Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China.

A Gram-positive, rod-shaped, motile, endospore-forming strain, DXFW5T, was isolated from the rhizosphere soil of tomato. Strain DXFW5T grew at 20-50 °C (optimum, 25-37 °C), pH 5-8 (optimum, pH 7) and in the presence of 3 % NaCl. It was positive for catalase and oxidase. Phylogenetic analysis using 16S rRNA gene sequences showed this strain was most closely related to Paenibacillus timonensis DSM 16943T (98.0 %) and Paenibacillus barengoltzii DSM 22255T (97.4 %). The DNA G+C content was 52.9 mol%. The digital DNA-DNA hybridization values between strain DXFW5T and P. timonensis DSM 16943T, P. barengoltzii DSM 22255T and P. macerans DSM 24T were 33.1, 24.9 and 21.2 %, respectively. The average nucleotide identity values between strain DXFW5T and P. timonensis DSM 16943T , P. barengoltzii DSM 22255T and P. macerans DSM 24T were 86.93, 81.77 and 75.98 %, respectively. The major fatty acids were anteiso-C15 : 0 (55.1 %), iso-C16 : 0 (13.2 %) and C16 : 0 (10 %). The polar lipids of strain DXFW5T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine two unidentified phospholipids and three unidentified lipids. MK-7 was the major isoprenoid quinone. Based on these results, it was concluded that the isolate represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rhizolycopersici sp. nov. is proposed, with DXFW5T (=ACCC 61751T=JCM 34488T) as the type strain.

Chitinophaga hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea.

A Gram-negative, rod-shaped aerobic bacterium designated as strain 2R12T was isolated from the rhizosphere soil of Hosta plantaginea. Phylogenetic analyses based on the 16S rRNA gene revealed that strain 2R12T should be assigned to the genus Chitinophaga with the highest sequence similarity to Chitinophaga arvensicola DSM 3695T (99.1 %) and Chitinophaga ginsengisegetis DSM 18108T (98.6 %). The major fatty acids of strain 2R12T (>10 %) were iso-C15 : 0, C16 :1 ω5c and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The predominant respiratory quinone was MK-7. The genomic DNA G+C content was 46.1 mol%. The average nucleotide identity values of strain 2R12T with C. arvensicola DSM 3695T and C. ginsengisegetis DSM 18108T were 77.9 and 78.8 %, respectively, while in silico DNA-DNA hybridization values for strain 2R12T with these strains were 22.8 and 23.3 %, respectively. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain 2R12T represents a novel species in the genus Chitinophaga, for which the name Chitinophaga hostae sp. nov. is proposed. The type strain is 2R12T (=ACCC 61757T=JCM 34719T).

Metabacillus rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants.

A Gram-positive, endospore-forming, rod-shaped and aerobic bacterium, with swarming and swimming motility, designated strain DBTR6T, was isolated from the rhizosphere soil of tomato plants. Strain DBTR6T grew at 20-45 â„ƒ (optimum 30-37℃), pH 4-9 (optimum 7-8) and at salinities from 0 to 5% (optimum 1%). Phylogenetic analysis using 16S rRNA gene sequences showed this strain belonged to the genus Metabacillus and was most closely related to Metabacillus litoralis DSM 16303 T (98.3%) and Metabacillus sediminilitoris MCCC 1K03777T (98.3%). The DNA G + C content of the genomic DNA was 36.4%. The digital DNA-DNA hybridization value between strain DBTR6T and reference strains M. sediminilitoris MCCC 1K03777T and "M. bambusae" BG109T were less than 70% (26.7% and 26.0%), and the average nucleotide identity score were less than 95% (78.55% and 78.38%), and the Amino Acid Identity values calculated were less than 96% (79.99% and 80.18%), respectively, suggesting that strain DBTR6T represented a novel species in the genus Metabacillus. Chemotaxonomic analysis showed that strain DBTR6T contained MK-7 as the major respiratory quinone. The predominant fatty acids (> 10.0%) were iso-C15:0, anteiso-C15:0 and C16:0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), glycolipids (GL) and three unidentified lipids (L). Based on the differential physiological properties, biochemical characteristics and genotypic data, strain DBTR6T represents a novel species of the genus Metabacillus, for which the name Metabacillus rhizolycopersici sp. nov. is proposed. The type strain is DBTR6T (= ACCC 61900 T = JCM 35080 T).

Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China.

During characterization of rhizobacteria, strain DBTS2T was isolated from the rhizosphere soil samples of healthy tomato plants and characterized using a polyphasic taxonomic approach. Phylogenetic analysis using 16S rRNA gene sequences showed this strain belonged to the genus Rhizobium and was most closely related to Rhizobium subbaraonis JC85T (99.1%) and Rhizobium daejeonense CCBAU 10050T (97%). Cells of strain DBTS2T were Gram-negative, short rod, aerobic and non-motile. This novel strain was found to grow at 20-45 °C (optimum 25-37 °C), pH 5-9 (optimum 8) and in the presence of 4% NaCl. It was positive for catalase and oxidase. The predominant cellular fatty acids were Summed Feature 8 (52.7%) and C19:0 cyclo ω8c (23.3%). The polar lipids of strain DBTS2T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipid, unidentified aminolipid, four unidentified phospholipids, unidentified lipid, phosphatidylcholine, unknown glycolipid and unknown aminophosphoglycolipids. Q-10 was the major quinone. The DNA-DNA hybridization similarity values between the strain DBTS2T and R. subbaraonis JC85T, R. daejeonense CCBAU 10050T and Rhizobium azooxidifex DSM100211T were 46.4%, 20.7% and 25.5%, respectively. The ANI value was 91.96% between strain DBTS2T and R. subbaraonis JC85T and 75.18% between strain DBTS2T and R. daejeonense CCBAU 10050T. The DNA G+C content of the genomic DNA was 63.1 mol%. Based on these results, it was concluded that the isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium rhizolycopersici sp. nov. is proposed, with DBTS2T (= CICC 24887T = ACCC61707 = JCM 34245) as the type strain.

Dickeya oryzae sp. nov., isolated from the roots of rice.

A novel Gram-stain-negative strain, designated ZYY5T, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5T was a member of the genus Dickeya, with a highest similarity to Dickeya zeae DSM 18068T (98.5%). The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Multi-locus sequence analysis using five concatenated genes (16S rRNA, atpD, infB, recA and gyrB) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5T formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of D. zeae. The orthologous average nucleotide identity (ANI) and digital DNA-DNAhybridization (dDDH) values among these six strains ranged from 96.8-99.9% and 73.7-99.8%, which supported that they were belonged to the same species. However, strain ZYY5T shared 58.4 of dDDH and 94.5% of ANI values with type strain D. zeae DSM 18068T, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5T contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus Dickeya. Based on the results of the polyphasic approaches, we propose that strain ZYY5T represents a novel species in the genus Dickeya, for which the name Dickeya oryzae sp. nov. (=JCM 33020 T=ACCC 61554 T) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of D. oryzae same as ZYY5T.

Gracilibacillus oryzae sp. nov., isolated from rice seeds.

A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8T should be placed within the genus Gracilibacillus (95.2-99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727T (99.0 %), 'Gracilibacillus xinjiangensis' CGMCC 1.12449T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0, which supported the allocation of the strain to the genus Gracilibacillus. The digital DNA-DNA hybridization value between strain TD8T and Gracilibacillus ureilyticus CGMCC 1.7727T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8T represented a novel species in the genus Gracilibacillus. The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8T (=ACCC 61556T=CICC 24889T=JCM 33537T).

Strain Conditions Monitoring on Corroded Prestressed Steel Strands in Beams Based on Fiber Bragg Grating Sensors.

Fiber Bragg Grating (FBG) sensors, with excellent properties, have been widely adopted to monitor the mechanical parameters in civil engineering in recent years. On the other hand, the current study on fatigue performance of corroded prestressed steel strands is still limited, and this is mainly because the long-term strain conditions monitoring is difficult to conduct. Based on the aforementioned considerations, a total of six beam specimens were fabricated in this study. The loading mode of four points bending was adopted in the form of sinusoidal waves in the experiments. On basis of the experimental results, it can be concluded that the fatigue life of the beam decreases sharply with the increase of the corrosion rate of steel strands. Besides, with the increase of the maximum fatigue load, the fatigue life of the beam will decrease significantly. Furthermore, the existing fatigue damage of steel strand inside the beam before corrosion may further accelerate its fatigue failure. As a result, the fatigue life of the beam is reduced because of the stress concentration. Under the same external load, the strain increment and the residual strain of steel strands in the stages of loading and unloading after corrosion increase significantly compared with other stages, while the existing residual strain always shows an increasing trend at various static loading stages. Therefore, the corrosion of steel strand seriously affects not only its mechanical properties, but also its fatigue performance. Finally, the FBG sensors are capable of measuring the steel strand strain, as well as the long-term strain conditions.

[Problems and countermeasures of soil health quality in urban green space]. / 城市绿地土壤健康质量问题与对策.

Soil quality of urban green space (UGS) is the basis for ensuring healthy growth of plants and maintaining the healthy ecosystem services for the residents and the sustainable development of city. At present, in order to improve the soil quality of UGS, more attention has been paid to fertility quality and environmental quality, but less to the health quality. We analyzed the concept, connotation, and assessment indicator of soil health quality, summarized the main problems and challenges of soil health quality of UGS. Finally, we put forward the ways and strategies to improve soil health quality of UGS, and prospected future research direction. Our aim was to attract the attention to the soil quality of UGS, especially soil health quality, and the importance of comprehensively improving soil quality of UGS, eventually providing strong technical support for urban sustainable development and eco-city construction.

[Effects of changes in water status on soil microbes and their response mechanism: A review]. / æ°´åˆ†æ¡ä»¶å˜åŒ–å¯¹åœŸå£¤å¾®ç”Ÿç‰©çš„å½±å“åŠå ¶å“åº”æœºåˆ¶ç ”ç©¶è¿›å±•.

Soil microbes play essential roles in maintaining terrestrial ecosystem services. Soil moisture is a primary determinant of soil microbial activities and ecosystem functions, which may fluctuate dramatically with the altered precipitation patterns and extreme drought caused by the ongoing global climate change. Due to the distinct soil microbial tolerance and life-strategy approaches to drought stress and different water status, fluctuation of soil moisture has a direct impact on microbial activities and community structure, thereby profoundly affecting microbial-mediated processes and ecosystem functions. Thus, it is of great significance to understand the dynamics and mechanisms that underlie the microbial responses to soil water status. In this review, we summarized recent progress in the study of responses of soil microbial activities (e.g. soil respiration and enzyme activities) and community structure to soil water status. We summarized underlying microbial physiological and ecological mechanisms, particularly 1) the cellular physiological accommodation such as osmolyte accumulation, exopolysaccharide production and transition into dormant states, and 2) the ecological strategies such as stress-resistant gene transfer and functional redundancy. Therefore, this investigation on the underlying relationship between soil microbial assembly and ecosystem functions under different water status could further demonstrate the microbially-mediated soil biogeochemical processes and provide a theoretical basis for future research and modelling of terrestrial ecosystem responses to climate change.

[Purification and cloning of an antifungal protein from the rice diseases controlling bacterial strain Paenibacillus polymyxa WY110].

Paenibacillus polymyxa WY110, a plant growth-promoting bacteria strain isolated from rice rhizosphere could suppress the growth of various plant pathogens effectively. With (NH4)2SO4 fractional precipitation, DEAE-Sephadex A-50 chromatography and Sephacryl S-200 chromatography followed by tracks of fraction antagonistic assay and SDS-PAGE, an antifungal protein P2 with in vitro anti-Pyricularia oxyzae activity was isolated and purified. It was showed with antagonistic activity on PDA plates that the growth of Pyricularia oryzae was inhibited by 1.5 microg of P2 protein effectively. N-terminal amino acid residues analysis showed 24 amino acid sequence: H2N-Ala-Asn-Val-Phe-Trp-Glu-Pro-Leu-Ser-Tyr-Tyr-Asn-Pro-Ser-Thr-Trp-Gln-Lys-Ala-Asp-Gly-Tyr-Ser-Asn-. Using this amino acid sequence as a target, the similarity of P2 protein was searched with BlastP program on Internet. It was showed a high homology between the P2 protein and the precursors of beta-1, 3-1, 4-glucanases from Bacillus. The beta-1, 3-1, 4-glucanase activity of P2 protein was identified with the specific substrate lichenan. According to the N-terminal partial sequence of P2 protein and the C-terminal conserved sequence of beta-1, 3-1, 4-glucanase, the primers for both terminals were synthesized. Using the genomic DNA of WY110 as the template, the full-length sequence of the gene encoding P2 was amplified by high fidelity PCR, then cloned into pMD18-T vecter. Sequence analysis showed the 72 nucleotide sequence on 5'-end matched with the known 24 amino acid sequence on N-terminal of P2 protein. The sequence (GenBank Accession Number: AF284449) was 636 bp in length encoding 212 amino acids. Comparing with a beta-1, 3-1, 4-glucanase gene (gluB) from Paenibacillus polymyxa, the sequence homology for nucleotides and deduced amino acids were 84% and 88.7% respectively. The cloning of the gene encoding P2 protein would be a new potential objective gene for plant gene engineering.

Plant-microbe association for rhizoremediation of chloronitroaromatic pollutants with Comamonas sp. strain CNB-1.

Comamonas sp. strain CNB-1, isolated from activated sludge and having a strong ability to degrade 4-chloronitrobenzene (4CNB), was applied for rhizoremediation of 4CNB-polluted soil through association with alfalfa. Confocal laser scanning microscopy revealed that strain CNB-1 successfully colonized alfalfa roots. Determination of strain CNB-1 populations by cultivation method and by quantitative competitive PCR technique targeting the chloronitrobenzene nitroreductase gene showed that the population of strain CNB-1 in the rhizosphere was about 10-100 times higher than that in the bulk soil. Gnotobiotic and outdoor experiments showed that pollutant 4CNB was completely removed within 1 or 2 days after 4CNB application into soil, and that its phytotoxicity to alfalfa was eliminated by inoculation of strain CNB-1. Results from PCR-denaturing gradient gel electrophoresis and analysis of 16S rRNA gene libraries revealed that the indigenous soil microbial community mainly consisted of alphaproteobacteria, betaproteobacteria, gammaproteobacteria, the CFB bacteria (Cytophaga-Flavabacterium-Bacteriodes), and Acidobacteria. This microbial community was not significantly influenced by inoculation of strain CNB-1. Thus, this study has developed a Comamonas-alfalfa system for rhizoremediation of 4CNB.