Interactions between trees such as Populus and their associated soil microbiome significantly impact the net plant productivity (NPP), carbon biosequestration and carbon allocation. In this chapter we discuss new insights learned from genomic-level studies involving Populus and its soil microbial community, especially symbiotic ectomycorrhizal interactions, focusing on the communication and signaling in the soil between the tree roots and the mycorrhizal fungi, effect of root exudates and fungal enzymes in the turn over and translocation of mineral nutrients, nitrogen and soil organic matter (SOM). Future prospects of functional genomic studies on plant and fungal components to improve carbon sequestration and partitioning are outlined. Studies of the Populus ectomycorrhizal interactome in the soil are critical to long-term ecosystem productivity and greatly impact planet's atmosphere.