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This study focused on the legacy effects of 8-year application of N (in gradient of 0, 140, 280, 470, and 660 kg N ha−1 year−1) on the bacterial community diversity, interactions, and assembly processes in the wheat rhizosphere. The rhizosphere bacterial α-diversity increased with the rate of historical N input, while it did not change at N addition rates of over 280 kg N ha−1 year−1. Historical N input clearly shifted the rhizosphere bacterial community composition, and soils with more N input were more dissimilar to those without N input. The net relatedness index (NRI) and nearest taxon index (NTI) analysis revealed that the rhizosphere bacterial communities in most samples were phylogenetically clustered, and the treatments with high N (> 470 kg N ha−1 year−1) showed higher levels of clustering than those with low N (< 140 kg N ha−1 year−1), indicating more environmental selection stress in soil with higher historical N input. Increased co-occurrence network size and connectivity were accompanied by increased aboveground biomass of wheat. Overall, with the increase in historical N input, the resulting legacy effects forced the bacterial community in the rhizosphere to undergo higher environmental selection pressure, and indirectly affected the complexity of wheat rhizosphere assemblages during subsequent crop growth. [ABSTRACT FROM AUTHOR]

Alkaline phosphomonoesterase (ALP) mainly originates from soil microbial secretion and plays a crucial role in the turnover of soil phosphorus (P). To examine the response of ALP-encoding microbial communities (analysed for the biomarker of the ALP gene, phoD) of soils and derivative soil fractions to different fertilisation regimes, soil samples were collected from a long-term experimental field (over 35 years). The different organic P (Po) pools of soil fractions and the ALP activity of soil were also determined. Compared with chemical-only fertilised soils, the ALP activity was 232-815% higher in organic-amended soils, and the highest enzyme activity was observed in the organic-only fertilised treatment. The abundance of the phoD gene harbouring in soil fractions, determined by quantitative PCR (qPCR), was affected by different fertilisations. The highest abundance of the phoD gene was generally detected in the 2-63-μm-sized fraction (silt), but most phoD-encoding microbial species were associated to the 0.1-2-μm-sized fraction (clay) in the chemical-only fertilised soil. The contents of labile Po (LPo), moderately labile Po (MLPo) and fulvic acid-associated Po (FAPo) were significantly correlated with the phoD gene abundance, whereas only LPo content was significantly correlated with the ALP activity. The dominant phoD-encoding phylas were Actinobacteria and Proteobacteria, according to a high-throughput sequencing. Bradyrhizobium, a N-fixer identified as a phoD-encoding genus, showed the highest abundance in fertilised soils. The abundance of Bradyrhizobium, Streptomyces, Modestobacter, Lysobacter, Frankia and Burkholderia increased with the organic-only amendment and was significantly correlated with the ALP activity. According to structure equation models (SEM), pH and LPo content significantly and directly affected the ALP activity; the soil organic C (C) content was related to composition and abundances of phoD-harbouring microbial communities; since both microbial properties were correlated to the ALP activity, the C content was indirectly related to the ALP activity. In conclusion, soil management practices can be used to optimise the contents of soil available P and the organic P with regulation of soil ALP activity and the community composition of corresponding microbes. [ABSTRACT FROM AUTHOR]

Particle-size soils were fractionated for evaluating changes in the composition of bacterial community and enzyme activity in response to 13 years of fertilization. This study focused on Mollisol and its particle-size fractions of 200-2,000 μm (coarse sand sized), 63 to 200 μm (fine sand sized), 2 to 63 μm (silt sized), and 0.1 to 2 to μm (clay-sized). Long-term chemical fertilization lowered the pH of all particle fractions, whereas organic fertilizer application mitigated soil acidification. Nutrient concentrations depended on both fertilizer treatment and particle fractions and enzymes were unevenly active throughout the soil. Generally, the highest enzyme activities were observed in the silt and clay fractions of control soil and the soil treated with chemical fertilizer (N, P, and K (NPK)) and in the sand-sized fraction of soil treated with manure and chemical fertilizer (MNPK). Except for acid phosphomonoesterase, the other tested enzyme activities in coarse-sized fractions of MNPK soil were significantly higher than those of the control and NPK soils. Fertilization and soil fraction interactively ( p < 0.05) affected the enzyme activity. Denaturing gradient gel electrophoresis analysis showed that the bacterial community structure significantly differed in different particle sizes with a higher bacterial diversity in small-sized than in coarse-sized fractions. Dominant bands were excised and sequenced. We have found the following bacterial groups: Actinobacteria, γ-proteobacteria, and Acidobacteria. In addition, enrichment of organic matter in coarser fractions was related to greater bacterial diversity than any other treatment. Principal component analysis showed a smaller variability among fractions of the organic amended treatment. Redundancy analysis showed that the tested properties significantly affected the composition of bacterial community with the exception of C/N and available P. No significant correlation between enzyme activity and bacterial community composition was detected, whereas positive correlations between other soil properties and enzyme activities were observed to various extents. Probably, enzyme activities might be affected by specific functional bacterial communities rather than by the overall bacterial community. We concluded that the long-term application of organic manures contributed to the increase of soil organic matter content of particles higher than 200 mm, with higher bacterial diversity and increases in most of the enzyme activities. [ABSTRACT FROM AUTHOR]

Rare bacteria in rhizospheres from natural watermelon vs chimeric watermelon were investigated to understand the rare rhizobacteria assembling processes along with plant development and effects of rare species on functional stability. Over 80% of the total OTUs were defined as rare taxa (i.e., transient, permanent, and conditionally rare) in the rhizosphere. Among these three rarities, transient rare taxa possessed the highest richness, while the conditionally rarity displayed the largest variations along growth stages and exhibited the greatest deterministic process for assembling. Pairs of conditionally rare taxa with high asynchrony and similar functional potentials were identified in the rhizobacterial communities. This suggests the functional stability of the rhizosphere through functional redundancy. The number of pairs within the rhizosphere of chimeric plant was ~ two fold higher than that of natural watermelon, which illustrated that chimeric plants can stabilize rhizospheric functions. [ABSTRACT FROM AUTHOR]

Watermelon Fusarium wilt is one of the most severe soil-borne diseases caused by Fusarium oxysporum f. sp. niveum. In this study, the population of F. oxysporum was quickly monitored by real-time PCR and DNA array in watermelon Fusarium wilt infected soils treated with Paenibacillus polymyxa SQR21 enhanced bio-organic fertilizer (BIO) at the beginning of nursery growth and/or at the beginning of transplanting. The fungal community composition was investigated by molecular cloning and DGGE techniques. The real-time PCR results showed the F. oxysporum population in the rhizosphere soil decreased from 8.56 × 10 colony-forming units (cfu) g rhizosphere soil to 9.41 × 10 cfu g rhizosphere soil after BIO application and the DNA array detection signals of F. oxysporum population weakened. The difference between F. oxysporum abundance of BIO amended and not amended bulk soils was lower than 10 cfu g soil. DGGE profile indicated that BIO application changed the fungal community structure in the rhizosphere soils; the molecular cloning data revealed that consecutive applications of BIO at nursery and transplanting stages not only decreased Ascomycota and increased Basidiomycota abundance in the rhizosphere soil but also caused the apperance of unique fungal group which were not found in the control. The beneficial fungi Chaetomium sp. Aspergillus penicillioides were found in the BIO amended treatment, while some harmful fungi such as F. oxysporum, Rhizoctonia solani, and Fusarium solani were only detected in the control. Data from this study indicated that BIO application can control watermelon Fusarium wilt by suppressing the population of F. oxysporum and changing the fungal community structure in the rhizosphere soils. [ABSTRACT FROM AUTHOR]

Fusarium wilt is one of the major constraints on cucumber production worldwide. Several strategies have been used to control the causative pathogen, Fusarium oxysporum f. sp. cucumerinum J. H. Owen, including soil solarization, fungicide seed treatment and biological control. In this study, F. oxysporum f. sp. cucumerinum was successfully controlled by a newly isolated strain, Bacillus subtilis SQR 9, in vitro and in vivo. Greenhouse experiments were carried out to evaluate the effect of inoculation and solid fermentation of organic fertilizer with B. subtilis SQR 9, hereby defined as bio-organic fertilizer (BIO), on the control of Fusarium wilt. In comparison with the control, the wilt incidence was significantly reduced (49-61% reduction) by application of BIO. The rhizosphere population of F. oxysporum f. sp. cucumerinum, as detected both by selective plating and realtime PCR, was significantly lower in BIO-treated plants than the control. The localization of bacterial cells, pattern of colonization and survival of B. subtilis SQR 9 in the rhizsosphere of cucumber, was examined by fluorescent microscopy and explored following recovery of the green fluorescent protein ( gfp)-labeled SQR 9 with the new gfp-marked shuttle vector pHAPII through selective plating. The preferential sites of the labeled strain were the differentiation and elongation zone, root hair and the lateral root junctions. The population of the strain was 10 cfu/g root in rhizoplane. These results indicate that the strain was able to survive well in the rhizosphere of cucumber, suppressed growth of F. oxysporum in the rhizosphere of cucumber and protected the host from the pathogen. [ABSTRACT FROM AUTHOR]

Partial substitution of chemical fertilizers by organic amendments is essential for improving the soil quality without yield loss. Fungi play an important role in soil quality because they decompose organic matter and cycle nutrients in the soil. However, there is limited information regarding the effect of different organic substitution rates (OSRs) on the soil quality and fungal community. This study investigated the relationship between the soil quality index and fungal community in a tea plantation under different OSRs of N, from a single application of synthetic fertilizer (NPK) to 100% N substitution with organic fertilizer (OM100). The OSRs were positively correlated with the soil physicochemical and biological soil quality index (SQI), but only the physicochemical SQI exhibited a significant relationship with tea production. The OSR also shifted the soil fungal community composition. Soil pH, soil organic C (SOC), microbial biomass C (MBC), and available potassium (AK) were the key characteristics that were significantly correlated with the variation of soil fungal community. Network analysis indicated that additional organic substitution can enhance the soil fungal network complexity, which also showed a positive correlation with the SQI. These results confirmed the feasibility of organic substitution for soil quality improvement, and implied that the soil fungal network complexity could be a new indicator for soil quality assessment. [ABSTRACT FROM AUTHOR]

Agricultural soils with (M+) or without (M−) organic amendment were collected from four long-term field experiments to investigate soil fungal community composition and its relationship to the soil ionome by employing both the sequencing of fungal internal transcription spacer (ITS) fragments and inductively coupled plasma mass spectrometry (ICP-MS). Fungal community composition was primarily impacted by physical location while organic amendment triggered community shifts in the same direction in all four sites. Overall, the fungal community was strongly correlated to soil pH that, conversely, impacted soil ion availability. Fungal community dissimilarity was strongly correlated to soil ionome (ionic profile) variability. Network analysis has been conducted to explore the biotic interactions in soil ecosystem, in which species (nodes) are connected by pairwise interactions (links). The results revealed that organic amendment led to a higher number of correlated nodes to soil ions, links, modules (a group of nodes more densely connected to each other than to nodes outside the group), and positive links within and between modules. Moreover, specific fungal modules were independently correlated with soil ions, suggesting that each module represents a functional guild or collection of similar fungal ecotypes. Module size (number of nodes in a module) exhibited no apparent influence on the scale of these correlations. The increase in cooperative/synergistic interactions with organic amendment suggests that application results in a better-organized and more efficient community with enhanced potential soil fungal interactions mediated by alterations in the soil ionome. Overall, this study indicates that these less commonly measured soil ions play an important role and may be used to reveal previously undetermined drivers of the soil microbial community. [ABSTRACT FROM AUTHOR]

The impact of long-term fertilizer on ammonia (NH) volatilization in a double rice-cropping system is not well documented. A long-term fertilizer experiment in Chinese double rice-cropping systems initiated in 1990 was used in this study to evaluate the NH volatilization. Six fertilizer treatments were designed, including inorganic fertilizer [nitrogen and phosphorus fertilizer (NP), nitrogen and potassium fertilizer (NK), and balanced mineral fertilizer (NPK)], combined inorganic/organic fertilizers at full and reduced rate (FOM and ROM), and no fertilizer application (served as control). Ammonia volatilization fluxes were measured using a continuous airflow enclosure method during double rice growing seasons from 2007 to 2009. Results showed that the cumulative NH volatilizations in the fertilizer plots ranged from 12.8 to 27.3 kg N ha for the early rice season and from 17.3 to 32.7 kg N ha for the late rice season, which accounted for 9.2-33.6 % and 17.8-32.2 % of the applied N, respectively. The NH concentration in floodwater is a predominant factor to NH losses in the double rice-cropping systems. Compared with the NPK, the cumulative NH volatilizations during double rice growing seasons were respectively increased by 9.7, 50.6, and 37.6 % for the NP, NK, and FOM plots, respectively, while they were decreased by 24.6 % for the ROM plots. Compared with the NPK, N uptakes by rice were decreased by 7.2-49.7 % with imbalanced fertilizer application (NP and NK), while they were increased by 9.6-41.0 % with combined inorganic/organic fertilizers application (ROM and FOM). Grain yields were comparable among the NPK, ROM, and FOM treatments, but they were declined by the treatments with imbalanced fertilizer application. These results suggested that agricultural economic viability and NH volatilization mitigation can be simultaneously achieved by balanced inorganic and organic fertilizers application. [ABSTRACT FROM AUTHOR]