Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essentialfor maintaining the health of terrestrial systems, but how climate change affects the richness and abundance of soil microbial communities remains unresolved. We examined the effects of warming, altered precipitation and annual biomass removal on grassland soil bacterial, fungal and protistan communities over 7 years to determine how these representative climate changes impact microbial biodiversity and ecosystem functioning. We show that experimental warming and the concomitant reductions in soil moisture played the predominant role in shaping microbial biodiversity by decreasing the richness of bacteria (9.6%), fungi (14.5%), and protists (7.5%). Our results also show positive associations between microbial biodiversity and ecosystem functional processes such as gross primary productivity and microbial biomass. We conclude that the detrimental effects of biodiversity loss might be more severe in a warmer world. MAINBiodiversity, the variety of genes, species, and ecosystems which constitute life on our planet 1 , is dramatically affected by human alterations of global environment 2 . Biodiversity underscores healthy ecosystem functions and assures the production of essential goods, services, and benefits to society, such as climate regulation, landscape stability, fibers, and food production 1 . However, such benefits are threatened by the unprecedented biodiversity loss 3,4 caused by anthropogenic global environmental changes like climate warming, altered precipitation patterns, and land use changes 5 . Studies demonstrate that biodiversity loss impairs the functioning of natural ecosystems * *

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Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.

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Nitrospira are the most widespread and well known nitrite-oxidizing bacteria (NOB) and putatively key nitrite-oxidizers in acidic ecosystems. Nevertheless, their ecology in agriculture soils has not been well studied. To understand the impact of straw incorporation on soil Nitrospira-like bacterial community, a cloned library analysis of the nitrite oxidoreductase gene-nxrB was performed for a long-term rapeseed-rice rotation system. In this study, most members of the Nitrospira-like NOB in the paddy soils from the Wuxue field experiment station were phylogenetically related with Nitrospira lineages II. The Shannon diversity index possessed a decrease trend in the straw applied soils. The relative abundances of 16 OTUs (accounting 72% of the total OTUs, including 11 unique OTUs and 5 shared OTUs) were different between in the straw applied and control soils. These data suggested a selection effect from the long-term straw fertilization. Canonical correspondence analysis data showed that a centralized group of Nitrospira-like NOB OTUs in the community was partly explained by the soil ammonium, nitrate, available phosphorus, and the available potassium. This could suggest that straw fertilization led to the soil Nitrospira-like NOB community shift, which was correlated with the change of available nutrients in the bulk soil.

Summary Soil aggregates, with complex spatial and nutritional heterogeneity, are clearly important for regulating microbial community ecology and biogeochemistry in soils. However, how the taxonomic composition and functional attributes of N‐cycling‐microbes within different soil particle‐size fractions under a long‐term fertilization treatment remains largely unknown. Here, we examined the composition and metabolic potential for urease activity, nitrification, N2O production and reduction of the microbial communities attached to different sized soil particles (2000–250, 250–53 and <53 μm) using a functional gene microarray (GeoChip) and functional assays. We found that urease activity and nitrification were higher in <53 μm fractions, whereas N2O production and reduction rates were greater in 2000–250 and 250–53 μm across different fertilizer regimes. The abundance of key N‐cycling genes involved in anammox, ammonification, assimilatory and dissimilatory N reduction, denitrification, nitrification and N2‐fixation detected by GeoChip increased as soil aggregate size decreased; and the particular key genes abundance (e.g., ureC, amoA, narG, nirS/K) and their corresponding activity were uncoupled. Aggregate fraction exerted significant impacts on N‐cycling microbial taxonomic composition, which was significantly shaped by soil nutrition. Taken together, these findings indicate the important roles of soil aggregates in differentiating N‐cycling metabolic potential and taxonomic composition, and provide empirical evidence that nitrogen metabolism potential and community are uncoupled due to aggregate heterogeneity.