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The ability of soil microorganisms to uphold a variety of ecosystem services is of increasing interest, but our understanding of the linkage between cropland ecosystem services and the soil microbiome under long-term different fertilizer regimes is still limited. Here, we measured 15 response variables commonly used as indicators of cropland ecosystem services, and employed a shotgun metagenomic sequencing technology to determine microbiome taxonomic composition and functional composition in a sandy loam soil amended with organic and inorganic fertilizers for 28 years. Long-term application of fertilizers had overall positive effects on the variables that indicate soil C and nutrient status, organic material decomposition, nutrient transformation, and plant productivity, but the strength of these effects differed between organic and inorganic fertilization. In long term, organic fertilizers significantly increased the abundance of Sphingomonas and Acidobacteria as well as genes involved in C and N metabolism and degradation of aromatic organic compounds. The observed differences in the indicators of overall biological activity, litter decomposition, nutrient transformation, cropland fertility and productivity were associated with changes in taxonomic composition and functional composition of the soil microbiome. Network analysis revealed that soil organic C, total N, L-leucine aminopeptidase, phosphatase, microbial biomass C and N, and the multifunctionality index showed strong positive associations with Acidobacterium, Lysobacter and Nitrososphaera. These microbes are implicated in the decomposition of organic material, soil C and N transformation, and plant growth promotion. The present study deepens our understanding of the relationship between the soil microbiome and agro-ecosystem functioning, and provides support for the use of organic fertilization strategy to enhance multiple ecosystem services in croplands.

Fertilization-induced changes in soil properties from the paddy soil and upland soil may directly regulate bacterial community composition, which usually coincide with shifts in molecular composition of soil organic carbon (SOC) in the upland soil. However, systematical comparisons lack on how regulators vary with cropping systems under the same weather conditions and soil parent materials. Here, we simultaneously investigated the changes of soil physicochemical parameters and shifts in the bacterial community and SOC molecular composition in two adjacent rice and maize fields that have received five fertilization regimes for more than 30 years. The separation of the bacterial community composition among the treatments from the paddy soil was mainly determined by soil nitrate-N, and that from the upland soil was mainly determined by soil available P (AP) and pH. The SOC molecular composition from the paddy soil was separated by the treatments with N application or not, with those treatments with N application being enriched with CCH3 and aromatic C C, and those without N application being enriched with aromatic C H. These changed C functional groups showed close association with amorphous Fe2O3. For the upland soil, the SOC molecular composition was separated by the treatments with P application or not, with those treatments with P application being enriched with OCH, and those without P application being enriched with CH/CH2. These changed C functional groups had close association with AP and total P. Our results indicated inconsistent separation patterns and regulators of the bacterial community and SOC molecular composition among the treatments of the paddy soil and upland soil, and suggested that the relatively dominant role of the fertilization-induced changes in soil properties or other soil microbes that controlled the SOC molecular composition over the bacteria measured in the present study.

The importance of soil saprotrophic fungi in agroecosystems is receiving increasing attention. However, the linkages between saprotrophic fungal communities and soil fertility and stoichiometry in agroecosystems are poorly understood. Here, four long-term field fertilization experiments with three treatments (i.e., no fertilizer (control), chemical nitrogen (N), phosphorus (P), and potassium (K) fertilizer (NPK), chemical combined with organic fertilizer (NPKM)) were performed to evaluate the associations of saprotrophic fungal communities with the soil fertility index (SFI) and stoichiometric carbon (C):N:P ratios. Long-term NPKM application increased the SFI by 57.66%–129.50% at the four sites, and the SFI was strongly correlated with the saprotrophic fungal community composition, which indicated that exogenous organic matter improved soil fertility to a large extent and stimulated the growth of saprotrophic fungi in arable soils. The soil C:P and N:P ratios were notably decreased in the fertilization treatment, indicated that P was sufficient. Further, the composition of saprotrophic fungi was significantly related to the C:N and N:P ratios, suggested that N status is an important factor for soil saprotrophic fungal communities. Our study provides empirical evidence that the saprotrophic fungal communities in arable soils are strongly associated with soil fertility and stoichiometry and offers guidance for improving soil fertility by regulating the saprophytic fungal community.

Soil microbes play a key role in terrestrial ecosystems. In the saline-sodic environment, the microbial communities and their community assembly processes, especially throughout soil profiles, however, are not well understood. Here, we characterized the soil microbial communities across three sodicity/salinity gradients to 1.0 m depth in the western Songnen Plain, Northeast China. Soil sodicity (exchangeable sodium percentage) and salinity (electrical conductivity) exerted a strong influence on bacterial community compositions compared with other soil properties. These filtering effects of sodicity/salinity were strong on the microbial communities in the layer of 0–60 cm across the three sites, with more contributions of deterministic processes over stochastic processes. As sodicity/salinity decreased, some potential biomarkers for a high community tolerance to salt or soda, such as KSA1, Halomonas, Euzebya and Bacillus, were depleted; meanwhile, some taxa associated with decomposition of organic matter and nutrient transformations, such as Arthrobacter, Mesorhizobium, Pseudomonas and Nitrospira, were enriched. Within each soil profile, the turnover in community composition was lower than between sites, and the stochastic processes (homogenizing dispersal) dominated the microbial assembly. Yet, the surface and deepest depth (80–100 cm) of saline-sodic soils still harbored some distinct microbial communities. The near-surface (20–40 cm) may serve as a gating role for limiting surface microbial penetrance into the deeper depth. Taken together, our results show that sodicity/salinity can strongly structure soil microbial communities, and emphasize the importance of soil depth as an environmental gradient on the assembly processes in saline-sodic soils.

The changes of chemical structure and decomposer community during straw degradation have been inconsistent in previous reports, showing either convergence or divergence of chemical structures or microbial communities among different straw types. Hence the strength of their relationship remains unclear. Here, we directly measured the chemical structures and bacterial and fungal communities of wheat (Triticum aestivum L.) and maize (Zea mays L.) residues after four-year decomposition in three Calcaric Fluvisols that varied in soil textures. Separation of the chemical structures among the six soil-straw combinations (two straw types × three soil textures) were generally coupled with trends in the communities of bacterial and fungal decomposers, but the nature of their coupling differed. In the sand soil, soil texture was the central feature that shaped bacterial and fungal communities for both straw types, driving in turn the convergence of chemical structures of both decomposing straws. In contrast, in the sandy loam and silty clay soils, straw type was the primary regulator of the colonizing bacterial and fungal communities, which resulted in the divergence of chemical structures according to straw type.

Improvement of Shajiang black soil in the Huanghuai plain is crucial for sustainable agricultural production; however, the effects of intensified fertilizer input on microbial communities in this soil type remain uncertain. Here, we conducted a long-term field trial using a wheat-soybean-maize cropping system, which had five treatments: organic material (soybean cake) (OM), mineral fertilizers (NPK), standard nitrogen (N) (half from OM and half from NPK) (MNPK), high N (1.6-fold higher than other treatments, with half from OM and half from NPK) (HMNPK), and unfertilized control. The organic carbon (C) composition of the soil was analyzed by 13C nuclear magnetic resonance spectroscopy, and bacterial community structure was determined based on 16S rRNA gene sequencing analysis. Addition of NPK resulted in soil acidification, which was effectively alleviated by organic amendment. NPK significantly (P

Soil bacteria and fungi are essential constituents of arable ecosystems. Long-term phosphorus (P) deficiency has been proven to significantly affect microbial community diversity and composition. However, how P deficiency impacts the interplay between bacteria and fungi remains unclear. The objective was to explore the bacterial-fungal co-occurrence patterns in soil as influenced by long-term P deficiency, using network analysis. Bacterial and fungal community datasets were obtained from soils which have consistently and continuously been fertilized with P (+P) or without P (−P) for >20 years in three long-term field experiments in China. Our results showed that the −P network was less complex and less efficient as indicated by fewer edges, lower average degree and higher average path length. Chronic P deficiency simultaneously decreased positive and negative bacterial-fungal edges, implying that both synergistic and antagonistic interactions were enhanced by P application. The keystone species differed between +P and −P network, and those from the +P network showed significant correlations with less soil properties, indicating the −P network was more sensitive to environmental disturbances. Four major modules were observed in both +P and −P networks, and they related with different soil properties, suggesting distinct habitat heterogeneity or niche partitioning. All the modules had similar ecological roles, while the module composition was altered by long-term P deficiency, indicating a possible ecological redundancy. Most of the fungi from the −P treatment were distributed in a special module negatively correlated with available P, indicating that fungi may prefer niches with low P concentration. Taken together, our results illustrated the crucial roles of P availability in microbial community assembly and investigated the responses of co-occurrence patterns to long-term P deficiency by regulating the topological properties, keystone species and module composition of the bacterial-fungal network.

It is of ecological significance to investigate microbial communities in response to straw amendment and moisture in arable soils. However, in Chinese fluvo-aquic soils, these responses are still poorly understood. We designed an incubation experiment involving two soils with and without the addition of maize stubble at two moisture levels, and bacterial community structure at days 20, 80, and 200 after the start of incubation was assessed via bar-coded pyrosequencing of the 16S rDNA amplicons. In the presence of stubble with identical moisture level, we observed higher bacterial diversity and richness in long-term organic manure-fertilized soil compared with the unfertilized soil at days 20 and 80, which we attributed to the different quality and quantity of organic matter between the two soils. However, there was no significant difference in bacterial diversity and richness between the two soils at day 200, indicating that long-term straw amendment probably lessens the difference in bacterial community structure between the two soils. In the amended soils bacterial diversity, richness, and community composition at 25% of the water-holding capacity distinctly differed from those at 55% of the water-holding capacity, indicating that moisture strongly affects bacterial distribution in the amended soils. As stubble-C availability declined over time, the dominance of copiotrophic population weakened, and oligotrophic population was moderately abundant. Finally, our study suggests that dissolved organic carbon, which drives redistribution in copiotrophic and oligotrophic categories in response to the varying water and stubble-C availability, is a determinant of bacterial community composition in the amended soils. (C) 2014 Elsevier B.V. All rights reserved.