Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River

Nanjing, China

Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River

Nanjing, China
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Zhao J.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Zhao J.,Nanjing Agricultural University | Zhang R.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Zhang R.,Nanjing Agricultural University | And 13 more authors.
Microbial Ecology | Year: 2014

Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems. © 2013 Springer Science+Business Media New York.


Qiu M.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Qiu M.,Nanjing Agricultural University | Li S.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Li S.,Nanjing Agricultural University | And 11 more authors.
Biology and Fertility of Soils | Year: 2013

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. © 2013 Springer-Verlag Berlin Heidelberg.


Weng J.,Nanjing Agricultural University | Weng J.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Wang Y.,Nanjing Agricultural University | Wang Y.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | And 6 more authors.
Applied Microbiology and Biotechnology | Year: 2013

Root colonization by antagonistic bacteria is a prerequisite for successful biological control, and the instability of colonization under varying environmental conditions has accentuated the need to improve the colonization activity. Root colonization by Bacillus spp. is mainly determined by chemotaxis and biofilm formation, and both functions are negatively controlled by the global transcription regulator AbrB. Here, we disrupted the gene abrB in Bacillus amyloliquefaciens SQR9, which has been proven to be a promising biocontrol agent of cucumber and watermelon wilt disease. Chemotaxis, biofilm formation, and colonization activities as well as biocontrol efficiency were measured and compared between the wild-type strain of SQR9 and the abrB mutant. The data presented in this article demonstrate that the colonization and biocontrol activity of B. amyloliquefaciens SQR9 could be significantly improved by abrB gene disruption. The results offer a new strategy to enhance the biocontrol efficacy of B. amyloliquefaciens SQR9. © 2012 Springer-Verlag Berlin Heidelberg.


Wang M.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Wang M.,Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization | Wang M.,Nanjing Agricultural University | Sun Y.,Nanjing Agricultural University | And 9 more authors.
Scientific Reports | Year: 2015

Fusarium wilt is caused by the infection and growth of the fungus Fusarium oxysporum in the xylem of host plants. The physiological responses of cucumbers that are infected with Fusarium oxysporum f. sp. cucumerinum (FOC) was studied in pot and hydroponic experiments in a greenhouse. The results showed that although water absorption and stem hydraulic conductance decreased markedly in infected plants, large amounts of red ink accumulated in the leaves of infected cucumber plants. The transpiration rate (E) and stomatal conductance (g s) of the infected plants were significantly reduced, but the E/g s was higher than healthy plants. We further found that there was a positive correlation between leaf membrane injury and E/g s, indicating that the leaf cell membrane injury increased the non-stomatal water loss from infected plants. The fusaric acid (FA), which was detected in the infected plant, resulted in damage to the leaf cell membranes and an increase in E/g s, suggesting that FA plays an important role in non-stomatal water loss. In conclusion, leaf cell membrane injury in the soil-borne Fusarium wilt of cucumber plants induced uncontrolled water loss from damaged cells. FA plays a critical role in accelerating the development of Fusarium wilt in cucumber plants.


Sun L.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Sun L.,Nanjing Agricultural University | Gao J.,Chinese Academy of Agricultural Sciences | Huang T.,Nanjing Agricultural University | And 6 more authors.
FEMS Microbiology Ecology | Year: 2015

Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate nitrogen during soil development. © FEMS 2015.


Xu Z.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Xu Z.,Nanjing Agricultural University | Zhang R.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Zhang R.,Nanjing Agricultural University | And 10 more authors.
Applied and Environmental Microbiology | Year: 2014

Bacillus amyloliquefaciens strain SQR9, isolated from the cucumber rhizosphere, suppresses the growth of Fusarium oxysporum in the cucumber rhizosphere and protects the host plant from pathogen invasion through efficient root colonization. In the Gram-positive bacterium Bacillus, the response regulator DegU regulates genetic competence, swarming motility, biofilm formation, complex colony architecture, and protease production. In this study, we report that stepwise phosphorylation of DegU in B. amyloliquefaciens SQR9 can influence biocontrol activity by coordinating multicellular behavior and regulating the synthesis of antibiotics. Results from in vitro and in situ experiments and quantitative PCR (qPCR) studies demonstrate the following: (i) that the lowest level of phosphorylated DegU (DegU~P) (the degQ mutation) impairs complex colony architecture, biofilm formation, colonization activities, and biocontrol efficiency of Fusarium wilt disease but increases the production of macrolactin and bacillaene, and (ii) that increasing the level of DegU~P by degQ and degSU overexpression significantly improves complex colony architecture, biofilm formation, colonization activities, production of the antibiotics bacillomycin D and difficidin, and efficiency of biocontrol of Fusarium wilt disease. The results offer a new strategy to enhance the biocontrol efficacy of Bacillus amyloliquefaciens SQR9. © 2014, American Society for Microbiology.


Zhang N.,Nanjing Agricultural University | Zhang N.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Wang D.,Nanjing Agricultural University | Wang D.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | And 8 more authors.
Plant and Soil | Year: 2014

Aim: It is necessary to understand the roles of root exudates involved in plant-microbe interactions to inform practical application of beneficial rhizosphere microbial strains. Methods: Colonization of Bacillus amyloliquefaciens SQR9 (isolated from cucumber rhizosphere) and Bacillus subtilis N11 (isolated from banana rhizosphere) of their original host was found to be more effective as compared to the colonization of the non-host plant. Organic acids in the root exudates of the two plants were identified by High performance liquid chromatography (HPLC). The chemotactic response and effects on biofilm formation were assessed for SQR9 and N11 in response to cucumber and banana root exudates, as well as their organic acids components. Results: Citric acid detected exclusively in cucumber exudates could both attract SQR9 and induce its biofilm formation, whereas only chemotactic response but not biofilm formation was induced in N11. Fumaric acid that was only detected in banana root exudates revealed both significant roles on chemotaxis and biofilm formation of N11, while showing only effects on biofilm formation but not chemotaxis of SQR9. Conclusion: The relationship between PGPR strain and root exudates components of its original host might contribute to preferential colonization. This study advances a clearer understanding of the mechanisms relevant to application of PGPR strains in agricultural production. © 2013 Springer Science+Business Media Dordrecht.


Xu Z.,Nanjing Agricultural University | Xu Z.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Shao J.,Nanjing Agricultural University | Shao J.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | And 7 more authors.
Applied and Environmental Microbiology | Year: 2013

Bacillus amyloliquefaciens strains are capable of suppressing soilborne pathogens through the secretion of an array of lipopeptides and root colonization, and biofilm formation ability is considered a prerequisite for efficient root colonization. In this study, we report that one of the lipopeptide compounds (bacillomycin D) produced by the rhizosphere strain Bacillus amyloliquefaciens SQR9 not only plays a vital role in the antagonistic activity against Fusarium oxysporum but also affects the expression of the genes involved in biofilm formation. When the bacillomycin D and fengycin synthesis pathways were individually disrupted, mutant SQR9M1, which was deficient in the production of bacillomycin D, only showed minor antagonistic activity against F. oxysporum, but another mutant, SQR9M2, which was deficient in production of fengycin, showed antagonistic activity equivalent to that of the wild-type strain of B. amyloliquefaciens SQR9. The results from in vitro, root in situ, and quantitative reverse transcription-PCR studies demonstrated that bacillomycin D contributes to the establishment of biofilms. Interestingly, the addition of bacillomycin D could significantly increase the expression levels of kinC gene, but KinC activation is not triggered by leaking of potassium. These findings suggest that bacillomycin D contributes not only to biocontrol activity but also to biofilm formation in strain B. amyloliquefaciens SQR9. © 2013, American Society for Microbiology.


Chen L.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Chen L.,Nanjing Agricultural University | Xun W.,Key Laboratory of Plant Nutrition and Fertilization in Low Middle Reaches of the Yangtze River | Xun W.,Nanjing Agricultural University | And 8 more authors.
European Journal of Soil Biology | Year: 2014

Fertilization plays a pivotal role on soil biological process and affects the soil bacterial community, which act as hosts for viruses. The effect of fertilization on soil viral community has not been well explored. In this study, a Haplic Acrisol soil, which is the soil type for 13 provinces in Southern China, was analyzed after 22 years different fertilization regimes for their viral composition. The soil responded to organic fertilizations with an increased amount of soil organic matter (SOM) and pH (increased from 5.7 to 6.6), while with the decreased SOM and pH for chemical fertilization, especially for single nitrogen fertilization. The combined effects of SOM and pH caused by long-term different fertilization regimes on soil viral communities were investigated by direct calculation of virus-like particles (VLPs) through epifluorescence microscopy. The highest VLP abundance (13.1×107 per gram dry soil) was detected in soil applied with chemical and organic fertilizers. The viral and bacterial abundances of organic soil were 4 and 5 times higher than those of inorganic soil respectively. Transmission electron microscopy observation revealed a higher frequency of Myoviridae viruses in soil with organic amendments than without organic amendments, and vice versa for Podoviridae viruses. These results demonstrate that organic fertilizer could increase viral abundance and morphological diversity through suppressing soil acidification and improving soil organic matter. © 2014 Elsevier Masson SAS.

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