisheries. PLoS One 2019; 14:e0210500. [PMID: 30633772 PMCID: PMC6329513 DOI: 10.1371/journal.pone.0210500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/23/2018] [Indexed: 11/19/2022] Open
Abstract
Shark depredation is an issue of concern in some Western Australian recreational and commercial fisheries where it can have economic, social and ecological consequences. Knowledge of the shark species involved is fundamental to developing effective management strategies to mitigate the impacts of depredation. Identification of the species responsible is difficult as direct observation of depredation events is uncommon and evaluating bite marks on fish has a high degree of uncertainty. The use of trace DNA techniques has provided an alternative method for species identification. We demonstrate proof of concept for a targeted DNA barcoding approach to identify shark species using trace DNA found at bite marks on recovered remains of hooked fish. Following laboratory validation, forensic analysis of swabs collected from samples of bitten demersal fish, led to the definitive identification of shark species involved in 100% of the incidences of depredation (n = 16).
Collapse
Affiliation(s)
- Seema Fotedar
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
- * E-mail:
| | - Sherralee Lukehurst
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
- Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Gary Jackson
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
| | - Michael Snow
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
| |
Collapse
|
26
|
Gillet B, Cottet M, Destanque T, Kue K, Descloux S, Chanudet V, Hughes S. Direct fishing and eDNA metabarcoding for biomonitoring during a 3-year survey significantly improves number of fish detected around a South East Asian reservoir. PLoS One 2018; 13:e0208592. [PMID: 30543655 PMCID: PMC6292600 DOI: 10.1371/journal.pone.0208592] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 11/20/2018] [Indexed: 11/18/2022] Open
Abstract
Biodiversity has to be accurately evaluated to assess more precisely possible dam effects on fish populations, in particular on the most biodiverse rivers such as the Mekong River. To improve tools for fish biodiversity assessment, a methodological survey was performed in the surroundings of a recent hydropower dam in the Mekong basin, the Nam Theun 2 project. Results of two different approaches, experimental surface gillnets capture and environmental DNA metabarcoding assays based on 12S ribosomal RNA and cytochrome b, were compared during 3 years (2014–2016). Pitfalls and benefits were identified for each method but the combined use of both approaches indisputably allows describing more accurately fish diversity around the reservoir. Importantly, striking convergent results were observed for biodiversity reports. 75% of the fish species caught by gillnets (62/82) were shown by the metabarcoding study performed on DNA extracted from water samples. eDNA approach also revealed to be sensitive by detecting 30 supplementary species known as present before the dam construction but never caught by gillnets during 3 years. Furthermore, potential of the marker-genes study might be underestimated since it was not possible to assign some sequences at lower taxonomic levels. Although 121 sequences were generated for this study, a third of species in the area, that exhibits high endemism, are still unknown in DNA databases. Efforts to complete local reference libraries must continue to improve the taxonomic assignment quality when using the non-invasive and promising eDNA approach. These results are of broader interest because of increasing number of hydropower projects in the Mekong Basin. They reveal the crucial importance to sample tissues/DNA of species before dam projects, i.e. before the species could become endangered and difficult to catch, to obtain more precise biomonitoring in the future as we believe eDNA metabarcoding will rapidly be integrated as a standard tool in such studies.
Collapse
Affiliation(s)
- Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche, Lyon, France
| | - Maud Cottet
- Nam Theun 2 Power Company Limited, Environment & Social Division, Environment Department, Gnommalath Office, Vientiane, Lao PDR
| | - Thibault Destanque
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche, Lyon, France
| | - Kaoboun Kue
- Nam Theun 2 Power Company Limited, Environment & Social Division, Environment Department, Gnommalath Office, Vientiane, Lao PDR
| | - Stéphane Descloux
- EDF, Hydro Engineering Centre, Environment and Social Department, Le Bourget-du-Lac, France
| | - Vincent Chanudet
- EDF, Hydro Engineering Centre, Environment and Social Department, Le Bourget-du-Lac, France
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche, Lyon, France
- * E-mail:
| |
Collapse
|
27
|
Clerissi C, Brunet S, Vidal-Dupiol J, Adjeroud M, Lepage P, Guillou L, Escoubas JM, Toulza E. Protists Within Corals: The Hidden Diversity. Front Microbiol 2018; 9:2043. [PMID: 30233528 PMCID: PMC6127297 DOI: 10.3389/fmicb.2018.02043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.
Collapse
Affiliation(s)
- Camille Clerissi
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Sébastien Brunet
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - Jeremie Vidal-Dupiol
- IFREMER, IHPE UMR 5244, Univ. Perpignan Via Domitia, CNRS, Univ. Montpellier, Montpellier, France
| | - Mehdi Adjeroud
- Institut de Recherche pour le Développement, UMR 9220 ENTROPIE & Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, France
| | - Pierre Lepage
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - Laure Guillou
- CNRS, UMR 7144, Sorbonne Universités, Université Pierre et Marie Curie - Paris 6, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Michel Escoubas
- CNRS, IHPE UMR 5244, Univ. Perpignan Via Domitia, IFREMER, Univ. Montpellier, Montpellier, France
| | - Eve Toulza
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| |
Collapse
|
28
|
Banchi E, Stankovic D, Fernández-Mendoza F, Gionechetti F, Pallavicini A, Muggia L. ITS2 metabarcoding analysis complements lichen mycobiome diversity data. Mycol Prog 2018; 17:1049-1066. [PMID: 30956650 PMCID: PMC6428334 DOI: 10.1007/s11557-018-1415-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/12/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023]
Abstract
Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.
Collapse
Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - David Stankovic
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia
| | | | - Fabrizia Gionechetti
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- Institute of Plant Sciences, Karl-Franzens University of Graz, Holteigasse 6, 8010 Graz, Austria
| |
Collapse
|
29
|
Bonato KO, Silva PC, Malabarba LR. Unrevealing Parasitic Trophic Interactions—A Molecular Approach for Fluid-Feeding Fishes. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
30
|
Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey tool to examine the potential use of uranium mine containment ponds as water sources by wildlife. We tested samples from surface water near mines and from one mine containment pond using two markers, 12S and 16S rRNA gene amplicons, to survey for vertebrate species. We recovered large numbers of sequence reads from taxa expected to be in the area and from less common or hard to observe taxa such as the tiger salamander and gray fox. Detection of these two species is of note because they were not observed in a previous species assessment, and tiger salamander DNA was found in the mine containment pond sample. We also found that sample concentration by centrifugation was a more efficient and more feasible method than filtration in these highly turbid surface waters. Ultimately, the use of eDNA metabarcoding could allow for a better understanding of the area’s overall biodiversity and community composition as well as aid current ecotoxicological risk assessment work.
Collapse
|
31
|
Yoon TH, Kang HE, Lee SR, Lee JB, Baeck GW, Park H, Kim HW. Metabarcoding analysis of the stomach contents of the Antarctic Toothfish ( Dissostichus mawsoni) collected in the Antarctic Ocean. PeerJ 2017; 5:e3977. [PMID: 29134141 PMCID: PMC5680711 DOI: 10.7717/peerj.3977] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/10/2017] [Indexed: 01/23/2023] Open
Abstract
Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species. A total of 19 species was identified from the stomach of D. mawsoni in this study, which included 14 fish species and five mollusks. More than 90% of contigs belonged to fish species, supporting the postulate that the major prey of D. mawsoni are fish. Two fish species, Macrourus whitsoni and Chionobathyscus dewitti, were the most important prey items (a finding similar to that of previous studies). We also obtained genotypes of prey items by NGS analysis, identifying an additional 17 representative haplotypes in this study. Comparison with three previous morphological studies and the NGS-based molecular identification in this study extended our knowledge regarding the prey of D. mawsoni, which previously was not possible. These results suggested that NGS-based diet studies are possible, if several current technical limitations, including the quality of the barcode database or the development of precise molecular quantification techniques to link them with morphological values, are overcome. To achieve this, additional studies should be conducted on various marine organisms.
Collapse
Affiliation(s)
- Tae-Ho Yoon
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Hye-Eun Kang
- Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
| | - Soo Rin Lee
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Jae-Bong Lee
- National Institute of Fisheries Science (NIFS), Busan, Republic of Korea
| | - Gun Wook Baeck
- Department of Seafood & Aquaculture Science/Institute of Marine Industry/Marine Bio-Education & Research Center, College of Marine Science, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Hyun Park
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, Republic of Korea
| | - Hyun-Woo Kim
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea.,Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
| |
Collapse
|
32
|
DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem. PLoS One 2017; 12:e0186929. [PMID: 29059215 PMCID: PMC5653352 DOI: 10.1371/journal.pone.0186929] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 10/10/2017] [Indexed: 11/27/2022] Open
Abstract
The three-spined stickleback (Gasterosteus aculeatus L., hereafter ‘stickleback’) is a common mesopredatory fish in marine, coastal and freshwater areas. In large parts of the Baltic Sea, stickleback densities have increased >10-fold during the last decades, and it is now one of the dominating fish species both in terms of biomass and effects on lower trophic levels. Still, relatively little is known about its diet—knowledge which is essential to understand the increasing role sticklebacks play in the ecosystem. Fish diet analyses typically rely on visual identification of stomach contents, a labour-intensive method that is made difficult by prey digestion and requires expert taxonomic knowledge. However, advances in DNA-based metabarcoding methods promise a simultaneous identification of most prey items, even from semi-digested tissue. Here, we studied the diet of stickleback from the western Baltic Sea coast using both DNA metabarcoding and visual analysis of stomach contents. Using the cytochrome oxidase (CO1) marker we identified 120 prey taxa in the diet, belonging to 15 phyla, 83 genera and 84 species. Compared to previous studies, this is an unusually high prey diversity. Chironomids, cladocerans and harpacticoids were dominating prey items. Large sticklebacks were found to feed more on benthic prey, such as amphipods, gastropods and isopods. DNA metabarcoding gave much higher taxonomic resolution (median rank genus) than visual analysis (median rank order), and many taxa identified using barcoding could not have been identified visually. However, a few taxa identified by visual inspection were not revealed by barcoding. In summary, our results suggest that the three-spined stickleback feeds on a wide variety of both pelagic and benthic organisms, indicating that the strong increase in stickleback populations may affect many parts of the Baltic Sea coastal ecosystem.
Collapse
|
33
|
Nelson EJH, Holden J, Eves R, Tufts B. Comparison of diets for Largemouth and Smallmouth Bass in Eastern Lake Ontario using DNA barcoding and stable isotope analysis. PLoS One 2017; 12:e0181914. [PMID: 28771612 PMCID: PMC5542617 DOI: 10.1371/journal.pone.0181914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 07/10/2017] [Indexed: 11/19/2022] Open
Abstract
Largemouth (LMB: Micropterus salmoides) and Smallmouth Bass (SMB: Micropterus dolomieu) are important species in the recreational fisheries of the Laurentian Great Lakes. The invasion of the Round Goby (Neogobius melanostomus) into these lakes has changed several facets of black bass biology, but there is still much to learn about the relationship between these species. Previous dietary analyses have shown Round Goby to be important prey for bass, but have been limited by low visual identification rates of dissected stomach items. Within the present study, DNA barcoding and stable isotope analysis improve prey identification and provide a more quantitative dietary analysis of adult black bass in Lake Ontario, comparing the importance of Round Goby as prey between these two species. Eighty-four LMB (406mm fork length ±4mm SEM) and two hundred sixty-four SMB (422mm ±2mm) obtained as tournament mortalities had prey identified using DNA-based methods. Round Goby was the most prevalent prey species for both predators. The diet of LMB was three times more diverse than that of SMB, which almost entirely consists of Round Goby. Our results provide further support that recent increases in the size of Lake Ontario bass are a result of Round Goby consumption, and that the effects of this dietary shift on body condition are greater for SMB. Techniques developed in this study include reverse-oriented dual priming oligonucleotides used as blocking primers for predator DNA, and an automated design approach of restriction fragment length polymorphism tests for identifying prey DNA barcodes.
Collapse
Affiliation(s)
- Erich J. H. Nelson
- Freshwater Fisheries Conservation Lab, Department of Biology, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
| | - Jeremy Holden
- Lake Ontario Management Unit, Glenora Fisheries Station, Ontario Ministry of Natural Resources and Forestry, Picton, Ontario, Canada
| | - Robert Eves
- Protein Function Discovery Lab, Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Bruce Tufts
- Freshwater Fisheries Conservation Lab, Department of Biology, Queen’s University, Kingston, Ontario, Canada
| |
Collapse
|
34
|
Olmos-Pérez L, Roura Á, Pierce GJ, Boyer S, González ÁF. Diet Composition and Variability of Wild Octopus vulgaris and Alloteuthis media (Cephalopoda) Paralarvae: a Metagenomic Approach. Front Physiol 2017; 8:321. [PMID: 28596735 PMCID: PMC5442249 DOI: 10.3389/fphys.2017.00321] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
The high mortality of cephalopod early stages is the main bottleneck to grow them from paralarvae to adults in culture conditions, probably because the inadequacy of the diet that results in malnutrition. Since visual analysis of digestive tract contents of paralarvae provides little evidence of diet composition, the use of molecular tools, particularly next generation sequencing (NGS) platforms, offers an alternative to understand prey preferences and nutrient requirements of wild paralarvae. In this work, we aimed to determine the diet of paralarvae of the loliginid squid Alloteuthis media and to enhance the knowledge of the diet of recently hatched Octopus vulgaris paralarvae collected in different areas and seasons in an upwelling area (NW Spain). DNA from the dissected digestive glands of 32 A. media and 64 O. vulgaris paralarvae was amplified with universal primers for the mitochondrial gene COI, and specific primers targeting the mitochondrial gene 16S gene of arthropods and the mitochondrial gene 16S of Chordata. Following high-throughput DNA sequencing with the MiSeq run (Illumina), up to 4,124,464 reads were obtained and 234,090 reads of prey were successfully identified in 96.87 and 81.25% of octopus and squid paralarvae, respectively. Overall, we identified 122 Molecular Taxonomic Units (MOTUs) belonging to several taxa of decapods, copepods, euphausiids, amphipods, echinoderms, molluscs, and hydroids. Redundancy analysis (RDA) showed seasonal and spatial variability in the diet of O. vulgaris and spatial variability in A. media diet. General Additive Models (GAM) of the most frequently detected prey families of O. vulgaris revealed seasonal variability of the presence of copepods (family Paracalanidae) and ophiuroids (family Euryalidae), spatial variability in presence of crabs (family Pilumnidae) and preference in small individual octopus paralarvae for cladocerans (family Sididae) and ophiuroids. No statistically significant variation in the occurrences of the most frequently identified families was revealed in A. media. Overall, these results provide new clues about dietary preferences of wild cephalopod paralarvae, thus opening up new scenarios for research on trophic ecology and digestive physiology under controlled conditions.
Collapse
Affiliation(s)
| | - Álvaro Roura
- Instituto de Investigaciones Marinas, Ecobiomar, CSICVigo, Spain.,La Trobe UniversityMelbourne, VIC, Australia
| | - Graham J Pierce
- Instituto de Investigaciones Marinas, Ecobiomar, CSICVigo, Spain.,CESAM and Departamento de Biologia, Universidade de AveiroAveiro, Portugal
| | - Stéphane Boyer
- Applied Molecular Solutions Research Group, Environmental and Animal Sciences, Unitec Institute of TechnologyAuckland, New Zealand
| | - Ángel F González
- Instituto de Investigaciones Marinas, Ecobiomar, CSICVigo, Spain
| |
Collapse
|
35
|
Coker DJ, Chaidez V, Berumen ML. Habitat Use and Spatial Variability of Hawkfishes with a Focus on Colour Polymorphism in Paracirrhites forsteri. PLoS One 2017; 12:e0169079. [PMID: 28125589 PMCID: PMC5268474 DOI: 10.1371/journal.pone.0169079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/12/2016] [Indexed: 11/19/2022] Open
Abstract
Identifying relationships between fishes and their environment is an integral part of understanding coral reef ecosystems. However, this information is lacking for many species, particularly in understudied and remote regions. With coral reefs continuing to face environmental pressures, insight into abundance and distribution patterns along with resource use of fish communities will aid in advancing our ecological understanding and management processes. Based on ecological surveys of hawkfish assemblages (Family: Cirrhitidae) in the Red Sea, we reveal distinct patterns in the distribution and abundance across the continental shelf, wave exposure, and with depth, particularly in the four colour morphs of Paracirrhites forsteri. Distinct patterns were observed among hawkfishes, with higher abundance of all species recorded on reefs farther from shore and on wave exposed reef zones. Cirrhitus spilotoceps was only recorded on the exposed crest, but unlike the other species, did not associate with live coral colonies. Overall, the most abundant species was P. forsteri. This species exploited a variety of habitats but showed an affinity for complex habitats provided by live and dead coral colonies. No difference in habitat use was observed among the four colour morphs, but distinct patterns were apparent in distribution and abundance with depth. This study suggests that in addition to P. forsteri exhibiting diverse colour morphologies, these various morphotypes appear to have corresponding ecological differences in the Red Sea. To better understand this, further studies are needed to identify what these differences extend to and the mechanisms involved.
Collapse
Affiliation(s)
- Darren J. Coker
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- * E-mail:
| | - Veronica Chaidez
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael L. Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| |
Collapse
|
36
|
Leal MC, Ferrier-Pagès C. Molecular trophic markers in marine food webs and their potential use for coral ecology. Mar Genomics 2016; 29:1-7. [PMID: 26896098 DOI: 10.1016/j.margen.2016.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 12/25/2022]
Abstract
Notable advances in ecological genomics have been driven by high-throughput sequencing technology and taxonomically broad sequence repositories that allow us to accurately assess species interactions with great taxonomic resolution. The use of DNA as a marker for ingested food is particularly relevant to address predator-prey interactions and disentangle complex marine food webs. DNA-based methods benefit from reductionist molecular approaches to address ecosystem scale processes, such as community structure and energy flow across trophic levels, among others. Here we review how molecular trophic markers have been used to better understand trophic interactions in the marine environment and their advantages and limitations. We focus on animal groups where research has been focused, such as marine mammals, seabirds, fishes, pelagic invertebrates and benthic invertebrates, and use case studies to illustrate how DNA-based methods unraveled food-web interactions. The potential of molecular trophic markers for disentangling the complex trophic ecology of corals is also discussed.
Collapse
Affiliation(s)
- Miguel Costa Leal
- Dept. of Fish Ecology Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry; Seestrasse 79, 6047 Kastanienbaum, Switzerland.
| | - Christine Ferrier-Pagès
- Centre Scientifique du Monaco, Ecophysiology team, 8 Quai Antoine ler, MC-98000 Monaco, Monaco.
| |
Collapse
|
37
|
Bourlat SJ, Haenel Q, Finnman J, Leray M. Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes Using Illumina MiSeq: The Dual-PCR Method. Methods Mol Biol 2016; 1452:197-207. [PMID: 27460379 DOI: 10.1007/978-1-4939-3774-5_13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
This protocol details the preparation of multiplexed amplicon libraries for metabarcoding (amplicon-based) studies of microscopic marine eukaryotes. Metabarcoding studies, based on the amplification of a taxonomically informative marker from a collection of organisms or an environmental sample, can be performed to analyze biodiversity patterns or predator-prey interactions. For Metazoa, we use the mitochondrial cytochrome oxidase 1 (CO1) or the small ribosomal subunit (SSU) markers. Here, we describe a strategy for the preparation of multiplexed Illumina MiSeq libraries using a dual-PCR approach for the addition of index and adaptor sequences.
Collapse
Affiliation(s)
- Sarah J Bourlat
- Department of Marine Sciences, University of Gothenburg, Box 463, SE-405 30, Gothenburg, Sweden.
| | - Quiterie Haenel
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-413 19, Gothenburg, Sweden
| | - Jennie Finnman
- Sahlgrenska Academy, Gothenburg University Genomics Core Facility, Gothenburg, Sweden
| | - Matthieu Leray
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| |
Collapse
|
38
|
Leray M, Meyer CP, Mills SC. Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 2015; 3:e1047. [PMID: 26137428 PMCID: PMC4485734 DOI: 10.7717/peerj.1047] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/02/2015] [Indexed: 11/20/2022] Open
Abstract
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction.
Collapse
Affiliation(s)
- Matthieu Leray
- USR 3278 CRIOBE CNRS-EPHE-UPVD, CBETM de l'Université de Perpignan , Perpignan Cedex , France ; Laboratoire d'Excellence "CORAIL" ; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, D.C. , USA
| | - Christopher P Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, D.C. , USA
| | - Suzanne C Mills
- USR 3278 CRIOBE CNRS-EPHE-UPVD, CBETM de l'Université de Perpignan , Perpignan Cedex , France ; Laboratoire d'Excellence "CORAIL"
| |
Collapse
|
39
|
DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol 2015; 30:25-35. [DOI: 10.1016/j.tree.2014.10.008] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 10/23/2014] [Accepted: 10/28/2014] [Indexed: 01/28/2023]
|
40
|
Mollot G, Duyck PF, Lefeuvre P, Lescourret F, Martin JF, Piry S, Canard E, Tixier P. Cover cropping alters the diet of arthropods in a banana plantation: a metabarcoding approach. PLoS One 2014; 9:e93740. [PMID: 24695585 PMCID: PMC3973587 DOI: 10.1371/journal.pone.0093740] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 03/06/2014] [Indexed: 11/27/2022] Open
Abstract
Plant diversification using cover crops may promote natural regulation of agricultural pests by supporting alternative prey that enable the increase of arthropod predator densities. However, the changes in the specific composition of predator diet induced by cover cropping are poorly understood. Here, we hypothesized that the cover crop can significantly alter the diet of predators in agroecosystems. The cover crop Brachiaria decumbens is increasingly used in banana plantations to control weeds and improve physical soil properties. In this paper, we used a DNA metabarcoding approach for the molecular analysis of the gut contents of predators (based on mini-COI) to identify 1) the DNA sequences of their prey, 2) the predators of Cosmopolites sordidus (a major pest of banana crops), and 3) the difference in the specific composition of predator diets between a bare soil plot (BSP) and a cover cropped plot (CCP) in a banana plantation. The earwig Euborellia caraibea, the carpenter ant Camponotus sexguttatus, and the fire ant Solenopsis geminata were found to contain C. sordidus DNA at frequencies ranging from 1 to 7%. While the frequencies of predators positive for C. sordidus DNA did not significantly differ between BSP and CCP, the frequency at which E. caraibea was positive for Diptera was 26% in BSP and 80% in CCP; the frequency at which C. sexguttatus was positive for Jalysus spinosus was 14% in BSP and 0% in CCP; and the frequency at which S. geminata was positive for Polytus mellerborgi was 21% in BSP and 3% in CCP. E. caraibea, C. sexguttatus and S. geminata were identified as possible biological agents for the regulation of C. sordidus. The detection of the diet changes of these predators when a cover crop is planted indicates the possible negative effects on pest regulation if predators switch to forage on alternative prey.
Collapse
Affiliation(s)
- Gregory Mollot
- CIRAD, UR 26 Systèmes de culture à base de bananiers, plantains et ananas, PRAM, Le Lamentin, Martinique, France
- INRA, UR-1115 Plantes et Systèmes de culture Horticoles, Avignon, France
| | - Pierre-François Duyck
- CIRAD, UR 26 Systèmes de culture à base de bananiers, plantains et ananas, PRAM, Le Lamentin, Martinique, France
- CIRAD, UMR PVBMT, CIRAD/Université de La Réunion, Pôle de Protection des Plantes, Saint-Pierre, La Réunion, France
- * E-mail:
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, CIRAD/Université de La Réunion, Pôle de Protection des Plantes, Saint-Pierre, La Réunion, France
| | | | | | | | - Elsa Canard
- CIRAD, UR 26 Systèmes de culture à base de bananiers, plantains et ananas, PRAM, Le Lamentin, Martinique, France
- CNRS-IRD, UMR 2724 MIVEGEC, Montpellier, France
| | - Philippe Tixier
- CIRAD, UR 26 Systèmes de culture à base de bananiers, plantains et ananas, PRAM, Le Lamentin, Martinique, France
- CIRAD – CATIE, Departamento de Agricultura y Agroforesteria, CATIE, Turrialba, Costa Rica
| |
Collapse
|
41
|
Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Boehm JT, Machida RJ. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool 2013; 10:34. [PMID: 23767809 PMCID: PMC3686579 DOI: 10.1186/1742-9994-10-34] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. RESULTS We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. CONCLUSIONS The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.
Collapse
Affiliation(s)
- Matthieu Leray
- Laboratoire d'Excellence "CORAIL", USR 3278 CRIOBE CNRS-EPHE, CBETM de l’Université de Perpignan, 66860, Perpignan Cedex, France
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC-163, Washington, DC 20013-7012, USA
| | - Joy Y Yang
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Christopher P Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC-163, Washington, DC 20013-7012, USA
| | - Suzanne C Mills
- Laboratoire d'Excellence "CORAIL", USR 3278 CRIOBE CNRS-EPHE, CBETM de l’Université de Perpignan, 66860, Perpignan Cedex, France
| | - Natalia Agudelo
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC-163, Washington, DC 20013-7012, USA
| | | | - Joel T Boehm
- Biology Department, City College of New York, New York, NY 10031, USA
- The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|