An important research component of any biofuels feedstock development program should include improving sustainability and the added benefits of carbon sequestration.  The potential for dramatic improvement in sustainability can be achieved via several avenues of research.  Sustainability for feedstocks research will require a need to identify (1) plant traits and other factors that enhance asymbiotic and symbiotic microbial processes; (2) plant traits that enable efficient resource use; (3) conditions that optimize the amount of nutrients supplied by the activities of symbiotic and associative microbial communities; (4) the importance of microbial functional diversity and its interdependence on plant diversity; and (5) plant and microbial traits that enhance carbon sequestration. To accomplish such research we will need to deepen our understanding of the mechanisms and genetics underlying plant-soil-microbial interactions and associations, especially the mycorrhizal symbioses. Research needs to encompass scales ranging from metagenomics and proteomics of mycorrhizal fungi and their habitats to the phenotypic expression of symbiotic traits. Success can be evaluated by identifying the relative contributions of plant traits vs. environmental conditions for expression of targeted pathways. Examples of potential approaches and research needs will be given for mycorrhizal fungi associated with switchgrass and poplar.  Tradeoffs between traits beneficial to sustainability and carbon sequestration will be discussed.