Soil organic carbon (SOC) is a critical component of soil health, farm productivity and climate control. It drives soil stability, nutrients cycling and erosion control. Soil microbes carry out a wide range of processes that are important for soil health and fertility including SOC turnover. However, microbial control over processes rate related to SOC turnover is not well understood. Changes in soil structural properties induced by agricultural management practices impact soil aggregation, which govern soil chemical and physical heterogeneity and consequently the distribution of microbial communities and their activities among aggregates of different sizes. Current knowledge of microbial communities and their activities within different microenvironments (i.e. aggregate size) is poor but is essential for understanding the regulation of SOC turnover at the farm system scale. In this presentation, we will present data from recent work employing a gene-genome-ecosystem based approach to address questions related to the regulatory and metabolic networks of microbes involved in SOC turnover. We will also identify the microbial drivers and key modulators of soil carbon cycling in grain producing agro-ecosystems. Dissecting the genome(s) of various bacteria has provided information about important traits related to differences in survival strategies and ability to influence SOC pool. Meta-analysis of a comprehensive next generation sequencing dataset from various soil environments suggests that few microbial groups can influence the availability of carbon on a global scale. The presentation will discuss detailed understanding on the mechanisms of microbial regulation of SOC turn-over which is the key challenge for predicting soil health and fertility under various management practices. Finally, we will highlight how empirical data on microbial community can be incorporated in the ecosystem models and enable us to better predict SOM processes in agricultural systems. Our presentation will conclude with an outline on how microbes in soils regulate the cycling of SOC with the particular aim of implementing practices that enable soil microbes to influence increased crop productivity and sustainability.