Abstract
Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.
Highlights
One of the largest extreme environments on Earth is the water under high hydrostatic pressure (HHP), i.e., the deep sea, which contributes up to approximately 95% of the oceans’ volume
Four L. aggregata strains SDL044, RF14, ZYF703, and ZYF612 were isolated from seawater samples from the Mariana Trench at depths of 0 m, 4,000 m, 9,600 m, and 9,600 m, respectively
Average nucleotide identities (ANIs) between each of the strains and the representative genome of L. aggregata are between 97 and 98%, which is higher than the empirical intra-species threshold – 95% (Goris et al, 2007; Supplementary Table S1), furtherly confirming the classification of the four isolates from the Mariana Trench
Summary
One of the largest extreme environments on Earth is the water under high hydrostatic pressure (HHP), i.e., the deep sea, which contributes up to approximately 95% of the oceans’ volume. Among the deep-sea ecosystems, hydrostatic pressure elevates greatly in oceanic trenches belonging to the hadal zone (deeper than 6,000 m). The Challenger Deep of the Mariana Trench is the deepest oceanic ecosystem on earth, in which the hydrostatic pressure elevates up to 110 MPa and the temperature remains low (1–2°C; Jamieson et al, 2010). Previous studies based on pure cultures focused on comparing piezophilic isolates from the same water depth, such as Actinomycetes isolates (Pathom-Aree et al, 2006) and Shewanella benthica (Zhang et al, 2019a), or on comparing deep-sea isolates with their counterparts from other surface waters (Peoples et al, 2020). An in-detail comparison based on pure cultures between vertically distributed ecotypes of the same species, especially between their mobile elements, is required to uncover the metabolic potentials and differentiation of these widely distributed bacteria in hadal environment
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