1
|
Revanales T, Lastra M, Sánchez-Mata A, García-Gallego MA, Mora J, Rodil IF. Biodiversity patterns of the benthic macrofaunal communities across the intertidal sedimentary shores of two Antarctic islands. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106333. [PMID: 38185002 DOI: 10.1016/j.marenvres.2023.106333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024]
Abstract
Antarctic benthic ecosystems support a unique fauna characterized by high levels of diversity and endemism. However, our knowledge of the macrofauna communities across the Antarctic intertidal sedimentary shore is limited, and their fundamental ecological features, including spatial variability, remain poorly understood. This study aimed to investigate the abundance, community structure (i.e. taxa-specific abundance), and biodiversity patterns (α-, β-, and λ-diversity) of benthic macrofauna communities on intertidal sedimentary shores of two Antarctic islands (South Shetland archipelago, N of Antarctic Peninsula): Livingston and Deception. We conducted a quantitative sampling during two Austral summer campaigns (2004 and 2005), studying eleven intertidal sites, with five sites located on Livingston and six on Deception. Our results demonstrated a significantly higher abundance of intertidal benthic macrofauna communities on Livingston than on Deception. Furthermore, significant differences in community structure were observed between the two islands. In terms of biodiversity patterns, there were no significant differences in the number of taxa within communities (α-diversity) between the two islands. However, significant differences in the variation of community composition (determined by the number and identity of taxa) between intertidal sites (β-diversity) were observed, shedding light on the higher total taxa count (λ-diversity) on Livingston compared to Deception. We suggest that the island-specific characteristics (e.g., granulometric characteristics, ice disturbance, sedimentation rates, and geothermal activity) determine the differences observed in macrofauna communities. However, other ecological processes and factors are operating on different spatial and temporal scales (e.g., population dynamics, biotic interactions, oceanographic conditions, and climate change) that influence the occurrence and abundance of macrofaunal taxa. Our findings contribute to the fundamental understanding of the spatial variability of these communities and provide essential information for better management decisions and conservation practices in Antarctic coastal ecosystems.
Collapse
Affiliation(s)
- T Revanales
- Department of Biology, Institute of Marine Research (INMAR), University of Cádiz, 11510, Puerto Real, Cádiz, Spain.
| | - M Lastra
- Marine Research Center, University of Vigo, Geoma, 36310, Vigo, Spain
| | - A Sánchez-Mata
- Department of de Ecology and Animal Biology, Faculty of Marine Science, University of Vigo, 36310, Vigo, Spain
| | - M A García-Gallego
- Department of de Ecology and Animal Biology, Faculty of Marine Science, University of Vigo, 36310, Vigo, Spain
| | - J Mora
- Department of Zoology, Faculty of Biology, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - I F Rodil
- Department of Biology, Institute of Marine Research (INMAR), University of Cádiz, 11510, Puerto Real, Cádiz, Spain
| |
Collapse
|
2
|
Van Steenkiste NWL, Wakeman KC, Söderström B, Leander BS. Patterns of host-parasite associations between marine meiofaunal flatworms (Platyhelminthes) and rhytidocystids (Apicomplexa). Sci Rep 2023; 13:21050. [PMID: 38030717 PMCID: PMC10687266 DOI: 10.1038/s41598-023-48233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
Microturbellarians are abundant and ubiquitous members of marine meiofaunal communities around the world. Because of their small body size, these microscopic animals are rarely considered as hosts for parasitic organisms. Indeed, many protists, both free-living and parasitic ones, equal or surpass meiofaunal animals in size. Despite several anecdotal records of "gregarines", "sporozoans", and "apicomplexans" parasitizing microturbellarians in the literature-some of them dating back to the nineteenth century-these single-celled parasites have never been identified and characterized. More recently, the sequencing of eukaryotic microbiomes in microscopic invertebrates have revealed a hidden diversity of protist parasites infecting microturbellarians and other meiofaunal animals. Here we show that apicomplexans isolated from twelve taxonomically diverse rhabdocoel taxa and one species of proseriate collected in four geographically distinct areas around the Pacific Ocean (Okinawa, Hokkaido, and British Columbia) and the Caribbean Sea (Curaçao) all belong to the apicomplexan genus Rhytidocystis. Based on comprehensive molecular phylogenies of Rhabdocoela and Proseriata inferred from both 18S and 28S rDNA sequences, as well as a molecular phylogeny of Marosporida inferred from 18S rDNA sequences, we determine the phylogenetic positions of the microturbellarian hosts and their parasites. Multiple lines of evidence, including morphological and molecular data, show that at least nine new species of Rhytidocystis infect the microturbellarian hosts collected in this study, more than doubling the number of previously recognized species of Rhytidocystis, all of which infect polychaete hosts. A cophylogenetic analysis examining patterns of phylosymbiosis between hosts and parasites suggests a complex picture of overall incongruence between host and parasite phylogenies, and varying degrees of geographic signals and taxon specificity.
Collapse
Affiliation(s)
- Niels W L Van Steenkiste
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada.
- Hakai Institute, Heriot Bay, Quadra Island, BC, Canada.
| | - Kevin C Wakeman
- Institute for the Advancement of High Education, Hokkaido University, Sapporo, Japan.
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
| | - Brian S Leander
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
3
|
Harbuzov Z, Farberova V, Tom M, Pallavicini A, Stanković D, Lotan T, Lubinevsky H. Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition. Mar Genomics 2022; 65:100980. [PMID: 35963148 DOI: 10.1016/j.margen.2022.100980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.
Collapse
Affiliation(s)
- Zoya Harbuzov
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel.
| | - Valeria Farberova
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Moshe Tom
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - David Stanković
- National institute of Biology, Department of Organisms and Ecosystems Research, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tamar Lotan
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Hadas Lubinevsky
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
| |
Collapse
|
4
|
Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
Collapse
Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
| |
Collapse
|
5
|
Fonseca VG, Kirse A, Giebner H, Vause BJ, Drago T, Power DM, Peck LS, Clark MS. Metabarcoding the Antarctic Peninsula biodiversity using a multi-gene approach. ISME COMMUNICATIONS 2022; 2:37. [PMID: 37938273 PMCID: PMC9723778 DOI: 10.1038/s43705-022-00118-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 07/04/2023]
Abstract
Marine sediment communities are major contributors to biogeochemical cycling and benthic ecosystem functioning, but they are poorly described, particularly in remote regions such as Antarctica. We analysed patterns and drivers of diversity in metazoan and prokaryotic benthic communities of the Antarctic Peninsula with metabarcoding approaches. Our results show that the combined use of mitochondrial Cox1, and 16S and 18S rRNA gene regions recovered more phyla, from metazoan to non-metazoan groups, and allowed correlation of possible interactions between kingdoms. This higher level of detection revealed dominance by the arthropods and not nematodes in the Antarctic benthos and further eukaryotic diversity was dominated by benthic protists: the world's largest reservoir of marine diversity. The bacterial family Woeseiaceae was described for the first time in Antarctic sediments. Almost 50% of bacteria and 70% metazoan taxa were unique to each sampled site (high alpha diversity) and harboured unique features for local adaptation (niche-driven). The main abiotic drivers measured, shaping community structure were sediment organic matter, water content and mud. Biotic factors included the nematodes and the highly abundant bacterial fraction, placing protists as a possible bridge for between kingdom interactions. Meiofauna are proposed as sentinels for identifying anthropogenic-induced changes in Antarctic marine sediments.
Collapse
Affiliation(s)
- V G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, UK.
| | - A Kirse
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - H Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - B J Vause
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - T Drago
- Portuguese Institute for Sea and Atmosphere (IPMA), Tavira, Portugal
- Institute Dom Luiz (IDL), University of Lisbon, Lisbon, Portugal
| | - D M Power
- Centre of Marine Sciences (CCMAR), Faro, Portugal
| | - L S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - M S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| |
Collapse
|
6
|
Cordier T, Angeles IB, Henry N, Lejzerowicz F, Berney C, Morard R, Brandt A, Cambon-Bonavita MA, Guidi L, Lombard F, Arbizu PM, Massana R, Orejas C, Poulain J, Smith CR, Wincker P, Arnaud-Haond S, Gooday AJ, de Vargas C, Pawlowski J. Patterns of eukaryotic diversity from the surface to the deep-ocean sediment. SCIENCE ADVANCES 2022; 8:eabj9309. [PMID: 35119936 PMCID: PMC8816347 DOI: 10.1126/sciadv.abj9309] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.
Collapse
Affiliation(s)
- Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
- Corresponding author. (T.C.); (A.J.G.); (C.d.V.); (J.P.)
| | - Inès Barrenechea Angeles
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP,, 29680 Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cédric Berney
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP,, 29680 Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Raphaël Morard
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, 28359 Bremen, Germany
| | - Angelika Brandt
- Department of Marine Zoology, Section Crustacea, Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt, Germany
- Institute for Ecology, Evolution, and Diversity, Goethe-University of Frankfurt, FB 15, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| | | | - Lionel Guidi
- Laboratoire d’océanographie de Villefranche (LOV), Observatoire Océanologique, Sorbonne Universités, UPMC Université Paris 06, CNRS, Villefranche-sur-Mer, 06230 Nice, France
| | - Fabien Lombard
- Laboratoire d’océanographie de Villefranche (LOV), Observatoire Océanologique, Sorbonne Universités, UPMC Université Paris 06, CNRS, Villefranche-sur-Mer, 06230 Nice, France
- Institut Universitaire de France (IUF), Paris, France
| | - Pedro Martinez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany
- FK V IBU, AG Marine Biodiversität, Universität Oldenburg, 26129 Oldenburg, Germany
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Covadonga Orejas
- Spanish Institute of Oceanography (IEO), Oceanographic Centre of Gijón,, Avda Príncipe de Asturias 70 bis, 33212 Gijón, Spain
| | - Julie Poulain
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University Evry, University Paris-Saclay, 91057 Evry, France
| | - Craig R. Smith
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University Evry, University Paris-Saclay, 91057 Evry, France
| | | | - Andrew J. Gooday
- National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Corresponding author. (T.C.); (A.J.G.); (C.d.V.); (J.P.)
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP,, 29680 Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
- Corresponding author. (T.C.); (A.J.G.); (C.d.V.); (J.P.)
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- ID-Gene ecodiagnostics, Confignon, 1232 Geneva, Switzerland
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
- Corresponding author. (T.C.); (A.J.G.); (C.d.V.); (J.P.)
| |
Collapse
|
7
|
GHELLER PAULAF, CORBISIER THAISN. Monitoring the anthropogenic impacts in Admiralty Bay using meiofauna community as indicators (King George Island, Antarctica). AN ACAD BRAS CIENC 2022; 94:e20210616. [DOI: 10.1590/0001-3765202220210616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/21/2021] [Indexed: 11/22/2022] Open
|
8
|
Clarke LJ, Suter L, Deagle BE, Polanowski AM, Terauds A, Johnstone GJ, Stark JS. Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 2021; 9:e12458. [PMID: 34820189 PMCID: PMC8601059 DOI: 10.7717/peerj.12458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
Collapse
Affiliation(s)
- Laurence J Clarke
- Australian Antarctic Division, Kingston, Tasmania, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Leonie Suter
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Bruce E Deagle
- Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, Australia
| | | | - Aleks Terauds
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | | | | |
Collapse
|
9
|
The occurrence of Nematoda in coastal sea ice on Svalbard (European Arctic) determined with the 18S small subunit rRNA gene. Polar Biol 2021. [DOI: 10.1007/s00300-021-02863-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractUnderstanding the diversity and functioning of Arctic sea ice ecosystems is vital to evaluate and predict the impact of current and future climate change. In the microscopic communities inhabiting the brine channels inside sea ice, nematodes often dominate numerically and act as bacterivores and herbivores. Despite nematodes great abundances and known ecological roles, molecular tools have not been applied to investigate their species diversity in sea ice. In an attempt to begin establishing a molecular baseline for species diversity of sea ice nematodes, we Sanger sequenced 74 specimens from four locations around Svalbard (European Arctic), using the 18S rRNA barcode. Currently available nucleotide reference databases are both underpopulated with representative marine nematode taxa and contain a substantial number of misidentified organisms. Together, these limitations inhibited the ability to identify marine specimens collected in this study with certainty. Nevertheless, our molecular data indicate the presence of two genera in sea ice on Svalbard—Theristus and Halomonhystera. While it is possible that the latter represents a novel ice nematode species, future studies, including morphometric analysis, are needed to verify our molecular findings. We leverage the assignment of molecular information to robustly identify nematodes and provide the first insight into the diversity of sea ice nematodes in the European Arctic. We advocate for an intensified cooperation between molecular and morphological taxonomists to expedite the establishment of baseline surveys that are required to predict biological consequences of the diminishing sea ice habitat in the future.
Collapse
|
10
|
Bowen BW, Forsman ZH, Whitney JL, Faucci A, Hoban M, Canfield SJ, Johnston EC, Coleman RR, Copus JM, Vicente J, Toonen RJ. Species Radiations in the Sea: What the Flock? J Hered 2021; 111:70-83. [PMID: 31943081 DOI: 10.1093/jhered/esz075] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Species flocks are proliferations of closely-related species, usually after colonization of depauperate habitat. These radiations are abundant on oceanic islands and in ancient freshwater lakes, but rare in marine habitats. This contrast is well documented in the Hawaiian Archipelago, where terrestrial examples include the speciose silverswords (sunflower family Asteraceae), Drosophila fruit flies, and honeycreepers (passerine birds), all derived from one or a few ancestral lineages. The marine fauna of Hawai'i is also the product of rare colonization events, but these colonizations usually yield only one species. Dispersal ability is key to understanding this evolutionary inequity. While terrestrial fauna rarely colonize between oceanic islands, marine fauna with pelagic larvae can make this leap in every generation. An informative exception is the marine fauna that lack a pelagic larval stage. These low-dispersal species emulate a "terrestrial" mode of reproduction (brooding, viviparity, crawl-away larvae), yielding marine species flocks in scattered locations around the world. Elsewhere, aquatic species flocks are concentrated in specific geographic settings, including the ancient lakes of Baikal (Siberia) and Tanganyika (eastern Africa), and Antarctica. These locations host multiple species flocks across a broad taxonomic spectrum, indicating a unifying evolutionary phenomenon. Hence marine species flocks can be singular cases that arise due to restricted dispersal or other intrinsic features, or they can be geographically clustered, promoted by extrinsic ecological circumstances. Here, we review and contrast intrinsic cases of species flocks in individual taxa, and extrinsic cases of geological/ecological opportunity, to elucidate the processes of species radiations.
Collapse
Affiliation(s)
- Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Jonathan L Whitney
- Joint Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI
| | - Anuschka Faucci
- Math & Sciences Division, Leeward Community College, University of Hawai'i, Pearl City, HI
| | - Mykle Hoban
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | | | - Erika C Johnston
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Richard R Coleman
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Jan Vicente
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| |
Collapse
|
11
|
Ceja-Navarro JA, Wang Y, Ning D, Arellano A, Ramanculova L, Yuan MM, Byer A, Craven KD, Saha MC, Brodie EL, Pett-Ridge J, Firestone MK. Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop. MICROBIOME 2021; 9:96. [PMID: 33910643 PMCID: PMC8082632 DOI: 10.1186/s40168-021-01042-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/26/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. RESULTS We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants (Panicum virgatum) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists' community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. CONCLUSIONS We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system. Video Abstract.
Collapse
Affiliation(s)
- Javier A. Ceja-Navarro
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA USA
| | - Yuan Wang
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Abelardo Arellano
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Leila Ramanculova
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | - Alyssa Byer
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | | | | | - Eoin L. Brodie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Mary K. Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| |
Collapse
|
12
|
Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes. PLoS One 2020; 15:e0236540. [PMID: 33147221 PMCID: PMC7641347 DOI: 10.1371/journal.pone.0236540] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/25/2020] [Indexed: 01/04/2023] Open
Abstract
The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification, and are capable of simultaneously providing valuable information on other taxonomic groups.
Collapse
|
13
|
Giebner H, Langen K, Bourlat SJ, Kukowka S, Mayer C, Astrin JJ, Misof B, Fonseca VG. Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes. Mol Ecol Resour 2020; 20:1333-1345. [PMID: 32462738 DOI: 10.1111/1755-0998.13201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/20/2020] [Accepted: 05/15/2020] [Indexed: 12/25/2022]
Abstract
Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence-capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence-capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence-capture recovered 80%-90% of the control sample species. DNA sequence-capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low-cost, whereas DNA-sequence capture for biodiversity assessment is still in its infancy, is more time-consuming but provides more taxonomic assignments.
Collapse
Affiliation(s)
- Hendrik Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Kathrin Langen
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sarah J Bourlat
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sandra Kukowka
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Christoph Mayer
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Jonas J Astrin
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Vera G Fonseca
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany.,Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| |
Collapse
|
14
|
Fegley SR, Smith JPS, Johnson D, Schirmer A, Jones-Boggs J, Edmonds A, Bursey J. Nourished, Exposed Beaches Exhibit Altered Sediment Structure and Meiofaunal Communities. DIVERSITY-BASEL 2020; 12. [PMID: 34168518 PMCID: PMC8221582 DOI: 10.3390/d12060245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To retain recreational uses and shoreline protection, a large proportion of ocean beaches have been, and continue to be, nourished. Adding sand from subtidal and terrestrial sources to nourish beaches rarely re-creates the original sediment structure of the beach. Numerous studies have demonstrated that meiofaunal communities are altered by changes in sediment composition in low-energy substrates, therefore, we have explored whether beach nourishment has affected exposed, ocean beach meiofaunal communities. Since the early 2000s, we have conducted a series of sampling and experimental studies on meiofauna and sediments on nourished beaches in coastal North Carolina USA that had been sampled previously in the early 1970s, prior to any beach nourishment. Most of our studies consider meiofauna at the level of major taxa only. However, a few studies examine free-living flatworm (turbellarian) species in detail because of the existence of historical studies examining this group. Comparison of contemporary results to historical data and of heavily nourished versus lightly nourished beaches reveals extensive changes to beach sediment structure and meiofaunal community composition, indicating that the beaches are a more heterogeneous habitat than in the past. The effects of these substantial physical and biological changes to the production of beach ecosystem services are unlikely to be inconsequential.
Collapse
Affiliation(s)
- Stephen R. Fegley
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC 28557, USA
| | - Julian P. S. Smith
- Department of Biology, Winthrop University, Rock Hill, SC 29733, USA
- Correspondence:
| | - Douglas Johnson
- Department of Biology, Winthrop University, Rock Hill, SC 29733, USA
| | - Amelia Schirmer
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC 28557, USA
| | | | - Austin Edmonds
- Department of Biology, Barton College, Wilson, NC 27893, USA
| | - Joseph Bursey
- Department of Biology, Winthrop University, Rock Hill, SC 29733, USA
| |
Collapse
|
15
|
Marine tardigrades from Lützow-Holm Bay, East Antarctica with the description of a new species. Polar Biol 2020. [DOI: 10.1007/s00300-020-02671-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
16
|
Zenker MM, Specht A, Fonseca VG. Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol. Ecol Evol 2020; 10:2352-2366. [PMID: 32184986 PMCID: PMC7069332 DOI: 10.1002/ece3.6042] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/24/2022] Open
Abstract
Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two-step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.
Collapse
Affiliation(s)
- Mauricio M. Zenker
- Zoological Research Museum Alexander KoenigBonnGermany
- Present address:
Rua Eulo MaroniSão PauloBrazil
| | - Alexandre Specht
- Embrapa CerradosBrasiliaBrazil
- Present address:
Embrapa CerradosPlanaltinaFederal DistrictBrazil
| | - Vera G. Fonseca
- Zoological Research Museum Alexander KoenigBonnGermany
- Present address:
Centre for EnvironmentFisheries and Aquaculture Science (Cefas)WeymouthUK
| |
Collapse
|
17
|
Vause BJ, Morley SA, Fonseca VG, Jażdżewska A, Ashton GV, Barnes DKA, Giebner H, Clark MS, Peck LS. Spatial and temporal dynamics of Antarctic shallow soft-bottom benthic communities: ecological drivers under climate change. BMC Ecol 2019; 19:27. [PMID: 31262299 PMCID: PMC6604130 DOI: 10.1186/s12898-019-0244-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background Marine soft sediments are some of the most widespread habitats in the ocean, playing a vital role in global carbon cycling, but are amongst the least studied with regard to species composition and ecosystem functioning. This is particularly true of the Polar Regions, which are currently undergoing rapid climate change, the impacts of which are poorly understood. Compared to other latitudes, Polar sediment habitats also experience additional environmental drivers of strong seasonality and intense disturbance from iceberg scouring, which are major structural forces for hard substratum communities. This study compared sediment assemblages from two coves, near Rothera Point, Antarctic Peninsula, 67°S in order to understand the principal drivers of community structure, for the first time, evaluating composition across all size classes from mega- to micro-fauna. Results Morpho-taxonomy identified 77 macrofaunal species with densities of 464–16,084 individuals m−2. eDNA metabarcoding of microfauna, in summer only, identified a higher diversity, 189 metazoan amplicon sequence variants (ASVs) using the 18S ribosomal RNA and 249 metazoan ASVs using the mitochondrial COI gene. Both techniques recorded a greater taxonomic diversity in South Cove than Hangar Cove, with differences in communities between the coves, although the main taxonomic drivers varied between techniques. Morphotaxonomy identified the main differences between coves as the mollusc, Altenaeum charcoti, the cnidarian Edwardsia sp. and the polychaetes from the family cirratulidae. Metabarcoding identified greater numbers of species of nematodes, crustaceans and Platyhelminthes in South Cove, but more bivalve species in Hangar Cove. There were no detectable differences in community composition, measured through morphotaxonomy, between seasons, years or due to iceberg disturbance. Conclusions This study found that unlike hard substratum communities the diversity of Antarctic soft sediment communities is correlated with the same factors as other latitudes. Diversity was significantly correlated with grain size and organic content, not iceberg scour. The increase in glacial sediment input as glaciers melt, may therefore be more important than increased iceberg disturbance. Electronic supplementary material The online version of this article (10.1186/s12898-019-0244-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Belinda J Vause
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, Cambridgeshire, CB30ET, UK
| | - Simon A Morley
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, Cambridgeshire, CB30ET, UK.
| | - Vera G Fonseca
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113, Bonn, Germany
| | - Anna Jażdżewska
- Laboratory of Polar Biology and Oceanobiology, Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha st., 90-237, Lodz, Poland
| | - Gail V Ashton
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, Cambridgeshire, CB30ET, UK.,Smithsonian Environmental Research Center, Romberg Tiburon Center, Tiburon, CA, USA
| | - David K A Barnes
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, Cambridgeshire, CB30ET, UK
| | - Hendrik Giebner
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113, Bonn, Germany
| | - Melody S Clark
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, Cambridgeshire, CB30ET, UK
| | - Lloyd S Peck
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, Cambridgeshire, CB30ET, UK
| |
Collapse
|
18
|
Saccò M, Blyth A, Bateman PW, Hua Q, Mazumder D, White N, Humphreys WF, Laini A, Griebler C, Grice K. New light in the dark - a proposed multidisciplinary framework for studying functional ecology of groundwater fauna. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 662:963-977. [PMID: 30795483 DOI: 10.1016/j.scitotenv.2019.01.296] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/12/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Groundwaters provide the vast majority of unfrozen freshwater resources on the planet, but our knowledge of subsurface ecosystems is surprisingly limited. Stygofauna, or stygobionts -subterranean obligate aquatic animals - provide ecosystem services such as grazing biofilms and maintaining water quality, but we know little about how their ecosystems function. The cryptic nature of groundwaters, together with the high degree of local endemism and stygofaunal site-specific adaptations, represent major obstacles for the field. To overcome these challenges, and integrate biodiversity and ecosystem function, requires a holistic design drawing on classical ecology, taxonomy, molecular ecology and geochemistry. This study presents an approach based on the integration of existing concepts in groundwater ecology with three more novel scientific techniques: compound specific stable isotope analysis (CSIA) of amino acids, radiocarbon analysis (14C) and DNA analyses of environmental samples, stygofauna and gut contents. The combination of these techniques allows elucidation of aspects of ecosystem function that are often obscured in small invertebrates and cryptic systems. Carbon (δ13C) and nitrogen (δ15N) CSIA provides a linkage between biogeochemical patterns and ecological dynamics. It allows the identification of stygofaunal food web structures and energy flows based on the metabolic pathway of specific amino groups. Concurrently, 14C provides complementary data on the carbon recycling and incorporation within the stygobiotic trophic webs. Changes in groundwater environmental conditions (e.g. aquifer recharge), and subsequent community adaptations, can be pinpointed via the measurementof the radiocarbon fingerprint of water, sediment and specimens. DNA analyses are a rapidly expanding approach in ecology. eDNA is mainly employed as a biomonitoring tool, while metabarcoding of individuals and/or gut contents provides insight into diet regimes. In all cases, the application of the approaches in combination provides more powerful data than any one alone. By combining quantitative (CSIA and 14C) and qualitative (eDNA and DNA metabarcoding) approaches via Bayesian Mixing Models (BMM), linkages can be made between community composition, energy and nutrient sources in the system, and trophic function. This suggested multidisciplinary design will contribute to a more thorough comprehension of the biogeochemical and ecological patterns within these undervalued but essential ecosystems.
Collapse
Affiliation(s)
- Mattia Saccò
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia.
| | - Alison Blyth
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Philip W Bateman
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Quan Hua
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Debashish Mazumder
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Nicole White
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - William F Humphreys
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6986, Australia; School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Alex Laini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale G.P. Usberti 33/A, 43124 Parma, Italy
| | - Christian Griebler
- Helmholtz Center Munich, Institute of Groundwater Ecology, Neuherberg, Germany; University of Vienna, Dept of Limnology and Bio-Oceanography, Vienna, Austria
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
| |
Collapse
|
19
|
Halanych KM, Mahon AR. Challenging Dogma Concerning Biogeographic Patterns of Antarctica and the Southern Ocean. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-121415-032139] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antarctica is enormous, cold, remote, and particularly sensitive to climate change. Most biological research below 60°S has focused on the isolated nature of the biota and how organisms have adapted to the cold and ice. However, biogeographic patterns in Antarctica and the Southern Ocean, and the processes explaining how those patterns came about, still await adequate explanation. Both terrestrial and marine organisms have been influenced by climatic change (e.g., glaciation), physical phenomena (e.g., oceanic currents), and/or potential barriers to gene flow (e.g., steep thermal gradients). Whereas the Antarctic region contains diverse and complex marine communities, terrestrial systems tend to be comparatively simple with limited diversity. Here, we challenge the current dogma used to explain the diversity and biogeographic patterns present in the Antarctic. We assert that relatively modern processes within the last few million years, rather than geo-logical events that occurred in the Eocene and Miocene, account for present patterns of biodiversity in the region. Additionally, reproductive life history stages appear to have little influence in structuring genetic patterns in the Antarctic, as currents and glacial patterns are noted to be more important drivers of organismal patterns of distribution. Finally, we highlight the need for additional sampling, high-throughput genomic approaches, and broad, multinational cooperation for addressing outstanding questions of Antarctic biogeography and biodiversity.
Collapse
Affiliation(s)
- Kenneth M. Halanych
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| |
Collapse
|
20
|
Magoga G, Sahin DC, Fontaneto D, Montagna M. Barcoding of Chrysomelidae of Euro-Mediterranean area: efficiency and problematic species. Sci Rep 2018; 8:13398. [PMID: 30194432 PMCID: PMC6128942 DOI: 10.1038/s41598-018-31545-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/03/2018] [Indexed: 11/16/2022] Open
Abstract
Leaf beetles (Coleoptera: Chrysomelidae), with more than 37,000 species worldwide and about 2,300 in the Euro-Mediterranean region, are an ecological and economical relevant family, making their molecular identification of interest also in agriculture. This study, part of the Mediterranean Chrysomelidae Barcoding project (www.c-bar.org), aims to: (i) develop a reference Cytochrome c oxidase I (COI) library for the molecular identification of the Euro-Mediterranean Chrysomelidae; (ii) test the efficiency of DNA barcoding for leaf beetles identification; (iii) develop and compare optimal thresholds for distance-based identifications estimated at family and subfamily level, minimizing false positives and false negatives. Within this study, 889 COI nucleotide sequences of 261 species were provided; after the inclusion of information from other sources, a dataset of 7,237 sequences (542 species) was analysed. The average intra-interspecific distances were in the range of those recorded for Coleoptera: 1.6–24%. The estimated barcoding efficiency (~94%) confirmed the usefulness of this tool for Chrysomelidae identification. The few cases of failure were recorded for closely related species (e.g., Cryptocephalus marginellus superspecies, Cryptocephalus violaceus - Cryptocephalus duplicatus and some Altica species), even with morphologically different species sharing the same COI haplotype. Different optimal thresholds were achieved for the tested taxonomic levels, confirming that group-specific thresholds significantly improve molecular identifications.
Collapse
Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Didem Coral Sahin
- Directorate of Plant Protection Central Research Institute, Yenimahalle, Ankara, Turkey
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche-Istituto per lo Studio degli Ecosistemi, Largo Tonolli 50, 28922, Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy.
| |
Collapse
|
21
|
Leasi F, Sevigny JL, Laflamme EM, Artois T, Curini-Galletti M, de Jesus Navarrete A, Di Domenico M, Goetz F, Hall JA, Hochberg R, Jörger KM, Jondelius U, Todaro MA, Wirshing HH, Norenburg JL, Thomas WK. Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach. Commun Biol 2018; 1:112. [PMID: 30271992 PMCID: PMC6123632 DOI: 10.1038/s42003-018-0119-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/24/2018] [Indexed: 01/05/2023] Open
Abstract
Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and time-effective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates.
Collapse
Affiliation(s)
- Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Avenue, Chattanooga, TN, 37403, USA.
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA.
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
| | - Eric M Laflamme
- Department of Mathematics, Plymouth State University, MSC29, 17 High Street, Plymouth, NH, 03264, USA
| | - Tom Artois
- Centre for Environmental Sciences, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium
| | - Marco Curini-Galletti
- Dipartimento di Medicina Veterinaria, University of Sassari, via Muroni 25, 07100, Sassari, Italy
| | - Alberto de Jesus Navarrete
- Departmento de Sistemática y Ecología Acuática, El Colegio de la Frontera Sur, Unidad Chetumal, Av. Centenario Km. 5.5 Chetumal Quintana Roo, 77014, Chetumal, Mexico
| | - Maikon Di Domenico
- Centro de Estudos do Mar, Universidade Federal do Paraná, Av. Beira-Mar, s/n, Pontal do Sul, PO Box 61, 83255-976, Pontal do Paraná, PR, Brazil
| | - Freya Goetz
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - Jeffrey A Hall
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
| | - Rick Hochberg
- Department of Biological Science, University of Massachusetts Lowell, Olsen Hall 414, 198 Riverside St., Lowell, MA, 01854, USA
| | - Katharina M Jörger
- Department of Biology, Ludwig-Maximilians-University of Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Munich, Germany
| | - Ulf Jondelius
- Swedish Museum of Natural History, POB 5007, SE-104 05, Stockholm, Sweden
| | - M Antonio Todaro
- Department of Life Sciences, University of Modena & Reggio Emilia, Via G. Campi 213/d, 41125, Modena, Italy
| | - Herman H Wirshing
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
| |
Collapse
|
22
|
Stephenson I, Van Steenkiste NWL, Leander BS. Molecular phylogeny of neodalyellid flatworms (Rhabdocoela), including three new species from British Columbia. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- India Stephenson
- Department of Zoology University of British Columbia Vancouver British Columbia Canada
| | | | - Brian S. Leander
- Department of Zoology University of British Columbia Vancouver British Columbia Canada
| |
Collapse
|
23
|
Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Sci Rep 2018; 8:11737. [PMID: 30082688 PMCID: PMC6078945 DOI: 10.1038/s41598-018-30179-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022] Open
Abstract
Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.
Collapse
|
24
|
Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|