Soil and plant root microbiota are crucial for plant growth, development and health. Comparative study of microbiota composition found that root systems of different plants select for completely different microbiota, when grown in identical conditions. It was shown that cereals (wheat and maize) root communities are similar in structure and composition, different from those of cucumber, and all were different from those of tomato. Moreover, plant species-specific stimulation of bacteria in the bulk soil suggested that the more active community was affected by root exudates. Metagenomics of root microbiota demonstrated high redundancy in functional potential between communities, highly disparate in their composition, pointing to a generalized root colonization toolbox. However, metatranscriptomic analysis revealed many plant specific traits. One of the main observations was that while in microbiota of wheat root, gene expression patterns suggested life under lack of available oxygen, in cucumber community metatranscriptome suggested high oxygen availability.
In wheat, all denitrification pathway genes but nosZ were highly expressed. The latter is the only enzyme known to perform conversion of N2O to N2, thus the end product of denitrification in such system is expected to be N2O. This may explain the extreme role of agriculture in global N2O emission. N2O reducing bacteria were isolated from wheat roots, and some of them, when augmented to soil, were shown to efficiently colonize the wheat root, causing a pronounced decrease in N2O emission. These results demonstrate the power of ecological studies and ‘ecology to engineering’ process for microbiota.