Structural and functional characterization of the microbial communities associated with the upland and irrigated rice rhizospheres in a neotropical Colombian savannah

There is limited information about the microbial communities associated with the rhizosphere of the rice plants grown under productive systems irrigated and upland in commercial lots. The objective of this research was to compare the structures and functions of the microbial communities of eight farmlands, four irrigated and four upland, located in the eastern Colombian savannahs (Orinoquia region). The characterization of the rhizosphere community of bacteria and fungi included the using of culture-independent techniques (PCR–DGGE), the enzymatic activity (nitrogenase protease, arylsulfatase and acid and alkaline phosphatase), as well as culture-dependent techniques for bacteria, fungi, actinomycetes, aerobic diazotrophs and phosphate solubilizing bacteria. Upland and irrigated crops with the same rice cultivar differed in terms of soil physical–chemical parameters, enzyme activity, microbial counts and the DGGE bacterial profiles. The irrigated farms had a higher pH and greater concentrations of iron and ammonium than the upland farms, while the upland farms showed higher concentrations of nitrate. The irrigated farms presented the highest counts of diazotrophs and had the greatest arylsulfatase activity, while the upland farmlands showed higher phosphatase activity. Nitrogenase activity was not detected in any farm. The bacterial PCR–DGGE profiles clustered farms by production system, but without significant differences in richness and diversity indices; the fungal community presented higher level of diversity in relation with other studies but it did not showed a clustering related with any production system.

► We studied the microbial function and structure of rice rhizosphere in commercial farms.
► The physicochemical and microbiological parameters differentiated the irrigated and upland systems.
► Arylsulfatase activity prevailed in irrigated and phosphatase activity in the upland systems.
►  Nitrogenase activity was not detected in any farm.
► PCR–DGGE showed a high diversity and richness of rice rhizosphere fungal community.