The nature of microbial diversity and assembly in the Nebraska Sandhills depends on organismal identity and habitat type

The ecoregion of the Nebraska Sandhills is the largest intact temperate grassland in the world and is impacted by climate change, specifically drought. Despite the well-established role microorganisms play in ecosystem functioning, little is known about microbial community diversity and assembly processes in the Sandhills. To address this gap of knowledge, we examined microbial communities in three habitats (prairie soils, lake sediments, and lake water) across four lake basins ranging in alkalinity (pH 7–11) over two years (October 2020 and 2021). Replicate soil, sediment, and water samples were characterized for bacterial and microbial eukaryotic communities with 16S and 18S rRNA metabarcoding. Analyses for alpha diversity, community composition, and assembly processes were examined with general linear models, β-NTI (nearest taxon indices) analyses, Mantel tests, and modified Hubbell’s neutral models. Overall, diversity and composition varied by habitat type and lake basin regardless of organismal identity or year. Community assembly processes varied by habitat type as well as by organismal identity, but not by year. However, the role of deterministic selection and stochastic dispersal of individual taxa (i.e., OTUs) was interannually variable. Finally, the prairie soil communities were identified as a reservoir for bacterial diversity and the lake sediment communities as a target group for potential monitoring of the effects of climate change in the western Nebraska Sandhills.