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The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH 4 + on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO 3 -manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO 3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO 3 . The ammonia monooxygenase ( amoA ) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO 3 + NH 4 + than NH 4 + during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO 3 -enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO 3 with or without NH 4 + supply may be ascribed to the lower activity of both AOB and AOA, especially AOA. [ABSTRACT FROM AUTHOR]

Plant responses to nitrogen (N) and phosphorus (P) deficiencies differ among genotypes. Although the rhizosphere microbiome can serve as an indicator of plant functional traits across different genotypes, whether and how genotypic differences in plant tolerance to N and P deficiencies are associated with the rhizosphere microbiome are unknown. In this study, we carried out a paddy field experiment using five previously screened rice (Oryza sativa L.) varieties and examined crop yield and mineral element concentrations as well as the chemical properties and bacterial community of bulk and rhizosphere soils in response to N and P deficiencies. The three high-yield rice genotypes were found to be tolerant to N and P deficiencies, whereas the two low-yield genotypes were sensitive. Rhizosphere bacterial community compositions under different fertilization treatments were clearly separated into two groups corresponding to tolerant and sensitive rice. Eighteen bacterial keystone taxa were identified across the five rice genotypes under different N and P conditions. Tolerant rice harbored more bacterial keystone taxa in the rhizosphere under N or P deficiency than did sensitive rice. The specific bacterial keystone taxa recruited by tolerant rice were functionally associated with soil N transformation, plant-promoting activity, carbon decomposition, and iron cycling. These results suggest that bacterial community selection in the rhizosphere is dependent on the tolerance of rice genotypes to N and P deficiencies. The findings help explain the intrinsic mechanism that potentially controls the yield gap of rice genotypes through rhizosphere-driven microbial functions under N/P-limited agroecosystem conditions. The identified bacterial keystone taxa, which are potentially useful bio-fertilizer inoculants for agricultural production and possible indicators of rice genotypes for breeding N- and P-efficient rice cultivars, may ultimately contribute to sustainable agricultural development, resulting in high crop yields while minimizing fertilizer input and environmental risks. • Fertilization has a greater effect than rice genotype on the bacterial community. • Bacterial community selection in the rhizosphere is rice-genotype dependent. • Rice tolerance to N/P deficiency drives separation of the bacterial community. • Compared with sensitive rice, tolerant rice harbors more bacterial keystone taxa. • Bacterial keystone taxa are associated with C/N transformation and Fe cycling. [ABSTRACT FROM AUTHOR]

Low soil nutrient availability severely constrains plant growth and productivity in acidic soil ecosystems. Diazotrophs and arbuscular mycorrhizal fungi (AMF) are the important microbial groups that improve the bioavailability of soil nitrogen (N) and phosphorus (P), respectively. Therefore, the objective was to investigate the biogeographic patterns and co-occurrence networks of the diazotrophic and AMF communities in the acidic soil ecosystem. We collected 52 soil samples from four long-term field observation stations with spatial distances of 961.3 km in the acidic soil region of southern China, and analyzed the community composition and biogeographic distributions of the diazotrophs and AMF using high-throughput sequencing of the functional gene amplicons. The variation partition analysis indicated that soil physicochemical factors provided more contributions than geographic distance, sampling stations and land-use types in the assembly of the diazotrophic and AMF community communities. Distance-decay relationships and Mantel tests showed that soil physicochemical factors had remarkable effects on both microbial community structures, whereas geographic distance only significantly affected the diazotrophic community variations. Co-occurrence network analysis revealed that AMF network was more complex and stable than the diazotrophic network. Furthermore, the dominant genera Bradyrhizbium and Glomus might be the more important keystone taxa in the diazotrophic and AMF networks, respectively. These findings suggest that the diazotrophic and AMF communities exhibit different assembly mechanisms and co-occurrence ecological networks in the acidic soil region of southern China, and both community assemblies were mainly driven by soil physicochemical factors. Unlabelled Image • Environmental factors clearly affected the diazotrophic and AMF community structures. • Geographic distance only significantly affected the diazotrophic community variations. • Diazotrophic and AMF communities exhibited different assembly mechanisms. • AMF network was more complex and stable than the diazotrophic network. • Bradyrhizbium and Glomus were the keystone taxa in the diazotrophic and AMF networks. [ABSTRACT FROM AUTHOR]