Quantitation of the glycoprotein spike area on the surface of enveloped viruses

The density of glycoprotein (GP) distribution on the virion surface substantially influences the virus infectivity and pathogenicity. A method to quantitatively determine the area occupied by surface GP spikes was proposed for influenza virus (Flu) strain A/PR/8/34 on the basis of data of tritium bombardment and dynamic light scattering. The latter was used to measure the diameter of intact virions and subviral particles (Flu virions lacking GP spikes after bromelain digestion). Intact virions and subviral particles were bombarded with a hot tritium atom flux, and the specific radioactivity of the matrix M1 protein was analyzed. The tritium label was incorporated into the amino acid residues of a thin exposed protein layer and partly penetrated through the lipid bilayer of the viral envelope, labeling M1, located under the lipid bilayer. The tritium label distribution among different amino acid residues was the same in M1 isolated from subviral particles and M1 isolated from intact virions, demonstrating that the M1 spatial structure remained unchanged during proteolysis of GP spikes. The difference in specific radioactivity between the M1 proteins isolated from intact virions and subviral particles was used to calculate the GP-free portion of the viral surface. Approximating the Flu virion as a sphere, the GP-covered area was estimated at 1.4 × 10⁴ nm², about 40% of the total virion surface. This was consistent with the cryoelectron tomography data published for Flu strain A/X-31. The approach can be applied for other enveloped high pathogenic viruses, such as HIV and the Ebola virus.     

Determination of concentration and aggregate size in influenza virus preparations using the true UV-absorption spectra

It is well-known that influenza virus (IV) preparations are characterized by very large contribution of light-scattering to their UV absorption spectra. With the help of so called extrapolation method we managed to measure true absorption spectra of IV preparations and to determine absorption coefficients (E0.1(1) (cm, 280)) for the intact IV virions and for IV subviral particles. These coefficients turned out to equal 1.26 +/- 0.17 and 0.96 +/- 0.11 for the virions and subviral particles respectively. The knowledge of exact IV concentration is necessary for quantitative physico-chemical studies of IV virions and their components. It is also shown that UV absorption spectra measurements allow to register IV virion aggregation. Aggregation properties of IV subviral particles were also studied.     

Inhibition effect of flavonoid compounds against neuraminidase expressed in Pichia pastoris

Neuraminidase (NA) is one of the two glycoproteins on the surface of influenza virus, which cleaves terminal sialic acid residues and facilitates the release of virions from infected cells. The recombinant NA from H5N1 influenza virus strain A/Vietnam/1203/04 was expressed in Pichia pastoris X33 as a 45 kDa protein that displayed a K _m of 9.96 ± 1.26 μM with fluorogenic substrate, 2′-(4-methylumbelliferyl)-α-D-N-acetyl neuraminic acid. Partially purified NA was used for the inhibition and kinetic assays with eight flavonoid compounds and gallic acid. Among them, gallocatechin gallate (GCG) showed the best inhibition against NA with the IC₅₀ of 8.98 ± 0.46 μM and showed a competitive inhibition pattern with K _i value of 8.34 ± 0.25 μM. In molecular docking experiments, GCG displayed a binding energy of ?13.71 kcal/mol to the active site of NA and the galloyl moiety was required for NA inhibition activity.     

Comparison of in vivo infectivity of tissue-cultured nonoccluded virus and alkali-liberated occluded virus of Baculovirus heliothis

Feeding and intrahemocelic injection studies using tissue-culture-derived-nonoccluded virus (TCNOV) and occluded virus liberated by alkaline solution (ALOV) from polyhedral inclusion bodies were conducted with the single-embedded Heliothis nuclear polyhedrosis virus, Baculo-virus heliothis (H_zSEV). Comparisons of infectivity between ALOV and NOV were based upon the number of adminstered plaque-forming-units (PFU). There was little, if any, difference in infectivity between ALOV and TCNOV of H_zSEV when injected into 4th-instar larvae of Heliothis virescens. The LD₅₀, from the multiple dose injection studies, for ALOV and TCNOV was 6.5 ± 1.2 PFU per larva and 3.4 ± 0.9 PFU per larva, respectively. Injection of a single dose (5 PFU per larva) resulted in a larval mortality of 83.2 ± 3.4 and 62.6 ± 5.7% for ALOV and TCNOV of the H_zSEV, respectively. The LC₅₀ of ALOV and TCNOV, from the multiple-dose feeding tests, was 3.1 ± 0.4 PFU/cm² and 4.5 ± 0.9 PFU/cm², respectively. Feeding 24-hr-old larvae on virus-treated diets at a single dose (50.0 PFU/cm²) resulted in a 1.5-fold difference in percentage larval mortality between ALOV (91.0 ± 4.0%) and TCNOV (61.2 ± 3.0%). Counts of viral particles (VP), based upon electron microscopy, were 14.3 ± 2.6 × 10¹⁰ and 5.2 ± 1.1 × 10⁷ VP/ml for the ALOV and TCNOV, respectively. Thus, each larva ingesting or injected with one PFU received ca. 3500 × more VP of ALOV than in did of TCNOV.     

Labeling of influenza viruses with synthetic fluorescent and biotin-labeled lipids

Direct labeling of virus particles is a powerful tool for the visualization of virus–cell interaction events. However, this technique involves the chemical modification of viral proteins that affects viral biological properties. Here we describe an alternative approach of influenza virus labeling that utilizes Function-Spacer-Lipid(FSL) constructs that can be gently inserted into the virus membrane. We assessed whether labeling with fluorescent(fluo-Ad-DOPE) or biotin-labeled(biot-CMG2-DOPE) probes has any deleterious effect on influenza virus hemagglutinin(HA) receptor specificity, neuraminidase(NA) activity, or replicative ability in vitro. Our data clearly show that neither construct significantly affected influenza virus infectivity or viral affinity to sialyl receptors. Neither construct influenced the NA activities of the influenza viruses tested, except the A/Puerto Rico/8/34(H1N1) strain. Our data indicate that lipid labeling provides a powerful tool to analyze influenza virus infection in vitro.     

Heterotrophic microorganisms and viruses in the water of the Gorky reservoir during a period of anomalously high water temperature

During the anomalously hot summer of 2010, the water temperature in the Gorky reservoir reached 27–33°C. Pronounced cyanobacterial blooms occurred in the limnetic part of the reservoir. The average values for bacterioplankton abundance (11.58 ± 1.25 × 10⁶ cell/mL), biomass (886 ± 96 mg/m³), and production [169 ± 32 mg C/(m³ day)] were twice as high as in the year with temperatures comparable to long-term average values. These parameters were higher in the limnetic part than in the river one. The abundance (4.86 ± 0.75 × 10³ cell/mL) and biomass (138 ± 9 mg/m³) of heterotrophic nanoflagellates were 2.3 and 1.7 times higher, respectively, than in years with regular temperature regimes. The average number of plank-tonic viral particles (N _v) in 2010 was 48.89 ± 9.54 × 10⁶ particles/mL, while virus-induced bacterial mortality (VMB) accounted for 26.9 ± 4.6% of the bacterial production. The N _v and VMB values in the limnetic part of the reservoir were, respectively, 1.5 and 1.8 times higher than in the river one.     

Crystalline Antigen from the Influenza Virus Envelope

THE envelope of influenza viruses contains two morphologically and chemically distinct glycoproteins, a haemagglu-tinin and a neuraminidase, which recent experiments have indicated¹ may be removed from the virion by treatment with the protease, bromelain. In an investigation of the mechanism of this phenomenon it was found that although the neuraminidase protein was completely degraded during proteolysis, the isolated haemagglutinin protein could be recovered almost unchanged from the incubation mixture. We report the subsequent purification and crystallization of the haemagglutinin and its preliminary chemical and antigenic characterization. The X-31 strain of A2/Hong Kong/68² was used in most of the experiments to be described. Viruses were grown in embryonated eggs, purified as described by Skehel and Schild³ and digested with bromelain as described by Compans et al.¹. The smooth-surfaced virus particles which resulted were removed from the incubation mixture by centrifuging for 60 min at 100,000g and purified by sucrose density gradient centrifugation (20–60% sucrose in phosphate buffered saline (PBS) (100,000g, 16 h). The morphology of these particles in comparison with intact virus is shown in Fig. 1. It is clear that all of the envelope spike proteins were removed during proteolytic digestion; in agreement with these observations the shaved particles were completely devoid of the haemagglutinating and neuraminidase activities of the virus envelope proteins. Polyacrylamide gel electrophoretic analyses of the polypeptide composition of the particles also indicated that they contained only four of the seven polypeptides of the virus⁴ in the same proportions as these were present in the intact virus particles (Fig. 2b and c). Both haemagglu-tination and neuraminidase activities were completely destroyed during protease treatment. Electrophoretic analyses of the proteins present in the protease incubation supernatant after removal of the subviral particles indicated, however (Fig. 2a), that the major components of this mixture were two polypeptides of similar mobility to the haemagglutinin polypeptides previously identified³. Thus, the mobility of the larger polypeptide of the supernatant was identical to that of the larger haemagglutinin component and the mobility of the smaller polypeptide indicated a molecular weight difference of approximately 3,000 between this and the smaller haemagglutinin polypeptide.     

Generation of Influenza Virus from Avian Cells Infected by Salmonella Carrying the Viral Genome

Domestic poultry serve as intermediates for transmission of influenza A virus from the wild aquatic bird reservoir to humans, resulting in influenza outbreaks in poultry and potential epidemics/pandemics among human beings. To combat emerging avian influenza virus, an inexpensive, heat-stable, and orally administered influenza vaccine would be useful to vaccinate large commercial poultry flocks and even migratory birds. Our hypothesized vaccine is a recombinant attenuated bacterial strain able to mediate production of attenuated influenza virus in vivo to induce protective immunity against influenza. Here we report the feasibility and technical limitations toward such an ideal vaccine based on our exploratory study. Five 8-unit plasmids carrying a chloramphenicol resistance gene or free of an antibiotic resistance marker were constructed. Influenza virus was successfully generated in avian cells transfected by each of the plasmids. The Salmonella carrier was engineered to allow stable maintenance and conditional release of the 8-unit plasmid into the avian cells for recovery of influenza virus. Influenza A virus up to 10⁷ 50% tissue culture infective doses (TCID₅₀)/ml were recovered from 11 out of 26 co-cultures of chicken embryonic fibroblasts (CEF) and Madin-Darby canine kidney (MDCK) cells upon infection by the recombinant Salmonella carrying the 8-unit plasmid. Our data prove that a bacterial carrier can mediate generation of influenza virus by delivering its DNA cargoes into permissive host cells. Although we have made progress in developing this Salmonella influenza virus vaccine delivery system, further improvements are necessary to achieve efficient virus production, especially in vivo.     

Neutralizing single-chain antibodies against the tick-borne encephalitis virus

A recombinant pSC13D6 plasmid DNA was constructed based on cDNA fragments of genes encoding variable domains of heavy and light chains of the MKA13D6 monoclonal antibody against glycoprotein of the tick-borne encephalitis (TBE) virus. This plasmid provided expression in Escherichia coli cells of the scl3D6 single-chain antibody against the TBE virus. The produced antibodies could bind to the TBE virus, strain 205, and the TBE virus recombinant E protein. The affinity constant of purified scl3D6 was (3.0 ± 0.2) × 10⁷ M^?1 for the equilibrium state and (2.8 ± 0.3) × 10⁷ M^?1 in the case of antigen-antibody formation on the surface. The obtained single-chain antibody could inhibit the infection potency of the TBE virus on a monolayer of eukaryotic cells. The calculated IC₅₀ value for scl3D6 was 16.7 μg/ml.     

Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses

Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids.     

Pyridine degradation characteristics of a newly isolated bacterial strain and its application with a novel reactor for the further treatment in pyridine wastewater

A pyridine-degrading strain Gemmobacter sp. ZP-12, isolated from an activated sludge, was able to use pyridine as the sole carbon and nitrogen source for the growth. The strain could effectively degrade pyridine and remove TOC over a wide range of initial pyridine concentrations. The pyridine degradation rate for 100, 500, 1000, 1500 and 2000 mg/L was 2.90 ± 0.17; 13.72 ± 0.21, 20.40 ± 0.24, 31.09 ± 0.26, 27.63 ± 0.17 mg/L/h, respectively. During the pyridine degraded, a large amount of NH₄⁺-N was released and accumulated. The accumulation of NH₄⁺-N increased with the increase of pyridine concentration. For further removing the NH₄⁺-N producing in pyridine degradation, an aerobic-moving bed biofilm reactor coupled with intermittent-aeration membrane biological reactor (a-MBBR-IMBR) was constructed, in which the strain and the aerobic / anoxic mixed sludge combined to remove the pollutants in the wastewater containing 500 mg/L pyridine. After 96 h of operation, the final TOC removal efficiency was 96.5 ± 1.05 %. The average residual concentration of NO₃⁻-N and NH₄⁺-N was respectively 9.09 ± 4.13 mg/L and 7.85 ± 3.88 mg/L. The study provides a viable option for treating pyridine wastewater.     

Histopathology and bioassay of Plathypena scabra granulosis virus

A granulosis virus was found infecting Plathypena scabra larvae in Iowa. The capsules averaged 377 ± 25 × 222 ± 19 nm. On the basis of light microscopical observations, the virus appeared to infect the epidermis, fat body, and tracheal matrix cells. The LC₅₀ and LC₉₅ were 6.7 × 10⁷ and 1.5 × 10⁹ capsules/acre, respectively. The LT₅₀ values varied from 3 to 9 days for 1 × 10¹² and 1 × 10⁸ capsules/acre, respectively.     

Biosynthesis of subviral oncogenic particles (virosomes) in mitochondria of rous sarcoma and Rauscher murine leukemia cells

Summary Experimental evidence for the presence and biosynthesis of subviral, leukemogenic particles in the isolated mitochondria of spleen cells of mice infected with Rauscher murine leukemia (RML) virus is presented. These subviral particles sediment at a density of 1.27–1.29 g/ml and induce splenomegaly and RML three weeks after i.v. or i.p. administration to white mice. Virosomes have been labelled with [³²P]phosphate in the isolated mitochondria from RML spleen cells and high molecular weight (70S) [³²P]RNA has been isolated from these subviral, leukemogenic particles. Rauscher virus group specific antigens were detected by immunodiffusion in the inner membrane and matrix fraction of the mitochondria of RML spleen cells. These results together with our earlier findings strongly suggest that mitochondria of the transformed cells participate in the biosynthesis of RNA tumor viruses. Possible mechanism of the penetration of viral genetic information of RNA tumor viruses into mitochondria of tumor cellsin vivo is discussed.     

<Emphasis Type="Italic">Nibribacter flagellatus</Emphasis> sp. nov., isolated from rhizosphere of <Emphasis Type="Italic">Hibiscus syriacus</Emphasis> and emended description of the genus <Emphasis Type="Italic">Nibribacter</Emphasis>

A Gram-stain negative, aerobic, motile by flagella, rod-shaped strain (THG-T16^T) was isolated from rhizosphere of Hibiscus syriacus. Growth occurred at 10–40 °C (optimum 28–30 °C), at pH 6.0–8.0 (optimum 7.0) and at 0–1.0% NaCl (optimum 0%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-T16^T were identified as Nibribacter koreensis KACC 16450^T (98.6%), Rufibacter roseus KCTC 42217^T (94.7%), Rufibacter immobilis CCTCC AB 2013351^T (94.5%) and Rufibacter tibetensis CCTCC AB 208084^T (94.4%). The DNA G+C content of strain THG-T16^T was determined to be 46.7 mol%. DNA–DNA hybridization values between strain THG-T16^T and N. koreensis KACC 16450^T, R. roseus KCTC 42217^T, R. immobilis CCTCC AB 2013351^T, R.tibetensis CCTCC AB 208084^T were 33.5?±?0.5% (31.7?±?0.7% reciprocal analysis), 28.1?±?0.2% (25.2?±?0.2%), 17.1?±?0.9% (10.2?±?0.6%) and 8.1?±?0.3% (5.2?±?0.1%). The polar lipids were identified as phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid and three unidentified lipids. The quinone was identified as MK-7 and the polyamine as sym-homospermidine. The major fatty acids were identified as C_16:1 ω5c, C_17:1 ω6c, iso-C_15:0, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B). On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics, and DNA–DNA hybridization data, strain THG-T16^T represents a novel species of the genus Nibribacter, for which the name Nibribacter flagellatus sp. nov. is proposed. The type strain is THG-T16^T(=?KACC 19188^T?=?CCTCC AB 2016246^T).     

Gracilibacillus xinjiangensis sp. nov., a new member of the genus Gracilibacillus isolated from Xinjiang region, China

A Gram-positive, endospore-forming, rod-shaped bacterium, designated isolate J2^T was isolated from a soil sample from Xinjiang Uyghur Autonomous Region, China. The isolate was observed to grow at 16–46 °C and pH 6.5–8.0. Chemotaxonomic analysis showed menaquinone-7 (MK-7) to be the major isoprenoid quinone; diphosphatidylglycerol, phosphatidylglycerol, one aminophospholipid, two phosphoglycolipids and one glycolipid as the major cellular polar lipids; and anteiso-C_15:0, iso-C_15:0, anteiso-C_17:0 and C_16:0 as the major fatty acids. Comparative analyses of the 16S rRNA gene sequence showed that strain J2^T is most closely related to Gracilibacillus ureilyticus (with 98.8 % similarity), Gracilibacillus dipsosauri (97.2 %), Gracilibacillus quinghaiensis (97.1 %) and Gracilibacillus thailandensis (97.0 %). The DNA–DNA reassociation values between strain J2^T and G. ureilyticus MF38^T, G. dipsosauri DD1^T, G. quinghaiensis YIM-C229^T and G. thailandensis TP2-8^T were 29.8 ± 3.7, 23.0 ± 3.5, 15.8 ± 4.9 and 15.9 ± 5.0 %, respectively. The genomic DNA G+C content of strain J2^T was determined to be 36.5 mol%. Based on these data, strain J2^T is considered as a novel species of the genus Gracilibacillus, for which the name Gracilibacillus xinjiangensis sp. nov. is proposed. The type species is J2^T (= CGMCC 1.12449^T = JCM 18859^T).     

Specific ion effects on the particle size distributions of cell culture–derived influenza A virus particles within the Hofmeister series

Virus particle (VP) aggregation can have serious implications on clinical safety and efficacy of virus‐based therapeutics. Typically, VP are suspended in buffers to establish defined product properties. Salts used to achieve these properties show specific effects in chemical and biological systems in a reoccurring trend known as Hofmeister series (HS). Hofmeister series effects are ubiquitous and can affect colloidal particle systems. In this study, influences of different ions (anions: SO₄^2?, HPO₄^2?, Cl^?, Br^?, NO₃^?, I^?; cations: K⁺, Na⁺, Li⁺, Mg²⁺, Ca²⁺) on particle size distributions of cell culture‐derived influenza VP were investigated. For the experimental setup, influenza virus A/Puerto Rico/8/34 (H1N1) VP produced in adherent and suspension Madin Darby canine kidney cells were used. Inactivated and concentrated virus harvests were dialyzed against buffers containing the ions of interest, followed by differential centrifugal sedimentation to measure particle size distributions. VP from both cell lines showed no aggregation over a wide range of buffers containing different salts in concentrations ≥60 mM. However, when dialyzed to low salt or Ca²⁺ buffers, VP produced in adherent cells showed increased aggregation compared to VP produced in suspension cells. Additionally, changes in VP diameters depending on specific ion concentrations were observed that partially reflected the HS trend.     

Halomonas zhaodongensis sp. nov., a slightly halophilic bacterium isolated from saline–alkaline soils in Zhaodong, China

A slightly halophilic bacterium (strain NEAU-ST10-25^T) was isolated from saline–alkaline soils in Zhaodong City, Heilongjiang Province, China. The strain is a Gram-negative, aerobic motile rod. It accumulates poly-β-hydroxyalkanoate and produces exopolysaccharide. It produces beige-yellow colonies. Growth occurs at NaCl concentrations (w/v) of 0–15 % (optimum 3 %), at temperatures of 4–60 °C (optimum 35 °C) and at pH 6–12 (optimum pH 9). Its G+C content is 53.8 mol%. Phylogenetic analyses based on the separate 16S rRNA gene and concatenation of the 16S rRNA, gyrB and rpoD genes indicate that it belongs to the genus Halomonas in the class Gammaproteobacteria. The most phylogenetically related species is Halomonas alkaliphila DSM 16354^T, with which strain NEAU-ST10-25^T showed 16S rRNA, gyrB and rpoD gene sequence similarities of 99.2, 82.3 and 88.2 %, respectively. The results of DNA–DNA hybridization assays showed 60.47 ± 0.69 % DNA relatedness between strain NEAU-ST10-25^T and H. alkaliphila DSM 16354^T, 42.43 ± 0.37 % between strain NEAU-ST10-25^T and Halomonas venusta DSM 4743^T and 30.62 ± 0.43 % between strain NEAU-ST10-25^T and Halomonas hydrothermalis DSM 15725^T. The major fatty acids are C_18:1 ω7c (62.3 %), C_16:0 (17.6 %), C_16:1 ω7c/C_16:1 ω6c (7.7 %), C_14:0 (2.9 %), C_12:0 3-OH (2.8 %), C_10:0 (2.1 %) and C_18:1 ω9c (1.6 %) and the predominant respiratory quinone is ubiquinone 9 (Q-9). The proposed name is Halomonas zhaodongensis, NEAU-ST10-25^T (=CGMCC 1.12286^T = DSM 25869^T) being the type strain.     

Kinetic and equilibrium studies of cyclomalto-octaose (γ-cyclodextrin)-methyl orange inclusion complexes

Measurements of the equilibrium and temperature-jump u.v., visible, and induced c.d. spectra of Methyl Orange (MO) in the presence of cyclomalto-octaose (γ-cyclodextrin, γ-CD) have been carried out. Three mechanistic steps were detected through the temperature-jump data (25.0°):

where K₁, K₂, and K₃ are 45 (±7), 2.0 (±1.1) × 10⁶, and 6.1 (±2.5) × 10³ dm³.mol^?1, respectively, k₂ = 9.4 (±5.1) × 10⁹ dm³.mol^?1.s^?1, and k_?2 = 4.8 (±0.8) × 10³ s^?1. The equilibrium u.v./visible data are also consistent with this reaction scheme. The high stability of the dimer inclusion complex (MO)₂ · γ-CD compared to that of the monomer inclusion complex MO · γ-CD appears to be related to the annular diameter of γ-CD and demonstrates a degree of selectivity in cyclodextrin inclusion complexes. The (MO)₂ · (γ-CD)₂ complex also contains a dimer, included by both γ-CD molecules.     

<Emphasis Type="Italic">Lysobacter pedocola</Emphasis> sp. nov., a novel species isolated from Korean soil

A Gram-negative, yellow-pigmented bacterial strain, designated IPC6^T, was isolated from soil in an arid region of Goyang-si (Gyeonggi-do, South Korea). Cells were strictly aerobic, non-spore-forming, rod-shaped. The strain grew within a temperature range of 10–42°C (optimum, 30°C) and pH of 5.0–11.0 (optimum, pH 8.0) in the presence of 0–2% (w/v) NaCl. Phylogenetically, the novel strain was closely related to members of the Lysobacter genus based on 16S rRNA sequence similarity, and showed the highest sequence similarity to Lysobacter niastensis KACC 11588^T (98.5%). The predominant fatty acids were iso-C_15:0, iso-C_16:0, and summed feature 9 (iso-C_17:1ω9c), with Q-8 identified as the major ubiquinone. The polar lipid content included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminophospholipid, and an unidentified phospholipid. DNA-DNA hybridization results indicated that the strain IPC6^T was distinct from Lysobacter niastensis KACC 11588^T (37.9 ± 0.14%), Lysobacter panacisoli KACC 17502^T (56.4 ± 0.13%), Lysobacter soli KCTC 22011^T (8.1 ± 0.04%), Lysobacter gummosus KCTC 12132^T (9.6 ± 0.03%), and Lysobacter cavernae KCTC 42875^T (37.5 ± 0.14%), respectively. The DNA G + C content of the novel strain was 71.1 mol%. Based on the collective phenotypic, genotypic and chemotaxonomic data, the IPC6^T strain is considered to represent a novel species in the genus Lysobacter, for which the name Lysobacter pedocola sp. nov. (= KCTC 42811^T = JCM 31020^T) is proposed.     

Halomonas nanhaiensis sp. nov., a halophilic bacterium isolated from a sediment sample from the South China Sea

A novel Gram-negative, aerobic, slightly halophilic, yellow-pigmented, oxidase-negative, Voges–Proskauer positive, non-spore-forming bacterium, designated YIM M 13059^T, was isolated from a sediment sample collected from the South China Sea at a depth of 310 m. Optimal growth was found to occur at 28–30 °C, pH 7.0 and in the presence of 3–4 % (w/v) NaCl. Cells were observed to be rod-shaped and motile by peritrichous flagella. The polar lipids of strain YIM M 13059^T were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a ninhydrin-positive phospholipid, one glycolipid and two unknown phospholipids. The predominant respiratory quinone was determined to be Q-9. The major fatty acids were identified as C_18:1 ω7c, C_16:1 ω6c/C_16:1 ω7c, C_16:0 and C_12:0 3-OH. The genomic DNA G+C content was determined to be 54.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belongs to the genus Halomonas in the family Halomonadaceae. The 16S rRNA gene sequence similarities between strain YIM M 13059 ^T and the type strains of members of the genus Halomonas were in the range 93.3–98.3 %. However, the levels of DNA–DNA relatedness values between YIM M 13059 and the type strains of the most closely related species, Halomonas zhangjiangensis, Halomonas variabilis, Halomonas neptunia, Halomonas boliviensis and Halomonas sulfadieris were 50.2 ± 0.68 %, 46.8 ± 1.9 %, 28.5 ± 0.74 %, 42.9 ± 0.55 % and 37.1 ± 0.68 %, respectively. Based on phylogenetic, chemotaxonomic and phenotypic data, the strain YIM M 13059^T is proposed to represent a novel member of the genus Halomonas, with the name Halomonas nanhaiensis sp. nov. The type strain is YIM M 13059^T (=JCM 18142^T =CCTCC AB 2012911^T).