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Soil aggregates provide different ecological niches for microorganisms, and in turn, the microbial interactions affect soil aggregation process. The response of the microbial community in bulk soil to different fertilization regimes has been well studied; however, the co-occurrence patterns of bacteria and fungi in different aggregates under various fertilization regimes remain unclear. Based on the long-term field experiment, we found that fertilization regimes contributed more to fungal than to bacterial community composition. Long-term fertilization decreased microbial interactions in large macroaggregates (LM), macroaggregates (MA) and silt and clay (SC) fractions, but increased in microaggregates (MI). The application of manure with inorganic fertilizers (NPKM) significantly increased the intensive cooperation between bacteria and fungi in LM and MA. Microbial communities in LM and MA were well separated and showed strong competition against microbes in MI and SC; hence, we concluded that the microbial habitat could be divided into two groups, large fractions (LM and MA) and small fractions (MI and SC). The bacterial genera Anaerolinea , Nocardioides , Ohtaekwangia , Geoalkalibacter , Lysobacter , Pedomicrobium , and Flavisolibacter were keystone taxa in inorganic fertilization, and Roseiflexus , Nitrospira , and Blastocatella were keystone taxa in NPKM, which were all sensitive to soil aggregation. In this study, we demonstrated that the NPKM decreased the microbial interactions within and between kingdoms in LM, MA, and SC, but enhanced nutrient availability and microbial interactions in MI, leading to the formation of biofilms and the strengthening of stress tolerance, which finally stimulated the formation and stabilization of soil aggregates. Thus, this study revealed how soil microbial competition or cooperation responded to different fertilization regimes at aggregate scales, and provided evidence for the stimulation of soil stability. [ABSTRACT FROM AUTHOR]

Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil. [ABSTRACT FROM AUTHOR]

Biochar (BC) addition to soil is a proposed strategy to enhance soil fertility and crop productivity. However, there is limited knowledge regarding responses of soil respiration and C-cycle enzyme activities to BC and nitrogen (N) additions in a calcareous soil. A 56-day incubation experiment was conducted to investigate the combined effects of BC addition rates (0, 0.5, 1.0, 2.5 and 5.0% by mass) and urea (U) application on soil nutrients, soil respiration and C-cycle enzyme activities in a calcareous soil in the North China Plain. Our results showed soil pH values in both U-only and U plus BC treatments significantly decreased within the first 14 days and then stabilized, and CO2emission rate in all U plus BC soils decreased exponentially, while there was no significant difference in the contents of soil total organic carbon (TOC), dissolved organic carbon (DOC), total nitrogen (TN), and C/N ratio in each treatment over time. At each incubation time, soil pH, electrical conductivity (EC), TOC, TN, C/N ratio, DOC and cumulative CO2 emission significantly increased with increasing BC addition rate, while soil potential activities of the four hydrolytic enzymes increased first and then decreased with increasing BC addition rate, with the largest values in the U + 1.0%BC treatment. However, phenol oxidase activity in all U plus BC soils showed a decreasing trend with the increase of BC addition rate. Our results suggest that U plus BC application at a rate of 1% promotes increases in hydrolytic enzymes, does not highly increase C/N and C mineralization, and can improve in soil fertility. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the effects of chemical fertilizer (NPK), NPK with livestock manure (NPK+M), NPK with straw (NPK+S), and NPK with green manure (NPK+G) on soil enzyme activities and microbial characteristics of albic paddy soil, which is a typical soil with low productivity in China. The responses of extracellular enzyme activities and the microbial community diversity (determined by phospholipid fatty acid analysis [PLFA] and denaturing gradient gel electrophoresis [DGGE]) were measured. The results showed that NPK+M and NPK+S significantly increased rice yield, with NPK+M being approximately 24% greater than NPK. The NPK+M significantly increased soil organic carbon (SOC) and available phosphate (P) and enhanced phosphatase, β-cellobiosidase, L-leucine aminopeptidase and urease activities. The NPK+S significantly increased SOC and available potassium (K) and significantly enhanced N-acetyl-glucosamidase, β-xylosidase, urease, and phenol oxidase activities. The NPK+G significantly improved total nitrogen (N), ammonium N, available P, and N-acetyl-glucosamidase activity. The PLFA biomass was highest under NPK+S, followed by NPK+M and NPK+G treatments. Principal component analysis (PCA) of the PLFA indicated that soils with NPK+M and NPK+S contained higher proportions of unsaturated and cyclopropane fatty acids (biomarkers of fungi and gram-negative bacteria) and soil under NPK+G contained more straight chain saturated fatty acids (representing gram-positive bacteria). PCA of the DGGE patterns showed that organic amendments had a greater influence on fungal community. Cluster analysis of fungal DGGE patterns revealed that NPK+G was clearly separated. Meanwhile, the bacterial community of NPK+M treatment was the most distinct. RDA analysis revealed changes of microbial community composition mostly depended on β-xylosidase, β-cellobiosidase activities, total N and available K contents. The abundances of gram-negative bacterial and fungal PLFAs probably effective in improving fertility of low-yield albic paddy soil because of their significant influence on DGGE profile. [ABSTRACT FROM AUTHOR]

Abstract: Ammonia oxidation is a critical step in the soil nitrogen (N) cycle and can be affected by the application of mineral fertilizers or organic manure. However, little is known about the rhizosphere effect on the function and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities, the most important organisms responsible for ammonia oxidation in agricultural ecosystems. Here, the potential nitrification activity (PNA), population size and composition of AOB and AOA communities in both the rhizosphere and bulk soil from a long-term (31-year) fertilizer field experiment conducted during two seasons (wheat and maize) were investigated using the shaken slurry method, quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis. N fertilization greatly enhanced PNA and AOB abundance, while manure application increased AOA abundance. The community structure of AOB exhibited more obvious shifts than that of AOA after long-term fertilization, resulting in more abundant AOB phylotypes similar to Nitrosospira clusters 3 and 4 in the N-fertilized treatments. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than that of AOA among soils during both seasons, indicating that AOB play an active role in ammonia oxidation. Conversely, the PNA and population sizes of AOB and AOA were typically higher in the rhizosphere than the bulk soil, implying a significant rhizosphere effect on ammonia oxidation. Cluster and redundancy analyses further showed that this rhizosphere effect played a more important role in shaping AOA community structure than long-term fertilization. Overall, the results indicate that AOB rather than AOA functionally dominate ammonia oxidation in the calcareous fluvo-aquic soil, and that rhizosphere effect and fertilization regime play different roles in the activity and community structures of AOB and AOA. [Copyright &y& Elsevier]

Abstract: The influence of inorganic or organic fertilization on soil microbial ecology has been emphasized recently, but less is known about rhizosphere effects on extracellular enzyme activities and microbial community structure. Eleven extracellular enzymes involved in C, N, P, and S cycling and microbial community structure in both the rhizosphere and bulk soil samples from a long-term (31-year) fertilizer experimental field at the wheat reproductive stage were investigated by microplate fluorometric assay and phospholipid fatty acid analysis (PLFA), respectively. The samples were taken from six treatments: control (CK, without fertilization), fertilizer N (N), fertilizer N and P (NP), fertilizer N, P and K (NPK), organic manure (M), and organic manure plus fertilizer N, P and K (MNPK). Responses to inorganic or organic fertilizers in the rhizosphere were significantly different from those in the bulk soil. Except for NO3 −-N, thus, nutrient concentrations were generally higher in the rhizosphere than in the bulk soil. M and MNPK treatments greatly increased organic C, total N, NH4 +-N and total S. Inorganic fertilizers (N, NP, and NPK) generally maintained or reduced most enzyme activities in the rhizosphere, but markedly increased these enzyme activities in the bulk soil. However, organic treatments (M and MNPK) enhanced most enzyme activities in both the rhizosphere and bulk soil. Higher total PLFA and lower ratios of bacteria to fungi and of actinomycetes to fungi were observed in the rhizosphere compared with the bulk soil. In the bulk soil, the ratios of bacteria to fungi and of actinomycetes to fungi were highest in the N treatment and lowest in the M treatment. However, in the rhizosphere there were no statistically significant differences in the abundance of bacteria, fungi and actinomycetes between the inorganic and organic treatments. Organic fertilization increased total PLFA and Gram+ to Gram− bacteria ratio in both the rhizosphere and bulk soil. Our results indicated that changes in fertilization regime had a greater impact on the bulk soil microbial community than in the rhizosphere. [Copyright &y& Elsevier]

Biochar addition to soil has been proposed as a strategy to enhance soil quality and crop productivity. However, little is known about responses of soil nutrients and microbial activities to additions of chemical fertilizer and biochar with different pyrolysis temperatures. To investigate the effects of control (CK), chemical fertilizer (NPK), and NPK with maize straw biochar (MC) produced at 300, 450, and 600 °C (NPK + MC300, NPK + MC450, and NPK + MC600) on crop yield, soil nutrients, soil enzyme activities, and microbial attributes in a calcareous soil, we conducted a pot experiment. The results showed that the NPK + MC450 treatment obtained the highest wheat yield and N, P, and K uptakes. The NPK + MC300 and NPK + MC450 treatments decreased significantly the soil available K content and increased the C/N ratio, contents of soil organic carbon (SOC) and available P compared to the NPK + MC600 treatment. The NPK + MC450 treatment promoted the increases in soil C- and N-cycling enzyme activities. The total N content, soil MBC and MBN were the main driving factors affecting soil enzyme activities. All the NPK plus MC soils significantly reduced the relative abundance of soil fungi and enhanced soil nutrient contents (excluding soil inorganic nitrogen) and total phospholipid fatty acid concentrations. A redundancy analysis revealed that the changes in soil microbial community depended mainly on the contents of MBC, MBN and available K as well as the C/N ratio. This study provides clear evidence that the co-application of NPK fertilizers and MC produced at 450 °C was more efficient for improving soil quality and potential crop productivity. [ABSTRACT FROM AUTHOR]

The application of organic fertilizers, such as straw and manure, is an efficient approach to maintain soil productivity. However, the effect of these organic fertilizers on soil microbial nutrient balance has not yet been established. In this study, the effects of the long-term combined organic-inorganic fertilization on microbial community were investigated by conducting a 30-year-long field test. Overall, the following five fertilizer groups were employed: inorganic NP fertilizer (NP), inorganic NK fertilizer (NK), inorganic NPK fertilizer (NPK), NPK + manure (MNPK), and NPK + straw (SNPK). The results indicated that the mean natural logarithm of the soil C:N:P acquisition enzyme ratio was 1.04:1.11:1.00 under organic-inorganic treatments, which showed a deviation from its overall mean ratio of 1:1:1. This indicates that microbial resources do not have a balance. Vector analysis (vector angle <45°) and threshold elemental ratio analysis (R C:N -TER C:N > 0) further demonstrated that the microbial metabolism was limited by Nitrogen (N) under SNPK and MNPK treatments. N limitation further influenced soil microbial community structure and its dominated SOC decomposition. Specifically, Microbial communities transformed into a more oligotrophic-dominant condition (fungal, Acidobacteria , Chloroflexi) from copiotrophic-dominant (Proteobacteria , Actinobacteria) condition with increasing N limitation. Lysobacter genus and Blastocatellaceae family, in the bacterial communities along with the Mortierella elongata species in fungal communities, were markedly associated with the N limitation, which could be the critical biomarker that represented N limitation. Both correlation analysis and partial least squares path modeling showed significant positive effects of N limitation on the ratio of bacterial functional genes (Cellulase/Amylase), involved in recalcitrant SOC degradation. [Display omitted] • Long-term combined organic-inorganic fertilization led to microbial N limitation. • The microbial N limitation increased with the increasing soil C/N ratio. • The N limitation affected the bacterial and fungal communities differently. • Three key biomarkers significantly correlated with N limitation were found. • N limitation promoted bacterial-dominated recalcitrant SOC decomposition. [ABSTRACT FROM AUTHOR]

Free-living nitrogen fixation (FLNF) by diazotrophs is a ubiquitous renewable resource and may constitute an attractive viable solution to the problem of environmental degradation caused by nitrogen over-fertilization. However, the biotic and abiotic control mechanisms of free-living nitrogen fixation are poorly understood. Moreover, there is rare information to link the composition and functions of diazotrophic communities; additionally, there are insufficient or inadequate predictors of the potential N fixation rate (PNFR) to help improve fertilization strategies. Here, through high-throughput sequencing, network analysis, and 15N 2 labelling methods, we investigated the long-term effects of partial substitution of mineral N by organic fertilizers on diazotroph abundance and composition in double rice cropping systems. The field trial was conducted for 34 years and included five treatments: control without fertilizer (CK); only mineral NPK fertilizer (NPK); 70% inorganic N + 30% organic N + PK (NPKM 1); 50% inorganic N + 50% organic N + PK (NPKM 2); 30% inorganic N + 70% organic N + PK (NPKM 3). Our results revealed that at the same nutrient input level, increasing the percentage of organic N substitution reduced diazotrophic abundance. Compared with the CK and NPK treatments, the organic substitution regimes reduced the fluctuation range of the PNFR between the early and late rice growing seasons. NH 4 +-N was the primary factor that negatively correlated (p < 0.01) with diazotrophic abundance, while the potential N fixation rate was positively correlated (p < 0.01) with soil C/N. Among abiotic factors, the models incorporating soil C/N and Fe2+/Mo could accurately predict the potential N fixation rate. High-throughput sequencing and network analyses revealed that Bradyrhizobium and Geobacter were the dominant genera in diazotrophic co-occurrence and keystone taxa patterns under all fertilization regimes. Soil pH and NH 4 +-N were the most important factors in shaping the diazotrophic co-occurrence and keystone patterns in paddy soils, respectively. Diazotrophic keystone composition was more suitable for predicting and characterising the potential N fixation rate than the co-occurrence pattern of diazotrophs. Moreover, compared with the CK and NPK regimes, partial substitution of mineral N with organic N fertilizer improved the prediction accuracy of potential N fixation rate more effectively. Overall, we highlight the benefits of organic substitution fertilizer regime in stabilizing and improving the potential N fixation rate. Our findings provide relevant insights into the potential of key microbial taxa for predictive N fixation for optimising chemical N fertilizer application strategies in paddy soils. • Bradyrhizobium and Geobacter were dominant genera in diazotrophic co-occurrence. • Collaborative diazotrophic community relationships outweighed competing ones. • Diazotrophic keystone taxa were suitable for predicting potential N fixation. • Organic substitution regime facilitated to stabilize and improve N fixation rate. [ABSTRACT FROM AUTHOR]

• The effect of 3-year fertilizations on soil bacterial community in 3 agroecosystems. • Geographic location was a main factor shaping soil bacterial community structure. • Short-term effect of chemical N fertilizer on bacterial community was much stronger. • N fertilizer reduced bacterial network complexity and connectivity in upland soil. Nitrogen (N) fertilization is a pivotal contributor to increasing crop yields. The substantial long-term effects of fertilization on soil microbial communities have been clearly verified. However, the short-term impacts of inorganic and organic fertilization are more stochastic and less deterministic in different agroecosystems, especially at a large spatial scale. Here, we examined the effect of 3 years of different fertilization strategies (i.e., no N fertilizer, inorganic N fertilization, and total or partial replacement of inorganic N by organic manure) on the soil bacterial community in three agroecosystem types spanning the middle temperate zone to the subtropical zone. The results showed that the main contribution to the changes in soil bacterial community structure were dominated by geographic location, which accounted for 61.60% of structural variation, while sampling season and fertilization practice explained 1.52% and 0.61%, respectively. Across three contrasting agroecosystem types, the inorganic N-alone application had greater impacts on the bacterial community structure than organic N fertilization, but the changes in composition were dependent on geographic location. Further, N fertilizer addition reduced soil bacterial network complexity and connectivity; specifically, some key module hubs belonging to non-dominant taxa were lost in N-fertilized upland soils, indicating reduced diversity and stability of the soil micro-ecosystem. Together, our results suggest that, when compared with the mild organic N source, the short-term stimulatory effect of chemical N fertilizer tended not to be beneficial for agroecosystem stability and sustainability. [ABSTRACT FROM AUTHOR]