The goal of a microbial community 'entity' model is to determine if a finely resolved study of microbial dynamics can be used as a large-scale biosensor to follow diversity patterns in the environment. It is thought that a microbial community is an assemblage of organisms, genes and gene functions. Transient, acute signals such as excessive nutrient loads or disturbance and chronic signals such as seasonal temperature or rainfall impact the total environmental system. With the development of new genomic tools, community-level studies have been designed that can interrogate the finer details of the biological components of a given habitat and correlate these components to the drivers shaping the ecosystem. We have characterized the microbial communities in situ in several different soil ecosystems and have linked the microbial structure with the system's 'drivers'. Amplicon length heterogeneity (ALH) interrogates the hypervariable domains of the ribosomal small subunit genes and separates these domains based on the naturally-occurring sequence lengths of DNA. The amplicons are phylogenetically relevant in that the various amplicons generated can be directly associated with specific taxonomic sequences archived in the databases. The microbial community model has been used to monitor the effect of nutrients or land management plans on the microbial community. The Shannon-Weaver diversity index and Pielou's evenness index were used to compare the impact of tillage practices on four Idaho sites. Native sagebrush communities (H= 2.68) differed significantly from irrigated moldboard plowed fields (H=2.26) and irrigated conservation tilled field (H= 2.36) but were not significantly different from irrigated pasture sites (H=2.50). The application of the ALH technique as a monitoring tool for microbial ecology has been shown to enhance and extend the current understanding of the dynamics of microbial communities in their specific environments and its use as a monitoring tool is rapidly expanding.