Unraveling the Molecular Mechanisms Underlying the Microbiome Response to Soil Rewetting

Soil microbes are highly sensitive to changes in their environment, and rapidly measuring their responses is necessary to fully understand the biological processes. Drought is one of the most common environmental stresses that soil microbiomes experience, and it is important to understand the mechanisms by which the soil microbiome respond to soil dehydration. We used ¹³C as a tracer of nutrient fluxes in desiccated soil microbiomes after rewetting to simultaneously measure aerobic respiration and track the metabolic state of the community. Here, we describe a Real Time Mass Spectrometry (RTMS) approach for rapid gas monitoring combined with omics approaches to track ¹³C flow through a soil system.

The mechanism(s) behind the burst of rapid mineralization of soil organic matter and increased rate of CO₂ release upon rewetting dry soil (termed the ‘Birch Effect’) are yet to be fully defined. One known mechanism used by microbes to protect against dehydration is the production of intracellular compounds known as osmolytes. We evaluated metabolic mechanisms produced upon rewetting a marginal soil testing the hypothesis that the rapid release of CO₂ arises from the microbial processing of putative intracellular osmolytes that build up during desiccation. RTMS allows for the simultaneous, rapid and fine scale (every 2 sec) evaluation and deconvolution of the production and consumption of a number of gasses including ¹²CO₂,¹³CO₂, O₂, N₂ and H₂O.  We compared the hydration response (production of CO₂ in real time) between the addition of water and ¹³C labeled glucose dissolved in water. The initial burst of ¹²CO₂ followed by a leveling off was identical in both treatments with an additional larger increase in ¹³CO₂ about 20 minutes later in the ¹³C labeled glucose experiment. Examination of the two minutes after the water addition revealed a rapid rate of ¹²CO₂ (38 sec) and H₂O (47 sec) production and slow rate of ¹³CO₂ (56 sec) production followed by the consumption of O₂ (67 sec) and N₂ (73 sec).  Evaluation of the soil metabolomes at specified time points within 3 hours after wetting revealed the immediate release of sugars from the cells into the extracellular matrix. These results provide evidence for respiration of putative intracellular osmolytes as one driving mechanism of the Birch Effect.