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Matric and osmotic stress have overlapping effects on Variovorax beijingensis transcription

ABSTRACT: Soil microbes must continuously adapt to changes in water availability, which dynamically fluctuates with weather and irrigation, and these adaptations are closely linked to climate effects. Soil water potential, which regulates microbe-available water, is controlled by both osmotic and matric potential, which both increase as soils dry. While both parameters can independently increase water potential, the genetic mechanisms of microbial response are unknown, with potentially different mechanisms available for microbes to respond to changes in soil osmolyte concentrations versus changes in water availability within a textured material. To explore microbial responses to matric versus osmotic potential shifts, we evaluated the activity, persistence, and transcription of Variovorax beijingensis in soils and liquid cultures subjected to either matrix or osmotic stress. We find this microbe respires in dilute minimal medium (-240 ±104 kPa), in liquid medium supplemented with sucrose (-1323 ±20.8 kPa), and in a pair of matrices that span a similar range of pressures (-183 ±55 and -1393 kPa ±200 kPa). Using principal-component analysis, we show that gene expression varies significantly across all four conditions, even in cases where the pressure is similar. However, the direction of gene expression changes arising from an increase in osmotic pressure within liquid medium and an increase in matric potential within the different soils covaried for 68% of the transcripts. Thus, as Variovorax transitions from conditions of low to high osmotic or matric potential, which both decrease water availability, there is large overlap in the transcriptional response, although the responses are not identical.

ORGANISM(S): Variovorax beijingensis

PROVIDER: GSE299872 | GEO | 2025/06/26

REPOSITORIES: GEO

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Project description:Spingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. The objectives of this study were to characterize how strain RW1 responses to changes in different components of the total water potential (solute and matric potential) and to then connect these responses to more realistic scenarios of soil desiccation. To accomplish this task, transcriptome profiling was used to investigate the effects of decreasing the solute potential with sodium chloride (solute stress), decreasing the matric potential with high-molecular weight polyethylene glycol (matric stress), or inoculating cells directly into unsaturated sand (sand desiccation stress). Transcriptome profiling revealed a general response to solute, matric, and sand desiccation stress that involved synthesizing trehalose and modifying the composition of exopolysaccarides. Transcriptome profiling also revealed responses that were unique to each stress. Only solute and matric stress triggered the down-regulation of flagella genes. Only solute and sand desiccation stress triggered the up-regulation of two RNA polymerase ECF-type sigma factors along with several membrane proteins, mechanosensitive channels, and solute transporters. Finally, only matric stress triggered the up-regulation of the RNA polymerase sigma-32 factor along with several molecular chaperones. Together, this study revealed a general response to solute, matric and sand desiccation stress but also unique responses to only a subset of these stresses, suggesting that each stress affects strain RW1 in a fundamentally different way. Comparative transcriptome profiling was performed to assess the effects of acute (30 min) solute and matric stress (3 samples for acute solute stress, 3 samples for acute matric stress, 3 controls), the effects of chronic (24 hours) solute and matric stress (3 samples for chronic solute stress, 3 samples for chronic matric stress, 3 controls), and the effects of sand desiccation stress (4 samples for sand desiccation treatment, 3 controls).

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Matric and osmotic stress have overlapping effects on Variovorax beijingensis transcription

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