Complete Genome Sequence of Phototrophic Betaproteobacterium Rubrivivax gelatinosus IL144

Abstract

e Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in freshwater ponds, sewage ditches, activated sludge, and food processing wastewater. There have not been many studies on photosynthetic betaproteobacteria. Here we announce the complete genome sequence of the best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC 100245).

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

“…Rhizobiales consisted of Bradyrhizobium, Starkeya, Rhizobium, and Mesorhizobium which were reported to degrade diverse organic matters and are typical symbiotic rhizobia that establish an N 2 -fixing symbiosis with its legume host soybean (Borodina et al 2005;Gourion et al 2011;Singh and Tabita 2010). Burkholderiales consisted of Variovorax paradoxus and Rubrivivax gelatinosus are capable of degrading diverse organic carbons including starch, cellulose, gelatin, chitin, and humic acids (Han et al 2011;Nagashima et al 2012;Satola et al 2013). These results suggest that the diverse metabolic versatility could be a key strategy for these microbial autotrophs to survive in harsh environments, which allows them to successfully compete with other microorganisms for resources.…”

The pathogenBatrachochytrium dendrobatidisdisturbs the frog skin microbiome during a natural epidemic and experimental infection

“…Bacteria in the genera Rubrivivax and Undibacterium responded positively to Bd infection in the laboratory and field. Rubrivivax are purple nonsulfur Betaproteobacteria in the widespread freshwater family Comamonadaceae that have been isolated from several environmental sources (54). Whereas a number of studies have examined metabolic properties of cultured isolates belonging to this genus, little is known about its ecology.…”

Essential Genes Predicted in the Genome of Rubrivivax gelatinosus

“…However, several of these tRNAs are functionally redundant, and in actuality, only 43 of 61 codons are accounted for by identified tRNAs. As noted in the original genome paper, three rRNA loci are found in the genome containing the 23S, 16S, and 5S rRNAs (11). Given that each locus also has the same Ala and Ile tRNAs, it is likely that the extra loci are the result of duplication; in fact, two of the loci are immediately adjacent to each other.…”

“…While the vast majority of ribosomal proteins were categorized as essential, the rRNAs were not. As noted in the original genome announcement, R. gelatinosus has a large number of redundant genes, including those for the rRNAs (11). The lack of essentiality suggests that at least two of the rRNA operons can be functionally expressed.…”

“…Its physiology has principally been studied for its photosynthetic capability (1)(2)(3)(4)(5)(6)(7)(8), but the organism is very metabolically versatile; it is capable of growing phototrophically (including photoheterotrophically) in anaerobic light conditions and chemoheterotrophically under aerobic conditions in light or dark (9,10). It has the necessary components for the Embden-Meyerhof-Parnas pathway and the Entner-Doudoroff pathway as well as for the pentose phosphate pathway (11). It is capable of carbon and nitrogen fixation, fermentation, and H 2 gas production, making it of interest in biofuel production.…”