I investigated the effects of carbon sources on both the bacterial composition of an agricultural bioinoculant product and the metabolism of a plant growth-promoting rhizobacterium, Bacillus megaterium. The first part of the study focused on evaluating an indigenous microorganism (IMO) bioinoculant that is mixed with water and a carbon source, such as maize bran or sugar, and incubated before applying to crops as an alternative to chemical fertilizers. Using Illumina 16S rRNA gene sequencing, I evaluated shifts in bacterial communities that resulted from incubating IMO with different carbon sources (maltose, glucose, sucrose, glucose with fructose, and maize bran) for varying lengths of time (48 and 72 hours) in limited aeration conditions. The following results were found: i) unaltered IMO paste consisted of primarily fermenting organisms, ii) incubating IMO with sterile growth media shifted the population towards dominance by Bacillus and Paenibacillus genera, iii) increased incubation time increased relative abundance of Clostridium (an anaerobic organism) and iv) non-sterile substrates encouraged growth of bacteria present on the substrate itself. These results indicate that variations in how the product is prepared can have a large impact on the final product that is ultimately applied to crops. For the second part of the study, I applied a 13C-assisted metabolomics profiling technique to Bacillus megaterium QM B1551, an organism similar to one identified in the IMO, to investigate the co-metabolism of glucose and three common disaccharides: sucrose, maltose, or cellobiose. Growth experiments indicated that each disaccharide can serve as a sole growth substrate, in accordance with genetic analysis that predicted diverse metabolic capabilities. However, intracellular metabolite labeling following growth on labeled and unlabeled mixed substrates revealed a hierarchy in disaccharide catabolism in the presence of glucose: (i) complete inhibition of cellobiose catabolism, (ii) minimal catabolism of maltose, and (iii) unbiased catabolism of sucrose. Our findings provide insights on selective carbon turnover by soil Bacillus species. Overall, this work contributes to the understanding of both mixed-species and single-species bioinoculants which are increasingly being looked towards as chemical fertilizer replacements.