Mountain areas harbor large climatic and geographic gradients and form numerous habitats that promote high overall biodiversity. Compared to macroorganisms, knowledge about drivers of biodiversity and distribution of soil bacteria in mountain regions is still scarce but a prerequisite for conservation of bacterial functions in soils. An important question is, whether soil bacterial communities with similar structures share environmental preferences. Using metabarcoding of the 16S rRNA gene marker, we assessed soil bacterial communities at 255 sites of a regular grid covering the mountainous landscape of Switzerland, which is characterized by close location of biogeographic regions that harbor different land-use types. Distribution of bacterial communities was mainly shaped by environmental selection, as revealed by 47.9% variance explained by environmental factors, with pH (29%) being most important. Little additional variance was explained by biogeographic regions (2.8%) and land-use types (3.3%). Cluster analysis of bacterial community structures revealed six bacterial community types (BCTs), which were associated to several biogeographic regions and land-use types but overall differed mainly in their preference for soil pH. BCT I and II occurred at neutral pH, showed distinct preferences for biogeographic regions mainly differing in elevation and nutrient availability. BCT III and IV differed only in their preferred soil pH. BCT VI occurred in most acidic soils (pH 3.6) and almost exclusively at forest sites. BCT V occurred in soils with a mean pH of 4 and differed from BCT VI in preference for lower values of organic C, total nitrogen and their ratio. Indicator species and bipartite network analyses revealed 3,998 OTUs associating to different levels of environmental factors and BCTs. Taxonomic classification revealed opposing associations of taxa deriving from the same phyla. The results revealed that pH, land-use type, biogeographic region, and nutrient availability were the main factors shaping bacterial communities across Switzerland. Indicator species and bipartite network analyses revealed environmental preferences of bacterial taxa. Combining information of environmental factors and BCTs yielded increased resolution of the factors shaping soil bacterial communities and provided an improved biodiversity framework. OTUs exclusively associated to BCTs provide a novel resource to identify unassessed environmental drivers.
