Search

A pineapple-banana rotation was studied as a model system to investigate the potential emergence of a fungal-mediated disease-suppression in a soil highly infested with the pathogen Fusarium oxysporum causing the banana wilt disease. By using both field and pot experiments, the pineapple-banana rotation system resulted in a significant decrease of the pathogen number and next-stubble banana disease incidence (P

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 (

The effect of genetic markers and reference databases on analyses of fungal communities were estimated using fungal large subunit (LSU) and internal transcribed spacer (ITS) amplicon datasets in consecutive years of rhizosphere samples from three candidate biofuel crops, corn (Zea mays), switchgrass (Panicum virgatum), and miscanthus (Miscanthus × giganteus). These two marker genes were selected to contrast possible differences in biological conclusions. In addition, two ITS schemes based on two ITS reference databases were used to assess differences due to reference database composition. A taxonomy-supervised method was invoked using the Ribosomal Database Project naive Bayesian classifier that accesses all three databases. The UNITE classification scheme had the highest number of classified taxa in the raw classification result; however, it also had the highest proportion of unknown taxa (sequences that were classified to “unclassified,” “unidentified,” incertae sedis or, in the case of Warcup, to matches containing two unique names). After removal of these unknown taxa, LSU had the highest classification rate followed by Warcup and UNITE. As expected, the communities resolved using the two ITS databases, based on the same sequences, were relatively more similar than those from the lower-coverage LSU classification scheme. The choice of marker gene or even the same reads with different classification databases revealed different community patterns due to database coverage, e.g., the relative abundance of the most abundant groups changed or were only detected in one or two of the classification schemes, such as for Mortierella, Fusarium, and Phoma. No marked difference in fungal beta-diversity was identified among the three methods. Differentiation between the three biofuel crops and between the drought and normal rainfall years was apparent, regardless of method. Though classification rates, taxonomic conflicts, and coverage differences within the high-abundance fungal groups varied according to classification scheme, there was no overall impact on beta diversity among the three methods.

Two seasonal pot experiments were conducted to investigate the effect of biofertilizer application after mixture of lime and ammonium bicarbonate (LA) fumigation, on banana Fusarium wilt disease suppression and soil microbial community composition. Biofertilizer application after LA fumigation decreased 80% of disease incidence compared to control of biofertilizer application to non-fumigated soil. Biofertilizer application after fumigation clearly manipulated soil microbial community composition as revealed by non-metric multidimensional scaling and Venn diagram. LA fumigation significantly reduced the abundance of F. oxysporum while biofertilizer application after fumigation could further decrease it. Furthermore, indigenous microbes, e.g., Bacillus, Pseudomonas, and Mortierella, were associated with disease suppression. Biofertilizer application after fumigation significantly (p

The asymbiotic diazotrophic bacteria are important for nitrogen (N) input to soil. Here, we investigated asymbiotic diazotrophic bacteria in an acidic red soil from functional, phylogenetic, and ecological perspectives. We firstly confirmed that phosphorus (P) availability determines the overall asymbiotic N fixation potential in the red soil. Then, we analyzed the soil bacterial community and N fixing (nifH) gene composition. Long-term different fertilizations significantly affected the composition of soil bacterial community. In addition, long-term organic cultivations increased most of the asymbiotic diazotrophic bacteria and the corresponding nifH gene abundances. Few asymbiotic diazotrophic bacteria, belonging to Chloroflexaceae, Methylocystaceae, Enterobacteriaceae, and Pseudomonadaceae, and their corresponding nifH genes were more abundant in N and P co-limited than in not co-limited soils, suggesting that some bacterial taxa from these families might be activated under nutrient limited conditions. Our findings provided new information for the distribution of asymbiotic diazotrophic bacteria in red soil and gave insights into the ecology of diazotrophic bacteria.

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.

Understanding the responses of soil microbiome composition to various farming practices is important for selecting suitable managements to maintain soil functions. In this study, the influences of heavy chemical fertilizer application (CF) and reduced chemical fertilizer supplemented with organic (OF) or bioorganic fertilizer (BF, BF = OF + Trichoderma) on composition of soil microbiome were investigated for monocropping cucumber systems using a five-season continuous pot experiment. The MiSeq sequencing data indicated that the CF treatment resulted in the lowest fungal diversity and the BF treatment resulted in a relatively higher one close to the initial soil (CK). The BF and OF treatments had similar impacts on the composition of bacterial community, and the CF treatment significantly reduced bacterial diversity. Although both OF and BF treatments had better plant growth responses, they had less disturbance on the composition of fungal community relative to the CF treatment. The BF treatment is more predictable than the other treatments for postponing fungal diversity as the inoculated fungal species significantly (p

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 N2-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 (Corg) content was related to composition and abundances of phoD-harbouring microbial communities; since both microbial properties were correlated to the ALP activity, the Corg 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.

The use of organic compost combined with inorganic fertilizer can enable balanced fertilization under intensive farming conditions, but little is known about how these fertilization practices affect the composition of microbial in arable soils. In this study, a field trial of a rice–wheat cropping system was established to examine the effects of 8 years of fertilization with inorganic fertilizers (IFs) and the organic manure–inorganic fertilizers (OMIFs) on composition of microbial communities. The fungal 18S and bacterial 16S rRNA gene fragments were amplified from each soil sample and sequenced. Significantly lower fungal richness and higher bacterial richness were observed for the OMIF treatment compared to the other treatments. No obvious changes in fungal diversity were observed among the treatments, with a decrease bacterial diversity detected in the IF treatment. Variations in relative abundance were observed in the fungal phyla Glomeromycota, Blastocladiomycota, and Schizoplasmodiida and in the bacterial phyla Acidobacteria, Gemmatimonadetes, and Cyanobacteria, most of which were significantly correlated with soil organic matter (OM) and/or nitrate N (NO3 −-N) contents. Additionally, the fungal abundance-based coverage estimator (ACE) showed a significant negative correlation with the soil NO3 −-N/OM content, while the correlation was positive for the bacterial ACE estimate. This study suggests that the fungal and bacterial communities respond differently to the long-term organic-inorganic fertilization, which may result from different effects of NO3 −-N/OM content of soil on the composition of fungal and bacterial communities.

Investigation of the properties and mechanisms of the interactions of root-colonizing biocontrol bacteria and plant pathogens is necessary to optimize the biocontrol strategies. In the present study, the interaction of a biocontrol strain Bacillus amyloliquefaciens T-5 tagged with a green fluorescent protein marker and a bacterial wilt pathogen Ralstonia solanacearum QL-Rs1115 tagged with red fluorescent protein marker was studied on tomato roots using different inoculation methods. The results showed that in the co-culture experiment, the population of pathogen QL-RFP was decreased by increasing the initial inoculum concentration of biocontrol strain. In the greenhouse experiment, both strains T-5-GFP and QL-RFP colonized tomato roots (root tips, root hairs, primary roots, and root junctions) and formed a biofilm on the root surfaces as determined by dilution plating and confocal laser scanning microscopy (CLSM) techniques. However, the root colonization of pathogen strain QL-RFP was almost completely suppressed in the presence of biocontrol strain T-5-GFP when both soil and plant seedlings were treated with T-5-GFP. The results of this study revealed the effectiveness of strain B. amyloliquefaciens T-5 as a biocontrol agent against tomato wilt pathogen and the significance of inoculation method used to inoculate biocontrol strain.

In our previous work, applying biofertilizer containing Bacillus amyloliquefaciens strain NJN-6 to a banana orchard infected by a serious Fusarium wilt disease over two consecutive years effectively controlled this soil-borne disease. In this study, deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) sequences was performed to investigate how the composition of rhizosphere microbial community responded to the application of biofertilizer (BIO), pig manure compost (PM), and chemical fertilizer (CF) and to explore the potential correlation between the microbial community composition and the Fusarium wilt disease. A total of 104,201 bacterial 16S rRNA genes and 154,953 fungal ITS sequence reads were obtained after basic quality control, and Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Ascomycota were the most abundant bacterial and fungal phyla across all samples. Compared with the PM and CF control, the alpha diversity of bacteria significantly (P

Tobacco bacterial wilt (TBW) is caused by Ralstonia solanacearum (R. solanacearum), a severe pathogenic agent with a wide host range. In this study, lime + ammonium bicarbonate (L + AB), organic fertilizer (OF), bio-organic fertilizer (BOF), and integrated treatment (L + AB + BOF) were assessed for the ability to control TBW and to influence the composition of native soil bacterial communities. The results showed that disease incidence of L + AB + BOF for two growth seasons in pot experiment was the lowest, with only 15.56 and 11.11 % at seasons 1 and 2, respectively. The integrated treatment could also significantly suppress TBW in the field, with a disease incidence of only 14.27 % compared with 35.41, 50.03, and 31.32 % in L + AB, OF, and BOF treatments, respectively. With application of the integrated treatment in pot and field experiments, the abundances of R. solanacearum were both significantly lower than those with other treatments. Denaturing gradient gel electrophoresis (DGGE) patterns showed that application of BOF significantly affected composition of bacterial communities of rhizosphere. The analysis of 454 sequencing data showed that application of integrated treatment recruited more beneficial bacteria than other treatments, such as Bacillus, Paenibacillus, Arthrobacter, and Streptomyces, while the abundance of Ralstonia with the integrated treatment was decreased. Overall, these results suggested that application of integrated agricultural management could effectively suppress bacterial wilt by affecting the composition of bacterial community and reducing the population of R. solanacearum.

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

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 × 104 colony-forming units (cfu) g−1 rhizosphere soil to 9.41 × 103 cfu g−1 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 104 cfu g−1 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.

The impact of long-term fertilizer on ammonia (NH3) 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 NH3 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 NH3 volatilizations in the fertilizer plots ranged from 12.8 to 27.3 kg N ha−1 for the early rice season and from 17.3 to 32.7 kg N ha−1 for the late rice season, which accounted for 9.2–33.6 % and 17.8–32.2 % of the applied N, respectively. The NH4 + concentration in floodwater is a predominant factor to NH3 losses in the double rice-cropping systems. Compared with the NPK, the cumulative NH3 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 NH3 volatilization mitigation can be simultaneously achieved by balanced inorganic and organic fertilizers application.

It was hypothesized that disruption of the root–microbiome association creates empty rhizosphere niches that could be filled by both soilborne pathogens and beneficial microbes. The effect of de-coupling root–microbiome associations related to improve soil suppressiveness was investigated in cucumber using the pathogen Fusarium oxysporum f. sp. Cucumerinum (FOC) and its antagonist Bacillus amyloliquefaciens SQR9 (SQR9) system. The root–soil microbiome association of cucumber was disrupted by applying the fungicide carbendazim to the soil, and then FOC or/and its antagonist SQR9 were inoculated in the rhizosphere. In the fungicide treatment, the FOC wilt disease incidence was significantly increased by 13.3 % on average compared to the FOC treatment without fungicide. However, when the fungicide treatment was applied to the soil with SQR9 and FOC, the SQR9 effectively reduced the disease incidence, and improved cucumber plant growth compared to a no fungicide control. These results indicate that de-coupling of root–microbiome associations followed by antagonist inoculation can improve rhizosphere soil suppressiveness, which may help to develop strategies for efficient application of rhizosphere beneficial microbes in agriculture.

Bacterial wilt caused by Ralstonia solanacearum is one of the most serious tobacco diseases worldwide. Brevibacillus brevis (L-25) and Streptomyces rochei (L-9) with strong inhibitory effects on R. solanacearum in vitro were isolated from the rhizosphere of a healthy tobacco plant in a severely wilt-diseased field. Pot and field experiments were conducted to evaluate the biocontrol effect of the isolated antagonists alone and in combination with organic fertilizer. In pot experiment, the control efficacy was 92.3–100 % in the treatments applied with L-25 and L-9 alone or together with organic fertilizers. When bioorganic fertilizer containing L-9 and L-25 was applied to the soil in field condition, the control efficacies were 95.4 and 30.0 in the Anhui and Guizhou field plots, respectively. The counts of bacteria and actinomycetes in rhizosphere soil were significantly increased (p ≤ 0.05) under all antagonist applications compared with CK (PR). In contrast, fungal and R. solanacearum densities in the rhizosphere soil applied with antagonists were much lower than the CK (PR) rhizosphere. Combined application of the two antagonists had better effect than single antagonist treatments. The antagonists were more effective when they were combined with organic fertilizer as compared with the antagonistic strains only. These results allow us to conclude that a combination of the biocontrol agents, L-25 and L-9, together with organic fertilizers can effectively control bacterial wilt by affecting soil microbial structure.

Banana production has been severely hindered by the long-term practice of monoculture agriculture. Fusarium wilt, caused by the Fusarium oxysporum f. sp. cubense (FOC), is one of the most destructive diseases that can afflict banana plants. It is both necessary and urgent to find an efficient method for protecting banana production worldwide. In this study, 57 antagonistic bacterial strains were isolated from the rhizospheres of healthy banana plants grown in a heavily wilt-diseased field; of the 57 strains, six strains with the best survival abilities were chosen for further study. Compared with the control and the other strains in the greenhouse experiment, W19 strain was found to observably decrease the incidence of Fusarium wilt and promote the growth of banana plants when combined with the organic fertilizer (OF). This strain was identified as Bacillus amyloliquefaciens based on its morphological, physiological, and biochemical properties, as well as 16S rRNA analysis. Two kinds of antifungal lipopeptides (iturin and bacillomycin D) produced by W19 strain were detected and identified using HPLC–ESI-MS. Another lipopeptide, called surfactin, was also produced by the thick biological film forming W19 strain. In addition to lipopeptides, 18 volatile antifungal compounds with significant antagonistic effect against F. oxysporum were detected and identified using gas chromatography–mass spectrometer (GC–MS). The work described herein not only highlights how the bioorganic fertilizer with B. amyloliquefaciens can be used to control Fusarium wilt of banana but also examines some of the potential mechanisms involved in the biocontrol of Fusarium wilt.

Cotton plants that are continuously subjected to monoculture suffer greatly from Verticillium wilt disease. The application of a novel bioorganic fertilizer (BOF) consisting of organic fertilizer combined with the antagonistic Bacillus subtilis strain HJ5 significantly suppressed Verticillium wilt of cotton. The disease incidence rates in soils that were treated with BOF (1 %, w/w) in the nursery stage, in the transplanted soil stage or in both stages, decreased by 42.9 %, 57.1 %, and 88.0 %, respectively, compared with controls. B. subtilis HJ5 was tagged with a plasmid-borne gfp gene encoding the green fluorescent protein to investigate its colonization behavior on cotton root surfaces. The results indicated that B. subtilis HJ5 predominantly colonizes the elongation and differentiation zones of the roots and forms micro-colonies in hydroponic and soil systems. The population of B. subtilis HJ5 in the rhizosphere and on cotton roots was also monitored. The number of B. subtilis HJ5 cells on the root surface reached a peak value of approximately 107 cfu per gram of roots 3 days after exposure of the cotton seedlings to the bacteria. Probably the colonization of B. subtilis HJ5 on cotton roots is one of the mechanisms involved in protecting cotton plants from fungal infection.

Intercropping with aerobic rice or arbuscular mycorrhizal fungi (AMF) colonization alleviated watermelon wilt disease, which is likely attributed to rice root exudates or AMF depressing watermelon wilt pathogen. However, it is unclear whether rice root exudates transfers to watermelon rhizosphere soil and whether AMF affects the transfer of rice root exudates to watermelon rhizosphere soil. A rhizobox experiment, with aerobic rice under 14 CO2, was conducted to investigate the effect of AMF colonization on carbon (C) transfer from rice to watermelon and on phosphorus (P) uptake by both watermelon and rice. The rhizobox was separated into labelling side (L side) and sampling side (S side) by inserting nylon mesh in the middle of the box. The L side was planted with aerobic rice, and the S side was aerobic rice (monocropping) or watermelon (intercropping). When 14 CO2 was added to rice canopy at the L side, 14 C activities of rice roots and rhizosphere soils in the L side were increased by intercropping with watermelon or AMF colonization. The 14 C was detected in roots and rhizosphere soils of rice and watermelon in the S side, but no differences were found among different treatments. 14 C activities in leaves were improved by AMF inoculation in the S side, regardless of rice or watermelon. Mycorrhizal colonization stimulated P absorption and translocation to rice in intercropping system. These findings suggest that AMF colonization could increase C transfer from rice to watermelon while intercropping with watermelon could promote AMF colonization and P uptake by rice.

Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum J. H. Owen, results in considerable yield losses for cucumber plants. A bio-organic fertilizer (BIO), which was a combination of manure composts with antagonistic microorganisms, and an organic fertilizer (OF) were evaluated for their efficiencies in controlling Fusarium wilt. Application of the BIO suppressed the disease incidence by 83% and reduced yield losses threefold compared with the application of OF. Analysis of microbial communities in rhizosphere soils by high-throughput pyrosequencing showed that more complex community structures were present in BIO than in OF treated soils. The dominant taxonomic phyla found in both samples were Proteobacteria, Firmicutes, Actinobacteria and Acidobacteria among bacteria and Ascomycota among fungi. Abundance of beneficial bacteria or fungi, such as Trichoderma, Hypoxylon, Tritirachium, Paenibacillus, Bacillus, Haliangium and Streptomyces, increased compared to the OF treatment, whereas the soil-borne pathogen, Fusarium, was markedly decreased. Overall, the results of this study demonstrate that the application of the BIO was a useful and effective approach to suppress Fusarium wilt and that the high-throughput 454 pyrosequencing was a suitable method for the characterization of microbial communities of rhizosphere soil of cucumber.

Tobacco black shank, caused by a soil-borne pathogen, Phytophthora parasitica var. nicotianae, is one of the most serious diseases which reduce tobacco production worldwide. In this study, P. parasitica var. nicotianae was successfully controlled in vitro and in vivo by a newly isolated strain, Paenibacillus polymyxa C5, which is a plant-growth-promoting rhizobacteria and an effective biocontrol agent. Pot experiments were carried out to evaluate the effect of a novel bio-organic fertilizer (BIO), produced by the solid fermentation of organic fertilizer amended P. polymyxa C5, on the control of tobacco black shank. In comparison with the control, the disease incidence was significantly (P

Cotton Verticillium wilt is a destructive soil-borne disease affecting cotton production. In this study, application of bio-organic fertilizer (BIO) at the beginning of nursery growth and/or at the beginning of transplanting was evaluated for its ability to control Verticillium dahliae Kleb. The most efficient control of cotton Verticillium wilt was achieved when the nursery application of BIO was combined with a second application in transplanted soil, resulting in a wilt disease incidence of only 4.4%, compared with 90.0% in the control. Denaturing gradient gel electrophoresis patterns showed that the consecutive applications of BIO at nursery and transplanting stage resulted in the presence of a unique group of fungi not found in any other treatments. Humicola sp., Metarhizium anisopliae, and Chaetomium sp., which were considered to be beneficial fungi, were found in the BIO treatment, whereas some harmful fungi, such as Alternaria alternate, Coniochaeta velutina, and Chaetothyriales sp. were detected in the control. After the consecutive applications of BIO at nursery and transplanting stage, the V. dahliae population in the rhizosphere soil in the budding period, flowering and boll-forming stage, boll-opening stage, and at harvest time were 8.5 × 102, 3.1 × 102, 4.6 × 102, and 1.7 × 102 colony-forming units per gram of soil (cfu g−1), respectively, which were significantly lower than in the control (6.1 × 103, 3.4 × 103, 5.2 × 103, and 7.0 × 103 cfu g−1, respectively). These results indicate that the suggested application mode of BIO could effectively control cotton Verticillium wilt by significantly changing the fungal community structure and reducing the V. dahliae population in the rhizosphere soil.

Laboratory tests and greenhouse experiments were carried out to investigate the abilities of Bacillus subtilis Y-IVI to promote plant growth and to colonize the rhizosphere and interior tissues of muskmelon. Laboratory tests showed that B. subtilis Y-IVI can produce indole acetic acid, siderophores, and ammonia. The inoculation of soil with green fluorescent protein-tagged Y-IVI (GY-IVI) significantly increased plant shoot and root dry weights as compared with the non-inoculated soils. The inoculation of soil with B. subtilis GY-IVI maintained approximately 108 colony-forming units (cfu) of GY-IVI per gram of dry rhizosphere soil for 1 month. The GY-IVI recovered from the interior of crowns and roots in the inoculated soil were 106 and 107 cfu g−1 dry weight, respectively, suggesting that GY-IVI acted as an endophyte. In the present study, we combined the two important growth promotion ingredients, colonization ability and growth promotion metabolites produced by biological agents, to investigate B. subtilis Y-IVI’s promotion effects on muskmelon growth.

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 106 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.

Rice seedling wilt frequently occurs in upland nurseries under well-aerated conditions and causes considerable economic loss. Whether the wilt is pathogenic or edaphic is not known. We hypothesize the use of composts to alleviate seedling wilt. The severity level of upland rice seedling wilt was significantly (p < 0.05) positively correlated with soil pH (r = 0.499; n = 19), but negatively correlated with soil organic matter (r = −0.745), microbial biomass C (r = −0.669), activities of dehydrogenase (r = −0.589), arylsulfatase (r = −0.272), fluorescein diacetate hydrolysis (r = −0.466), and β-glucosidase (r = −0.280). Correlations between severity level and soil inorganic N and exchangeable potassium K were not significant. Contents of Fe, Zn, Cu, and Mn in healthy seedlings were not significantly (p < 0.05) different from those in infected seedlings. These data suggest that seedling wilts are not associated with nutrient constraints. Compost amendment at the rate of 3% or above in pot experiments significantly improved seedling growth and reduced the wilt symptoms. Field trials further showed that aboveground weight of seedlings in compost-amended treatment ranged from 11.5 to 14.9 mg per plant, significantly higher than the range from 6.38 to 12.1 mg per plant in the control treatment; in addition to rice growth compost significantly increased microbial biomass and enzyme activities of soils. Soil fumigation significantly increased rice growth and alleviation symptoms in 11 out of 19 soils, suggesting the involvement of pathogens. It is concluded that upland seedling wilt is a pathogen-associated disease. Probably high soil pH and low soil biochemical activities may favor pathogen activities.

Pot experiments were carried out over two growing periods to assay the biocontrol efficacy and rhizosphere colonization of Trichoderma harzianum SQR-T037 (SQR-T037) applied as SQR-T037 conidia suspension (TCS), SQR-T037 conidia suspension blended with organic fertilizer (TBF), or SQR-T037 fermented organic fertilizer (TFF). Each formulation had three T. harzianum numbers. In two experiments, Percent Disease Indexes (PDIs) decreased with the increase of SQR-T037 number added to soils. The TFF treatment consistently exhibited the lowest PDIs at same amendment rate of SQR-T037 and 0–8.9%, 25.6–78.9%, and 4.4–50.0% of PDIs were found in TFF, TCS, and TBF treatment, respectively. Soils treated with TFF showed the highest SQR-T037 population in rhizosphere and bulk soil. Decrease of Fusarium oxysporum population in both bulk and rhizosphere soils occurred in the treatment SQR-T037 at 105 and 106 cfug−1 soil rate. The TFF treatment at the SQR-T037 rate of 103 cfug−1 soil significantly (p < 0.05) increased SQR-T037 population within the rhizoplane but had no effect on F. oxysporum population when compared to TCS and TBF. Generally, TFF treatments were superior to TCS and TBF treatments on disease control by sustaining colonization of SQR-T037 and decreasing F. oxysporum abundance in the rhizosphere soil. We propose that TFF treatment at SQR-T037 rate of 107 cfug−1 (i.e., 105 cfug−1 soil after applied to soil) was the best formulation for controlling Fusarium wilt of cucumber.

The present study was carried out on pot experiments with rice (Oryza sativa L. cv. Wuyujing 7) and winter wheat (Triticum aestivum L. cv. Yangmai 6) rotation in a sandy and a clayey soil fertilized with 15N-labeled ammonium sulfate (AS) and 15N-labeled rabbit feces so as to study the mechanisms of reduction of fertilizer N loss by organic fertilizers. The treatments included: (1) control without any N fertilizer application; (2) fertilization with 15N-labeled AS (IF); (3) fertilization with labeled rabbit feces (OF); (4) fertilization with either 40% 15N-labeled rabbit feces and 60% unlabeled AS (IOF1) or (5) 40% unlabeled rabbit feces and 60% 15N-labeled AS (IOF2). In the rice season, the IOF treatments compared to the IF treatment decreased the percentage of lost fertilizer N from the sandy and clayey soils, whereas it increased the percentage of fertilizer N, present as mineral N and microbial biomass N (MBN). During the second season, when soils were cropped to winter wheat, the IOF treatments in comparison with the IF or OF treatment increased mineral N and MBN contents of soils sampled at tillering, jointing, and heading stages, and such increases were derived from the organic N fertilizer in the sandy soil and from the inorganic N fertilizer in the clayey soil. The increased MBN in the IOF treatments was derived from inorganic fertilizers applied both soils. Therefore, in the IOF treatment, during the rice season, the organic N increased the immobilization of inorganic N in MBN, while the inorganic N fertilizer applied to both soils stimulated the uptake of organic N and the organic N fertilizer increased the uptake of inorganic N by winter wheat; the inorganic N increased the recovery of organic N in the plant-soil system after harvesting the winter wheat.

To assess the influence of phenolic acids from plant root exudates on soil pathogens, we studied the effect of sinapic acid added to chemically defined media on the growth and virulence factors of Fusarium oxysporum f. sp. niveum. Sinapic acid inhibited the growth and conidial formation and germination of F. oxysporum f. sp. niveum by 6.7–8.8% and 11.2–37.3%, respectively. Mycotoxin production by F. oxysporum f. sp. niveum was stimulated by 81.6–230.7%. Pectinase, proteinase, cellulase, and amylase activities were stimulated at a lower concentration of sinapic acid, while they were inhibited at a higher concentration. It is concluded that sinapic acid inhibited the growth and conidial germination of F. oxysporum f. sp. niveum and decreased the pathogenic enzymes’ activity at higher doses.

Two field experiments were conducted to evaluate the effect of organic fertilizer application either with or without antagonistic bacteria (Bacillus subtilis SQR-5 and Paenibacillus polymyxa SQR-21) on the control of Fusarium oxysporum f. sp. Cucumerinum J. H. Owen wilt disease in cucumber. The incidence of Fusarium wilt disease was 5.3–13.5% for cucumber plants treated with bioorganic fertilizer, while it was 30.3–51% in controls (only with organic fertilizer). Higher yields and lower disease incidences were observed in the dry season when compared with the wet season for both types of organic fertilizer treatments. Biolog analysis showed a significant change in soil bacterial composition and activity after bioorganic fertilizer application. The numbers of colony-forming units of F. oxysporum f. sp. Cucumerinum J. H. Owen for bioorganic-fertilizer-treated soils were significantly decreased compared with control. Scanning electron micrographs of cucumber basal stems showed a presence of mycelia-like mini strands accompanied by an amorphous substance within the xylem vessels. This amorphous substance and mini strands were richer in calcium and phosphorus but had low carbon and oxygen than the living mycelia. Reverse-phase high-pressure liquid chromatography and mass spectroscopic analysis showed that the antagonistic bacteria produced the antifungal compounds fusaricidin A, B, C, and D with molecular weights of 883.5, 897.5, 947.5, and 961.5 Da, respectively. The application of bioorganic fertilizer has a great potential for the control of F. oxysporum wilt disease in cucumber plants.

An innovative method was used to treat rice straw based on a mixed dilute acid treatment followed by neutralization with ammonia water. This treatment decreased the Si content of the rice straw, thus improving its degradation by soil microorganisms. The plant-available N of soil was greatly improved after the application of the treated rice straw with urea. Soil microbial biomass N was about 50 mg kg−1 in the soil amended with the treated rice straw and urea but only 40 mg kg−1 in the soil amended with untreated rice straw and urea. Better synchronization of N supply with the plant requirement for N uptake was obtained when treated rice straw was applied with urea. Recovery of urea-N was 61% when soil was amended with treated rice straw and urea, whereas it was only 46% in soil amended with untreated rice straw and urea, and only 30% in soil treated with urea alone.

Soil nitrification rate is very different among soil types, as a result of differences in physical and chemical properties. Little is known about the composition of the nitrifying bacteria community. In this investigation, three soils (fluvo-aquic soil, permeable paddy soil and red earth) from different geo-ecological regions in China were characterized for their nitrification activities and their nitrifying bacteria communities determined either by molecular approaches or by conventional culture methods. A 28-day long-term soil incubation showed that the maximum nitrification potential was found in the fluvo-aquic soil with almost 100% of inorganic N present as NO 3 − -N, while the minimum nitrification potential was in red earth with only a 4.9% conversion rate from ammonium into nitrate. There was no relationship between nitrification potential and numbers of nitrifiers in the soil. The conventional most probable number (MPN) method could enumerate ammonia oxidizers, but failed in enumerating nitrite oxidizers. Therefore, we used an MPN-PCR procedure which gave a convincing nitrite oxidizer count result, instead of MPN-diphylamine. Soils were characterized by denaturing gradient gel electrophoresis (DGGE) of DNA extracted from soils and amplified using a primer specific for the 16S rRNA gene and/or for the amoA gene. The DGGE columns of the three soils differed from each other. There were two similar bands present in DGGE columns of the fluvo-aquic and permeable paddy soils, but no similar band was found in DGGE columns of the red earth. The sequence of amoA indicated that all ammonia oxidizers in these soils were grouped into Nitrosospira clusters 1 and 3, and each soil had a common band similar to the other soils and a special band which differed from the other soils.

Three separate greenhouse experiments were conducted to determine the bi-directional N transfer in a peanut and rice intercropping system using the direct 15N foliar feeding technique at N application rates of 15, 75 and 150 kg ha−1. When peanut was used as the 15N donor plant, the atom % 15N in the rice shoot was consistently higher than in control rice, indicating that 15N transfer from peanut to the associated rice crop occurred. The percentage of N transfer (%NT) from peanut to the associated rice was 9.9%, 5.7% and 4.2% at the three N application rates, respectively. The N transferred from peanut to rice was 22.6, 15.5 and 8.2 mg N plant−1, accounting for 10.9%, 6.4% and 3.1% of the total N accumulated in rice plants at the three N application rates, respectively. When rice functioned as the 15N donor plant, the %NTs were 4.4%, 2.1% and 1.4% and represented about 5.2%, 3.4% and 2.4% of total N accumulated in peanut shoot at the three N application rates, respectively. The net directional N transfer was from peanut to rice and this was calculated by the difference in the bi-directional transfers and was mainly due to peanut root decomposition. Thus, the %NTs were 10.7%, 6.3%, 5.1% and 3.5% on 28 July (the day on which peanut shoots were cut), 8 August, 28 August and 8 September, respectively, and correspondingly, the N transferred from peanut to rice represented 6.0%, 5.8%, 5.1% and 3.2% of the total N accumulated in the rice plants.

Cultivation of rice in unsaturated soils covered with mulch is receiving more attention in China because of increasingly serious water shortage; however, greenhouse gas emission from this cultivation system is still poorly understood. A field experiment was conducted in 2001 to compare nitrous oxide (N2O) and methane (CH4) emission from rice cultivated in unsaturated soil covered with plastic or straw mulch and the traditional waterlogged production system. Trace gas fluxes from the soil were measured weekly throughout the entire growth period using a closed chamber method. Nitrous oxide emissions from unsaturated rice fields were large and varied considerably during the rice season. They were significantly affected by N fertilizer application rate. In contrast, N2O emission from the waterlogged system was very low with a maximum of 0.28 mg N2O m−2 h−1. However, CH4 emission from the waterlogged system was significantly higher than from the unsaturated system, with a maximum emission rate of 5.01 mg CH4 m−2 h−1. Our results suggested that unsaturated rice cultivation with straw mulch reduce greenhouse gas emissions.

Bacillus amyloliquefaciens SQR9, isolated from the rhizosphere of cucumber, can control Fusarium wilt of cucumber and directly stimulate plant growth. To evaluate its potential agricultural use, the plant growth promotion of B. amyloliquefaciens SQR9 was evaluated, and the relative mechanisms, especially the production of the phytohormone indole-3-acetic acid (IAA), were investigated. The related plant-growth-promoting factors were genetically and chemically analyzed, and a mutant library was constructed for selecting strains with different IAA production. B. amyloliquefaciens SQR9 showed a growth-promoting activity in greenhouse experiments. Plant-growth-promoting factors like extracellular phytase, volatile components including acetoin, 2,3-butanediol, and phytohormone IAA were detected in B. amyloliquefaciens SQR9 cultures grown under laboratory conditions. Three IAA production mutant strains showed variation in plant-growth-promoting effect. IAA production in B. amyloliquefaciens SQR9 was related to its plant-growth-promoting effect, but IAA alone could not account for the overall observed plant-growth-promoting effect. The promoted plant growth by the rhizospheric strain B. amyloliquefaciens SQR9 can be attributed to multiple factors, including production of phytohormones, volatile compounds, and extracellular enzymes. Therefore, the strain B. amyloliquefaciens SQR9 may be used as a plant-growth-promoting agent to increase crop yield.