Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean

Abstract

Microbial eukaryotes are key components of the ocean plankton. Yet, our understanding of their community composition and activity in different water layers of the ocean is limited, particularly for picoeukaryotes (0.2-3 µm cell size). Here, we examined the picoeukaryotic communities inhabiting different vertical zones of the tropical and subtropical global ocean: surface, deep chlorophyll maximum, mesopelagic (including the deep scattering layer and oxygen minimum zones), and bathypelagic. Communities were analysed by high-tthroughput sequencing of the 18S rRNA gene (V4 region) as represented by DNA (community structure) and RNA (metabolism), followed by delineation of Operational Taxonomic Units (OTUs) at 99% similarity. We found a stratification of the picoeukaryotic communities along the water column, with assemblages corresponding to the sunlit and dark ocean. Specific taxonomic groups either increased (e.g., Chrysophyceae or Bicosoecida) or decreased (e.g., Dinoflagellata or MAST-3) in abundance with depth. We used the rRNA:rDNA ratio of each OTU as a proxy of metabolic activity. The highest relative activity was found in the mesopelagic layer for most taxonomic groups, and the lowest in the bathypelagic. Altogether, we characterize the change in community structure and metabolic activity of picoeukaryotes with depth in the global ocean, suggesting a hotspot of activity in the mesopelagic.

A metagenomic assessment of microbial eukaryotic diversity in the global ocean

“…The image retrieved in our study on the picosized fraction was broadly similar to that reported in Giner et al (2020) using V4 rDNA amplicons, with MALV groups dominating the photic zone along with Dinoflagellata, Pelagophyceae and Prymnesiophyceae, although this last group was only detected by metagenomics and represented a critical difference. In the aphotic layer, both approaches revealed a dominance of MALV, Polycystinea, Acantharia, and RAD‐B, together with Diplonemea only detected by metagenomics.…”

“…V4 amplicon sequences. Deposited at European Nucleotide Archive, accession number PRJEB23771, from a previous study (Giner et al, 2020). V9 amplicon sequences.…”

“…We then compared the obtained results with the more common amplicon sequencing of the V4 region (using the data from Giner et al, 2020; Figure S1), and the V9 region (newly obtained here). Giner et al (2020) focused on vertical changes of picoeukaryotic (0.2–3 µm) diversity in the global ocean assessed by V4‐metabarcoding and here we complement this study using V9‐metabarcoding, metagenomic data, and add the still unexplored nanoeukaryotic fraction (3–20 µm) of the Malaspina data set. Finally, we increased the taxonomic information of microbial eukaryotes by retrieving long sequences of the ribosomal DNA operon from assembled metagenomes.…”

Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench

“…The hadal zone (exclusively comprised of trenches) constitutes the deepest 45% of the vertical depth of the global ocean ( Jamieson et al, 2010 ; Jamieson, 2015 ) and was known to host active and diverse biological communities ( Jamieson et al, 2010 ; Nunoura et al, 2015 ; Xu et al, 2018 ; Liu et al, 2019b ), indicating the hadal ecosystem is crucial to ocean food web. Previous surveys on the distribution of microbial eukaryotes along the water column on a global scale ( Giner et al, 2020 ) and in specific oceanic regions ( Countway et al, 2007 ; Not et al, 2007 ; Brown et al, 2009 ; Hu et al, 2016 ; Xu et al, 2017 ) have revealed unexpected high phylogenetic diversity of microbial eukaryotes in deep seas and a clear differentiation between surface photic and deep aphotic ocean communities. However, the maximum depth of these studies was limited to the bathypelagic zone.…”

Relating network analyses to phylogenetic relatedness to infer protistan co-occurrences and co-exclusions in marine and terrestrial environments

“…While the "paradox of the plankton" and its resolution based on the theory of chaos support the co-occurrence of functionally similar plankton (Huisman & Weissing, 1999;Hutchinson, 1961), here we show that indeed phylogenetic related plankton co-occur but could simultaneously co-exclude themselves more than expected by chance at the marine surface. Other large-scale processes affect the assembly patterns of marine sunlight exposure and currents responsible of the depth stratification in the water column (Giner et al, 2020;Ibarbalz et al, 2019). However, geographical structures, natural fluctuations and absence of equilibrium state in marine plankton communities are not enough to avoid exclusion among related organisms, as observed here, and would refute the existence of any plankton paradox under phylogenetic niche conservatism.…”