Green manuring relocates microbiomes in driving the soil functionality of nitrogen cycling to obtain preferable grain yields in thirty years

Fertilizers are widely used to produce more food, inevitably altering the diversity and composition of soil organisms. The role of soil biodiversity in controlling multiple ecosystem services remains unclear, especially after decades of fertilization. Here, we assess the contribution of the soil functionalities of carbon(C), nitrogen(N), and phosphorus(P) cycling to crop production and explore how soil organisms control these functionalities in a 33-year field fertilization experiment. The long-term application of green manure or cow manure produced wheat yields equivalent to those obtained with chemical N, with the former providing higher soil functions and allowing the functionality of N cycling(especially soil N mineralization and biological N fixation) to control wheat production. The keystone phylotypes within the global network rather than the overall microbial community dominated the soil multifunctionality and functionality of C,N, and P cycling across the soil profile(0–100 cm). We further confirmed that these keystone phylotypes consisted of many metabolic pathways of nutrient cycling and essential microbes involved in organic C mineralization, N_(2)O release, and biological N fixation. The chemical N, green manure, and cow manure resulted in the highest abundances of amoB, nifH, and GH48 genes and Nitrosomonadaceae,Azospirillaceae, and Sphingomonadaceae within the keystone phylotypes, and these microbes were significantly and positively correlated with N_(2)O release, N fixation, and organic C mineralization, respectively. Moreover, our results demonstrated that organic fertilization increased the effects of the network size and keystone phylotypes on the subsoil functions by facilitating the migration of soil microorganisms across the soil profiles and green manure with the highest migration rates. This study highlights the importance of the functionality of N cycling in controlling crop production and keystone phylotypes in regulating soil functions, and provides selectable fertilization strategies for maintaining crop production and soil functions across soil profiles in agricultural ecosystems.

Inhibition of ammonia-oxidizing bacteria promotes the growth of ammonia-oxidizing archaea in ammonium-rich alkaline soils

Disparities in the substrate affinity and tolerance threshold for ammonia have been believed to play a key role in driving niche differentiation between ammonia-oxidizing archaea (AOA) and bacteria (AOB);however, recent surveys argue that direct competition between AOA and AOB is also important in this phenomenon. Accordingly, it is reasonable to predict that diverse AOA lineages would grow in ammonium (NH_(4)^(+))-rich alkaline arable soils if AOB growth is suppressed. To test this hypothesis, a microcosm study was established using three different types of alkaline arable soils, in which a high NH_(4)^(+) concentration (200 μg N g^(-1) dry soil) was maintained by routinely replenishing urea and the activities of AOB were selectively inhibited by 1-octyne or 3,4-dimethylpyrazole phosphate (DMPP). Compared with amendment with urea alone, 1-octyne partially retarded AOB growth, while DMPP completely inhibited AOB. Both inhibitors accelerated the growth of AOA, with significantly higher ratios of abundance of AOA to AOB observed with DMPP amendment across soils. Nonmetric multidimensional scaling analysis (NMDS) indicated that different treatments significantly altered the community structures of both AOA and AOB and AOA OTUs enriched by high-NH_(4)^(+) amendment were taxonomically constrained across the soils tested and closely related to Nitrososphaera viennensis EN76 and N. garnensis. Given that these representative strains have been demonstrated to be sensitive to high ammonia concentrations, our results suggest that it is the competitiveness for ammonia, rather than disparities in substrate affinity and tolerance threshold for ammonia, that drives niche differentiation between these phylotypes and AOB in NH_(4)^(+)-rich alkaline soils.