Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas

Abstract

Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.

Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59T and Sphingomonas glaciei S8-45T, Two Novel Bacteria from the North Slope of Mount Everest

“…For the genome of strain S5-59 T , the unique genes accounted for 34.4% (1065 unique genes), and the S8-45 T had just 301 unique genes with a percentage of 10.9% ( Figure 7 A). The unique genes are usually associated with the species’ genetic diversity, environmental adaptation, and other special characteristics [ 78 ].…”

Microbial diversity and community dynamics in an active, high CO2subsurface rift ecosystem

“…Members of the taxon Desulfosporosinus are sulfate reducers, moderate acidophiles, and have the metabolic capability to fix CO 2 into acetyl-CoA via the Wood-Ljungdahl pathway [75]. Similarly, Sulfurimonas are characterized by diverse energy metabolisms, which includes the potential to drive carbon fixation by rTCA cycling, via pathways of sulfur/hydrogen oxidation [76]. Additional, on-going work in our group also showed Eger sediment enrichments incubated under a H 2 /CO 2 atmosphere to be highly abundant in Desulfosporosinus (Data not shown).…”

“…Another striking finding was the high representation of Hadarchaeales sequences in several samples, as this relatively newly established group of Candidatus microorganisms is closely associated with both the marine and terrestrial subsurface settings and was first discovered in acidic hot springs [8, 93]. Phylogenetically, Hadarchaeales have been classified as Euryarchaeota, and are known for their versatile metabolism, which has been described to include the capability to oxidize hydrogen and one carbon compounds [76, 94]. Further evidence for a diverse and thriving archaeal community in the Eger subsurface were the detection of several Proteoarcheota taxa.…”

“…Phylogenetically, Hadarchaeales have been classified as Euryarchaeota, and are known for their versatile metabolism, which has been described to include the capability to oxidize hydrogen and one carbon compounds [76,94]. Further evidence for a diverse and thriving archaeal community in the Eger subsurface were the detection of several Proteoarcheota taxa.…”

Conspicuous Smooth and White Egg-Shaped Sulfur Structures on a Deep-Sea Hydrothermal Vent Formed by Sulfide-Oxidizing Bacteria

“…Sulfurimonas can oxidize a range of reduced sulfur compounds, such as sulfide, elemental sulfur, and thiosulfate ( 17 ). Sulfurimonas is able to oxidize sulfide, usually completely, to sulfate ( 17 ) and produce crystalline sulfur only as intermediate product under low-oxygen conditions ( 18 ). We therefore regarded it likely that Arcobacter is responsible for the formation of the abundant and structured filaments.…”