Abstract
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.
Highlights
Supplementary information The online version of this article contains supplementary material, which is available to authorised users.Marine sediments are microbially driven ecosystems and encompass one of the largest reservoirs of organic carbon on Earth [1,2,3]
Fungi perform key osmotrophic/ lysotrophic/saprotrophic (OLS) biogeochemical functions in terrestrial environments, the equivalent role remains underexplored in marine sediments [13]
These results suggest a hitherto underexplored OLS protistan community in marine sediments and implicate a diverse range of ribosomally active eukaryotic microbes in multiple aspects of the marine carbon cycle in the surface sediments
Summary
Marine sediments are microbially driven ecosystems and encompass one of the largest reservoirs of organic carbon on Earth [1,2,3]. Osmotrophy [11] and other lifestyles that involve degradation of organic matter are considered important in marine sediments [12]. These processes are responsible for the breakdown of complex compounds that reach the sea floor [3]. A number of studies have shown the presence of fungal DNA and RNA in marine sediments [9, 14,15,16] but the diversity of wider OLS protist groups remain untested, even though such groups encode lifestyle strategies often critical for biogeochemical process [12, 13]
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