Yong-Guang Zhang

Streptomyces hundungensis sp. nov., a novel actinomycete with antifungal activity and plant growth promoting traits

A novel actinobacterium MBRL 251T, isolated from a sample collected from a limestone quarry at Hundung, Manipur, India, was characterized using a polyphasic approach. The 16S ribosomal RNA gene sequence of strain MBRL 251T showed closest similarities with Streptomyces xanthochromogenes NRRL B-5410T (99.6%) and Streptomyces michiganensis NBRC 12797T (99.6%). The DNA relatedness between MBRL 251T and S. xanthochromogenes NBRC 12828T, and S. michiganensis NBRC 12797T was 46.6% and 40.7%, respectively. Strain MBRL 251T contained LL-diaminopimelic acid as the diagnostic diamino acid, with glucose and xylose as the main cell wall sugars, whereas small amounts of galactose, mannose, rhamnose and ribose were also detected in the whole-cell wall hydrolysates. The major fatty acids identified were anteiso-C15:0 (35.1%), iso-C16:0 (21.1%) and anteiso-C17:1 (13.2%). The predominant menaquinones detected were MK-9(H6) and MK-9(H8), whereas the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositolmannosides. The G+C content of the genomic DNA was 72.3%. The phenotypic and genotypic data showed that strain MBRL 251T merits the recognition as a representative of a novel species of the genus Streptomyces. It is proposed that the isolate should be classified in the genus Streptomyces as a novel species, Streptomyces hundungensis sp. nov. The type strain is MBRL 251T (=JCM 17577T=KCTC 29124T).

Description of Streptomonospora sediminis sp. nov. and Streptomonospora nanhaiensis sp. nov., and reclassification of Nocardiopsis arabia Hozzein & Goodfellow 2008 as Streptomonospora arabica comb. nov. and emended description of the genus Streptomonospora.

Two actinomycete strains isolated from marine sediment samples, designated YIM M11335(T) (from the Indian Ocean) and 12A09(T) (from the South China Sea), were obtained and examined by a polyphasic approach. The two Gram-staining-positive, aerobic strains produced branched substrate mycelia and aerial hyphae that were not fragmented, and no diffusible pigment was produced on the media tested. At maturity, spore chains and single spores were formed on aerial hyphae and substrate mycelium, respectively. Whole-organism hydrolysates of both strains contained meso-diaminopimelic acid and the diagnostic sugars glucose and galactose. Their predominant menaquinones were MK-10(H4), MK-10(H6), MK-11(H4), MK-11(H6) and MK-11(H8) for strain YIM 11335(T) and MK-10(H4), MK-10(H6), MK-11(H4), MK-11(H6) and MK-11(H8) for strain 12A09(T). The polar lipids detected in the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, phosphatidylcholine, an unknown phosphoglycolipid and several unknown glycolipids, phospholipids and polar lipids. The major fatty acids (>10%) were iso-C16 : 0 and C16:0 for strain YIM 11335(T) and iso-C16:0 for strain 12A09(T). The G+C contents of the genomic DNA of strains YIM 11335(T) and 12A09(T) were 70.7% and 74.4%, respectively. DNA-DNA hybridization relatedness values of these two isolates with the type strains Nocardiopsis arabia DSM 45083(T) and Streptomonospora halophila YIM 91355(T) supported the hypothesis they are representatives of two different species. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the two isolates belong to the genus Streptomonospora of the family Nocardiopsaceae and that the type strain of N. arabia should be reclassified as a representative of Streptomonospora arabica comb. nov. The names proposed for the two novel species are Streptomonospora sediminis sp. nov. (type strain YIM M11335(T) = DSM 45723(T) = CCTCC AB 2012051(T)) and Streptomonospora nanhaiensis sp. nov. (type strain 12A09(T) = KCTC 29145(T) = CCTCC AB 2013140(T)), respectively. An emended description of the genus Streptomonospora is also proposed in the light of the new data.

Quantitative Proteomics Reveals Membrane Protein-Mediated Hypersaline Sensitivity and Adaptation in Halophilic Nocardiopsis xinjiangensis.

The genus Nocardiopsis is one of the most dominant Actinobacteria that survives in hypersaline environments. However, the adaptation mechanisms for halophilism are still unclear. Here, we performed isobaric tags for relative and absolute quantification based quantitative proteomics to investigate the functions of the membrane proteome after salt stress. A total of 683 membrane proteins were identified and quantified, of which 126 membrane proteins displayed salt-induced changes in abundance. Intriguingly, bioinformatics analyses indicated that these differential proteins showed two expression patterns, which were further validated by phenotypic changes and functional differences. The majority of ABC transporters, secondary active transporters, cell motility proteins, and signal transduction kinases were up-regulated with increasing salt concentration, whereas cell differentiation, small molecular transporter (ions and amino acids), and secondary metabolism proteins were significantly up-regulated at optimum salinity, but down-regulated or unchanged at higher salinity. The small molecule transporters and cell differentiation-related proteins acted as sensing proteins that played a more important biological role at optimum salinity. However, the ABC transporters for compatible solutes, Na(+)-dependent transporters, and cell motility proteins acted as adaptive proteins that actively counteracted higher salinity stress. Overall, regulation of membrane proteins may provide a major protection strategy against hyperosmotic stress.

Frigoribacterium endophyticum sp. nov., an endophytic actinobacterium isolated from the root of Anabasis elatior (C. A. Mey.) Schischk

A novel endophytic actinobacterium, designated EGI 6500707(T), was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10-45 °C (optimum 25-30 °C), at pH 5-10 (optimum pH 8) and in presence of 0-4% (w/v) NaCl (optimum 0-3%). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0). The DNA G+C content of strain EGI 6500707(T) was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707(T) should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265(T) (99.1%) and Frigoribacterium mesophilum MSL-08(T) (96.5%). DNA-DNA relatedness between strain EGI 6500707(T) and F. faeni JCM 11265(T) was 47.2%. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain EGI 6500707(T) represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707(T) ( = JCM 30093(T) = KCTC 29493(T)).

Nesterenkonia rhizosphaerae sp. nov., an alkaliphilic actinobacterium isolated from rhizosphere soil in a saline-alkaline desert.

An alkaliphilic actinobacterial strain, designated EGI 80099(T), was isolated from a rhizosphere soil sample of Reaumuria soongorica found in the desert soils of Fukang, Xinjiang, north-west China. Cells of strain EGI 80099(T) were Gram-stain-positive, non-motile, non-endospore-forming cocci. The predominant menaquinones were MK-7, MK-8 and MK-9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0 and anteiso-C17 : 0. Analysis of the cell wall showed the presence of peptidoglycan of the type l-Lys-Gly-l-Glu, variation A4α. Cells of the isolate contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown phospholipid and an unidentified glycolipid as polar lipids. The genomic DNA G+C content was 63.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80099(T) belongs to the genus Nesterenkonia, sharing 95.68-97.37 % sequence similarities with the type strains of recognized species within this genus. DNA-DNA hybridization of strain EGI 80099(T) with the type strains of species that showed the highest sequence similarities, Nesterenkonia aethiopica DSM 17733(T) (97.37 %), Nesterenkonia flava CAAS 251(T) (97.23 %) and Nesterenkonia xinjiangensis YIM 70097(T) (97.02 %), gave relatedness values of 8.7-62.2 %. Data from DNA-DNA hybridizations and physiological and biochemical tests indicated that strain EGI 80099(T) represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia rhizosphaerae sp. nov. is proposed. The type strain is EGI 80099(T) ( = BCRC 16947(T) = JCM 19129(T)).

Halopelagius fulvigenes sp. nov., a halophilic archaeon isolated from a lake

Two extremely halophilic archaea, designated YIM 94188(T) and YIM 94189, were isolated from Qijiaojing lake in Xinjiang province, north-west China and subjected to taxonomic characterization using a polyphasic approach. The cells of the two strains were coccoid, non-motile and Gram-stain-negative. Colonies were pink-white-pigmented and aerobic. Growth occurred at 10-30% (w/v) NaCl, 20-55 °C and pH 6.0-8.0 (optimum: 20-25% NaCl, 37-42 °C, pH 6.5-7.0). Magnesium was necessary for growth in the range of 0.2-1.2 M. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the two strains belonged to the genus Halopelagius showing 98.5% sequence similarity to the closest phylogenetic neighbour, Halopelagius inordinatus RO5-2(T). In addition, the DNA-DNA hybridization values of strains YIM 94188(T) and YIM 94189 to Halopelagius inordinatus RO5-2(T) were 35.7% and 37.7%, respectively. Polar lipid analyses revealed that the two strains contained phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). The DNA G+C contents of strains YIM 94188(T) and YIM 94189 were 66.3 mol% and 64.6 mol%, respectively. On the basis of physiological and chemotaxonomic data, and phylogenetic analysis, strains YIM 94188(T) and YIM 94189 were classified as representing a novel species in the genus Halopelagius. The name Halopelagius fulvigenes sp. nov. is proposed, with YIM 94188(T) (=CCTCC AB 2010456(T)=JCM 17506(T)) as the type strain.

Micromonospora kangleipakensis sp. nov., isolated from a sample of limestone quarry.

Strain MBRL 34(T), isolated from a sample of limestone quarry located at Hundung, Manipur, India, was characterized by polyphasic taxonomy. The strain showed the highest 16S rRNA gene sequence similarity with Micromonospora echinaurantica DSM 43904(T) (98.4 %), but formed a monophyletic clade with Micromonospora coerulea DSM 43143(T) (98.3 %) in the neighbour-joining tree. DNA-DNA hybridization experiments gave a DNA-DNA relatedness value of 53.1 % between MBRL 34(T) and M. coerulea DSM 43143(T). Strain MBRL 34(T) contained meso-diaminopimelic acid, galactose and glucose in the whole-cell hydrolysates along with small amounts of mannose, xylose, rhamnose and ribose. The major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside, along with an unknown lipid. MK-10(H6), MK-10(H2) MK-11(H4) and MK-10(H4) were the predominant menaquinones detected. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 73.5 %. Based on the taxonomic characteristics from a polyphasic study, strain MBRL 34(T) merits recognition as a representative of a novel species of the genus Micromonospora for which the name Micromonospora kangleipakensis sp. nov. is proposed; the type strain is MBRL 34(T) ( = DSM 45612(T) = JCM 17696(T)).

Aurantimonas endophytica sp. nov., a novel endophytic bacterium isolated from roots of Anabasis elatior (C. A. Mey.) Schischk.

An orange-coloured, aerobic, motile, short-rod-shaped bacterial strain, designated EGI 6500337T, was isolated from the surface-sterilized root of a halophyte, Anabasis elatior (C. A. Mey.) Schischk, collected from Urumqi, Xinjiang province, north-west China. Growth occurred at 5-35 °C (optimum 30 °C), at pH 6.0-9.0 (optimum pH 7.0) and in the presence of 0-6 % (w/v) NaCl (optimum 0-1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EGI 6500337T formed a distinct lineage in the cluster that comprised the genera Aurantimonas and Aureimonas in the family Aurantimonadaceae. The 16S rRNA gene sequence of strain EGI 6500337T shared highest similarity with those of Aurantimonas coralicida DSM 14790T (97.15 %) and Aurantimonas manganoxydans DSM 21871T (97.15 %). Strain EGI 6500337T contained Q-10 as the dominant isoprenoid quinone. The major cellular fatty acids were C18 : 1ω7c and C19 : 0ω8c cyclo. The polar lipid profile of strain EGI 6500337T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as major components, similarly to members of the genus Aurantimonas. The DNA G+C content of strain EGI 6500337T was 66.8 mol%. The level of DNA-DNA relatedness between strain EGI 6500337T and Aurantimonas coralicida DSM 14790T was 24.7±2.9 %. On the basis of the phylogenetic analysis, chemotaxonomic data and phenotypic characteristics, strain EGI 6500337T represents a novel species of the genus Aurantimonas, for which the name Aurantimonas endophytica sp. nov. is proposed. The type strain is EGI 6500337T (=KCTC 52296T=CPCC 100904T).

Nocardiopsis ansamitocini sp. nov., a new producer of ansamitocin P-3 of the genus Nocardiopsis.

An alkalitolerant actinomycete strain, designated EGI 80425T, capable of producing ansamitocin P-3, was isolated from a saline-alkali soil sample of Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80425T formed non-fragmented substrate mycelia and white aerial hyphae with long spore chains. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and rhamnose as the major sugar. The major fatty acids were anteiso-C17 : 0, iso-C16 : 0 and C18 : 1ω9c. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-9(H4). The G+C content of the genomic DNA of strain EGI 80425T was 70.2 mol%. Strain EGI 80425T showed highest 16S rRNA gene sequence similarity to Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T (96.44 %). Phylogenetic analysis showed that strain EGI 80425T clustered with the members of the genus Nocardiopsis. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain EGI 80425T represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis ansamitocini sp. nov. is proposed. The type strain is EGI 80425T ( = CGMCC 9969T = KCTC 39605T).

Biogeography of Nocardiopsis strains from hypersaline environments of Yunnan and Xinjiang Provinces, western China.

The genus Nocardiopsis is a widespread group within the phylum Actinobacteria and has been isolated from various salty environments worldwide. However, little is known about whether biogeography affects Nocardiopsis distribution in various hypersaline environments. Such information is essential for understanding the ecology of Nocardiopsis. Here we analyzed 16S rRNA, gyrB, rpoB and sodA genes of 78 Nocardiopsis strains isolated from hypersaline environments in Yunnan and Xinjiang Provinces of western China. The obtained Nocardiopsis strains were classified into five operational taxonomic units, each comprising location-specific phylo- and genotypes. Statistical analyses showed that spatial distance and environmental factors substantially influenced Nocardiopsis distribution in hypersaline environments: the former had stronger influence at large spatial scales, whereas the latter was more influential at small spatial scales.