Matric and osmotic stress have overlapping effects on Variovorax beijingensis transcription

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. Overall design: V. beijingensis was grown in liquid mM9 (low osmotic potential), mM9 with 425 mM sucrose (high osmotic potential), artificial soil Q2 (low matric potential), and artificial soil M2 (high matric potential) for 72 hours in six replicates. The total RNA was extracted (followed by rRNA depletion), and the library was prepared for RNA-seq.