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Jossart Q, Bauman D, Moreau CV, Saucède T, Christiansen H, Brasier MJ, Convey P, Downey R, Figuerola B, Martin P, Norenburg J, Rosenfeld S, Verheye M, Danis B. A pioneer morphological and genetic study of the intertidal fauna of the Gerlache Strait (Antarctic Peninsula). ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:514. [PMID: 36973586 DOI: 10.1007/s10661-023-11066-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The underexplored intertidal ecosystems of Antarctica are facing rapid changes in important environmental factors. Associated with temperature increase, reduction in coastal ice will soon expose new ice-free areas that will be colonized by local or distant biota. To enable detection of future changes in faunal composition, a biodiversity baseline is urgently required. Here, we evaluated intertidal faunal diversity at 13 locations around the Gerlache Strait (western Antarctic Peninsula), using a combination of a quadrat approach, morphological identification and genetic characterization. Our data highlight a community structure comprising four generally distributed and highly abundant species (the flatworm Obrimoposthia wandeli, the bivalve Kidderia subquadrata, and the gastropods Laevilitorina umbilicata and Laevilitorina caliginosa) as well as 79 rarer and less widely encountered species. The most abundant species thrive in the intertidal zone due to their ability to either survive overwinter in situ or to rapidly colonize this zone when conditions allow. In addition, we confirmed the presence of multiple trophic levels at nearly all locations, suggesting that complex inter-specific interactions occur within these communities. Diversity indices contrasted between sampling locations (from 3 to 32 species) and multivariate approaches identified three main groups. This confirms the importance of environmental heterogeneity in shaping diversity patterns within the investigated area. Finally, we provide the first genetic and photographic baseline of the Antarctic intertidal fauna (106 sequences, 137 macrophotographs), as well as preliminary insights on the biogeography of several species. Taken together, these results provide a timely catalyst to assess the diversity and to inform studies of the potential resilience of these intertidal communities.
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Affiliation(s)
- Quentin Jossart
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Marine Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
- UMR CNRS 6282, Université de Bourgogne, Dijon, France.
| | - David Bauman
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, Montpellier, IRD, France
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Camille Ve Moreau
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Madeleine J Brasier
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Peter Convey
- British Antarctic Survey, NERC, Cambridge, United Kingdom
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
- Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (MI-BASE), Santiago, Chile
| | - Rachel Downey
- Fenner School of Environment & Society, Australian National University, Canberra, Australia
| | | | - Patrick Martin
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Jon Norenburg
- Smithsonian Institution National Museum of Natural History, Washington, United States of America
| | - Sebastian Rosenfeld
- Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (MI-BASE), Santiago, Chile
- Laboratorio de Ecosistemas Marinos Antarticos y Subantarticos, Universidad de Magallanes, Punta Arenas, Chile
- Centro de Investigación Gaia‑Antártica, Universidad de Magallanes, Punta Arenas, Chile
| | - Marie Verheye
- Laboratory of Trophic and Isotopes Ecology (LETIS), Université de Liège, Liège, Belgium
- Laboratory of Evolutionary Ecology, Université de Liège, Liège, Belgium
| | - Bruno Danis
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Sultana S, Azlan A, Desa MNM, Mahyudin NA. Multiplex platforms in biosensor based analytical approaches: Opportunities and challenges for the speciation of animal species in food chain. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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Matassa CM, Hitchcock CB. Bioblitz Assessment of Rocky Intertidal Biodiversity within the Boston Harbor Islands National Recreation Area. Northeast Nat (Steuben) 2021. [DOI: 10.1656/045.025.s908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Colleen B. Hitchcock
- Biology Department and Environmental Studies Program, Brandeis University, Waltham, MA 02453
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Parker SS, Pauly GB, Moore J, Fraga NS, Knapp JJ, Principe Z, Brown BV, Randall JM, Cohen BS, Wake TA. Adapting the bioblitz to meet conservation needs. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:1007-1019. [PMID: 29493001 DOI: 10.1111/cobi.13103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/30/2018] [Accepted: 02/23/2018] [Indexed: 06/08/2023]
Abstract
When conservation strategies require new, field-based information, practitioners must find the best ways to rapidly deliver high-quality survey data. To address this challenge, several rapid-assessment approaches have been developed since the early 1990s. These typically involve large areas, take many months to complete, and are not appropriate when conservation-relevant survey data are urgently needed for a specific locale. In contrast, bioblitzes are designed for quick collection of site-specific survey data. Although bioblitzes are commonly used to achieve educational or public-engagement goals, conservation practitioners are increasingly using a modified bioblitz approach to generate conservation-relevant data while simultaneously enhancing research capacity and building working partnerships focused on conservation concerns. We term these modified events expert bioblitzes. Several expert bioblitzes have taken place on lands of conservation concern in Southern California and have involved collaborative efforts of government agencies, nonprofit organizations, botanic gardens, museums, and universities. The results of expert bioblitzes directly informed on-the-ground conservation and decision-making; increased capacity for rapid deployment of expert bioblitzes in the future; and fostered collaboration and communication among taxonomically and institutionally diverse experts. As research and conservation funding becomes increasingly scarce, expert bioblitzes can play an increasingly important role in biodiversity conservation.
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Affiliation(s)
- Sophie S Parker
- The Nature Conservancy, 445 S. Figueroa Street, Suite 1950, Los Angeles, CA, 90071, U.S.A
| | - Gregory B Pauly
- Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, 90007, U.S.A
| | - James Moore
- The Nature Conservancy, 915 E. Bonneville Avenue, Las Vegas, NV, 89101, U.S.A
| | - Naomi S Fraga
- Rancho Santa Ana Botanic Garden, 1500 N. College Avenue, Claremont, CA, 91711, U.S.A
| | - John J Knapp
- The Nature Conservancy, 532 E. Main Street, Suite 200, Ventura, CA, 93001, U.S.A
| | - Zachary Principe
- The Nature Conservancy, 402 W. Broadway, Suite 1350, San Diego, CA, 92101, U.S.A
| | - Brian V Brown
- Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, 90007, U.S.A
| | - John M Randall
- The Nature Conservancy, 402 W. Broadway, Suite 1350, San Diego, CA, 92101, U.S.A
| | - Brian S Cohen
- The Nature Conservancy, 402 W. Broadway, Suite 1350, San Diego, CA, 92101, U.S.A
| | - Thomas A Wake
- Zooarchaeology Laboratory, The Cotsen Institute of Archaeology, University of California, Los Angeles, CA, 90095, U.S.A
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Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries. Sci Rep 2015. [PMID: 26199185 PMCID: PMC4510495 DOI: 10.1038/srep12162] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections.
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Shokralla S, Porter TM, Gibson JF, Dobosz R, Janzen DH, Hallwachs W, Golding GB, Hajibabaei M. Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep 2015; 5:9687. [PMID: 25884109 PMCID: PMC4401116 DOI: 10.1038/srep09687] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/16/2015] [Indexed: 01/26/2023] Open
Abstract
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.
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Affiliation(s)
- Shadi Shokralla
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Teresita M Porter
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Joel F Gibson
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Rafal Dobosz
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
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Meier R, Wong W, Srivathsan A, Foo M. $1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics 2015; 32:100-110. [DOI: 10.1111/cla.12115] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2015] [Indexed: 12/01/2022] Open
Affiliation(s)
- Rudolf Meier
- Lee Kong Chian Natural History Museum; National University of Singapore; 6 Science Drive 2 Singapore 117546 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
- University Scholars Programme; National University of Singapore, University Town; 18 College Avenue East Singapore 138593 Singapore
| | - Winghing Wong
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Amrita Srivathsan
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Maosheng Foo
- Lee Kong Chian Natural History Museum; National University of Singapore; 6 Science Drive 2 Singapore 117546 Singapore
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Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proc Natl Acad Sci U S A 2014; 111:8007-12. [PMID: 24808136 DOI: 10.1073/pnas.1406468111] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Conventional assessments of ecosystem sample composition are based on morphology-based or DNA barcode identification of individuals. Both approaches are costly and time-consuming, especially when applied to the large number of specimens and taxa commonly included in ecological investigations. Next-generation sequencing approaches can overcome the bottleneck of individual specimen isolation and identification by simultaneously sequencing specimens of all taxa in a bulk mixture. Here we apply multiple parallel amplification primers, multiple DNA barcode markers, 454-pyrosequencing, and Illumina MiSeq sequencing to the same sample to maximize recovery of the arthropod macrobiome and the bacterial and other microbial microbiome of a bulk arthropod sample. We validate this method with a complex sample containing 1,066 morphologically distinguishable arthropods from a tropical terrestrial ecosystem with high taxonomic diversity. Multiamplicon next-generation DNA barcoding was able to recover sequences corresponding to 91% of the distinguishable individuals in a bulk environmental sample, as well as many species present as undistinguishable tissue. 454-pyrosequencing was able to recover 10 more families of arthropods and 30 more species than did conventional Sanger sequencing of each individual specimen. The use of other loci (16S and 18S ribosomal DNA gene regions) also added the detection of species of microbes associated with these terrestrial arthropods. This method greatly decreases the time and money necessary to perform DNA-based comparisons of biodiversity among ecosystem samples. This methodology opens the door to much cheaper and increased capacity for ecological and evolutionary studies applicable to a wide range of socio-economic issues, as well as a basic understanding of how the world works.
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Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE. The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics 2013; 4:43. [PMID: 24330602 PMCID: PMC3904460 DOI: 10.1186/2041-1480-4-43] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/30/2013] [Indexed: 12/20/2022] Open
Abstract
As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO;
http://www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, content, structure, adoption, and governance approach. The ontology is available from
http://purl.obolibrary.org/obo/envo.owl - an OBO format version is also available by switching the file suffix to “obo”.
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Affiliation(s)
- Pier Luigi Buttigieg
- HGF-MPG Research Group on Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.
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