Nitrogen cycling communities associated to roots of arable crops in relation to management

Abstract: Management of terrestrial nitrogen (N) has been identified as a key challenge in the implementation of sustainable agricultural practices. Transformations of inorganic N are mainly performed by microbial functional guilds that regulate the retention or loss of N. Soil management may affect the diversity, composition, and functioning of N-cycling microbial communities. The aim was to define the influence of soil properties, crops and intercropping on root- and soil-associated N-cycling communities with a special focus on the genetic and enzymatic potential for denitrification and nitrous oxide (N₂O) reduction. A greenhouse experiment comparing intercropped cocksfoot and lucerne with sole cropping practices showed that plant species and intercropping significantly affected the abundances of root associated communities that drive the retention or loss of N, suggesting altered plant-microbial and/or microbial-microbial interactions. Addition of biogas digestate as fertilizer did not alter the intercropping effects. A higher N₂O production rate was found in root-associated microbial communities in cocksfoot during intercropping, which coincided with decreased genetic potential for N₂O reduction by organisms within nosZ clade II compared to sole cropped cocksfoot. Sequencing revealed that these N₂O reducers were related to Ignavibacteria, which have a truncated denitrification pathway that lacks the genetic capacity to produce N₂O. Soil type also had a strong influence on root-associated N-cycling communities. In a full-factorial experiment with two soil types and two different crops (barley and sunflower), soil type overrode crop effects regarding both genetic and enzymatic potential for denitrification. Thus, soil physical and chemical properties rather than plant species determine the denitrification and N₂O production rates of the root-associated communities. The genetic potential for the various N-cycling communities differed between bulk soil and roots, indicating that N-cycling functional organisms were favored in different compartments in the soil-root environment. The N₂O reducing organisms carrying nosZI were shown to have an affinity to plant roots, whereas those with nosZII prefer the bulk soil thus indicating a possible niche differentiation between the two clades.

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