Comparative Genomic Analysis of Labrenzia aggregata (Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions

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.

Linking coral fluorescence phenotypes to thermal bleaching in the reef-building Galaxea fascicularis from the northern South China Sea

“…Previous studies have shown that the DMSP in coral holobionts is produced by both coral and Symbiodiniaceae (Raina et al 2013 ). The bacteria detected in corals, such as L. aggregate , might be able to degrade the generated DMSP into the climate-active gas DMS via the bacterial cleavage pathway (Zhong et al 2021 ). Prosthecochloris (photoautotrophic bacteria) participates in sulfur metabolism.…”

Identification and genomic analysis of a novel temperate bacteriophage infecting Labrenzia aggregata isolated from the Mariana Trench

“…A single colony was carefully selected and purified three times before strain identification (Zhao et al, 2020). The genome of the host strain was also obtained (accession number: CP045617) (Zhong et al, 2021).…”

“…Labrenzia aggregata, a member of order Hyphomicrobiales, class Alphaproteobacteria, is widespread in marine environments and actively contributes to nitrogen and sulfur cycles, playing roles in denitrification, dissimilatory nitrate reduction to ammonium (DNRA) (King, 2003;King and Weber, 2007), thiosulfate oxidation, as well as the biosynthesis and degradation of dimethylsulfoniopropionate (DMSP) (Curson et al, 2017). Recent studies revealed their presence in deep-sea environments, such as the Mariana Trench, due to their ability to survive and grow under high hydrostatic pressure conditions (Priyanka et al, 2014;Zhong et al, 2021). In addition, extensive horizontal gene transfer (HGT) events have been identified in L. aggregata genome, likely mediated by viruses (Zhong et al, 2021).…”

“…Recent studies revealed their presence in deep-sea environments, such as the Mariana Trench, due to their ability to survive and grow under high hydrostatic pressure conditions (Priyanka et al, 2014;Zhong et al, 2021). In addition, extensive horizontal gene transfer (HGT) events have been identified in L. aggregata genome, likely mediated by viruses (Zhong et al, 2021).…”

“…In our previous study, the L. aggregata RF14 strain was isolated from the Mariana Trench at a depth of 4,000 m and potential prophage sequences were identified in its genome. However, whether this prophage can be induced remains unknown (Zhong et al, 2021). In this study, we successfully induced a prophage from the L. aggregata RF14 strain using mitomycin C, named as vB_LagS-V1.…”