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

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.

Biomineralization of struvite induced by indigenous marine bacteria of the genus Alteromonas

“…However, to our knowledge, there are few marine bacteria that have been reported to be responsible for the formation of struvite. As mentioned above, the genus Alteromonas comprises versatile microorganisms playing essential roles in marine biogeochemical cycles (Lelchat et al, 2015;Chen et al, 2020;Cusick et al, 2021;Gago et al, 2021). In this study, we suggest that Alteromonas spp.…”

“…Prevalence analysis of ammonification metabolism pathways suggested that ammonium production was ubiquitous among the genus Alteromonas. Considering Alteromonas is indigenous in marine environments and has adapted to high salinity (Ivars-Martinez et al, 2008;Gonzaga et al, 2012;Chen et al, 2020;Gago et al, 2021), it is reasonable to question the role of Alteromonas spp. in struvite deposition in the ocean and sea.…”

Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity

“…The variable part of the pan-genome relates to the accessory or unique features, common to several or limited to individual strains, respectively, and associates with metabolic variability and ecological differentiation within the species or population, resulting in “microdiversity” of phenotypic traits [ 40 , 50 , 51 ]. It is interesting that each of the P. distincta and P. arctica A 37-1-1 T genomes contain from 7 to 210 unique genes, the orthologues of which are absent in other Pseudoalteromonas genomes ( Figure 4 and Figure 9 ).…”

Pontibrevibacter nitratireducens gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from seawater of the Indian Ocean and intertidal zone

“…Some desirable physiological and biochemical features such as aerobic anoxygenic photosynthesis, degradation of aromatics, quorum sensing and other characteristics [4] have been found in the Roseobacter group, which are widely distributed in marine ecosystems, including coastal zones, hydrothermal vents and sediments. The species of the Roseobacter group were shown to share 89 % 16S rRNA gene sequence similarity [5–7]. Wirth et al suggested that the 16S rRNA gene showed poor resolution of phylogenetic relationships among this group [8].…”