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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 co-metabolize 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 oligo-saccharides 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.

SUBMITTER: Segura A

PROVIDER: S-EPMC8360164 | biostudies-literature |

REPOSITORIES: biostudies-literature

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PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influence its survival in soil and rhizosphere.

Project description:In this work we describe the role of paht gene from Novosphingobium sp. HR1a, as a regulator that seems to be involved in the control over the utilization of carbon and sulfur sources mainly involved in the control of pyruvate production and in the acetyl-CoA biosynthesis and PEP recycling from pyruvate.

2021-07-01 | GSE163593 | GEO

PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influence its survival in soil and rhizosphere.

Project description:PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influence its survival in soil and rhizosphere.

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Transcriptome analysis of Novosphingobium sp. THN1 during microcystin-LR degradation under different carbon concentrations

Project description:The bacterium Novosphingobium sp. THN1 (THN1) is capable of degrading microcystin-LR (MCLR). To get an insight into genes expression during MCLR degradation and the regulation of different carbon concentrations on MCLR degradation, we performed RNA-seq of THN1 during MCLR degradation under different carbon concentrations.

2019-01-30 | GSE125827 | GEO

LuxR402 of <i>Novosphingobium</i> sp. HR1a regulates the correct configuration of cell envelopes.

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Identification of opsA, a gene involved in solute stress mitigation and survival in soil, in the polycyclic aromatic hydrocarbon-degrading bacterium Novosphingobium sp. strain LH128.

Project description:The aim of this study was to identify genes involved in solute and matric stress mitigation in the polycyclic aromatic hydrocarbon (PAH)-degrading Novosphingobium sp. strain LH128. The genes were identified using plasposon mutagenesis and by selection of mutants that showed impaired growth in a medium containing 450 mM NaCl as a solute stress or 10% (wt/vol) polyethylene glycol (PEG) 6000 as a matric stress. Eleven and 14 mutants showed growth impairment when exposed to solute and matric stresses, respectively. The disrupted sequences were mapped on a draft genome sequence of strain LH128, and the corresponding gene functions were predicted. None of them were shared between solute and matric stress-impacted mutants. One NaCl-affected mutant (i.e., NA7E1) with a disruption in a gene encoding a putative outer membrane protein (OpsA) was susceptible to lower NaCl concentrations than the other mutants. The growth of NA7E1 was impacted by other ions and nonionic solutes and by sodium dodecyl sulfate (SDS), suggesting that opsA is involved in osmotic stress mitigation and/or outer membrane stability in strain LH128. NA7E1 was also the only mutant that showed reduced growth and less-efficient phenanthrene degradation in soil compared to the wild type. Moreover, the survival of NA7E1 in soil decreased significantly when the moisture content was decreased but was unaffected when soluble solutes from sandy soil were removed by washing. opsA appears to be important for the survival of strain LH128 in soil, especially in the case of reduced moisture content, probably by mitigating the effects of solute stress and retaining membrane stability.

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LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes

Project description:In this work, we report that the knockout mutant in other of this luxR-like genes (named luxR402) in Novosphingobium sp. HR1a; floculated faster than the wild-type when cultures are in repose. Transcriptomic analysis allowed us to determine the LuxR402 regulon; we have identified that the carbohydrate assimilation pathway and TCA cycle are affected in the mutant. Accordingly, the mutant presented poorer growth than the wild-type when growing in different carbon sources. At stationary phase of growth the pili biosynthesis, trehalose utilization and capside-related proteins were affected in the mutant strain. Microscopy assays determined that the mutant strain cultures presented cells aggrupations and that the extracellular matrix is less abundant than in the wild-type cultures.

2023-07-13 | GSE223267 | GEO

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Carbon fluxes and soil carbon dynamics along a gradient of biogeomorphic succession in alpine wetlands of Tibetan Plateau.

Project description:Hydrological changes under climate warming drive the biogeomorphic succession of wetlands and may trigger substantial carbon loss from the carbon-rich ecosystems. Although many studies have explored the responses of wetland carbon emissions to short-term hydrological change, it remains poorly understood how the carbon cycle evolves with hydrology-driven wetland succession. Here, we used a space-for-time approach across hydrological gradients on the Tibetan Plateau to examine the dynamics of ecosystem carbon fluxes (carbon dioxide (CO2) and methane (CH4)) and soil organic carbon pools during alpine wetland succession. We found that the succession from mesic meadow to fen changed the seasonality of both CO2 and CH4 fluxes, which was related to the shift in plant community composition, enhanced regulation of soil hydrology and increasing contribution of spring-thaw emission. The paludification caused a switch from net uptake of gaseous carbon to net release on an annual timescale but produced a large accumulation of soil organic carbon. We attempted to attribute the paradox between evidence from the carbon fluxes and pools to the lateral carbon input and the systematic changes of historical climate, given that the wetlands are spatially low-lying with strong temporal climate-carbon cycle interactions. These findings demonstrate a systematic change in the carbon cycle with succession and suggest that biogeomorphic succession and lateral carbon flows are both important for understanding the long-term dynamics of wetland carbon footprints.

| S-EPMC11197537 | biostudies-literature

Microcystin-LR Degradation and Gene Regulation of Microcystin-Degrading <i>Novosphingobium</i> sp. THN1 at Different Carbon Concentrations.

Project description:The bacterium Novosphingobium sp. THN1 (THN1) is capable of degrading microcystin-LR (MC-LR). To study the ability of THN1 to degrade MC-LR and its possible mechanism(s) of regulation, we analyzed the effect of carbon concentrations on the degradation process. The MC-LR degradation rate peaked early and then declined during MC-LR biodegradation. Decreased levels of carbon in the medium caused the degradation peak to occur earlier. The expression of the functional gene mlrA, encoding a microcystinase, showed a similar trend to the MC-LR degradation rate at various carbon concentrations (r2 = 0.717, p < 0.05), suggesting that regulation of mlrA expression may play an important role in MC-LR degradation by THN1. The total bacterial biomass decreased when the carbon source was limited and did not correlate with the MC-LR degradation rate. Transcriptomic analysis showed that MC-LR degradation differentially regulated 62.16% (2597/4178) of THN1 genes. A considerable number of differentially expressed genes (DEGs) during MC-LR degradation encoded proteins related to carbon-, nitrogen-, and amino acid-related pathways. At 2 h of MC-LR degradation, most DEGs (29/33) involved in carbon and nitrogen metabolism were downregulated. This indicated that MC-LR may regulate carbon and nitrogen pathways of Novosphingobium sp. THN1. KEGG pathway analysis indicated that the upregulated DEGs during MC-LR degradation were mainly related to amino acid degradation and substrate metabolism pathways. Particularly, we detected increased expression of glutathione metabolism-related genes from transcriptomic data at 2 h of MC-LR degradation compared with the gene expression of 0 h, such as GST family protein, glutathione peroxidase, S-(hydroxymethyl) glutathione dehydrogenase, and glutathione-dependent disulfide-bond oxidoreductase that have been reported to be involved in microcystin degradation.

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Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid.

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| S-EPMC9944591 | biostudies-literature

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