Abstract
Sphingomonads comprises a group of interesting aerobic bacteria because of their ubiquity and metabolic capability of degrading many recalcitrant contaminants. The tetralin-degrader Sphingopyxis granuli strain TFA has been recently reported as able to anaerobically grow using nitrate as the alternative electron acceptor and so far is the only bacterium with this ability within the sphingomonads group. To understand how strain TFA thrives under anoxic conditions, a differential transcriptomic analysis while growing under aerobic or anoxic conditions was performed. This analysis has been validated and complemented with transcription kinetics of representative genes of different functional categories. Results show an extensive change of the expression pattern of this strain in the different conditions. Consistently, the most induced operon in anoxia codes for proteases, presumably required for extensive changes in the protein profile. Besides genes that respond to lack of oxygen in other bacteria, there are a number of genes that respond to stress or to damage of macromolecules, including genes of the SOS DNA-damage response, which suggest that anoxic conditions represent a hostile environment for this bacterium. Interestingly, growth under anoxic conditions also resulted in repression of all flagellar and type IV pilin genes, which suggested that this strain shaves its appendages off while growing in anaerobiosis.
Highlights
Bacteria of the sphingomonads group belong to the physiologically diverse Sphingomonadaceae Family, within the Class α-proteobacteria, and were originally clustered within the genus Sphingomonas
In order to characterise the global regulation during anaerobiosis of S. granuli strain TFA and to establish what genes could be directly regulated by anaerobiosis or by other conditions intrinsic to limited growth of this bacterium[8], such as slow growth, nutrient or energy limitation or responses to other forms of stress, we compared the transcriptomic profiles by differential RNA-Seq in a number of conditions including aerobic growth on β-hydroxybutirate (BHB), which is its conventional carbon source, or on tetralin as the only carbon and energy sources, growth on BHB under anoxic conditions while respiring nitrate, and aerobic response to nitric oxide while growing on BHB
Differential expression represented as fold induction or repression of each gene in the wild type strain while growing in (i) anoxic condition with nitrate using BHB as the carbon and energy source, (ii) in aerobiosis using tetralin as the carbon and energy source, and (iii) in aerobiosis using BHB as the carbon and energy source in the presence of nitric oxide, each of these conditions compared to the condition aerobic growth using BHB as the carbon and energy source, is shown in Supplementary Table S1
Summary
Bacteria of the sphingomonads group belong to the physiologically diverse Sphingomonadaceae Family, within the Class α-proteobacteria, and were originally clustered within the genus Sphingomonas. Phylogenetic analyses of the new described species in the past two decades have shown the relative genetic diversity of the species, which can be classified into at least 5 genera, Sphingomonas, Novosphingobium, Sphingopyxis and Sphingobium[1] and, more recently, Sphingosinicella[2] This group of bacteria have attracted attention because of its ubiquity -since they can be isolated from many different environments, many of them thrive in marine environments-their biodiversity, and their metabolic versatility. Analyses of their genomes showed that they are quite diverse in size, ranging from 3 Mb of S. baekryungensis DSM 16222 to 5 Mb of S. fribergensis Kp5.2, and in organization[3]. Nitrate reduction to nitrite has been reported in two other Sphingopyxis strains[14,15], this reduction has not been characterised at all and anaerobic growth has not been reported for these strains, TFA represents the only strain within the sphingomonads group able to anaerobically grow using nitrate as the electron acceptor
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