Abstract
Rhizobia have two major life styles, one as free-living bacteria in the soil, and the other as bacteroids within the root/stem nodules of host legumes where they convert atmospheric nitrogen into ammonia. In the soil, rhizobia have to cope with changing and sometimes stressful environmental conditions, such as nitrogen limitation. In the beta-rhizobial strain Paraburkholderia phymatum STM815, the alternative sigma factor σ54 (or RpoN) has recently been shown to control nitrogenase activity during symbiosis with Phaseolus vulgaris. In this study, we determined P. phymatum’s σ54 regulon under nitrogen-limited free-living conditions. Among the genes significantly downregulated in the absence of σ54, we found a C4-dicarboxylate carrier protein (Bphy_0225), a flagellar biosynthesis cluster (Bphy_2926-64), and one of the two type VI secretion systems (T6SS-b) present in the P. phymatum STM815 genome (Bphy_5978-97). A defined σ54 mutant was unable to grow on C4 dicarboxylates as sole carbon source and was less motile compared to the wild-type strain. Both defects could be complemented by introducing rpoNin trans. Using promoter reporter gene fusions, we also confirmed that the expression of the T6SS-b cluster is regulated by σ54. Accordingly, we show that σ54 affects in vitro competitiveness of P. phymatum STM815 against Paraburkholderia diazotrophica.
Highlights
Symbioses between legumes and rhizobia increase soil fertility and crop yield by means of biological nitrogen fixation [1]
We recently showed that the alternative σ factor σ54 is a key regulator of P. phymatum STM815 symbiotic nitrogen fixation inside root nodules of Phaseolus vulgaris [25]
By using RNA-Seq and metabolomics on bean root nodules formed by P. phymatum STM815 wild type and a σ54 mutant [26], we found that in addition to the symbiotic genes, σ54 controls several genes potentially important for P. phymatum STM815 to persist in soil
Summary
Symbioses between legumes and rhizobia increase soil fertility and crop yield by means of biological nitrogen fixation [1]. Paraburkholderia phymatum STM815 is an interesting strain since it is able to nodulate mimosoid as well as papilionoid legumes It has been shown by several groups to be highly competitive in infecting the roots of mimosoid and papilionoid legumes [17,19,20,21]. Our group has shown that P. phymatum STM815 harbors two type VI secretion systems (T6SS) in its genome, which contribute to the competitive ability of this strain in vitro and in infecting plants [22]. These characteristics partly explain the success of this strain in competing with other rhizobia in the soil. T6SS-b gene cluster and rendered P. phymatum STM815 slightly less competitive against Paraburkholderia diazotrophica [27], suggesting that σ54 is involved in the control of interbacterial competition
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