Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110

Abstract

Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. V. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggest V. paradoxus S110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbeplant and microbe-microbe interactions.Variovorax paradoxus is a metabolically diverse, aerobic bacterium that engages in mutually beneficial interactions with a variety of bacteria and plants. V. paradoxus belongs to the subclass of Proteobacteria and can metabolically utilize natural compounds produced by other biota, such as acyl homoserine lactones (AHLs) (25) and alkyl/aryl-sulfonates (38). This metabolic capacity suggests that Variovorax plays an essential role in the natural cycling of biogenic chemicals. Variovorax species are also able to degrade a variety of contaminants, including pesticides and crude oil-associated S-metabolites (5,19,37,41,42,46,50,51,52), often in synergistic and mutually beneficial interactions with other bacteria. In addition, a close relative of Variovorax was found to be the central, nonphotosynthetic partner within the phototrophic consortium "Chlorochromatium aggregatum" (22). Moreover, V. paradoxus is resistant to various heavy metals, including cadmium and mercury (2).V. paradoxus belongs to a group referred to as plant growthpromoting rhizobacteria (PGPR), which exert beneficial effects on plant growth. As a common plant symbiont found in the rhizosphere (2, 3), the metabolic diversity of V. paradoxus appears to be related to its role as a PGPR. By degrading toxic contaminants, this bacterium can prevent harm otherwise experienced by the plant and thus can promote plant growth. Strains of Variovorax can enhance the host plant's stress tolerance and disease resistance (2, 3) and aid in nutrient availability and uptake (38). The effectiveness of Variovorax as a PGPR is likely to be more potent because it also appears to be a good endophytic symbiont (34,36,39,43,44,45,47) and thus interacts more closely with the host plant. Conversely, endospheric habitats are known to offer microbes the advantage of a more uniform and protective niche compared to the competitive, high-stress environment of the soil (36).The diverse metabol...

Microbial community structure and function of Nitrobenzene reduction biocathode in response to carbon source switchover

“…Genome sequencing of Variovorax paradoxus S110 indicated that it carried corresponding genes for CO 2 fixation (Han et al, 2010). Moreover, GeoChip analysis detected three carbon fixation genes (Gene ID 220718833 and 221082971 for propionylCoA carboxylase and 239801525 for ribulose-bisphosphate carboxylase) from V. paradoxus S110 and Paracoccus denitrificans PD1222 (Gene ID 69936694 and 119386345 for propionyl-CoA carboxylase and 69153892 for ribulosebisphosphate carboxylase) respectively, which further supported the function of Variovorax and Paracoccus in the autotrophic bBC.…”

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.…”

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

“…Among these, 42 genera were significantly affected by willows at both contamination levels, and the 24 bacterial and fungal genera among those are listed in Supplementary Table S2. Among the genera consistently activated by willows at both contamination levels, some were previously reported as having interesting characteristics for phytoremediation, for instance, Methylibium petroleiphilum is involved in aromatic hydrocarbon and methyl tertbutyl ether degradation (Nakatsu et al, 2006), Mesorhizobium is a well-known genus involved in nitrogen fixation, some species are resistant to metals (Vidal et al, 2009;Huang et al, 2010) and can degrade acetonitrile (Feng and Lee, 2009), some Variovorax species display plant growth promoting activities and are able to degrade various contaminants (Han et al, 2011) and Parvibaculum species are able to degrade linear carbon chains, including alkanes (Schleheck et al, 2004;Rosario-Passapera et al, 2012). Some other genera showed contrasting responses to willows when exposed to different concentrations of contaminants (Supplementary Table S2).…”