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• Fertilization regimes affected straw-C incorporation into amino sugars. • Higher 13C-fungal residues accumulated in NPK plus manure supplied soil. • Higher straw-13C transformed into bacterial C in NPK-treated soil. • NPKM soil sustained greater recovery of 13C in total amino sugars by the end. • Straw-13C amino sugars contributed differentially to 13C-SOC in different soils. Emerging evidences have emphasized the primacy of microorganisms as executor in soil organic C (SOC) formation. Yet, whether and how microbial transformation of crop residue-derived C into necromass is affected by fertilization regimes remains poorly understood. To address this, soils subjected to 3-year applications of chemical fertilizer (NPK) vs manure plus chemical fertilizer (NPKM) were incubated with or without addition of 13C-labelled rice straw for 60 days. The 13C incorporation into amino sugars (microbial necromass biomarker) was identified by using an amino sugar-based stable isotope probing approach. The straw-C were transformed more rapidly into total amino sugars (13C-AS s) in NPK-treated soil, while more pronounced 13C-AS s accumulation occurred in NPKM soil at later stage, indicating temporal microbial C uptake to generate necromass varied depending on fertilization regimes. Moreover, straw-derived fungal C was significantly higher in NPKM over NPK while bacterial counterpart reversed during the incubation. Our results reinforced changes in microbial communities and their C utilization capacities for efficient residue production in different fertilized soils. Additionally, NPKM-treated soil sustained a prolonged but likely more efficient utilization of straw-C with increasing time as evidenced by significantly higher percentage of straw-dervied C enrichment in 13C amino sugar pools by the end of incubation. These findings reveal that fertilization regimes can alter response strategies of microbial transformation of plant C into microbial-derived C. Together with differential contributions of these newly-formed microbial C to SOC pool, our work highlights the key role of microbial anabolisms in building up SOC following crop residue return to soils under different fertilization regimes. [ABSTRACT FROM AUTHOR]

Ammonia oxidation, the primary and rate-limiting step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the dominant environmental driver of the activity, abundance, diversity and composition of ammonia-oxidizers has not been well understood enough, and the relative contribution of AOA and AOB to nitrification is still under debate. Soils treated with different fertilization regimes in an over 35-year field experiment were collected to explore the variation in function and structure of ammonia-oxidizer communities and corresponding driver. The highest nitrification activity (44.49 mg N kg −1 soil d −1 ) was found in only organic fertilizer (O) treated soil, whereas the lowest activity (2.81 mg N kg −1 soil d −1 ) was observed in only mineral fertilizer (NPK) treated soil. Moreover, as 1-octyne was employed to discriminate AOA- and AOB-supported nitrification, AOA dominated (93.53%) the nitrification in the Control soil, while AOB contributed dominantly (84.73–89.10%) in all of the organic amended soils, and NPK-treated soil showed an almost equal contribution to AOA (45.79%) and AOB (54.21%). Compared with the Control soil, AOA abundance increased in soils with organic and low chemical fertilizer but decreased in only chemically treated soil, whereas the AOB abundance in all fertilized soils was greatly enhanced. The AOA activity was linearly dependent on AOA abundance, whereas the AOB activity was exponentially correlated with AOB abundance. The sequences of AOA and AOB in the Control soil were mostly affiliated with group I.1b thaumarchaeota and genus Nitrosospira clusters 3a.1. Soil treated with NPK increased the abundance of AOA that belonged to group I.1a-associated lineage, whereas more abundant AOB was related to Nitrosospira clusters 3a.2 and 8b. In contrast, the O-treated soil showed more abundant AOB that belonged to Nitrosospira clusters 3b and 8b. As revealed by aggregated boosted tree analysis, the soil ammonium (NH 4 + ) content was identified as the dominant driver of activity and diversity of AOA, and soil pH was considered to be the major influencing factor in abundance and composition of AOA; the AOB composition was mainly affected by soil NH 4 + content, the relative activity and diversity by soil pH, and the relative abundance by soil electrical conductivity (EC). Collectively, different fertilization regimes will result in variations in activity, abundance, diversity and composition of ammonia-oxidizers with distinct drivers. Our research could be helpful to identify better strategies for the mitigation of nitrate production in agricultural soils. [ABSTRACT FROM AUTHOR]

Significant differences in the microbial biomass and diversity in soil have been observed following long-term fertilization, but little research has explored the co-occurrence patterns among microbial taxa or functions. Soil samples from four long-term experiments in China were collected, and an Illumina amplicon sequencing of 16S rDNA amplicon was performed to decipher the differences in interactions and network organization arising from fertilization with organic amendment (OA) or chemical fertilizer (CF) across the sampling sites. We thus aimed to extend the analysis beyond the basic inventory descriptions of the composition and diversity of the microbiome and toward an assessment of relationships and effects. Nonmetric multidimensional scaling analysis revealed a clear difference between the soil microbiomes associated with the OA and CF treatments. Fertilization can interact with the soil chemical properties and sampling site, thereby significantly impacting the associated soil microbiome. Distinct network structures indicated that the OA network was characterized by more functionally interrelated operational taxonomic units (OTUs) than the CF network. The topological roles of individual OTUs and key microbial populations were distinctly different, although the generalists mainly belonging to Actinobacteria and Proteobacteria were observed in both networks. The different fertilization treatments had distinct effects on the soil pH, which represented a key variable to impact the associated microbial community modularity. Most functional groups involving carbon-, nitrogen- and phosphorus-related metabolism and recycling and antibiotic biosynthesis were present at significantly high abundance in the organic-amended soils. All of the functions with statistical significance could be traced to corresponding responsible major modules in the CF network, but it was not the case in OA soil. These results suggested that the soil functions were decentralized and assigned to small groups in OA soil. Overall, we demonstrated that long-term organic amendment supports stronger functional potentials and more interactions within soil community relative to long-term chemical-only fertilization, which may be related to OA benefits to soil stability and buffering capacity. These results explore the correlations, inter-taxa and between major groups and functional traits, to gain a more integrated understanding of microbiome and ecological rules guiding soil community fostered by fertilization regimes. [ABSTRACT FROM AUTHOR]

Abstract: The application method for a novel bioorganic fertilizer (BIO) was developed to improve its biocontrol efficacy of Fusarium wilt (Ling et al. 2010). However, its efficacy on controlling Fusarium wilt and the variations of microbial community after long-term application for watermelon production had not been elucidated. To clarify, a 4-years pot experiment of mono-cropping watermelon was conducted. The results revealed that though the disease incidences were increased in all treatments with the increase of continuous cropping years, the treatment of BIO application both in nursery and pot soil always maintained the lowest disease incidence. The real-time PCR results showed that the population of Paenibacillus polymyxa was decreased with continuous cropping years, but in all seasons, the treatment with BIO application both in nursery and pot soil had a highest population of P. polymyxa than the other treatments. On the other hand, the abundance of the pathogen FON was increased with the increase of continuous cropping years and the lowest rate of increase was found by BIO application in both nursery and pot soil. DGGE patterns showed that the bacterial diversity was weakened after mono-cropping of watermelon for 4 years, but the consecutive applications of BIO at nursery and transplanting stage resulted in the minimal change of bacterial diversity. More detailed differences on bacterial diversity between control and double application of BIO treatment after 4-years monoculture were analyzed by 454 pyrosequencing, which showed the dominant phyla found in both samples were Firmicutes, Proteobacteria and Actinobacteria, and the consecutive applications of BIO recruited more beneficial bacteria than control, such as Bacillus, Paenibacillus, Haliangium, Streptomyces. Overall, these results, to a certain extent, approved that the consecutive applications of BIO at nursery and transplanting stage could effectively suppress watermelon Fusarium wilt by regulating the rhizosphere bacterial diversity. These results could give some clues that how to regulate the soil microbial community to an appropriate level which can keep the plant healthy and thus control the soil-borne diseases. [Copyright &y& Elsevier]

Cotton production in a long-term, consecutive, mono-cropping cotton field has greatly suffered from soil-borne diseases. In this study, a 4-year field experiment was conducted to investigate the effects of organic fertilizer (OF) or bio-fertilizer (BF) combined with a reduced chemical fertilizer (CF) on soil physicochemical properties, biological activities, antagonistic bacteria ( Bacillus, Trichoderma and Pseudomonas ) and pathogen( Fusarium and Verticillium dahliae ). Soil physicochemical and biological properties were significantly affected by different fertilization scenarios. Soil bulk density (BD) decreased by 4.69% more with 60% CF + BF treatment than with 60% CF + OF treatment. Compared with CF treatment, 60% CF + BF treatment significantly increased soil chemical properties of total nitrogen (TN), available phosphorus (AP), available potassium (AK), soil organic carbon (SOC) and dissolved organic carbon (DOC). The resistant enzymatic activities of catalase (CAT), peroxidase (POD), polyphenoloxidase (PPO) and fluorescein diacetate (FDA) were improved by the bio-fertilizer addition. The abundances of Bacillus , Trichoderma and Pseudomonas followed the order of BF > OF > CF > control. The gene copy numbers of Fusarium and Verticillium dahliae were 3.18 and 2.25 cfu × 10 3 · (g · soil) −1 with CF treatment; these decreased by 47% and 32% with 80% CF + OF treatment, respectively, and they further decreased by 86% and 46% with 80% CF + BF treatment, respectively. Together, our results demonstrated that both OF and BF significantly strengthened the enzyme activities, and the antagonistic bacterial abundance but suppressed pathogens, BF was superior to OF in regulating soil microbial abundance, particularly at a high application rate, and highlighted that SOC and AP ( P < 0.05) were positively correlated with antagonistic bacteria, whereas soil BD and pH were the dominant environment factors impacting soil pathogens. Therefore, ameliorating soil TN, AP and SOC statuses using organic or bio-fertilizer combined with chemical fertilizer is a promising approach to maintaining soil microbiota balance in a continuous, mono-cropping cotton field. [ABSTRACT FROM AUTHOR]

Even though organic fertilization is known to promote soil nitrogen cycling ( N -cycling), it is unclear how this effect is mediated. Here we studied the potential roles of soil physiochemical properties and soil particle-size fraction (PSF) in relation to the diversity and abundance of N -cycling-related prokaryotes by sampling field sites that had been subjected to either mineral or organic fertilization for over 30 years (two independent fields subjected to both fertilization treatments). We found that organic fertilization increased the 63–200 μm sized soil fraction and the abundance of various N -cycling-related prokaryotes including diazotrophs, ammonia-oxidizers and denitrifiers. Moreover, increase in the abundance of different N -cycling-related prokaryotes varied between different size fractions: the abundance of ammonia-oxidizers and nitrate-reducers was the highest in the 63–200 μm size fraction, while the abundance of diazotrophs, ammonifiers and denitrifiers was the highest in the 200–2000 μm, 2–63 μm and 0.1–2 μm size fractions, respectively. According to structural equation modelling (SEM), soil PSF, physiochemical properties and the community structure of N -cycling-related prokaryotes within different PSFs were associated with the abundance of N -cycling-related prokaryotes in non-fractionated bulk soils. In conclusion, these results suggest that organic, but not mineral, fertilization can support the abundance of N -cycling-related prokaryotes and that the strength of the effects depends on their association with specific particle-size fractions. [ABSTRACT FROM AUTHOR]

The complexity of soil processes involved in the production, consumption and accumulation of volatile organic compounds (VOCs) makes hard to access the overall dynamics of VOCs in the soil. In this study, the field soil, applied with inorganic (CF), organic (OF) and inorganic-organic mixed (CFOF) fertilizers for ten years was evaluated for the emission of VOCs at different temperature and moisture levels. We identified 30–50 soil emitted VOCs representing the most common soil VOCs groups by using the solid-phase microextraction (SPME) fiber and gas chromatography-mass spectroscopy. The highest total emission of VOCs was found in OF treatment, but it was non-significantly different with CF treatment. The emission of VOCs was significantly increased with the decrease in moisture contents and increase in the temperature of the soil. Among different fertilizer treatments, the emission of VOCs was significantly higher in OF treatment at 5% moisture, and in CF and OF treatments at 35 °C. Further, the VOCs emitted from soil treated with CFOF showed the highest increase in plant growth while CF and OF treatments showed similar results. The VOCs were also extracted from the soil using methanol to better understand the dynamics of VOCs. The abundance of VOCs extracted from the soil was 44–61%, while the richness was 65–70% higher than the VOCs emitted from the soil in different treatments. Taken together the results of emitted and extracted VOCs from the soil, we conclude that the fertilizers are able to discriminate among the VOC patterns of soil. In addition, most of the VOCs are retained in the soil and the emission of VOCs from soil depends on the type of VOCs, soil properties and environmental conditions; however, more research is required to find out better soil VOCs analysis methods. [ABSTRACT FROM AUTHOR]

Although the enrichment of antibiotic resistance genes (ARGs) in diverse organic soils have been explored, understanding of the ecological processes governing the composition of ARGs in long-term organically fertilized soils still remains limited across typical agricultural regions. Thus, the distribution and assembly of ARG profile in three typical agricultural soils (black soil, fluvo-aquic soil, and red soil) under long-term contrasting fertilization regimes (chemical-only vs organic-only) were investigated using high-throughput qPCR (HT-qPCR). The application of organic manure significantly increased the abundance and number of ARGs across soils, as compared to those with chemical fertilizer. Organic manure application enriched the abundance of mobile genetic elements (MGEs), which were positively associated with ARGs. In addition, it is long-term organic fertilizer that enriched the number and abundance of opportunist and specialist ARGs in the fluvo-aquic and red soils, but not black soils. The number and abundance of most generalist ARGs did not change significantly among different fertilization or soil types. The assembly process of the ARG profiles tends to be more deterministic in organically fertilized soils than in chemically fertilized soils. These results suggest that long-term organic fertilizer application may contribute to the persistence and health risk of the soil antibiotic resistomes (especially specialist ARGs). [Display omitted] • Animal manures inputs increased the abundance and number of total ARGs in typical agricultural soils. • Opportunist, specialist, and generalist ARGs were identified in the over 30 years of fertilized soils. • Long-term organic fertilizer enriched the number and abundance of opportunist and specialist ARGs. • Deterministic processes mainly shaped ARGs community in organically fertilized soils. [ABSTRACT FROM AUTHOR]

Partial organic fertilizer substitution for chemical fertilizer has been proven to reduce the synthetic nitrogen (N) fertilizer requirement while maintaining or improving rice yield. However, little is known about the underlying physiological mechanisms of such an effect. Field trials were conducted to investigate the effect of organic fertilizer substitution for chemical fertilizer on rice yield and the source – sink relationship in two growing seasons. The treatments were as follows: no N fertilizer application (CK); farmers' fertilizer practice (FFP); optimal chemical N management (OPT); and organic fertilizer substitution based on the OPT treatment (OPT-SN). Compared with treatments of chemical N fertilizer alone, rice yield was maintained in the OPT-SN treatment. The value of the sink – source difference in rice was positive during the grain filling period irrespective of the treatments, implying that the grain yield was source-limited. Although the effects on sink growth were similar among the different N addition treatments, organic fertilizer substitution improved source capacity by extending the duration of source activity when compared with treatments only containing chemical N fertilizer. The source – sink relationship was more balanced (lower sink – source difference) in the OPT-SN treatment relative to treatments of chemical N fertilizer alone, and a significant negative relationship between sink – source difference and grain yield was observed. Overall, organic fertilizer substitution could maintain grain yield by establishing a more balanced source – sink relationship during the grain filling period. Our findings clarify the positive effect of organic fertilizer substitution on source – sink balance and provide a basis for fertilization strategies to improve crop productivity. • Organic substitution extended the duration of source growth. • Organic substitution was beneficial for source capacity. • Organic substitution maintained yield through a balanced source–sink relationship. [ABSTRACT FROM AUTHOR]