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Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink

Rodríguez-Martínez Raquel, Leonard Guy, Milner David S., Sudek Sebastian, Conway Mike, Moore Karen, Hudson Theresa, Mahé Frédéric, Keeling Patrick J., Santoro Alyson E., Worden Alexandra Z., Richards Thomas A.. 2020. Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink. ISME Journal, 14 (4) : 984-998.

Article de revue ; Article de recherche ; Article de revue à facteur d'impact
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Quartile : Outlier, Sujet : ECOLOGY / Quartile : Outlier, Sujet : MICROBIOLOGY

Résumé : Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the 'ribosomally active' eukaryotic diversity present in sediments close to the water/sediment interface. We demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms. We also observe many groups that include, or branch close to, osmotrophic–saprotrophic protists (e.g. labyrinthulomycetes and Pseudofungi), microbes likely to be important for detrital decomposition. The sequence data also included a diversity of abundant amplicon-types that branch close to the Fonticula slime moulds. Taken together, our data identifies additional roles for eukaryotic microbes in the marine carbon cycle; where putative osmotrophic–saprotrophic protists represent a significant active microbial-constituent of the upper sediment layer.

Mots-clés Agrovoc : sédiment, écologie marine, écologie microbienne, biodiversité, Bacillariophyceae, Ciliophora, arn ribosomal, caractéristique du peuplement, population composite, analyse qualitative

Mots-clés géographiques Agrovoc : océan Pacifique

Mots-clés complémentaires : sédiment marin, Labyrinthulea

Mots-clés libres : Biodiversity, Microbial ecology, Water microbiology

Classification Agris : M40 - Écologie aquatique

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Rodríguez-Martínez Raquel, University of Exeter (GBR) - auteur correspondant
  • Leonard Guy, University of Exeter (GBR)
  • Milner David S., University of Exeter (GBR)
  • Sudek Sebastian, Monterey Bay Aquarium Research Institute (USA)
  • Conway Mike, Monterey Bay Aquarium Research Institute (USA)
  • Moore Karen, University of Exeter (GBR)
  • Hudson Theresa, University of Exeter (GBR)
  • Mahé Frédéric, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0002-2808-0984
  • Keeling Patrick J., University of British Columbia (CAN)
  • Santoro Alyson E., UC (USA)
  • Worden Alexandra Z., Monterey Bay Aquarium Research Institute (USA)
  • Richards Thomas A., University of Exeter (GBR) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/597388/)

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