Abstract
Roseobacter clade bacteria are ubiquitous in marine environments and now thought to be significant contributors to carbon and sulfur cycling. However, only a few strains of roseobacters have been isolated from the deep-sea water column and have not been thoroughly investigated. Here, we present the complete genomes of phylogentically closed related Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014 isolated from deep-sea water of the Southeastern Pacific. The genome sequences showed that the two deep-sea roseobacters carry genes for versatile metabolisms with functional capabilities such as ribulose bisphosphate carboxylase-mediated carbon fixation and inorganic sulfur oxidation. Physiological and biochemical analysis showed that T. profunda JLT2016 was capable of autotrophy, heterotrophy, and mixotrophy accompanied by the production of exopolysaccharide. Heterotrophic carbon fixation via anaplerotic reactions contributed minimally to bacterial biomass. Comparative proteomics experiments showed a significantly up-regulated carbon fixation and inorganic sulfur oxidation associated proteins under chemolithotrophic conditions compared to heterotrophic conditions. Collectively, rosebacters show a high metabolic flexibility, suggesting a considerable capacity for adaptation to the marine environment.
Highlights
Pathway[6,19]
Pelagibaca bermudensis HTCC2601 isolated from surface water of the Sargasso Sea has genes that encode all CBB cycle enzymes[20], indicating a potential autotrophic carbon fixation; there is no physiological evidence of this
Cultivated isolates of Roseobacter clade bacteria (RCB) are currently classified into 72 genera and 222 species with a valid name, and only 8 species from 7 genera recently have been isolated from bathypelagic water (Thiobacimonas profunda[24], Pelagibaca abyssi[25], Salipiger nanhaiensis[26], Roseovarius halotolerans[27], Roseovarius indicus[28], Palleronia abyssalis[29], Roseivivax marinus[30] and Seohaeicola westpacificensis31)
Summary
13C content in T. profunda JLT2016 when grown with glucose and NaH13CO3 is signifcantly less than that in autotrophic and mixotrophic cells (paired t-test, p < 0.001) (Fig. 4C), accounting for only 0.5–1.2% of the total carbon of cells This finding suggests that the level of anaplerotic carbon fixation is low and bacterial growth relies primarily on heterotrophic metabolism ( referred as heterotrophy). Most of proteins in the CBB cycle and the Sox enzymes in chemolithoheterotrophic and mixotrophic growth were present at higher levels than those in heterotrophic growth (Fig. 5) T. profunda JLT2016 has the bare minimum proteome for survival under different trophic conditions, and follows an opportunitrophic lifestyle of maintaining broad functional potential to exploit spatially and temporally variable substrates as carbon and energy resources
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