Protein kinase Ime2 is associated with mycelial growth, conidiation, osmoregulation, and pathogenicity in Fusarium oxysporum.

Fusarium oxysporum f.sp. niveum is one of the most serious diseases impairing watermelon yield and quality. Inducer of meiosis 2 (Ime2) is the founding member of a family of serine/threonine protein kinases and plays important roles in yeasts and other filamentous fungi. In this study, we analyzed the functions of FoIme2, the ortholog of Saccharomyces cerevisiae Ime2 in F. oxysporum f.sp. niveum. The FoIme2-deleted mutants exhibited obvious morphological abnormalities, including slower vegetative growth, more branches in the edge hyphae and a reduction in conidia production. Compared to the wild type, the mutants were hypersensitive to the osmotic stressor NaCl but were more insensitive to the membrane stressor SDS. The deletion of FoIme2 also caused a reduction in pathogenicity. Transcriptional analysis revealed that FoIme2 acts downstream of FoOpy2 which is an upstream sensor of the MAPK kinase cascade. These results indicate that FoIme2 is important in the development and pathogenicity of F. oxysporum, and provide new insight for the analysis of the pathogenic mechanism of F. oxysporum.

Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors.

BACKGROUND: Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent disease, resistance genes in rice have been cloned and introduced into susceptible cultivars. However, introduced resistance can often be broken within few years of release, often due to mutation of cognate avirulence genes in fungal field populations. RESULTS: To better understand the pattern of mutation of M. oryzae field isolates under natural selection forces, we used a next generation sequencing approach to analyze the genomes of two field isolates FJ81278 and HN19311, as well as the transcriptome of FJ81278. By comparing the de novo genome assemblies of the two isolates against the finished reference strain 70-15, we identified extensive polymorphisms including unique genes, SNPs (single nucleotide polymorphism) and indels, structural variations, copy number variations, and loci under strong positive selection. The 1.75 MB of isolate-specific genome content carrying 118 novel genes from FJ81278, and 0.83 MB from HN19311 were also identified. By analyzing secreted proteins carrying polymorphisms, in total 256 candidate virulence effectors were found and 6 were chosen for functional characterization. CONCLUSIONS: We provide results from genome comparison analysis showing extensive genome variation, and generated a list of M. oryzae candidate virulence effectors for functional characterization.

The Effects of Accompanying Ryegrass on Bayberry Trees by Change of Soil Property, Rhizosphere Microbial Community Structure, and Metabolites.

As a subtropical and tropical tree, bayberry (Myrica rubra) is an important fruit tree grown commercially in southern China. Interestingly, our studies found that the fruit quality of bayberry with accompanying ryegrass was significantly improved, but its mechanism remains unclear. The aim of this study was to explore the mechanism of accompanying ryegrass on the beneficial effect of the fruit quality of bayberry by measuring the vegetative growth parameters, fruit parameters with economic impact, physical and chemical properties of rhizosphere soil, microbial community structure, and metabolites of the bayberry with/without ryegrass. Notably, the results revealed a significant difference between bayberry trees with and without accompanying ryegrass in fruit quality parameters, soil physical and chemical properties, microbial community structure, and metabolites. Compared with the control without accompanying ryegrass, the planting of ryegrass increased the titratable sugar, vitamin C, and titratable flavonoid contents of bayberry fruits by 2.26%, 28.45%, and 25.00%, respectively, and decreased the titratable acid contents by 9.04%. Furthermore, based on 16S and ITS amplicon sequencing of soil microflora, the accompanying ryegrass caused a 12.47% increment in Acidobacteriota while a 30.04% reduction in Actinobacteria was recorded, respectively, when compared with the bayberry trees without ryegrass. Redundancy discriminant analysis of microbial communities and soil properties indicated that the main variables of the bacterial community included available nitrogen, available phosphorus, exchangeable aluminum, and available kalium, while the main variables of the fungal community included exchangeable aluminum, available phosphorus, available kalium, and pH. In addition, the change in microbial community structure was justified by the high correlation analysis between microorganisms and secondary metabolites. Indeed, GC-MS metabolomics analysis showed that planting ryegrass caused a 3.83%-144.36% increase in 19 metabolites such as 1,3-Dipentyl-heptabarbital and carbonic acid 1, respectively, and a 23.78%-51.79% reduction of 5 metabolites compared to the bayberry trees without the accompanying ryegrass. Overall, the results revealed the significant change caused by the planting of ryegrass in the physical and chemical properties, microbiota, and secondary metabolites of the bayberry rhizosphere soils, which provides a new insight for the ecological improvement of bayberry.

Molecular mapping of the blast resistance genes Pi2-1 and Pi51(t) in the durably resistant rice 'Tianjingyeshengdao'.

Tianjingyeshengdao' (TY) is a rice cultivar with durable resistance to populations of Magnaporthe oryzae (the causal agent of blast) in China. To understand the genetic basis of its resistance to blast, we developed a population of recombinant inbred lines from a cross between TY and the highly susceptible 'CO39' for gene mapping analysis. In total, 22 quantitative trait loci (QTLs) controlling rice blast resistance were identified on chromosomes 1, 3, 4, 5, 6, 9, 11, and 12 from the evaluation of four disease parameters in both greenhouse and blast nursery conditions. Among these QTLs, 19 were contributed by TY and three by CO39. Two QTL clusters on chromosome 6 and 12 were named Pi2-1 and Pi51(t), respectively. Pi2-1 was detected under both growth chamber and natural blast nursery conditions, and explained 31.24 to 59.73% of the phenotypic variation. Pi51(t) was only detected in the natural blast nursery and explained 3.67 to 10.37% of the phenotypic variation. Our results demonstrate that the durable resistance in TY is controlled by two major and seven minor genes. Identification of the markers linked to both Pi2-1 and Pi51(t) in this study should be useful for marker-aided selection in rice breeding programs as well as for molecular cloning of the identified resistance genes.

Molecular mapping of the new blast resistance genes Pi47 and Pi48 in the durably resistant local rice cultivar Xiangzi 3150.

The indica rice cultivar Xiangzi 3150 (XZ3150) confers a high level of resistance to 95% of the isolates of Magnaporthe oryzae (the agent of rice blast disease) collected in Hunan Province, China. To identify the resistance (R) gene(s) controlling the high level of resistance in this cultivar, we developed 286 F(9) recombinant inbred lines (RILs) from a cross between XZ3150 and the highly susceptible cultivar CO39. Inoculation of the RILs and an F(2) population from a cross between the two cultivars with the avirulent isolate 193-1-1 in the growth chamber indicated the presence of two dominant R genes in XZ3150. A linkage map with 134 polymorphic simple sequence repeat and single feature polymorphism markers was constructed with the genotype data of the 286 RILs. Composite interval mapping (CIM) using the results of 193-1-1 inoculation showed that two major R genes, designated Pi47 and Pi48, were located between RM206 and RM224 on chromosome 11, and between RM5364 and RM7102 on chromosome 12, respectively. Interestingly, the CIM analysis of the four resistant components of the RILs to the field blast population revealed that Pi47 and Pi48 were also the major genetic factors responsible for the field resistance in XZ3150. The DNA markers linked to the new R genes identified in this study should be useful for further fine mapping, gene cloning, and marker-aided breeding of blast-resistant rice cultivars.

Efficacy of Plant Growth-Promoting Bacteria Bacillus cereus YN917 for Biocontrol of Rice Blast.

Bacillus cereus YN917, obtained from a rice leaf with remarkable antifungal activity against Magnaporthe oryzae, was reported in our previous study. The present study deciphered the possible biocontrol properties. YN917 strain exhibits multiple plant growth-promoting and disease prevention traits, including production of indole-3-acetic acid (IAA), ACC deaminase, siderophores, protease, amylase, cellulase, and ß-1,3-glucanase, and harboring mineral phosphate decomposition activity. The effects of the strain YN917 on growth promotion and disease prevention were further evaluated under detached leaf and greenhouse conditions. The results revealed that B. cereus YN917 can promote seed germination and seedling plant growth. The growth status of rice plants was measured from the aspects of rice plumule, radicle lengths, plant height, stem width, root lengths, fresh weights, dry weights, and root activity when YN917 was used as inoculants. YN917 significantly reduced rice blast severity under detached leaf and greenhouse conditions. Genome analysis revealed the presence of gene clusters for biosynthesis of plant promotion and antifungal compounds, such as IAA, tryptophan, siderophores, and phenazine. In summary, YN917 can not only be used as biocontrol agents to minimize the use of chemical substances in rice blast control, but also can be developed as bio-fertilizers to promote the rice plant growth.

Scale-Dependent Effects of Growth Stage and Elevational Gradient on Rice Phyllosphere Bacterial and Fungal Microbial Patterns in the Terrace Field.

The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.

[Construction of microbial metagenomic library and screening of a nematicidal protease gene in greenhouse cucumber soil infested with root-knot nematodes].

OBJECTIVE: In order to search novel nematicidal protease genes, a metagenomic fosmid library was constructed and screened by uncultured method. METHODS: Density gradient centrifugation was used to extract and purify total greenhouse soil microbial DNA. After end-repair, ligation, packing and transformation, metagenomic fosmid library was constructed. At the same time, in order to screen the library, function-driven screening was used as a potential strategy, skim milk was served as substrate and root-knot nematodes as targets. RESULTS: The library contained 31,008 clones with the average insert fragment of 36.5 kb, including 1.13 Gbp microbial genetic information, so it was suitable for large-scale microbial functional gene screening. By the function-driven screening, fosmid clone pro12 which contained the nematicidal protease gene was screened. Then, subclones were constructed and screened. A subclone named espro124a5 was screened. After analysis of gene structure, espro124a5 is a secreted extracellular protease and a database search for homologies revealed it possessed 45% identities with peptidase S15 from Maricaulis maris MCS10 (accession no. YP_ 756822 at NCBI). It is a novel serine protease. Besides these, it has the serine protease-conserved catalytic triad residues, Asp469, His541 and the catalytic nucleophile Ser348. CONCLUSION: DNA obtained from the method of Nycodenz density gradient centrifugation had high purity, long fragment, and can meet the requirements of constructing metagenomic fosmid library. At the same time, the metagenomic fosmid library contains a lot of microbial genetic information, which is suitable for the screening of the other microbial genetic resources.

Novel methodologies for automatically and simultaneously determining BTEX components using FTIR spectra.

This study introduced a patented novel methodological system for automatically analysis of Fourier Transform Infrared Spectrometer (FTIR) spectrum data located at 'fingerprint' region (wavenumber 670-800 cm(-1)), to simultaneously determinate multiple petroleum hydrocarbons (PHs) in real mixture samples. This system includes: an object oriented baseline correction; Band decomposition (curve fitting) method with mathematical optimization; and Artificial Neural Network (ANN) for determination, which is suitable for the characteristics of this IR regions, where the spectra are normally with low signal to noise ratio and high density of peaks. BTEX components are potentially lethal carcinogens and contained in many petroleum products. As a case study, six BTEX components were determinate automatically and simultaneously in mixture vapor samples. The robustness of the BTEX determination was validated using real petroleum samples, and the prediction results were compared with gas chromatography-mass spectrometry (GC-MS).

Fabrication of macro-mesoporous titania/alumina core-shell materials in oil/water interface.

A series of macro-mesoporous TiO2/Al2O3 nanocomposites with different morphologies were synthesized. The materials were calcined at 723 K and were characterized by X-ray diffraction (XRD), Scanning electron microscopy (SEM), Transmission electron microscope (TEM), N2 adsorption/desorption, Infrared Emission Spectroscopy (IES), X-ray photoelectron spectroscopy (XPS) and UV-visible spectroscopy (UV-visible). A modified approach was proposed for the synthesis of 1D (fibrous) nanocomposite with higher Ti/Al molar ratio (2:1) at lower temperature (<100°C), which makes it possible to synthesize such materials on industrial scale. The performance-morphology relationship of as-synthesized TiO2/Al2O3 nanocomposites was investigated by the photocatalytic degradation of a model organic pollutant under UV irradiation. The samples with 1D (fibrous) morphology exhibited superior catalytic performance than the samples without, such as titania microspheres.

[Diversity analysis of archaeal and fungal communities in adjacent cucumber root soil samples in greenhouse by small-subunit rRNA gene cloning].

Soil archaea and fungi play important roles in the greenhouse soil ecosystem. To develop and apply rich microbial resources in greenhouse ecological environment, and to understand the interaction between microbes and plants, we constructed archaeal 16S rRNA and fungal 18S rRNA gene libraries to analyze the compositions of archaeal and fungal communities. Total greenhouse soil DNA was directly extracted and purified by skiving-thawing-lysozyme-proteinase K-SDS hot treatment and treatment of cetyltriethylammnonium bromide (CTAB). After PCR amplification, retrieving, ligating, transforming, screening of white clones, archaeal 16S rRNA and fungal 18S rRNA gene libraries were constructed. The sequences of archaea and fungi were defined into operational taxonomic units (OTUs) when 97% similarity threshold for OTU assignment was performed by using the software DOTUR. Phylogenetic analysis showed that crenarchaeota and unidentified-archaea were the two major sub-groups and only a few of euryarchaeota existed in the archaeal clone library, total 45 OTUs. All the crenarchaeota belonged to thermoprotei; except for Basidiomycotina, the other four sub-group fungi were discovered in the fungal library, total 24 OTUs. The diversities of archaea were very abundant and a few euryarchaeota (methanebacteria) existed in the archaeal clone library, it might be directly related to the long-term high temperature, high humidity, and high content of organic matter. The limitation of oxygen was the other reason for causing this phenomenon; Ascomycotina (over 80%) was the dominant sub-groups in fungal library. It was because most of the plant fungal diseases belonged to soil-borne diseases which gone through the winter by the ways of scierotium or perithecium and became the sources of primary infection.

Alumina nanofibers grafted with functional groups: a new design in efficient sorbents for removal of toxic contaminants from water.

A new design in efficient sorbents for the removal of trace pollutants from water was proposed: grafting the external surface of gamma-alumina (gamma-Al(2)O(3)) nanofibers with functional groups that have a strong affinity to the contaminants. This new grafting strategy greatly improves the accessibility of these sorption sites to adsorbates and thus efficiency of the fibrous sorbents. The product sorbents could capture the pollutants selectively even when the concentration of the contaminants is extremely low. Two types of gamma-Al(2)O(3) nanofibers with different size were prepared via facile hydrothermal methods. Thiol groups were then grafted on the gamma-Al(2)O(3) fibers by refluxing the toluene solution of 3-mercaptopropyltrimethoxysilane (MPTMS). The thiol group modified fibers not only can efficiently remove heavy metal ions (Pb(2+) and Cd(2+)) from water at a high flux, but also display high sorption capacity under sorption equilibrium conditions. Similar result was obtained from the nanofibers grafted with octyl groups which are employed to selectively adsorb highly diluted hydrophobic 4-nonylphenol molecules from water. This study demonstrates that grafting nanofibers is a new and effective strategy for developing efficient sorbents.

[Isolation, identification and field control efficacy of an endophytic strain against tobacco bacterial wilt (Ralstonia solanacarum)].

In this paper, an endophytic strain B-001 against tobacco bacterial wilt (Ralstonia solanacarum) was isolated from the stem of healthy tobacco in R. solanacarum-infected fields, which had a stronger inhibitory effect on some kinds of gram-positive bacteria, gram-negative bacteria, and pathogenic fungi. This strain belonged to Bacillus, and its 16S rDNA after PCR and sequencing had an accession of GenBank being DQ444283. The 16S rDNA phylogenetic tree was constructed with MEGA3, and compared with the published 16S rDNA sequences of relative bacteria species. B-001 had a 99.2% sequence similarity with Bacillus subtilis (DQ415893). According to the morphological, physiological and biochemical characteristics, and based on phylogenetic analysis, B-001 was identified as a strain of B. subtilis. Field experiments in Guiyang and Ningxiang counties of Hunan Province showed that in 2005 and 2006, the control efficacy of B-001 on R. solanacarum ranged from 40.03% to 78. 14%, better than that of Streptomycini.