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Shen Z.,Nanjing Agricultural University | Wang D.,Nanjing Institute of Vegetable Science | Ruan Y.,Hainan University | Xue C.,Nanjing Agricultural University | And 3 more authors.
PLoS ONE | Year: 2014

Our previous work demonstrated that application of a bio-organic fertilizer (BIO) to a banana mono-culture orchard with serious Fusarium wilt disease effectively decreased the number of soil Fusarium sp. and controlled the soil-borne disease. Because bacteria are an abundant and diverse group of soil organisms that responds to soil health, deep 16 S rRNA pyrosequencing was employed to characterize the composition of the bacterial community to investigate how it responded to BIO or the application of other common composts and to explore the potential correlation between bacterial community, BIO application and Fusarium wilt disease suppression. After basal quality control, 137,646 sequences and 9,388 operational taxonomic units (OTUs) were obtained from the 15 soil samples. Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria were the most frequent phyla and comprised up to 75.3% of the total sequences. Compared to the other soil samples, BIO-treated soil revealed higher abundances of Gemmatimonadetes and Acidobacteria, while Bacteroidetes were found in lower abundance. Meanwhile, on genus level, higher abundances compared to other treatments were observed for Gemmatimonas and Gp4. Correlation and redundancy analysis showed that the abundance of Gemmatimonas and Sphingomonas and the soil total nitrogen and ammonium nitrogen content were higher after BIO application, and they were all positively correlated with disease suppression. Cumulatively, the reduced Fusarium wilt disease incidence that was seen after BIO was applied for 1-year might be attributed to the general suppression based on a shift within the bacteria soil community, including specific enrichment of Gemmatimonas and Sphingomonas. © 2014 Shen et al.

Ling N.,Nanjing Agricultural University | Wang D.,Nanjing Institute of Vegetable Science | Zhu C.,Nanjing Agricultural University | Song Y.,Nanjing Agricultural University | And 5 more authors.
Plant and Soil | Year: 2014

Background and aims: Paenibacillus spp. are widely considered to impact the fertility and health of soil. The aim of this study was to evaluate how different fertilization regimes affect the population size and community structure of Paenibacillus spp. over a long period of time in red soil.Methods: Soil samples were collected from a long-term experiment and were then analyzed using real-time PCR and PCR-DGGE. The correlation analysis, PCA and RDA were used to explore the relationships among Paenibacillus spp. population, community structure and soil properties in different treatments.Results: The pH was seriously decreased only by the application of chemical fertilizer. The largest population of Paenibacillus spp. was found in the soil treated with organic fertilizer application, while the richest diversity was observed in the soil treated only with the chemical fertilizer. The Paenibacillus spp., Paenibacillus alkaliterrae, Paenibacillus campinasensis, and Paenibacillus xylanilyticus were found in all treatments. Paenibacillus castaneae was found in the soil treated with NPK, and Paenibacillus pabuli was specifically observed in the lime-amended treatment. Paenibacillus taichungensis and Paenibacillus prosopidis were detected in the soil treated with only chemical fertilizer. Except for the ammonium and pH, all the tested soil fertility parameters (total C, total N, nitrate, available K and available P) could significantly affect both the Paenibacillus spp. population number and diversity. The soil pH was significantly correlated with Paenibacillus spp. diversity only.Conclusions: Our results indicate that the different long-term fertilization regimes have varied impact on both the Paenibacillus spp. population size and the diversity of the community associated with the soil properties tested. These results can help to enrich the information on the response of beneficial soil microbes to different long-term fertilization regimes. © 2014, Springer International Publishing Switzerland.

Yang X.,Nanjing Agricultural University | Sun F.,Nanjing Institute of Vegetable Science | Xiong A.,Nanjing Agricultural University | Wang F.,Nanjing Agricultural University | And 6 more authors.
Molecular Biology Reports | Year: 2012

A nitrate transporter, BcNRT1, was isolated from non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) cultivar 'Suzhouqing'. The full-length cDNA was obtained using the rapid amplification of cDNA ends technique and contains an open reading frame of 1,770 bp that predicts a protein of 589 acid residues that possesses 12 putative transmembrane domains. Using the GUS marker gene driven by the BcNRT1 promoter, we found BcNRT1 expression to be concentrated in primary and lateral root tips and in shoots of transgenic Arabidopsis plants. The YFP fused to BcNRT1 and transformed into cabbage protoplasts indicated that BcNRT1 was localized to the plasma membrane. The expression of BcNRT1 in roots was induced by exposure to 25 mM nitrate, and the BcNRT1 cRNA heterologously expressed in Xenopus laevis oocytes showed nitrate conductance when nitrate was included in the medium. Moreover, mutant chl1-5 plants harboring 35S::BcNRT1 showed sensitivity to chlorate treatment and exhibited restored nitrate uptake. In conclusion, the results indicate that BcNRT1 functions as a low affinity nitrate transporter in non-heading Chinese cabbage. © 2012 Springer Science+Business Media B.V.

Lin F.,Jiangsu Academy of Agricultural Sciences | Jiang L.,Jiangsu Academy of Agricultural Sciences | Liu Y.,University of Illinois at Urbana - Champaign | Lv Y.,Jiangsu Academy of Agricultural Sciences | And 2 more authors.
Plant Molecular Biology | Year: 2014

In the wake of recent progress of high throughput transcriptome profiling technologies, extensive housekeeping gene mining has been conducted in humans. However, very few studies have been reported in maize (Zea mays L.), an important crop plant, and none were conducted on a genome -wide level. In this study, we surveyed housekeeping genes throughout the maize transcriptome using RNA-seq and microarray techniques, and validated the housekeeping profile with quantitative polymerase chain reaction (qPCR) under a series of conditions including different genotypes and nitrogen supplies. Seven microarray datasets and two RNA-seq libraries representing 40 genotypes at more than 20 developmental stages were selected to screen for commonly expressed genes. A total of 1,661 genes showed constitutive expression in both microarray and RNA-seq datasets, serving as our starting housekeeping gene candidates. To determine for stably expressed housekeeping genes, NormFinder was used to select the top 20 % invariable genes to be the more likely candidates, which resulted in 48 and 489 entries from microarray and RNA-seq data, respectively. Among them, nine genes (2OG-Fe, CDK, DPP9, DUF, NAC, RPN, SGT1, UPF1 and a hypothetical protein coding gene) were expressed in all 40 maize diverse genotypes tested covering 16 tissues at more than 20 developmental stages under normal and stress conditions, implying these as being the most reliable reference genes. qPCR analysis confirmed the stable expression of selected reference gene candidates compared to two widely used housekeeping genes. All the reference gene candidates showed higher invariability than ACT and GAPDH. The hypothetical protein coding gene exhibited the most stable expression across 26 maize lines with different nitrogen treatments with qPCR, followed by CDK encoding the cyclin-dependent kinase. As the first study to systematically screen for housekeeping genes in maize, we identified candidates by examining the transcriptome atlas generated from RNA-seq and microarray technologies. The nine top-ranked qPCR-validated novel housekeeping genes provide a valuable resource of reference genes for maize gene expression analysis. © 2014, Springer Science+Business Media Dordrecht.

Liu T.,Nanjing Agricultural University | Dai W.,Nanjing Agricultural University | Sun F.,Nanjing Institute of Vegetable Science | Yang X.,Nanjing Agricultural University | And 2 more authors.
Acta Physiologiae Plantarum | Year: 2014

To improve the efficiency of nitrogen use and to reduce the accumulation of nitrates in vegetables, an improved understanding of the mechanisms that regulate nitrate uptake and signaling is essential. Nitrogen use is regulated largely by the nitrate transporter genes, but few studies have examined the nitrate transporter genes in non-heading Chinese cabbage (Brassica rapa ssp. Chinensis Makino), one of the most important leafy vegetables in East Asia. In this study, the nitrate transporter gene BraNRT2.1 was isolated from non-heading Chinese cabbage. The cDNA for this gene contains an open reading frame of 1593 base pairs and encodes a predicted protein of 530 amino acid residues. Analysis of the BraNRT2.1 showed that BraNRT2.1 was expressed mainly in the roots and that the transcription of the gene was induced following exposure to 250 μM and 25 mM nitrate. In addition, GUS staining revealed that the BraNRT2.1 promoter directed expression to the roots. The BraNRT2.1-YFP fusion protein was observed to be localized to the plasma membrane. Finally, we observed that BraNRT2.1 could restore nitrate uptake in the presence of 200 μM nitrate in Arabidopsis thaliana plants lacking AtNRT2.1 function. Together, these results demonstrate that BraNRT2.1 encodes a high-affinity nitrate transporter that participates in nitrate uptake. These findings provide a foundation for future studies and plant breeding to improve the efficiency of nitrogen use and to reduce the accumulation of nitrates in vegetables. © 2013 Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków.

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