Abstract
The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.
Highlights
The marine habitat is the largest on Earth and marine microbes play fundamental roles in global biogeochemical nutrient cycling [1]
A broad overview of presence of phylum Chloroflexi representatives in the water column of marine and brackish environments using 16S rRNA metagenomic reads is shown in Supplementary Fig. S1A (See Supplementary Table S4)
While SAR202 were barely detectable in the photic zone and deep chlorophyll maximum (DCM) datasets (Western and Eastern Mediterranean, Caspian and Red Sea, HOTs and BATs), they comprised a substantial fraction of the microbial community in the datasets from the deep aphotic zones of eastern Mediterranean (Aegean ca. 5% and Ionian ca. 10%)
Summary
The marine habitat is the largest on Earth and marine microbes play fundamental roles in global biogeochemical nutrient cycling [1]. Insitu substrate uptake experiments suggested that a large fraction of SAR202 cells utilize L-aspartic acid at all depths in favor of the more refractory D-asp. This is in contrast to the global bacterial and archaeal community that shows decreased uptake rates for L-Asp with increasing depth, suggesting adaptability of SAR202 to available dissolved organic matter in the deep sea [12]. FISH analyzes showed that SAR202 cells have a coccoid morphology with a diameter of > 1 μm [10] that does not vary with depth. Reports are sometimes conflicting in this respect, e.g., correlation to high oxygen concentrations found by Giovannoni et al [7] and lack thereof by Schattenhofer et al [11]
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