A study of microbiome structure and function associated with plants roots will be presented. the study showed that the microbiome structure is determined by the plant type, with root microbiome is related in cereals (corn, wheat) and in cucumber and tomato is different from that of the cereals and from each other. When examining gene expression in these communities we realized that while denitrification genes are highly expressed, the final gene (nosZ), responsible to the reduction of N2O (a potent greenhouse gas) to N2 is not. That may explain the fact that most of anthropogenic emission is from agricultural soils. N2O reducing bacteria, isolated from wheat roots, could prevent up to 40% of the emission