Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

Type Article
Date 2021-05
Language English
Author(s) Lejzerowicz Franck1, 2, Gooday Andrew John3, 4, Barrenechea Angeles Inés5, 6, Cordier Tristan5, 7, Morard Raphaël8, Apothéloz-Perret-Gentil Laure9, Lins Lidia10, Menot LenaickORCID11, Brandt Angelika12, 13, Levin Lisa Ann14, Martinez Arbizu Pedro15, Smith Craig Randall16, Pawlowski Jan5, 9, 17
Affiliation(s) 1 : Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, United States
2 : Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
3 : National Oceanography Centre, Southampton, United Kingdom
4 : Life Sciences Department, Natural History Museum, London, United Kingdom
5 : Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
6 : Department of Earth Sciences, University of Geneva, Geneva, Switzerland
7 : NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Bergen, Norway
8 : MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
9 : ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
10 : Marine Biology Research Group, Ghent University, Ghent, Belgium
11 : IFREMER, REM/EEP/LEP, Centre de Bretagne, Plouzané, France
12 : Senckenberg Research Institute and Natural History Museum, Frankfurt, Germany
13 : Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt, Germany
14 : Integrative Oceanography Division, Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
15 : German Centre for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
16 : Department of Oceanography, University of Hawai‘i at Mānoa, Honolulu, HI, United States
17 : Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
Source Frontiers In Marine Science (2296-7745) (Frontiers Media SA), 2021-05 , Vol. 8 , P. 671033 (23p.)
DOI 10.3389/fmars.2021.671033
WOS© Times Cited 2
Keyword(s) deep-sea sediment, eukaryotic biodiversity, Foraminifera, metazoans, 18S rRNA gene, bioinformatics, seafloor bathymetry
Abstract

The abyssal seafloor is a mosaic of highly diverse habitats that represent the least known marine ecosystems on Earth. Some regions enriched in natural resources, such as polymetallic nodules in the Clarion-Clipperton Zone (CCZ), attract much interest because of their huge commercial potential. Since nodule mining will be destructive, baseline data are necessary to measure its impact on benthic communities. Hence, we conducted an environmental DNA and RNA metabarcoding survey of CCZ biodiversity targeting microbial and meiofaunal eukaryotes that are the least known component of the deep-sea benthos. We analyzed two 18S rRNA gene regions targeting eukaryotes with a focus on Foraminifera (37F) and metazoans (V1V2), sequenced from 310 surface-sediment samples from the CCZ and other abyssal regions. Our results confirm huge unknown deep-sea biodiversity. Over 60% of benthic foraminiferal and almost a third of eukaryotic operational taxonomic units (OTUs) could not be assigned to a known taxon. Benthic Foraminifera are more common in CCZ samples than metazoans and dominated by clades that are only known from environmental surveys. The most striking results are the uniqueness of CCZ areas, both datasets being characterized by a high number of OTUs exclusive to the CCZ, as well as greater beta diversity compared to other abyssal regions. The alpha diversity in the CCZ is high and correlated with water depth and terrain complexity. Topography was important at a local scale, with communities at CCZ stations located in depressions more diverse and heterogeneous than those located on slopes. This could result from eDNA accumulation, justifying the interim use of eRNA for more accurate biomonitoring surveys. Our descriptions not only support previous findings and consolidate our general understanding of deep-sea ecosystems, but also provide a data resource inviting further taxon-specific and large-scale modeling studies. We foresee that metabarcoding will be useful for deep-sea biomonitoring efforts to consider the diversity of small taxa, but it must be validated based on ground truthing data or experimental studies.

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Lejzerowicz Franck, Gooday Andrew John, Barrenechea Angeles Inés, Cordier Tristan, Morard Raphaël, Apothéloz-Perret-Gentil Laure, Lins Lidia, Menot Lenaick, Brandt Angelika, Levin Lisa Ann, Martinez Arbizu Pedro, Smith Craig Randall, Pawlowski Jan (2021). Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding. Frontiers In Marine Science, 8, 671033 (23p.). Publisher's official version : https://doi.org/10.3389/fmars.2021.671033 , Open Access version : https://archimer.ifremer.fr/doc/00696/80856/