1
|
Barrenechea Angeles I, Nguyen NL, Greco M, Tan KS, Pawlowski J. Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity. PLoS One 2024; 19:e0298440. [PMID: 38422100 PMCID: PMC10903905 DOI: 10.1371/journal.pone.0298440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.
Collapse
Affiliation(s)
- Inès Barrenechea Angeles
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Ngoc-Loi Nguyen
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- Institute of Marine Sciences, Spanish National Research Council, Barcelona, Spain
| | - Koh Siang Tan
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- ID-Gene Ecodiagnostics Ltd., Plan-les-Ouates, Switzerland
| |
Collapse
|
2
|
Benthic Foraminifera Diversity of the Abyssal Northwest Atlantic. DIVERSITY 2023. [DOI: 10.3390/d15030381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The species diversity of benthic foraminifera at four abyssal working areas in the Labrador Sea, Labrador Basin, and Southwest of the Azores is documented. One hundred and fifty taxa (forty-three not assigned to a species) were found and their diversity was recorded. One hundred and twenty-four taxa (fifteen not assigned to a species) were illustrated with optical and/or SEM (Scanning Electron Microscope) images on twelve plates. The material was sampled during RV Sonne cruise SO286 as part of IceDivA2 (Icelandic marine Animals meets Diversity along latitudinal gradients in the deep sea of the Atlantic Ocean 2). IceDivA2 investigated the biodiversity within key groups of the marine benthic abyssal habitats of the North Atlantic. Thirty-two samples from four sliced and three full cores, from six stations sampled with a MUC (Multiple corer), were analyzed. Given low sedimentation rates in such environments the material is assumed to be of Holocene to late Pleistocene age. Due to the scarcity of living specimens this study was based on total assemblages. Four species-based clusters are identified, which correspond to the four working areas. The samples of each cluster show specific characteristics markedly different from those of the samples of the other clusters. It indicates that abyssal faunas are heterogeneous. Three clusters are dominated by Epistominella exigua (Brady, 1884), which is recorded as not rare to dominant in many abyssal plains worldwide. The faunal differences are manifested in the long tail of less important species and differing abundances of E. exigua.
Collapse
|
3
|
Martin JL, Santi I, Pitta P, John U, Gypens N. Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor.
Collapse
|
4
|
Macher JN, Wideman JG, Girard EB, Langerak A, Duijm E, Jompa J, Sadekov A, Vos R, Wissels R, Renema W. First report of mitochondrial COI in foraminifera and implications for DNA barcoding. Sci Rep 2021; 11:22165. [PMID: 34772985 PMCID: PMC8589990 DOI: 10.1038/s41598-021-01589-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences ("barcodes") of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.
Collapse
Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Elsa B Girard
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Anouk Langerak
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Elza Duijm
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | | | - Aleksey Sadekov
- ARC Centre of Excellence for Coral Reef Studies, Ocean Graduate School, The University of Western Australia, Crawley, Australia
| | - Rutger Vos
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Richard Wissels
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Willem Renema
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
5
|
Moles J, Derkarabetian S, Schiaparelli S, Schrödl M, Troncoso JS, Wilson NG, Giribet G. An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods. Sci Rep 2021; 11:8473. [PMID: 33875688 PMCID: PMC8055997 DOI: 10.1038/s41598-021-87244-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/25/2021] [Indexed: 02/02/2023] Open
Abstract
Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.
Collapse
Affiliation(s)
- Juan Moles
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
- SNSB-Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, Munich, Germany.
- Biozentrum Ludwig Maximilians University and GeoBio-Center LMU Munich, Munich, Germany.
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Stefano Schiaparelli
- DiSTAV, University of Genoa, C.so Europa 26, 16132, Genoa, Italy
- Italian National Antarctic Museum (MNA, Section of Genoa), Viale Benedetto XV n. 5, 16132, Genoa, Italy
| | - Michael Schrödl
- SNSB-Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, Munich, Germany
- Biozentrum Ludwig Maximilians University and GeoBio-Center LMU Munich, Munich, Germany
| | - Jesús S Troncoso
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus Lagoas-Marcosende s/n, 36200, Vigo, Spain
| | - Nerida G Wilson
- Collections and Research, Western Australian Museum, Welshpool DC, Locked Bag 49, Perth, WA, 6986, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| |
Collapse
|
6
|
Affiliation(s)
- Craig R. McClain
- Louisiana Universities Marine Consortium (LUMCON) Chauvin LA USA
| |
Collapse
|
7
|
Gooday AJ, Schoenle A, Dolan JR, Arndt H. Protist diversity and function in the dark ocean - Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists. Eur J Protistol 2020; 75:125721. [PMID: 32575029 DOI: 10.1016/j.ejop.2020.125721] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/27/2022]
Abstract
The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.
Collapse
Affiliation(s)
- Andrew J Gooday
- National Oceanography Centre, University of Southampton Waterfront Campus, Southampton, UK; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - John R Dolan
- Sorbonne Université, CNRS UMR 7093, Laboratoroire d'Océanographie de Villefranche-sur-Mer, Villefranche-sur-Mer, France
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
| |
Collapse
|
8
|
McCarthy AH, Peck LS, Hughes KA, Aldridge DC. Antarctica: The final frontier for marine biological invasions. GLOBAL CHANGE BIOLOGY 2019; 25:2221-2241. [PMID: 31016829 PMCID: PMC6849521 DOI: 10.1111/gcb.14600] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 05/26/2023]
Abstract
Antarctica is experiencing significant ecological and environmental change, which may facilitate the establishment of non-native marine species. Non-native marine species will interact with other anthropogenic stressors affecting Antarctic ecosystems, such as climate change (warming, ocean acidification) and pollution, with irreversible ramifications for biodiversity and ecosystem services. We review current knowledge of non-native marine species in the Antarctic region, the physical and physiological factors that resist establishment of non-native marine species, changes to resistance under climate change, the role of legislation in limiting marine introductions, and the effect of increasing human activity on vectors and pathways of introduction. Evidence of non-native marine species is limited: just four marine non-native and one cryptogenic species that were likely introduced anthropogenically have been reported freely living in Antarctic or sub-Antarctic waters, but no established populations have been reported; an additional six species have been observed in pathways to Antarctica that are potentially at risk of becoming invasive. We present estimates of the intensity of ship activity across fishing, tourism and research sectors: there may be approximately 180 vessels and 500+ voyages in Antarctic waters annually. However, these estimates are necessarily speculative because relevant data are scarce. To facilitate well-informed policy and management, we make recommendations for future research into the likelihood of marine biological invasions in the Antarctic region.
Collapse
Affiliation(s)
- Arlie H. McCarthy
- Department of ZoologyUniversity of CambridgeCambridgeUK
- British Antarctic Survey, NERCCambridgeUK
| | | | | | - David C. Aldridge
- Department of ZoologyUniversity of CambridgeCambridgeUK
- BioRISC, St Catharine's CollegeCambridgeUK
| |
Collapse
|
9
|
Voltski I, Gooday AJ, Pawlowski J. Eyes of the Deep-sea Floor: The Integrative Taxonomy of the Foraminiferal Genus Vanhoeffenella. Protist 2018; 169:235-267. [PMID: 29649777 DOI: 10.1016/j.protis.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 11/17/2017] [Accepted: 11/18/2017] [Indexed: 11/16/2022]
Abstract
Vanhoeffenella is a common deep-sea monothalamous foraminifer, some species of which have a unique eye-like test morphology. Owing to its world-wide distribution, it has been recorded numerous times since the "heroic age" of the deep-sea exploration in the early 20th century. So far, only 4 species have been described, and no attempts have been made to estimate the real diversity of this peculiar genus. Over the last fifteen years, we have collected specimens of Vanhoeffenella from various deep-sea areas, providing the basis for an integrative taxonomy and biogeography of this genus. Here, we clarify the phylogenetic position of Vanhoeffenella and give an account of its diversity in the Atlantic, Arctic and Southern Oceans (the Weddell Sea) as revealed by genetic marker (SSU rDNA) and morphology. Our study shows that Vanhoeffenella branches within Clade F of monothalamids and incorporates at least 10 putative species. Some could be distinguished by either morphological or molecular features, but only the integrative taxonomic approach provides a robust way to assess their diversity. We examine the new material of the type species (V. gaussi Rhumbler), redescribe the poorly-known V. oculus Earland and describe formally a fifth species, V. dilatata sp. nov.
Collapse
Affiliation(s)
- Ivan Voltski
- Department of Genetics and Evolution, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland.
| | - Andrew J Gooday
- National Oceanography Centre, Southampton, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland
| |
Collapse
|
10
|
Worldwide sampling reveals low genetic variability in populations of the freshwater ciliate Paramecium biaurelia (P. aurelia species complex, Ciliophora, Protozoa). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-017-0357-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
11
|
Borrelli C, Hou Y, Pawlowski JW, Holzmann M, Katz ME, Chandler GT, Bowser SS. Assessing SSU rDNA Barcodes in Foraminifera: A Case Study using Bolivina quadrata. J Eukaryot Microbiol 2017; 65:220-235. [PMID: 28865158 DOI: 10.1111/jeu.12471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 08/07/2017] [Accepted: 08/22/2017] [Indexed: 12/15/2022]
Abstract
The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences (KY468817-KY468826) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus).
Collapse
Affiliation(s)
- Chiara Borrelli
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, 12180, New York, USA
| | - Yubo Hou
- Wadsworth Center, New York State Department of Health, Albany, 12201, New York, USA
| | - Jan W Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, 1211, Switzerland
| | - Maria Holzmann
- Department of Genetics and Evolution, University of Geneva, Geneva, 1211, Switzerland
| | - Miriam E Katz
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, 12180, New York, USA
| | - G Thomas Chandler
- Arnold School of Public Health, University of South Carolina, Columbia, 29208, South Carolina, USA
| | - Samuel S Bowser
- Wadsworth Center, New York State Department of Health, Albany, 12201, New York, USA
| |
Collapse
|
12
|
Volkova E, Kudryavtsev A. Description of Neoparamoeba longipodia n. sp. and a new strain of Neoparamoeba aestuarina (Page, 1970) (Amoebozoa, Dactylopodida) from deep-sea habitats. Eur J Protistol 2017; 61:107-121. [DOI: 10.1016/j.ejop.2017.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
|
13
|
Taylor ML, Roterman CN. Invertebrate population genetics across Earth's largest habitat: The deep-sea floor. Mol Ecol 2017; 26:4872-4896. [PMID: 28833857 DOI: 10.1111/mec.14237] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/04/2023]
Abstract
Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made.
Collapse
Affiliation(s)
- M L Taylor
- Department of Zoology, University of Oxford, Oxford, UK
| | - C N Roterman
- Department of Zoology, University of Oxford, Oxford, UK
| |
Collapse
|
14
|
De Groote A, Hauquier F, Vanreusel A, Derycke S. Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea. BMC Evol Biol 2017; 17:154. [PMID: 28668078 PMCID: PMC5494145 DOI: 10.1186/s12862-017-1003-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/21/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. RESULTS Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. CONCLUSIONS The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.
Collapse
Affiliation(s)
- Annelies De Groote
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Freija Hauquier
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
- Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences (RBINS), Rue Vautier 29, 1000 Brussels, Belgium
| |
Collapse
|
15
|
Verheye ML, Backeljau T, d'Udekem d'Acoz C. Locked in the icehouse: Evolution of an endemic Epimeria (Amphipoda, Crustacea) species flock on the Antarctic shelf. Mol Phylogenet Evol 2017; 114:14-33. [PMID: 28528744 DOI: 10.1016/j.ympev.2017.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/12/2017] [Accepted: 05/14/2017] [Indexed: 11/24/2022]
Abstract
The Antarctic shelf's marine biodiversity has been greatly influenced by the climatic and glacial history of the region. Extreme temperature changes led to the extinction of some lineages, while others adapted and flourished. The amphipod genus Epimeria is an example of the latter, being particularly diverse in the Antarctic region. By reconstructing a time-calibrated phylogeny based on mitochondrial (COI) and nuclear (28S and H3) markers and including Epimeria species from all oceans, this study provides a temporal and geographical framework for the evolution of Antarctic Epimeria. The monophyly of this genus is not supported by Bayesian Inference, as Antarctic and non-Antarctic Epimeria form two distinct well-supported clades, with Antarctic Epimeria being a sister clade to two stilipedid species. The monophyly of Antarctic Epimeria suggests that this clade evolved in isolation since its origin. While the precise timing of this origin remains unclear, it is inferred that the Antarctic lineage arose from a late Gondwanan ancestor and hence did not colonize the Antarctic region after the continent broke apart from the other fragments of Gondwanaland. The initial diversification of the clade occurred 38.04Ma (95% HPD [48.46Ma; 28.36Ma]) in a cooling environment. Adaptation to cold waters, along with the extinction of cold-intolerant taxa and resulting ecological opportunities, likely led to the successful diversification of Epimeria on the Antarctic shelf. However, there was neither evidence of a rapid lineage diversification early in the clade's history, nor of any shifts in diversification rates induced by glacial cycles. This suggests that a high turnover rate on the repeatedly scoured Antarctic shelf could have masked potential signals of diversification bursts.
Collapse
Affiliation(s)
- Marie L Verheye
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium; Catholic University of Louvain-la-Neuve, Department of Biology, Marine Biology Laboratory, Croix du Sud 3 bte L7.06.04, 1348 Louvain-la-Neuve, Belgium.
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium; University of Antwerp, Evolutionary Ecology Group, Universiteitsplein 1, 2160 Antwerp, Belgium
| | - Cédric d'Udekem d'Acoz
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium
| |
Collapse
|
16
|
Moles J, Wägele H, Uhl G, Avila C. Bipolarity in sea slugs: a new species of Doridunculus (Mollusca: Nudibranchia: Onchidoridoidea) from Antarctica. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0309-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
17
|
Easton EE, Thistle D. Do some deep‐sea, sediment‐dwelling species of harpacticoid copepods have 1000‐km‐scale range sizes? Mol Ecol 2016; 25:4301-18. [DOI: 10.1111/mec.13744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- E. E. Easton
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
| | - D. Thistle
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
| |
Collapse
|
18
|
Protist metabarcoding and environmental biomonitoring: Time for change. Eur J Protistol 2016; 55:12-25. [DOI: 10.1016/j.ejop.2016.02.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/29/2016] [Accepted: 02/12/2016] [Indexed: 01/06/2023]
|
19
|
Georgieva MN, Wiklund H, Bell JB, Eilertsen MH, Mills RA, Little CTS, Glover AG. A chemosynthetic weed: the tubeworm Sclerolinum contortum is a bipolar, cosmopolitan species. BMC Evol Biol 2015; 15:280. [PMID: 26667806 PMCID: PMC4678467 DOI: 10.1186/s12862-015-0559-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sclerolinum (Annelida: Siboglinidae) is a genus of small, wiry deep-sea tubeworms that depend on an endosymbiosis with chemosynthetic bacteria for their nutrition, notable for their ability to colonise a multitude of reducing environments. Since the early 2000s, a Sclerolinum population has been known to inhabit sediment-hosted hydrothermal vents within the Bransfield Strait, Southern Ocean, and whilst remaining undescribed, it has been suggested to play an important ecological role in this ecosystem. Here, we show that the Southern Ocean Sclerolinum population is not a new species, but more remarkably in fact belongs to the species S. contortum, first described from an Arctic mud volcano located nearly 16,000 km away. RESULTS Our new data coupled with existing genetic studies extend the range of this species across both polar oceans and the Gulf of Mexico. Our analyses show that the populations of this species are structured on a regional scale, with greater genetic differentiation occurring between rather than within populations. Further details of the external morphology and tube structure of S. contortum are revealed through confocal and SEM imaging, and the ecology of this worm is discussed. CONCLUSIONS These results shed further insight into the plasticity and adaptability of this siboglinid group to a range of reducing conditions, and into the levels of gene flow that occur between populations of the same species over a global extent.
Collapse
Affiliation(s)
- Magdalena N Georgieva
- Life Sciences Department, Natural History Museum, London, UK.
- School of Earth and Environment, University of Leeds, Leeds, UK.
| | - Helena Wiklund
- Life Sciences Department, Natural History Museum, London, UK.
| | - James B Bell
- Life Sciences Department, Natural History Museum, London, UK.
- School of Geography, University of Leeds, Leeds, UK.
| | - Mari H Eilertsen
- Centre for Geobiology, University of Bergen, Bergen, Norway.
- Department of Biology, University of Bergen, Bergen, Norway.
| | - Rachel A Mills
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.
| | | | - Adrian G Glover
- Life Sciences Department, Natural History Museum, London, UK.
| |
Collapse
|
20
|
Yasuhara M, Tittensor DP, Hillebrand H, Worm B. Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model. Biol Rev Camb Philos Soc 2015; 92:199-215. [PMID: 26420174 DOI: 10.1111/brv.12223] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Abstract
There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology-palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross-scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep-time perspective based on high-resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future.
Collapse
Affiliation(s)
- Moriaki Yasuhara
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.,Swire Institute of Marine Science, The University of Hong Kong, Cape d'Aguilar Road, Shek O, Hong Kong SAR, China.,Department of Earth Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Derek P Tittensor
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada.,United Nations Environment Programme World Conservation Monitoring Centre, 219 Huntingdon Road, Cambridge, CB3 0DL, UK
| | - Helmut Hillebrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University of Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Boris Worm
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| |
Collapse
|
21
|
Zhang B, Xu M, Bian S, Hou L, Tang D, Li Y, Gu M, Cheng Z, Yu H. Global Identification of Genes Specific for Rice Meiosis. PLoS One 2015; 10:e0137399. [PMID: 26394329 PMCID: PMC4578934 DOI: 10.1371/journal.pone.0137399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 08/17/2015] [Indexed: 11/23/2022] Open
Abstract
The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homologue of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq combined with bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast.
Collapse
Affiliation(s)
- Bingwei Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modem Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Meng Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modem Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Shiquan Bian
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modem Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Lili Hou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modem Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modem Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modem Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
- * E-mail:
| |
Collapse
|
22
|
Tyml T, Kostka M, Ditrich O, Dyková I. Vermistella arctica n. sp. Nominates the Genus Vermistella as a Candidate for Taxon with Bipolar Distribution. J Eukaryot Microbiol 2015; 63:210-9. [PMID: 26384711 DOI: 10.1111/jeu.12270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 08/28/2015] [Accepted: 08/29/2015] [Indexed: 11/26/2022]
Abstract
A new amoebozoan species, Vermistella arctica n. sp., is described from marine habitats in the central part of Svalbard archipelago. This is the first report on Arctic amoebae belonging to the genus Vermistella Moran and Anderson, 2007, the type species of which was described from the opposite pole of the planet. Psychrophily proved in the new strains qualifies the genus Vermistella as a bipolar taxon. Molecular phylogenetic analyses based on 18S rDNA and actin sequences did not show any affinity of the genus Vermistella to Stygamoeba regulata ATCC(®) 50892(™) strain. A close phylogenetic relationship was found between Vermistella spp. and a sequence originating from an environmental sample from Cariaco basin, the largest marine permanently anoxic system in the world. Possible mechanisms of bipolar distribution are discussed.
Collapse
Affiliation(s)
- Tomáš Tyml
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Institute of Parasitology, Biology Centre ASCR, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Martin Kostka
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Institute of Parasitology, Biology Centre ASCR, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Oleg Ditrich
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Iva Dyková
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| |
Collapse
|
23
|
Abstract
Abstract
Benthic foraminifera are a major component of the Antarctic biota. Coastal foraminiferal morphospecies are widely distributed in Antarctic waters. The question is whether these morphotypes are genetically identical or, rather, they represent a cohort of cryptic species. Here, we compared genetically nine benthic foraminiferal morphospecies from Admiralty Bay (South Shetlands) and the western Ross Sea (McMurdo Sound, Terra Nova Bay), separated by a distance of ~4500 km. Additionally, for three of these morphospecies, we included specimens from Rothera (Marguerite Bay), which is located between the two main areas of interest. Our study, based on SSU and ITS rDNA sequence data, shows that all examined morphospecies share the same genotypes despite the presence of considerable intra-individual genetic variability.
Collapse
|
24
|
Cunea n. g. (Amoebozoa, Dactylopodida) with two cryptic species isolated from different areas of the ocean. Eur J Protistol 2015; 51:197-209. [DOI: 10.1016/j.ejop.2015.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 11/17/2022]
|
25
|
Moles J, Figuerola B, Campanyà-Llovet N, Monleón-Getino T, Taboada S, Avila C. Distribution patterns in Antarctic and Subantarctic echinoderms. Polar Biol 2015. [DOI: 10.1007/s00300-014-1640-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
26
|
Burkett AM, Rathburn AE, Pérez ME, Levin LA, Cha H, Rouse GW. Phylogenetic placement of Cibicidoides wuellerstorfi (Schwager, 1866) from methane seeps and non-seep habitats on the Pacific margin. GEOBIOLOGY 2015; 13:44-52. [PMID: 25407814 DOI: 10.1111/gbi.12118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
Benthic foraminifera are among the most abundant groups found in deep-sea habitats, including methane seep environments. Unlike many groups, no endemic foraminiferal species have been reported from methane seeps, and to our knowledge, genetic data are currently sparse for Pacific deep-sea foraminifera. In an effort to understand the relationships between seep and non-seep populations of the deep-sea foraminifera Cibicidoides wuellerstorfi, a common paleo-indicator species, specimens from methane seeps in the Pacific were analyzed and compared to one another for genetic similarities of small subunit rDNA (SSU rDNA) sequences. Pacific Ocean C. wuellerstorfi were also compared to those collected from other localities around the world (based on 18S gene available on Genbank, e.g., Schweizer et al., 2009). Results from this study revealed that C. wuellerstorfi living in seeps near Costa Rica and Hydrate Ridge are genetically similar to one another at the species level. Individuals collected from the same location that display opposite coiling directions (dextral and sinstral) had no species level genetic differences. Comparisons of specimens with genetic information available from Genbank (SSU rDNA) showed that Pacific individuals, collected for this study, are genetically similar to those previously analyzed from the North Atlantic and Antarctic. These observations provide strong evidence for the true cosmopolitan nature of C. wuellerstorfi and highlight the importance of understanding how these microscopic organisms are able to maintain sufficient genetic exchange to remain within the same species between seep and non-seep habitats and over global distances.
Collapse
Affiliation(s)
- A M Burkett
- Earth and Environmental Systems, Indiana State University, Terre Haute, IN, USA
| | | | | | | | | | | |
Collapse
|
27
|
Pawlowski J, Lejzerowicz F, Esling P. Next-generation environmental diversity surveys of foraminifera: preparing the future. THE BIOLOGICAL BULLETIN 2014; 227:93-106. [PMID: 25411369 DOI: 10.1086/bblv227n2p93] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Foraminifera are commonly defined as marine testate protists, and their diversity is mainly assessed on the basis of the morphology of their agglutinated or mineralized tests. Diversity surveys based on environmental DNA (eDNA) have dramatically changed this view by revealing an unexpected diversity of naked and organic-walled lineages as well as detecting foraminiferal lineages in soil and freshwater environments. Moreover, single-cell analyses have allowed discrimination among genetically distinctive types within almost every described morphospecies. In view of these studies, the foraminiferal diversity appeared to be largely underestimated, but its accurate estimation was impeded by the low speed and coverage of a cloning-based eDNA approach. With the advent of high-throughput sequencing (HTS) technologies, these limitations disappeared in favor of exhaustive descriptions of foraminiferal diversity in numerous samples. Yet, the biases and errors identified in early HTS studies raised some questions about the accuracy of HTS data and their biological interpretation. Among the most controversial issues affecting the reliability of HTS diversity estimates are (1) the impact of technical and biological biases, (2) the sensitivity and specificity of taxonomic sequence assignment, (3) the ability to distinguish rare species, and (4) the quantitative interpretation of HTS data. Here, we document the lessons learned from previous HTS surveys and present the current advances and applications focusing on foraminiferal eDNA. We discuss the problems associated with HTS approaches and predict the future trends and avenues that hold promises for surveying foraminiferal diversity accurately and efficiently.
Collapse
Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland; and
| | - F Lejzerowicz
- Department of Genetics and Evolution, University of Geneva, Switzerland; and
| | - P Esling
- IRCAM, UMR 9912, Université Pierre et Marie Curie, Paris, France
| |
Collapse
|
28
|
Naughton K, O’Hara T, Appleton B, Cisternas P. Antitropical distributions and species delimitation in a group of ophiocomid brittle stars (Echinodermata: Ophiuroidea: Ophiocomidae). Mol Phylogenet Evol 2014; 78:232-44. [DOI: 10.1016/j.ympev.2014.05.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 10/25/2022]
|
29
|
Weber AAT, Pawlowski J. Wide Occurrence of SSU rDNA Intragenomic Polymorphism in Foraminifera and its Implications for Molecular Species Identification. Protist 2014; 165:645-61. [DOI: 10.1016/j.protis.2014.07.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/09/2014] [Accepted: 07/16/2014] [Indexed: 11/28/2022]
|
30
|
Havermans C, Sonet G, d’Udekem d’Acoz C, Nagy ZT, Martin P, Brix S, Riehl T, Agrawal S, Held C. Genetic and morphological divergences in the cosmopolitan deep-sea amphipod Eurythenes gryllus reveal a diverse abyss and a bipolar species. PLoS One 2013; 8:e74218. [PMID: 24086322 PMCID: PMC3783426 DOI: 10.1371/journal.pone.0074218] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/30/2013] [Indexed: 11/18/2022] Open
Abstract
Eurythenes gryllus is one of the most widespread amphipod species, occurring in every ocean with a depth range covering the bathyal, abyssal and hadal zones. Previous studies, however, indicated the existence of several genetically and morphologically divergent lineages, questioning the assumption of its cosmopolitan and eurybathic distribution. For the first time, its genetic diversity was explored at the global scale (Arctic, Atlantic, Pacific and Southern oceans) by analyzing nuclear (28S rDNA) and mitochondrial (COI, 16S rDNA) sequence data using various species delimitation methods in a phylogeographic context. Nine putative species-level clades were identified within E. gryllus. A clear distinction was observed between samples collected at bathyal versus abyssal depths, with a genetic break occurring around 3,000 m. Two bathyal and two abyssal lineages showed a widespread distribution, while five other abyssal lineages each seemed to be restricted to a single ocean basin. The observed higher diversity in the abyss compared to the bathyal zone stands in contrast to the depth-differentiation hypothesis. Our results indicate that, despite the more uniform environment of the abyss and its presumed lack of obvious isolating barriers, abyssal populations might be more likely to show population differentiation and undergo speciation events than previously assumed. Potential factors influencing species' origins and distributions, such as hydrostatic pressure, are discussed. In addition, morphological findings coincided with the molecular clades. Of all specimens available for examination, those of the bipolar bathyal clade seemed the most similar to the 'true' E. gryllus. We present the first molecular evidence for a bipolar distribution in a macro-benthic deep-sea organism.
Collapse
Affiliation(s)
- Charlotte Havermans
- Direction Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Biodiversity Research Centre, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
- * E-mail:
| | - Gontran Sonet
- Direction Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Cédric d’Udekem d’Acoz
- Direction Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Zoltán T. Nagy
- Direction Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Patrick Martin
- Direction Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Direction Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Saskia Brix
- Centre for Marine Biodiversity Research, Senckenberg Research Institute c/o Biocentrum Grindel, Hamburg, Germany
| | - Torben Riehl
- Centre for Marine Biodiversity Research, Senckenberg Research Institute c/o Biocentrum Grindel, Hamburg, Germany
| | - Shobhit Agrawal
- Section Functional Ecology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Christoph Held
- Section Functional Ecology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| |
Collapse
|
31
|
Heger TJ, Mitchell EAD, Leander BS. Holarctic phylogeography of the testate amoebaHyalosphenia papilio(Amoebozoa: Arcellinida) reveals extensive genetic diversity explained more by environment than dispersal limitation. Mol Ecol 2013; 22:5172-84. [DOI: 10.1111/mec.12449] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/26/2013] [Accepted: 07/01/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Thierry J. Heger
- Departments of Botany and Zoology; University of British Columbia; #3529- 6270 University Blvd Vancouver, British Columbia, Canada V6T 1Z4
| | - Edward A. D. Mitchell
- Laboratory of Soil Biology; University of Neuchâtel; Rue Emile-Argand 11 Neuchâtel CH-2000 Switzerland
| | - Brian S. Leander
- Departments of Botany and Zoology; University of British Columbia; #3529- 6270 University Blvd Vancouver, British Columbia, Canada V6T 1Z4
| |
Collapse
|
32
|
Di Giuseppe G, Barbieri M, Vallesi A, Luporini P, Dini F. Phylogeographical pattern ofEuplotes nobilii, a protist ciliate with a bipolar biogeographical distribution. Mol Ecol 2013; 22:4029-37. [DOI: 10.1111/mec.12363] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/19/2013] [Accepted: 04/25/2013] [Indexed: 11/26/2022]
Affiliation(s)
| | | | - Adriana Vallesi
- Laboratory of Eukaryotic Microbiology and Animal Biology; Department of Environmental Sciences; University of Camerino; 62032 Camerino MC Italy
| | - Pierangelo Luporini
- Laboratory of Eukaryotic Microbiology and Animal Biology; Department of Environmental Sciences; University of Camerino; 62032 Camerino MC Italy
| | - Fernando Dini
- Department of Biology; University of Pisa; 56126 Pisa Italy
| |
Collapse
|
33
|
Winkelmann I, Campos PF, Strugnell J, Cherel Y, Smith PJ, Kubodera T, Allcock L, Kampmann ML, Schroeder H, Guerra A, Norman M, Finn J, Ingrao D, Clarke M, Gilbert MTP. Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species. Proc Biol Sci 2013; 280:20130273. [PMID: 23516246 PMCID: PMC3619516 DOI: 10.1098/rspb.2013.0273] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 11/12/2022] Open
Abstract
Despite its charismatic appeal to both scientists and the general public, remarkably little is known about the giant squid Architeuthis, one of the largest of the invertebrates. Although specimens of Architeuthis are becoming more readily available owing to the advancement of deep-sea fishing techniques, considerable controversy exists with regard to topics as varied as their taxonomy, biology and even behaviour. In this study, we have characterized the mitochondrial genome (mitogenome) diversity of 43 Architeuthis samples collected from across the range of the species, in order to use genetic information to provide new and otherwise difficult to obtain insights into the life of this animal. The results show no detectable phylogenetic structure at the mitochondrial level and, furthermore, that the level of nucleotide diversity is exceptionally low. These observations are consistent with the hypotheses that there is only one global species of giant squid, Architeuthis dux (Steenstrup, 1857), and that it is highly vagile, possibly dispersing through both a drifting paralarval stage and migration of larger individuals. Demographic history analyses of the genetic data suggest that there has been a recent population expansion or selective sweep, which may explain the low level of genetic diversity.
Collapse
Affiliation(s)
- Inger Winkelmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Paula F. Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Museu da Ciência da Universidade de Coimbra, Largo Marquês de Pombal, 3000-272 Coimbra, Portugal
| | - Jan Strugnell
- Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, 3086 Victoria, Australia
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UPR1934 du CNRS, BP 14, 79360 Villiers-en-Bois, France
| | - Peter J. Smith
- National Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Tsunemi Kubodera
- National Museum of Nature and Science, Collection Center, 4-1-1 Amakubo, Tsukuba-shi, Ibaragi-Pref 305-0005, Japan
| | - Louise Allcock
- Department of Zoology, Martin Ryan Marine Science Institute, National University of Ireland, University Road, Galway, Ireland
| | - Marie-Louise Kampmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Angel Guerra
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Mark Norman
- Melbourne Museum, Museum Victoria, 11 Nicholson Street, Carlton, Victoria 3053, Australia
| | - Julian Finn
- Melbourne Museum, Museum Victoria, 11 Nicholson Street, Carlton, Victoria 3053, Australia
| | | | - Malcolm Clarke
- Rua do Porto18, 9939 430 Sao Joao, Lajes do Pico, Açores, Portugal
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| |
Collapse
|
34
|
Surviving rapid climate change in the deep sea during the Paleogene hyperthermals. Proc Natl Acad Sci U S A 2013; 110:9273-6. [PMID: 23690593 DOI: 10.1073/pnas.1300579110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Predicting the impact of ongoing anthropogenic CO2 emissions on calcifying marine organisms is complex, owing to the synergy between direct changes (acidification) and indirect changes through climate change (e.g., warming, changes in ocean circulation, and deoxygenation). Laboratory experiments, particularly on longer-lived organisms, tend to be too short to reveal the potential of organisms to acclimatize, adapt, or evolve and usually do not incorporate multiple stressors. We studied two examples of rapid carbon release in the geological record, Eocene Thermal Maximum 2 (∼53.2 Ma) and the Paleocene Eocene Thermal Maximum (PETM, ∼55.5 Ma), the best analogs over the last 65 Ma for future ocean acidification related to high atmospheric CO2 levels. We use benthic foraminifers, which suffered severe extinction during the PETM, as a model group. Using synchrotron radiation X-ray tomographic microscopy, we reconstruct the calcification response of survivor species and find, contrary to expectations, that calcification significantly increased during the PETM. In contrast, there was no significant response to the smaller Eocene Thermal Maximum 2, which was associated with a minor change in diversity only. These observations suggest that there is a response threshold for extinction and calcification response, while highlighting the utility of the geological record in helping constrain the sensitivity of biotic response to environmental change.
Collapse
|
35
|
Evidence from morphological and genetic data confirms that Colossendeis tenera Hilton, 1943 (Arthropoda: Pycnogonida), does not belong to the Colossendeis megalonyx Hoek, 1881 complex. ORG DIVERS EVOL 2013. [DOI: 10.1007/s13127-012-0120-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
36
|
Herrera S, Shank TM, Sánchez JA. Spatial and temporal patterns of genetic variation in the widespread antitropical deep-sea coralParagorgia arborea. Mol Ecol 2012; 21:6053-67. [DOI: 10.1111/mec.12074] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/28/2012] [Accepted: 09/01/2012] [Indexed: 01/20/2023]
Affiliation(s)
| | - T. M. Shank
- Biology Department; Woods Hole Oceanographic Institution; 266 Woods Hole Road; Woods Hole; MA; 02543; USA
| | - J. A. Sánchez
- Laboratorio de Biologia Molecular Marina (BIOMMAR), Departamento Ciencias Biologicas; Universidad de los Andes; Carrera 1E No 18A - 10; Bogota; Colombia
| |
Collapse
|
37
|
Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc Natl Acad Sci U S A 2012; 109:17633-8. [PMID: 23045668 DOI: 10.1073/pnas.1208160109] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.
Collapse
|
38
|
Gentekaki E, Lynn D. Spatial genetic variation, phylogeography and barcoding of the peritrichous ciliate Carchesium polypinum. Eur J Protistol 2012; 48:305-13. [PMID: 22595653 DOI: 10.1016/j.ejop.2012.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 03/12/2012] [Accepted: 04/05/2012] [Indexed: 11/30/2022]
Abstract
Most recent studies of geographic distribution of microbial eukaryotes have focused on marine rather than freshwater protists. Here, we used the freshwater peritrich ciliate Carchesium polypinum to quantify the degree of genetic diversity of four closely related and previously described lineages and to determine whether patterns of genetic differentiation showed geographic partitioning. Using an expanded dataset of 100 isolates and employing the mitochondrial marker cytochrome oxidase c subunit I (cox-1), we enriched the 6 previously identified clades of Carchesium polypinum. We found a large degree of geographic overlap among the different clades (e.g. to the level of range of sampling), but also a spatially restricted clade (e.g. to the level of one river basin). Furthermore, we present evidence of a clear geographic separation in one of the lineages with Canadian and North Carolinian isolates grouping in two distinct clusters.
Collapse
Affiliation(s)
- Eleni Gentekaki
- Department of Integrative Biology, University of Guelph, ON, Canada.
| | | |
Collapse
|
39
|
Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK. Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol Ecol 2012; 21:1048-59. [PMID: 21985648 PMCID: PMC3261328 DOI: 10.1111/j.1365-294x.2011.05297.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and probably play pivotal roles in maintaining ecosystem function. Although the deep-sea benthos represents one of the world's largest habitats, we lack a firm understanding of the biodiversity and community interactions amongst meiobenthic organisms in this ecosystem. Within this vast environment, key questions concerning the historical genetic structure of species remain a mystery, yet have profound implications for our understanding of global biodiversity and how we perceive and mitigate the impact of environmental change and anthropogenic disturbance. Using a metagenetic approach, we present an assessment of microbial eukaryote communities across depth (shallow water to abyssal) and ocean basins (deep-sea Pacific and Atlantic). Within the 12 sites examined, our results suggest that some taxa can maintain eurybathic ranges and cosmopolitan deep-sea distributions, but the majority of species appear to be regionally restricted. For Operationally Clustered Taxonomic Units (OCTUs) reporting wide distributions, there appears to be a taxonomic bias towards a small subset of taxa in most phyla; such bias may be driven by specific life history traits amongst these organisms. In addition, low genetic divergence between geographically disparate deep-sea sites suggests either a shorter coalescence time between deep-sea regions or slower rates of evolution across this vast oceanic ecosystem. While high-throughput studies allow for broad assessment of genetic patterns across microbial eukaryote communities, intragenomic variation in rRNA gene copies and the patchy coverage of reference databases currently present substantial challenges for robust taxonomic interpretations of eukaryotic data sets.
Collapse
Affiliation(s)
- Holly M Bik
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA.
| | | | | | | | | | | | | |
Collapse
|
40
|
Gooday AJ, Jorissen FJ. Benthic foraminiferal biogeography: controls on global distribution patterns in deep-water settings. ANNUAL REVIEW OF MARINE SCIENCE 2012; 4:237-62. [PMID: 22457975 DOI: 10.1146/annurev-marine-120709-142737] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Benthic foraminifera, shell-bearing protists, are familiar from geological studies. Although many species are well known, undescribed single-chambered forms are common in the deep sea. Coastal and sublittoral species often have restricted distributions, but wide ranges are more frequent among deep-water species, particularly at abyssal depths. This probably reflects the transport of tiny propagules by currents across ocean basins that present few insurmountable barriers to dispersal, combined with slow rates of evolution. Undersampling of the vast deep-sea habitat, however, makes it very difficult to establish the ranges of less common foraminiferal species, and endemism may be more prevalent than currently realized. On continental slopes, some species have restricted distributions, but wide-ranging bathyal species that exhibit considerable morphological variation are more common. This may be linked to the greater heterogeneity of continental slopes compared with oceans basins. Improved knowledge of deep-sea foraminiferal biogeography requires sound morphology-based taxonomy combined with molecular genetic studies.
Collapse
Affiliation(s)
- Andrew J Gooday
- National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, United Kingdom.
| | | |
Collapse
|
41
|
Analysis of the community structure of abyssal kinetoplastids revealed similar communities at larger spatial scales. ISME JOURNAL 2011; 6:713-23. [PMID: 22071346 DOI: 10.1038/ismej.2011.138] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Knowledge of the spatial scales of diversity is necessary to evaluate the mechanisms driving biodiversity and biogeography in the vast but poorly understood deep sea. The community structure of kinetoplastids, an important group of microbial eukaryotes belonging to the Euglenozoa, from all abyssal plains of the South Atlantic and two areas of the eastern Mediterranean was studied using partial small subunit ribosomal DNA gene clone libraries. A total of 1364 clones from 10 different regions were retrieved. The analysis revealed statistically not distinguishable communities from both the South-East Atlantic (Angola and Guinea Basin) and the South-West Atlantic (Angola and Brazil Basin) at spatial scales of 1000-3000 km, whereas all other communities were significantly differentiated from one another. It seems likely that multiple processes operate at the same time to shape communities of deep-sea kinetoplastids. Nevertheless, constant and homogenous environmental conditions over large spatial scales at abyssal depths, together with high dispersal capabilities of microbial eukaryotes, maintain best the results of statistically indistinguishable communities at larger spatial scales.
Collapse
|
42
|
Morard R, Quillévéré F, Douady CJ, de Vargas C, de Garidel-Thoron T, Escarguel G. Worldwide genotyping in the planktonic foraminifer Globoconella inflata: implications for life history and paleoceanography. PLoS One 2011; 6:e26665. [PMID: 22028935 PMCID: PMC3197684 DOI: 10.1371/journal.pone.0026665] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/30/2011] [Indexed: 11/19/2022] Open
Abstract
The planktonic foraminiferal morpho-species Globoconella inflata is widely used as a stratigraphic and paleoceanographic index. While G. inflata was until now regarded as a single species, we show that it rather constitutes a complex of two pseudo-cryptic species. Our study is based on SSU and ITS rDNA sequence analyses and genotyping of 497 individuals collected at 49 oceanic stations covering the worldwide range of the morpho-species. Phylogenetic analyses unveil the presence of two divergent genotypes. Type I inhabits transitional and subtropical waters of both hemispheres, while Type II is restricted to the Antarctic subpolar waters. The two genetic species exhibit a strictly allopatric distribution on each side of the Antarctic Subpolar Front. On the other hand, sediment data show that G. inflata was restricted to transitional and subtropical environments since the early Pliocene, and expanded its geographic range to southern subpolar waters ∼700 kyrs ago, during marine isotopic stage 17. This datum may correspond to a peripatric speciation event that led to the partition of an ancestral genotype into two distinct evolutionary units. Biometric measurements performed on individual G. inflata from plankton tows north and south of the Antarctic Subpolar Front indicate that Types I and II display slight but significant differences in shell morphology. These morphological differences may allow recognition of the G. inflata pseudo-cryptic species back into the fossil record, which in turn may contribute to monitor past movements of the Antarctic Subpolar Front during the middle and late Pleistocene.
Collapse
Affiliation(s)
- Raphaël Morard
- CNRS UMR 5276 Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France.
| | | | | | | | | | | |
Collapse
|
43
|
Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proc Natl Acad Sci U S A 2011; 108:13177-82. [PMID: 21788523 DOI: 10.1073/pnas.1018426108] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deep-sea floors represent one of the largest and most complex ecosystems on Earth but remain essentially unexplored. The vastness and remoteness of this ecosystem make deep-sea sampling difficult, hampering traditional taxonomic observations and diversity assessment. This problem is particularly true in the case of the deep-sea meiofauna, which largely comprises small-sized, fragile, and difficult-to-identify metazoans and protists. Here, we introduce an ultra-deep sequencing-based metagenetic approach to examine the richness of benthic foraminifera, a principal component of deep-sea meiofauna. We used Illumina sequencing technology to assess foraminiferal richness in 31 unsieved deep-sea sediment samples from five distinct oceanic regions. We sequenced an extremely short fragment (36 bases) of the small subunit ribosomal DNA hypervariable region 37f, which has been shown to accurately distinguish foraminiferal species. In total, we obtained 495,978 unique sequences that were grouped into 1,643 operational taxonomic units, of which about half (841) could be reliably assigned to foraminifera. The vast majority of the operational taxonomic units (nearly 90%) were either assigned to early (ancient) lineages of soft-walled, single-chambered (monothalamous) foraminifera or remained undetermined and yet possibly belong to unknown early lineages. Contrasting with the classical view of multichambered taxa dominating foraminiferal assemblages, our work reflects an unexpected diversity of monothalamous lineages that are as yet unknown using conventional micropaleontological observations. Although we can only speculate about their morphology, the immense richness of deep-sea phylotypes revealed by this study suggests that ultra-deep sequencing can improve understanding of deep-sea benthic diversity considered until now as unknowable based on a traditional taxonomic approach.
Collapse
|
44
|
Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One 2011; 6:e18169. [PMID: 21483744 PMCID: PMC3070721 DOI: 10.1371/journal.pone.0018169] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 02/22/2011] [Indexed: 11/26/2022] Open
Abstract
Background The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes.
Collapse
|
45
|
ETTER RONJ, BOYLE ELIZABETHE, GLAZIER AMANDA, JENNINGS ROBERTM, DUTRA EDIANE, CHASE MIKER. Phylogeography of a pan-Atlantic abyssal protobranch bivalve: implications for evolution in the Deep Atlantic. Mol Ecol 2011; 20:829-43. [DOI: 10.1111/j.1365-294x.2010.04978.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
46
|
Lowe CD, Montagnes DJS, Martin LE, Watts PC. High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae) uncovered by microsatellite loci. PLoS One 2010; 5:e15557. [PMID: 21203414 PMCID: PMC3009739 DOI: 10.1371/journal.pone.0015557] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/12/2010] [Indexed: 11/18/2022] Open
Abstract
Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites) has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e)) of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST) values indicated weak to moderate population sub-division (0.01-0.12), but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.
Collapse
Affiliation(s)
- Chris D Lowe
- School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom.
| | | | | | | |
Collapse
|
47
|
Bik HM, Thomas WK, Lunt DH, Lambshead PJD. Low endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida). BMC Evol Biol 2010; 10:389. [PMID: 21167065 PMCID: PMC3022606 DOI: 10.1186/1471-2148-10-389] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/18/2010] [Indexed: 11/27/2022] Open
Abstract
Background Nematodes represent the most abundant benthic metazoa in one of the largest habitats on earth, the deep sea. Characterizing major patterns of biodiversity within this dominant group is a critical step towards understanding evolutionary patterns across this vast ecosystem. The present study has aimed to place deep-sea nematode species into a phylogenetic framework, investigate relationships between shallow water and deep-sea taxa, and elucidate phylogeographic patterns amongst the deep-sea fauna. Results Molecular data (18 S and 28 S rRNA) confirms a high diversity amongst deep-sea Enoplids. There is no evidence for endemic deep-sea lineages in Maximum Likelihood or Bayesian phylogenies, and Enoplids do not cluster according to depth or geographic location. Tree topologies suggest frequent interchanges between deep-sea and shallow water habitats, as well as a mixture of early radiations and more recently derived lineages amongst deep-sea taxa. This study also provides convincing evidence of cosmopolitan marine species, recovering a subset of Oncholaimid nematodes with identical gene sequences (18 S, 28 S and cox1) at trans-Atlantic sample sites. Conclusions The complex clade structures recovered within the Enoplida support a high global species richness for marine nematodes, with phylogeographic patterns suggesting the existence of closely related, globally distributed species complexes in the deep sea. True cosmopolitan species may additionally exist within this group, potentially driven by specific life history traits of Enoplids. Although this investigation aimed to intensively sample nematodes from the order Enoplida, specimens were only identified down to genus (at best) and our sampling regime focused on an infinitesimal small fraction of the deep-sea floor. Future nematode studies should incorporate an extended sample set covering a wide depth range (shelf, bathyal, and abyssal sites), utilize additional genetic loci (e.g. mtDNA) that are informative at the species level, and apply high-throughput sequencing methods to fully assay community diversity. Finally, further molecular studies are needed to determine whether phylogeographic patterns observed in Enoplids are common across other ubiquitous marine groups (e.g. Chromadorida, Monhysterida).
Collapse
Affiliation(s)
- Holly M Bik
- Department of Zoology, The Natural History Museum, London, UK.
| | | | | | | |
Collapse
|
48
|
McClain CR, Hardy SM. The dynamics of biogeographic ranges in the deep sea. Proc Biol Sci 2010; 277:3533-46. [PMID: 20667884 PMCID: PMC2982252 DOI: 10.1098/rspb.2010.1057] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 07/05/2010] [Indexed: 11/12/2022] Open
Abstract
Anthropogenic disturbances such as fishing, mining, oil drilling, bioprospecting, warming, and acidification in the deep sea are increasing, yet generalities about deep-sea biogeography remain elusive. Owing to the lack of perceived environmental variability and geographical barriers, ranges of deep-sea species were traditionally assumed to be exceedingly large. In contrast, seamount and chemosynthetic habitats with reported high endemicity challenge the broad applicability of a single biogeographic paradigm for the deep sea. New research benefiting from higher resolution sampling, molecular methods and public databases can now more rigorously examine dispersal distances and species ranges on the vast ocean floor. Here, we explore the major outstanding questions in deep-sea biogeography. Based on current evidence, many taxa appear broadly distributed across the deep sea, a pattern replicated in both the abyssal plains and specialized environments such as hydrothermal vents. Cold waters may slow larval metabolism and development augmenting the great intrinsic ability for dispersal among many deep-sea species. Currents, environmental shifts, and topography can prove to be dispersal barriers but are often semipermeable. Evidence of historical events such as points of faunal origin and climatic fluctuations are also evident in contemporary biogeographic ranges. Continued synthetic analysis, database construction, theoretical advancement and field sampling will be required to further refine hypotheses regarding deep-sea biogeography.
Collapse
Affiliation(s)
- Craig R McClain
- National Evolutionary Synthesis Center, 2024 West Main Street, Durham, NC 27705, USA.
| | | |
Collapse
|
49
|
Long-distance island hopping without dispersal stages: transportation across major zoogeographic barriers in a Southern Ocean isopod. Naturwissenschaften 2010; 97:583-94. [DOI: 10.1007/s00114-010-0674-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/25/2010] [Accepted: 04/26/2010] [Indexed: 10/19/2022]
|
50
|
Lowe CD, Montagnes DJ, Martin LE, Watts PC. Patterns of Genetic Diversity in the Marine Heterotrophic Flagellate Oxyrrhis marina (Alveolata: Dinophyceae). Protist 2010; 161:212-21. [DOI: 10.1016/j.protis.2009.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 08/01/2009] [Indexed: 11/28/2022]
|