In an incipient soil system, the biotic component of soil development is microbially driven. However, there is limited understanding of microbial community establishment, functional associations, and community assembly processes in such systems. Additionally, in a incipient system lacking higher life forms like plants, microbes are the first biotic entity to participate in carbon dynamics. This study presents a unique approach of examining microbial signatures in a incipient terrestrial basalt soil system conducted under controlled conditions at the Landscape Evolution Observatory at University of Arizona. A combination of phylogenetic analysis, ultra-high resolution carbon compound characterization, and ecological null models were employed to highlight the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in incipient environmental systems.