Biological Soil Crust metatranscriptomes constructed using Total RNA and Duplex-Specific thermostable nuclease (DSN) enzyme

Biological Soil Crusts (BSCs) are “organosedimentary assemblages” comprised of microbial communities in the top centimeters of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems, with soil structure and nutrient status due to the activity of pioneering species such as Microcoleus vaginatus. These phototrophic cyanobacteria produce polysaccharide filaments that bind the soil and are thought to excrete a range of compounds that stimulate the development of heterotrophic microorganisms that in turn contribute to the stability and biogeochemistry of these systems. In the age of genomics, the value of isolated microorganisms is often overlooked and in order to facilitate detailed analysis of the patterns of metabolite flow and exchange in these systems, we attempted to isolate in pure culture, a broad range of numerically significant and phylogenetically representative heterotrophic bacteria from BSCs. Using a combination of simple pre-treatment (hydration of BSCs mats under dark and light conditions) and isolation strategies (media with varying compositions, nutrient availability and protection from oxidative stress) we recovered 402 bacterial and 1 fungal isolate in axenic culture, which at 97% phylogenetic similarity comprised 116 (115 bacterial and 1 fungal) OTUs. We found that each medium recovered mostly distinct OTUs and that our view of the true diversity was significantly impacted by the physiological state of the BSC when sampled, with dominant organisms frequently obscuring our detection of less abundant members. We related the recovered isolates to the fraction of biomass (estimated abundance) of common OTUs in the BSC and found that more than 8% of relative abundance of OTUs was represented by our isolates. This demonstrates that simple cultivation procedures combined with specific pre-treatment of samples can allow for cultivation of numerically significant members of the BSC microbial community and allow us to reduce the culturability gap and enable physiological and metabolic assays that rely on axenic cultures.