Soil depths and developmental stages of biological soil crusts are more important than shrub cover in structuring prokaryotic communities

•Microhabitats are important in shaping soil prokaryotic communities in deserts.•Alpha diversity differs in soil depths, biocrust stages, with/without shrub cover.•With/without shrub cover do not change prokaryotic community compositions.•Cyanobacteria dominates in biocrusts and in cyano- and lichen crusts than others.•Soil pH and TP respectively drive patterns of alpha and beta diversities.