Lingfang Zhu

Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum

A yellow-pigmented bacterium, designated strain ZFGT-11(T), was isolated from roots of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain ZFGT-11(T) were Gram-stain-negative, strictly aerobic rods that were surrounded by a thick capsule and were motile by means of a single polar flagellum. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFGT-11(T) was a member of the genus Sphingomonas and was closely related to Sphingomonas naasensis KACC 16534(T) (97.6% similarity), Sphingomonas kyeonggiense JCM 18825(T) (96.8%), Sphingomonas asaccharolytica IFO 15499(T) (96.7%) and Sphingomonas leidyi DSM 4733(T) (96.6%). The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major cellular fatty acids were summed feature 8 (comprising C(18 : 1)ω7c and/or C(18 : 1)ω6c), C(17 : 1)ω6c, C(14 : 0) 2-OH, C(16 : 0) and C(15 : 0) 2-OH. The major polyamine of strain ZFGT-11(T) was sym-homospermidine. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, two unidentified aminoglycolipids, two unidentified phospholipids and two unidentified lipids were detected in the polar lipid profile. The DNA G+C content was 66.8 mol%. DNA-DNA relatedness for strain ZFGT-11(T) with respect to its closest phylogenetic relative S. naasensis KACC 16534(T) was 26.2±4.8% (mean±SD). On the basis of data from the present polyphasic taxonomic study, strain ZFGT-11(T) is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas gei sp. nov. is proposed. The type strain is ZFGT-11(T) ( = CCTCC AB 2013306(T) = KCTC 32449(T) = LMG 27608(T)).

Pontibacter toksunensis sp. nov., isolated from soil, and emended descriptions of Pontibacter roseus and Pontibacter akesuensis.

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented bacterial strain, designated ZLD-7(T), was isolated from a soil sample collected from an arid area in Xinjiang Province in north-west China, and characterized by using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that strain ZLD-7(T) was a member of the genus Pontibacter in the family Cytophagaceae, with sequence similarities of 93.7-96.2 % to type strains of other Pontibacter species. The only isoprenoid quinone of strain ZLD-7(T) was MK-7, and its major cellular fatty acids were summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I), iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profile consisted of phosphatidylethanolamine, one unidentified aminolipid and four unidentified polar lipids. The DNA G+C content was 47.8 mol%. On the basis of the evidence presented, it is proposed that strain ZLD-7(T) represents a novel species of the genus Pontibacter, for which the name Pontibacter toksunensis sp. nov. is proposed. The type strain is ZLD-7(T) ( = CCTCC AB 208003(T) = KCTC 23984(T)). Emended descriptions of Pontibacter roseus and Pontibacter akesuensis are also proposed.

Asticcacaulis endophyticus sp. nov., a prosthecate bacterium isolated from the root of Geum aleppicum.

A strictly aerobic, light-yellow-coloured, stalked bacterium, designated strain ZFGT-14(T), was isolated from the root of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi province, north-west China, and was subjected to a taxonomic study using a polyphasic approach. This novel isolate grew at 7-33 °C (optimum 25-28 °C) and pH 6.0-10.0 (optimum pH 7.0-8.0). Flexirubin-type pigments were not produced. Cells were Gram-stain-negative, rod-shaped and motile with a single polar flagellum. The predominant respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C19 : 0 cyclo ω8c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and the major polar lipids were phosphatidylglycerol and glycolipids. The DNA G+C content was 57.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFGT-14(T) was most closely related to the genus Asticcacaulis and had low sequence similarity (95.0-95.9 %) with all species with validly published names within the genus Asticcacaulis. Based on the phenotypic, phylogenetic and genotypic data, strain ZFGT-14(T) is considered to represent a novel species of the genus Asticcacaulis, for which the name Asticcacaulis endophyticus sp. nov. is proposed. The type strain is ZFGT-14(T) ( = CCTCC AB 2013012(T) = KCTC 32296(T) = LMG 27605(T)).

The Type VI Secretion System Engages a Redox-Regulated Dual-Functional Heme Transporter for Zinc Acquisition

The type VI secretion system was recently reported to be involved in zinc acquisition, but the underlying mechanism remains unclear. Here, we report that Burkholderia thailandensis T6SS4 is involved in zinc acquisition via secretion of a zinc-scavenging protein, TseZ, that interacts with the outer membrane heme transporter HmuR. We find that HmuR is a redox-regulated dual-functional transporter that transports heme iron under normal conditions but zinc upon sensing extracellular oxidative stress, triggered by formation of an intramolecular disulfide bond. Acting as the first line of defense against oxidative stress, HmuR not only guarantees an immediate response to the changing environment but also provides a fine-tuned mechanism that allows a gradual response to perceived stress. The T6SS/HmuR-mediated active zinc transport system is also involved in bacterial virulence and contact-independent bacterial competition. We describe a sophisticated bacterial zinc acquisition mechanism affording insights into the role of metal ion transport systems.

Sphingomonas hylomeconis sp. nov., isolated from the stem of Hylomecon japonica.

A yellow-pigmented bacterium, designated strain GZJT-2T, was isolated from the stem of Hylomecon japonica (Thunb.) Prantl et Kündig collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain GZJT-2T were Gram-reaction-negative, strictly aerobic, rod-shaped, non-spore-forming and non-motile. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GZJT-2T was a member of the genus Sphingomonas, with sequence similarities of 92.1-96.9 % to type strains of recognized species of the genus Sphingomonas (92.1 % to Sphingomonas oligoaromativorans SY-6T and 96.9 % to Sphingomonas oligophenolica JCM 12082T). Strain GZJT-2T contained ubiquinone-10 (Q-10) as the predominant respiratory quinone and sym-homospermidine as the major polyamine. The major cellular fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C14 : 0 2-OH. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, four unidentified phospholipids, an unidentified aminolipid and four unidentified lipids were detected in the polar lipid profile. The DNA G+C content was 62.5 ± 0.3 mol%. On the basis of data from phenotypic, phylogenetic and DNA-DNA relatedness studies, strain GZJT-2T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas hylomeconis sp. nov. is proposed. The type strain is GZJT-2T ( = CCTCC AB 2013304T = KCTC 42739T).

Rhizobacter bergeniae sp. nov., isolated from the root of Bergenia scopulosa.

A yellowish-pigmented bacterium, designated strain PLGR-1(T), was isolated from the root of Bergenia scopulosa collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain PLGR-1(T) were Gram-stain-negative, strictly aerobic, rod-shaped, non-spore-forming and motile with a single polar flagellum. Growth occurred at 7-33 °C (optimum, 25-28 °C), at pH 5.0-10.0 (optimum, pH 6.0-7.0) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). The predominant respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polyamines were putrescine and 2-hydroxyputrescine and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 69.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain PLGR-1(T) belonged to the class Betaproteobacteria and formed a tight phyletic lineage with members of the genus Rhizobacter. Strain PLGR-1(T) was most closely related to Rhizobacter dauci DSM 11587(T) and Rhizobacter fulvus DSM 19916(T), with 16S rRNA gene sequence similarities of 98.5 and 98.0 %, respectively. The DNA-DNA relatedness values between strain PLGR-1(T) and the type strains of Rhizobacter dauci and Rhizobacter fulvus were 46.3 and 14.7 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain PLGR-1(T) is considered to represent a novel species of the genus Rhizobacter, for which the name Rhizobacter bergeniae sp. nov. is proposed. The type strain is PLGR-1(T) ( = CCTCC AB 2013018(T) = KCTC 32299(T) = LMG 27607(T)).

A starvation-induced regulator, RovM, acts as a switch for planktonic/biofilm state transition in Yersinia pseudotuberculosis

The transition between the planktonic state and the biofilm-associated state is a key developmental decision for pathogenic bacteria. Biofilm formation by Yersinia pestis is regulated by hmsHFRS genes (β-1, 6-N-acetyl-D-glucosamine synthesis operon) in its flea vector and in vitro. However, the mechanism of biofilm formation in Yersinia pseudotuberculosis remains elusive. In this study, we demonstrate that the LysR-type regulator RovM inversely regulates biofilm formation and motility in Y. pseudotuberculosis by acting as a transcriptional regulator of these two functions. RovM is strongly induced during growth in minimal media but strongly repressed in complex media. On one hand, RovM enhances bacterial motility by activating the expression of FlhDC, the master regulator of flagellar genes, via the recognition of an operator upstream of the flhDC promoter. On the other hand, RovM represses β-GlcNAc production under nutrition-limited conditions, negatively regulating hmsHFRS expression by directly binding to the −35 element of its promoter. Compared to wild-type bacteria, the rovM mutant established denser biofilms and caused more extensive mortality in mice and silkworm larvae. These results indicate that RovM acts as a molecular switch to coordinate the expression of genes involved in biofilm formation and motility in response to the availability of nutrients.

Rhizobium gei sp. nov., a bacterial endophyte of Geum aleppicum

A bacterial strain, designated as ZFJT-2T, was isolated from the stem of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain ZFJT-2T were Gram-stain-negative, strictly aerobic, rod-shaped and motile by means of a single polar flagellum. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, 11-methyl C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), and the DNA G+C content was 58.3 mol% (HPLC). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFJT-2T was a member of the genus Rhizobium and was most closely related to Rhizobium giardinii KACC 10720T (98.6 % similarity) and Rhizobium herbae CCBAU 83011T (98.5 %). The low levels of sequence similarity found between the atpD, recA and glnII gene sequences of strain ZFJT-2T and those of recognized species of the genus Rhizobium (no more than 94.4, 87.2 and 89.5 %, respectively) indicated that it may represent a separate species of the genus Rhizobium. The DNA-DNA relatedness values for strain ZFJT-2T with respect to R. giardinii KACC 10720T and R. herbae CCBAU 83011T were 17.6 and 41.9 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, strain ZFJT-2T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium gei sp. nov. is proposed. The type strain is ZFJT-2T (=CCTCC AB 2013015T=KCTC 32301T=LMG 27603T).

RovM and CsrA Negatively Regulate Urease Expression in Yersinia pseudotuberculosis

Urease acts as an important acid resistance system and virulence factor that is widespread among microorganisms. RovM is a global regulator that regulates a series of genes and pathways including acid survival systems in the enteric bacterium Yersinia pseudotuberculosis (Yptb). However, whether RovM regulates the urease activity in Yptb was still unknown. In this study, by using qualitative and quantitative urease assays, we show that the urease expression responds to nutrient conditions and the RovM protein represses urease expression by binding to its promoter. A previously reported positive regulator OmpR activates urease activity but RovM plays a dominant role in different nutrient conditions. In addition, carbon storage regulator system A (CsrA), the upstream regulator of RovM, dramatically down-regulates urease activity possibly by its binding to the Shine-Dalgarno (SD) sequence of the mRNA encoding the urease. In conclusion, this study demonstrates that urease activity is strictly controlled by nutrient conditions and is down-regulated by the CsrA-RovM pathway.

Draft Genome Sequence of Nafulsella turpanensis ZLM-10T, a Novel Member of the Family Flammeovirgaceae

ABSTRACT Nafulsella turpanensis ZLM-10T is a slightly halophilic, Gram-negative, rod-shaped, gliding, pale-pink-pigmented bacterium in the family Flammeovirgaceae, and it shows resistance to gentamicin, kanamycin, neomycin, and streptomycin. Here, we report the genome sequence of N. turpanensis strain ZLM-10T, which has a 4.8-Mb genome and a G+C content of 45.67%.