Pontibacter harenae sp. nov., isolated from the soil of a Populus euphratica forest.

A Gram-negative, rod-shaped, aerobic and light pink-pigmented bacterium, designated XAAS-A31T, was isolated from the soil of a Populus euphratica forest located near Hotan City, Xinjiang, PR China. Polyphasic, taxonomic and phylogenomic analyses were used to determine the taxonomy position of the strain. Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that XAAS-A31T belongs to the genus Pontibacter, family Hymenobacteraceae, and shows highest sequence similarity to Pontibacter silvestris XAAS-R86T (96.2 %). The digital DNA-DNA hybridization (22.0 %-19.2 %) and orthologous average nucleotide identity (74.1 %-72.7 %) values relative to closest validly published Pontibacter species were lower than the recommended thresholds of 70 and 96 %, respectively. The cells grew at 4-40 °C (optimum, 28-30 °C), at pH 6.5-8.5 (pH 7.0-7.5) and with 0-8% NaCl (0.5-2.0% NaCl). The main respiratory quinone of XAAS-A31T is MK-7, and the principal cellular fatty acids are iso-C15 : 0, iso-C17 : 0 3OH and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The major polar lipids are phosphatidylethanolamine, three unidentified amino-phospholipids, one unidentified glycolipid and eight unidentified lipids. The genome length of strain XAAS-A31T is 5.48 Mbp with a DNA G+C content of 44.2 mol% and 4013 protein-coding genes. Phenotypic and genotypic data suggested that XAAS-A31T represents a novel Pontibacter species, for which we propose the name Pontibacter harenae sp. nov. and type strain XAAS-A31T (=CCTCC AB 2017162T=KCTC 62049T).

Pontibacter kalidii sp. nov., isolated from rhizosphere soil of Kalidium foliatum.

A Gram-negative, aerobic, gliding motile, rod-shaped bacterium, designated XAAS-72T, was isolated from the rhizosphere soil of Kalidium foliatum sampled in the Xinjiang Uyghur Autonomous Region, PR China. Cells grew at 4-45 °C, pH 5.0-8.0 and 0-8% NaCl, with optimal growth at 20-30 °C, pH 6.0-7.0 and 1-2 % NaCl. Strain XAAS-72T is closely related to members of the genus Pontibacter, namely Pontibacter korlensis CCTCC AB 206081T (97.6%) and Pontibacter flavimaris ACCC 19859T (97.2 %), and <94.6 % related to other currently described Pontibacter strains. The average nucleotide identity values between XAAS-72T and P. korlensis CCTCC AB 206081T and P. flavimaris ACCC 19859T were 77.9 and 86.9 %, respectively; the corresponding digital DNA-DNA hybridization values were 21.7 and 31.8 %. Menaquinone-7 was the predominant respiratory menaquinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified glycolipids and five unidentified lipids. The major cellular fatty acids were summed feature 4 (containing iso-C17 : 1 I/anteiso-C17 : 1 B), summed feature 3 (containing C16 : 1 ω7c/C16 : 1 ω6c) and iso-C15 : 0. The genome length of strain XAAS-72T was 5 054 860 bp with a genomic DNA G+C content of 54.5 mol%. The phenotypic and genotypic data suggest that strain XAAS-72T represents a novel species of the genus Pontibacter, for which the name Pontibacter kalidii sp. nov. is proposed. The strain is XAAS-72T (CGMCC 16594T=KCTC 72095T).

Screening and Identification of a Streptomyces Strain with Quorum-Sensing Inhibitory Activity and Effect of the Crude Extracts on Virulence Factors of Pseudomonas aeruginosa.

Quorum-sensing (QS) is involved in numerous physiological processes in bacteria, such as biofilm formation, sporulation, and virulence formation. Therefore, the search for new quorum-sensing inhibitors (QSI) is a promising strategy that opens up a new perspective for controlling QS-mediated bacterial pathogens. To explore new QSIs, a strain named Streptomyces sp. D67 with QS inhibitory activity was isolated from the soil of the arid zone around the Kumutag Desert in Xinjiang. Phylogenetic analyses demonstrated that strain D67 shared the highest similarity with Streptomyces ardesiacus NBRC 15402T (98.39%), which indicated it represented a potential novel species in the Streptomyces genus. The fermentation crude extracts of strain D67 can effectively reduce the violacein production produced by Chromobacterium violaceum CV026 and the swarming and swimming abilities of Pseudomonas aeruginosa. It also has significant inhibitory activity on the production of virulence factors such as biofilm, pyocyanin, and rhamnolipids of P. aeruginosa in a significant concentration-dependent manner, but not on protease activity. A total of 618 compounds were identified from the fermentation crude extracts of strain D67 by LC-MS, and 19 compounds with significant QS inhibitory activity were observed. Overall, the strain with QS inhibitory activity was screened from Kumutag Desert in Xinjiang for the first time, which provided a basis for further research and development of new QSI.

Bacterial Community Composition and Isolation of Actinobacteria from the Soil of Flaming Mountain in Xinjiang, China.

In this work, bacterial community composition and actinobacteria resources were explored in extremely hot and hyper-arid areas of Flaming Mountain. This was achieved through a combination of PCR amplicon sequencing of bacterial 16S rRNA gene and cultivation-dependent isolation and characterization efforts. According to the high-throughput sequencing results and soil characteristics, 11 kinds of media were firstly designed to isolate actinobacteria, following the screening and identification of related strains. The results showed that a total of 2994 operational taxonomic units (OTUs) were obtained, involving 22 phyla, 77 orders and 121 genera. Among them, actinobacteria with the relative abundance of 8% ranked third, accounting for 33 genera and 47 species. A total of 132 strains distributed by eight families and 11 genera of actinobacteria were isolated from 11 media, of which six strains were potential new species. Furthermore, the functional characteristics of isolated strains were preliminarily evaluated. The results showed that the obtained strains generally had tolerance against heat, salt and alkali. Fifty-two strains had antibacterial activity, 69 strains could produce hydrolases, and 12.4% of the strains had quorum sensing inhibitory activity. The present study has laid a solid foundation for further understanding the bacterial diversity and exploiting actinobacteria resources in the Flaming Mountain area.

Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum.

Endophytic bacteria and fungi colonize plants that grow in various types of terrestrial and aquatic ecosystems. Our study investigates the communities of endophytic bacteria and fungi of halophyte Kalidium schrenkianum growing in stressed habitats with ionizing radiation. The geochemical factors and radiation (at low, medium, high level and control) both affected the structure of endophytic communities. The bacterial class Actinobacteria and the fungal class Dothideomycetes predominated the endophytic communities of K. schrenkianum. Aerial tissues of K. schrenkianum had higher fungal diversity, while roots had higher bacterial diversity. Radiation had no significant effect on the abundance of bacterial classes. Soil pH, total nitrogen, and organic matter showed significant effects on the diversity of root endophytes. Radiation affected bacterial and fungal community structure in roots but not in aerial tissues, and had a strong effect on fungal co-occurrence networks. Overall, the genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments, however negative correlations were found between endophytic bacteria and fungi in the plant. The genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments. Our findings suggest that radiation affects root endophytes, and that the endophytes associated with aerial tissues and roots of K. schrenkianum follow different mechanisms for community assembly and different paradigms in stress response.

Biochar induced improvement in root system architecture enhances nutrient assimilation by cotton plant seedlings.

BACKGROUND: Raising nitrogen use efficiency of crops by improving root system architecture is highly essential not only to reduce costs of agricultural production but also to mitigate climate change. The physiological mechanisms of how biochar affects nitrogen assimilation by crop seedlings have not been well elucidated. RESULTS: Here, we report changes in root system architecture, activities of the key enzymes involved in nitrogen assimilation, and cytokinin (CTK) at the seedling stage of cotton with reduced urea usage and biochar application at different soil layers (0-10 cm and 10-20 cm). Active root absorption area, fresh weight, and nitrogen agronomic efficiency increased significantly when urea usage was reduced by 25% and biochar was applied in the surface soil layer. Glutamine oxoglutarate amino transferase (GOGAT) activity was closely related to the application depth of urea/biochar, and it increased when urea/biochar was applied in the 0-10 cm layer. Glutamic-pyruvic transaminase activity (GPT) increased significantly as well. Nitrate reductase (NR) activity was stimulated by CTK in the very fine roots but inhibited in the fine roots. In addition, AMT1;1, gdh3, and gdh2 were significantly up-regulated in the very fine roots when urea usage was reduced by 25% and biochar was applied. CONCLUSION: Nitrogen assimilation efficiency was significantly affected when urea usage was reduced by 25% and biochar was applied in the surface soil layer at the seedling stage of cotton. The co-expression of gdh3 and gdh2 in the fine roots increased nitrogen agronomic efficiency. The synergistic expression of the ammonium transporter gene and gdh3 suggests that biochar may be beneficial to amino acid metabolism.

[Effects of cotton stalk biochar on microbial community structure and function of continuous cropping cotton rhizosphere soil in Xinjiang, China].

In this study, field trials were conducted to examine the effects of cotton stalk biochar on microbial population, function and structural diversity of microorganisms in rhizosphere soil of continuous cotton cropping field in Xinjiang by plate count, Biolog and DGGE methods. The experiment was a factorial design with four treatments: 1) normal fertilization with cotton stalk removed (NPK); 2) normal fertilization with cotton stalk powdered and returned to field (NPKS); 3) normal fertilization plus cotton stalk biochar at 22.50 t · hm⁻² (NPKB1); and 4) normal fertilization plus cotton stalk biochar at 45.00 t · hm⁻² (NPKB2). The results showed that cotton stalk biochar application obviously increased the numbers of bacteria and actinomycetes in the rhizospheric soil. Compared with NPK treatment, the number of fungi was significantly increased in the NPKB1treatment, but not in the NPKB2 treatment. However, the number of fungi was generally lower in the biochar amended (NPKB1, NPKB2) than in the cotton stalk applied plots (NPKS). Application of cotton stalk biochar increased values of AWCD, and significantly improved microbial richness index, suggesting that the microbial ability of utilizing carbohydrates, amino acids and carboxylic acids, especially phenolic acids was enhanced. The number of DGGE bands of NPKB2 treatment was the greatest, with some species of Gemmatimonadetes, Acidobacteria, Proteobacteria and Actinobacteria being enriched. UPGMC Cluster analysis pointed out that bacterial communities in the rhizospheric soil of NPKB2 treatment were different from those in the NPK, NPKS and NPKB1treatments, which belonged to the same cluster. These results indicated that application of cotton stalk biochar could significantly increase microbial diversity and change soil bacterial community structure in the cotton rhizosphere soil, thus improving the health of soil ecosystem.

Rufibacter roseus sp. nov., isolated from radiation-polluted soil.

A rose, Gram-stain-negative, aerobic, rod-shaped bacterium that was motile by gliding, and designated strain H359(T), was isolated from radiation-polluted soil (with high Cs(137)) from the Xinjiang Uygur Autonomous Region of PR China and subjected to a polyphasic taxonomic analysis. The isolate grew optimally at 30 °C and pH 7.0. It grew with NaCl up to 4% (w/v). 16S rRNA gene sequence analysis indicated that strain H359(T) belonged to the genus Rufibacter, a member of the family Cytophagaceae, with Rufibacter tibetensis CCTCC AB 208084(T) as its closest phylogenetic relative, having 96.1% 16S rRNA gene sequence similarity to the type strain. Strain H359(T) contained menaquinone-7 (MK-7) as the predominant menaquinone, and the major fatty acids were iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c. The polar lipid profile had phosphatidylethanolamine as the major component. The DNA G+C content was 43.9 mol%. Based on phenotypic, genotypic and phylogenetic evidence, strain H359(T) represents a novel species of the genus Rufibacter, for which the name Rufibacter roseus sp. nov. is proposed. The type strain is H359(T) ( =CPCC 100615(T) =KCTC 42217(T)).

Paenibacillus algorifonticola sp. nov., isolated from a cold spring.

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259(T), was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20-30 °C and pH 7.3-7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259(T) belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538(T) (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1(T) (96.3 %) and Paenibacillus castaneae Ch-32(T) (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15:0 and C16:0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259(T) ( = CGMCC 1.10223(T)  = JCM 16598(T)).