The Northern Great Plains of the United States and Canada have seen an increase in pulse crops like pea, lentil, and chickpea acreage in dryland and irrigated systems. Rotating pulse crops into cereal crop production systems could reduce the demand for nitrogen fertilizer due to the symbiotic relationship with nitrogen fixing bacteria called diazotrophs. Legume-diazotroph relationships are well studied, but little is known about the free-living bacteria of the bulk soil in the legume-cereal rotation systems. Here we determine the community structure of the overall (16S) and diazotroph (nifH) soil microbiome in pulse-cereal rotations across the state of Montana. Many variables influenced the microbial community structure, but and among them, irrigation caused a significant shift in the composition of the communities and co-occurrence network topology. Interestingly, the diazotrophic communities in dryland soil are more robust and contain more generalist compared to irrigated soils. Co-occurrence networks support the identification of different diazotrophic keystone taxa such as Firmicutes in irrigated and Proteobacteria in dryland soils. Linking farm management practices and crop productivity with microbial community structure dynamics is an initial step in establishing a knowledge base for farmers to exploit the soil microbiota to maintain healthy soil for crop production.