Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses.

Mingming Chen,Jiwei Tian,Kai Tang,Xiaoyuan Feng,Yu Song,Yao Zhang,Nianzhi Jiao

doi:10.3389/fmicb.2020.01739

Mingming Chen, Jiwei Tian + Show 5 more

Open Access

https://doi.org/10.3389/fmicb.2020.01739

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Abstract

Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.

Highlights

The hadal zone constitutes the deepest 45% of the vertical depth gradient of oceans (6000–11000 m), and corresponds to the highest hydrostatic pressure within the seawater environment (60–110 MPa) (Jamieson et al, 2009)
We recovered multiple single amplified genomes (SAGs) belonging to the Roseobacter group and genus Alteromonas from the hadal zone in the Mariana Trench
Phylogenomic analyses showed that these hadal SAGs have a closer relationship to surface-associated strains despite recruitment analyses indicating that their relative abundance was mainly higher in the hadal zone

Summary

Introduction

The hadal zone constitutes the deepest 45% of the vertical depth gradient of oceans (6000–11000 m), and corresponds to the highest hydrostatic pressure within the seawater environment (60–110 MPa) (Jamieson et al, 2009). The gene composition of trench-adapted microorganisms is distinct from that of their shallower deep-sea relatives (León-Zayas et al, 2015). Within the Rhodobacterales, group Roseobacter is a diverse alphaproteobacterial lineage whose members share > 89% identity of the 16S rRNA gene and include > 70 validly named genera and > 170 validly named species (Simon et al, 2017). This group is found ubiquitously in marine environments, accounting for up to 25% of microbial communities in coastal oceans (Buchan et al, 2005). Comparative genomic analyses suggested that many of the genes unique to this hadal Marinosulfonomonas lineage were of unknown function (León-Zayas et al, 2015)

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