Microbes Persist: how soil moisture regimes shape the ecophysiology and C cycling of wild soil microbiomes

Soil water availability is a key driver of microbial function and exerts influence on a variety of temporal scales—ranging from short-term pulse dynamics to long-term seasonal and annual precipitation patterns. Determining the impact of changing water dynamics on microbial growth and activity is crucial for assessing how changes in weather patterns may impact soil functionality. In Mediterranean grasslands, the first substantial annual rainfall after months of drought is a driver of substantial soil microbial activity and coincides with a pulse of CO₂ emissions that can equal 10% of annual ecosystem productivity. To understand how altered precipitation regimes in semi-arid soils affect the microbial ecophysiological traits associated with soil carbon cycling, we use quantitative stable isotope probing (qSIP) to interrogate Who is where? and What are they doing? in wild soil communities collected during multiple points in the Mediterranean climate water-year. We also use multi-omics approaches, including metagenomics, metatranscriptomics, lipidomics, and metabolomics. Our qSIP results indicate only a fraction of the microbial community is actively growing at any moment or location; at the start of the growing season, the growing portion was 28%, 48% and 58% at wet, intermediate and dry sites. In a year-long study examining growth rates (measured with metagenomic qSIP) at three soil depths, we found distinct groups of actively growing organisms associated with seasonal changes in soil moisture. In a second study, we examined short-term pulse dynamics following the rewetting of dry soil. The first rain event after the dry season is a period of high growth and mortality where a large portion of annual carbon cycling occurs. To assess the impact of drought intensity on the rewetting response, soils were collected from two precipitation treatments in the field (50 or 100% mean annual precipitation) and rewet in a laboratory incubation. Wet-up triggered a rapid succession of bacterial populations, a large increase in the number of viruses (vOTUs), and strong indications of active viral lysis. We found that reduced precipitation influenced the composition of organic compounds in the soil—increasing tannin-like compounds and reducing the concentration of lipid-like compounds and changes the structure of trophic networks. Using metagenomics and 16S rRNA gene qSIP, we tracked growth and mortality following rewetting. We found that a history of limited moisture (50% precipitation) reduced both growth and mortality, demonstrating the interplay between annual/seasonal dynamics and short-term responses. Additionally, we found that growth after rewetting can be predicted from genomic traits such as genome size, codon bias, and GC content—indicating key features of fast-responding taxa to soil water pulse-dynamics. These results point to genome level traits that are predictive of microbial growth responses, and show how differences in legacy precipitation can influence microbial activities long after changes in soil moisture are no longer detectable.