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Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.These authors contributed equally:

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Rose (Rosa sp.) plants (`Mercedes') were grown in yellow tuff (YT) (volcanic ash, scoria) and pumice from Italy (PI) and Greece (PG) for which physical and hydraulic characteristics were determined. The differences among the measured retention curves of these materials result in significant differences among their relative hydraulic conductivity functions. The hydraulic conductivity of YT is much higher than that of PI, which is higher than that of PG. The plants were subjected to optimal growth and nutrition conditions. Irrigation was controlled using electronic tensiometers, at suction values well within the range of easily available water: 13 cm for YT and 8 cm for the two pumice types. Nonetheless, yields were significantly higher in YT than in PI; yields were even lower in PG. We suggest that the limiting factor was the dynamic water availability to the plants, which is affected mainly by the unsaturated hydraulic conductivity. The relative hydraulic conductivity of YT at 13 cm is more than an order of magnitude higher than that of PI at 8 cm. The relative hydraulic conductivity of PG at 8 cm is two orders of magnitude lower than that of YT at 13 cm. It seems that the current concept of easily available water, based on a predetermined suction range, independent of the hydraulic characteristics of the media, is not an appropriate parameter for irrigation management in soilless culture. The unsaturated hydraulic conductivity, being a characteristic function of the medium and highly sensitive to moisture variation, indicates better the actual availability of water to the roots. Therefore, it should be used for irrigation control in containers filled with porous substrates.