Defining Spatial and Ecological Niches of Denitrifying Bacteria in Soils

Global surface temperatures gradually increase as consequence of steadily increasing atmospheric greenhouse gas concentrations. Nitrous oxide (N2O) is a potent greenhouse gas primarily emitted from agricultural soils. Responsible for this are microbial processes like denitrification where nitrate is sequentially reduced to molecular nitrogen (N2) with N2O emitted as an intermediate. With unfavorable conditions for complete denitrification N2O can occur as end product and thus further accelerate climate change. Denitrification and N2O emissions are well known to be driven by different environmental factors but information about the impact on soil denitrifier community traits (abundance, composition, diversity) remains marginal. This study comprehensively investigates how various biotic and abiotic factors impact both process-level and genetic denitrification potentials as well as microbial community dynamics in different soils. Combination of soil slurry experiments and molecular analyses allowed investigation of the effects of proximity to air-filled macropores, soil pH, plant growth, fertilization and microbial community composition on denitrification activity. Additionally, the influence of soil pH and plant growth on denitrifier community dynamics has been analyzed. The results confirm that denitrification potentials on process-level are strongly driven by soil pH, N-input as well as microbial community composition, whereas the proximity to air-filled macropores has a minor influence. Furthermore, the studies evinced that environmental factors not only shape denitrification potentials but also microbial community structure. Differences in denitrifier community structures of investigated soils led to differing kinetic parameters for N2O production and reduction. Here, Bradyrhizobium sp. has been revealed as keystone taxa for complete denitrification, even under changing environmental conditions. Denitrifier gene abundances were thought to provide insights into denitrification potential but, however, they do not reliably predict actual denitrification activities or N2O emissions. Only nirS appears to be a good predictor for denitrification rates in soils. Overall, the results indicate that denitrification potentials are shaped not only by environmental factors, such as soil pH or soil structure, but also by denitrifier community traits and their enzyme kinetics. Genetic denitrification potential alone was found to be a poor predictor of actual denitrification activity, highlighting the importance of microbial resilience and the need to consider both functional and compositional aspects of the soil microbiome.