PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres

Abstract

Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to cometabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono-and oligosaccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.

Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut

“…Though we could not directly correlate biological and physiological functions of these core bacteria that occupied the small nodules either as beneficial or commensal and/or pathogenic (Brader et al, 2017), some previous reports highlighted the beneficial role and importance of these endophytic bacterial taxa (Aserse et al, 2013;Khan et al, 2014;Rodriguez-Conde et al, 2016;McKee et al, 2019;Olanrewaju and Babalola, 2019;Asaf et al, 2020;Segura et al, 2021). For example, the genus Niastella, from the Chitinophagales order under phylum Bacteroidota, can degrade a variety of carbohydratebased biomass, releasing sugars as nutrients for their own growth as well as for other microbial communities (McKee et al, 2019).…”

“…For example, the genus Niastella, from the Chitinophagales order under phylum Bacteroidota, can degrade a variety of carbohydratebased biomass, releasing sugars as nutrients for their own growth as well as for other microbial communities (McKee et al, 2019). Recent studies found that bacterial species from Novosphingobium, Sphingomonas, and Niastella genera play significant roles: from remediation of environmental contamination to producing highly beneficial phytohormones (gibberellins and indole acetic acid, sphingan, and gellan gum), improving plant-growth attributes (i.e., shoot length, chlorophyll contents, and shoot and root dry weight) protecting plants from stress conditions such as drought, salinity, and heavy metals in agriculture soils, co-metabolizing nutrients existing in root exudates, and producing the N-acyl-homoserine lactone quorum-sensing (QS) signals (Gan et al, 2009;Khan et al, 2014;Rodriguez-Conde et al, 2016;Asaf et al, 2017Asaf et al, , 2020Segura et al, 2021). Heatmap of the predicted KEGG Orthology (KO) pathway genes of bacterial communities from three developmental stages of big and small nodules in peanut roots related to N cycling processes.…”

Metagenomic and proteomic insights into the self‐adaptive cell surface hydrophobicity of Sphingomonas sp. strain PAH02 reducing the migration of cadmium‐phenanthrene co‐pollutant in rice

“…Results showed that differential expression proteins (DEPs) were involved in the catabolic process of aromatic compounds and the transport of HMs (Figure 3A–D). For instance, some key proteins were up‐regulated at the coexistence of Cd and Phe, such as MerR, ARHDs, MhpF, BenD, CatB2, BenB and CatA (Segura et al, 2021; Xu et al, 2017). However, some HM‐related proteins were significantly downregulated, including CadA (Shi et al, 2021), CusA/CzcA (Bhagwat et al, 2021) and PobA (Reid et al, 2018).…”

Tetrahydroisoquinoline N-methyltransferase from Methylotenera Is an Essential Enzyme for the Biodegradation of Berberine in Soil Water

“…It has been confirmed that Methylotenera can be used as a degradation agent for environmental pollutants such as petroleum, motor oil and methane [ 26 , 27 , 28 ]. In addition, Novosphingobium is an excellent phenanthrene degrader [ 29 ]. Delftia can biodegrade organic pollutants, such as phenolic compounds and chlorobenzene [ 30 ].…”