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Sample records for photosynthetic bacterium isolated

  1. Identification, isolation, and sequence of the reaction center protein genes of the photosynthetic purple bacterium Rhodopseudomonas capsulata

    SciTech Connect

    Hearst, J.E.

    1984-07-01

    Reaction centers in photosynthetic membranes are the centers to which electronic excitation due to light absorption is transferred. This excitation brings about a charge separation between a bacteriochlorophyll molecule and two quinone molecules which ultimately leads to the formation of a hydroquinone. The reduced hydroquinone is then utilized to produce a proton gradient across the membrane and ultimately to produce ATP. We have focused our interest on the structure of the reaction center in the photosynthetic purple bacterium, Rhodopseudomonas capsulata, with the intention of establishing a detailed understanding of these first chemical steps in the natural fixation of sunlight. The methods used to identify and isolate the genes for the three reaction center subunits, L, M, and H, in Rps. capsulata are outlined. These genes have then been sequenced, and the sequences analyzed in detail for their similarity with sequences of comparable proteins from more advanced photosynthetic bacteria such as Anabena, from algae such as Euglena and Chlamydomonas, and from higher plants such as amaranthus, soybean, tobacco and spinach. Homology was found which has been tentatively interpreted to be in the region of quinone binding in all of these reaction centers. There is growing optimism that there will be substantial structural similarity between the reaction centers of the purple bacteria and those of photosystem II in higher plants. This conclusion is important because the x-ray crystal structures of several of the purple bacteria reaction center complexes are presently being worked on and will ultimately be solved.

  2. Isolation and Characterization of a Purple Non-Sulfur Photosynthetic Bacterium Rhodopseudomonas faecalis Strain A from Swine Sewage Wastewater.

    PubMed

    Wei, Hongyi; Okunishi, Suguru; Yoshikawa, Takeshi; Kamei, Yuto; Maeda, Hiroto

    2016-01-01

    A purple non-sulfur photosynthetic bacterium (PNSB), PSB Strain A was isolated from swine sewage wastewater. Phylogenetic analysis revealed that PSB Strain A was most closely related to Rhodopseudomonas faecalis. Growth of the isolate under anaerobic-light conditions with a variety of carbon sources was investigated. Both PSB Strain A and the standard strain showed good growth with acetic acid, propionic acid, and n-butyric acid at a concentration of 20 mM. At the high concentration of 200 mM, PSB Strain A showed better growth in pyruvate, acetate, propionate, succinate and malate. By applying PSB Strain A to treat swine sewage wastewater, the concentration of VFAs, which were acetic acid and propionic acid, decreased from 158.0 mM to 120.2±2.9 mM, and 14.9 mM to 9.3±0.9 mM, respectively, after 216-h incubation. After 330-h incubation, the concentrations of TOC and ammonia nitrogen dropped from 4508.0 mg/L to 3104.0±451.5 mg/L, and 629.7 mg/L to 424.1±7.4 mg/L, respectively. The isolated PSB Strain A showed almost the same efficiency compared with the standard strain on the removal of VFAs and TOC. The results suggest the possibility of using the isolated strain to treat swine sewage wastewater. PMID:27009507

  3. Isolation, characterization, and amino acid sequences of auracyanins, blue copper proteins from the green photosynthetic bacterium Chloroflexus aurantiacus

    NASA Technical Reports Server (NTRS)

    McManus, J. D.; Brune, D. C.; Han, J.; Sanders-Loehr, J.; Meyer, T. E.; Cusanovich, M. A.; Tollin, G.; Blankenship, R. E.

    1992-01-01

    Three small blue copper proteins designated auracyanin A, auracyanin B-1, and auracyanin B-2 have been isolated from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus. All three auracyanins are peripheral membrane proteins. Auracyanin A was described previously (Trost, J. T., McManus, J. D., Freeman, J. C., Ramakrishna, B. L., and Blankenship, R. E. (1988) Biochemistry 27, 7858-7863) and is not glycosylated. The two B forms are glycoproteins and have almost identical properties to each other, but are distinct from the A form. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis apparent monomer molecular masses are 14 (A), 18 (B-2), and 22 (B-1) kDa. The amino acid sequences of the B forms are presented. All three proteins have similar absorbance, circular dichroism, and resonance Raman spectra, but the electron spin resonance signals are quite different. Laser flash photolysis kinetic analysis of the reactions of the three forms of auracyanin with lumiflavin and flavin mononucleotide semiquinones indicates that the site of electron transfer is negatively charged and has an accessibility similar to that found in other blue copper proteins. Copper analysis indicates that all three proteins contain 1 mol of copper per mol of protein. All three auracyanins exhibit a midpoint redox potential of +240 mV. Light-induced absorbance changes and electron spin resonance signals suggest that auracyanin A may play a role in photosynthetic electron transfer. Kinetic data indicate that all three proteins can donate electrons to cytochrome c-554, the electron donor to the photosynthetic reaction center.

  4. Isolation, characterization, and primary structure of rubredoxin from the photosynthetic bacterium, Heliobacillus mobilis

    NASA Technical Reports Server (NTRS)

    Lee, W. Y.; Brune, D. C.; LoBrutto, R.; Blankenship, R. E.

    1995-01-01

    Rubredoxin is a small nonheme iron protein that serves as an electron carrier in bacterial systems. Rubredoxin has now been isolated and characterized from the strictly anaerobic phototroph, Heliobacillus mobilis. THe molecular mass (5671.3 Da from the amino acid sequence) was confirmed and partial formylation of the N-terminal methionyl residue was established by matrix-assisted laser desorption mass spectroscopy. The complete 52-amino-acid sequence was determined by a combination of N-terminal sequencing by Edman degradation and C-terminal sequencing by a novel method using carboxypeptidase treatment in conjunction with amino acid analysis and laser desorption time of flight mass spectrometry. The molar absorption coefficient of Hc. mobilis rubredoxin at 490 nm is 6.9 mM-1 cm-1 and the midpoint redox potential at pH 8.0 is -46 mV. The EPR spectrum of the oxidized form shows resonances at g = 9.66 and 4.30 due to a high-spin ferric iron. The amino acid sequence is homologous to those of rubredoxins from other species, in particular, the gram-positive bacteria, and the phototrophic green sulfur bacteria, and the evolutionary implications of this are discussed.

  5. Role of Rhodobacter sp. Strain PS9, a Purple Non-Sulfur Photosynthetic Bacterium Isolated from an Anaerobic Swine Waste Lagoon, in Odor Remediation

    PubMed Central

    Do, Young S.; Schmidt, Thomas M.; Zahn, James A.; Boyd, Eric S.; de la Mora, Arlene; DiSpirito, Alan A.

    2003-01-01

    Temporal pigmentation changes resulting from the development of a purple color in anaerobic swine waste lagoons were investigated during a 4-year period. The major purple photosynthetic bacterium responsible for these color changes and the corresponding reductions in odor was isolated from nine photosynthetic lagoons. By using morphological, physiological, and phylogenetic characterization methods we identified the predominant photosynthetic bacterium as a new strain of Rhodobacter, designated Rhodobacter sp. strain PS9. Rhodobacter sp. strain PS9 is capable of photoorganotrophic growth on a variety of organic compounds, including all of the characteristic volatile organic compounds (VOC) responsible for the odor associated with swine production facilities (J. A. Zahn, A. A. DiSpirito, Y. S. Do, B. E. Brooks, E. E. Copper, and J. L. Hatfield, J. Environ. Qual. 30:624-634, 2001). The seasonal variations in airborne VOC emitted from waste lagoons showed that there was a 80 to 93% decrease in the concentration of VOC during a photosynthetic bloom. During the height of a bloom, the Rhodobacter sp. strain PS9 population accounted for 10% of the total community and up to 27% of the eubacterial community based on 16S ribosomal DNA signals. Additional observations based on seasonal variations in meteorological, biological, and chemical parameters suggested that the photosynthetic blooms of Rhodobacter sp. strain PS9 were correlated with lagoon water temperature and with the concentrations of sulfate and phosphate. In addition, the photosynthetic blooms of Rhodobacter sp. strain PS9 were inversely correlated with the concentrations of protein and fluoride. PMID:12620863

  6. Photosynthetic inhibition and oxidative stress to the toxic Phaeocystis globosa caused by a diketopiperazine isolated from products of algicidal bacterium metabolism.

    PubMed

    Tan, Shuo; Hu, Xiaoli; Yin, Pinghe; Zhao, Ling

    2016-05-01

    Algicidal bacteria have been turned out to be available for inhibiting Phaeocystis globosa which frequently caused harmful algal blooms and threatened to economic development and ecological balance. A marine bacterium Bacillus sp. Ts-12 exhibited significant algicidal activity against P. globosa by indirect attack. In present study, an algicidal compound was isolated by silica gel column, Sephadex G-15 column and HPLC, further identified as hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, cyclo-(Pro-Gly), by GC-MS and (1)H-NMR. Cyclo-(Pro-Gly) significantly increased the level of reactive oxygen species (ROS) within P. globosa cells, further activating the enzymatic and non-enzymatic antioxidant systems, including superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and ascorbic acid (AsA). The increase in methane dicarboxylic aldehyde (MDA) content showed that the surplus ROS induced lipid peroxidation on membrane system. Transmission electron microscope (TEM) and flow cytometry (FCM) analysis revealed that cyclo-(Pro-Gly) caused reduction of Chl-a content, destruction of cell membrane integrity, chloroplasts and nuclear structure. Real-time PCR assay showed that the transcriptions of photosynthesis related genes (psbA, psbD, rbcL) were significantly inhibited. This study indicated that cyclo-(Pro-Gly) from marine Bacillus sp. Ts-12 exerted photosynthetic inhibition and oxidative stress to P. globosa and eventually led to the algal cells lysis. This algicidal compound might be potential bio-agent for controlling P. globosa red tide. PMID:27095455

  7. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    SciTech Connect

    Brown, A.E.; Gilbert, C.W.; Guy, R.; Arntzen, C.J.

    1984-10-01

    The photoaffinity herbicide azidoatrazine (2-azido-4-ethylamino-6-isopropylamino-s-triazine) selectively labels the L subunit of the reaction center of the photosynthetic bacterium Rhodopseudomonas sphaeroides. Herbicide-resistant mutants retain the L subunit and have altered binding properties for methylthio- and chloro-substituted triazines as well as altered equilibrium constants for electron transfer between primary and secondary electron acceptors. We suggest that a subtle alteration in the L subunit is responsible for herbicide resistance and that the L subunit is the functional analog of the 32-kDa Q/sub B/ protein of chloroplast membranes. 42 references, 6 figures, 1 table.

  8. Determination of the number of detergent molecules associated with the reaction center protein isolated from the photosynthetic bacterium Rhodopseudomonas viridis. Effects of the amphiphilic molecule 1,2,3-heptanetriol.

    PubMed

    Gast, P; Hemelrijk, P; Hoff, A J

    1994-01-01

    Detergent-free reaction center (RC) proteins from the photosynthetic bacterium Rhodopseudomonas viridis were obtained using Bio-Beads SM-2. With these RCs, the amount of detergent molecules associated with the protein was measured by determining the detergent concentration at which re-solubilization occurred as a function of the RC concentration. For N,N-dimethyl dodecylamine-N-oxide (LDAO), Triton X-100 and beta-octylglucoside 260 +/- 30,105 +/- 10 and 360 +/- 100 detergent molecules were necessary to dissolve the protein, respectively. With this technique we have studied the effect of the amphiphilic molecule 1,2,3-heptanetriol, which is essential in the crystallization process of these RCs. Addition of 5% 1,2,3-heptanetriol reduces the value for LDAO to 120 +/- 20 LDAO/RC, supporting the notion that crystallization of the RCs is promoted by increasing the number of protein-protein contacts. PMID:8276109

  9. Isolation of Rhp-PSP, a member of YER057c/YjgF/UK114 protein family with antiviral properties, from the photosynthetic bacterium Rhodopseudomonas palustris strain JSC-3b

    PubMed Central

    Su, Pin; Feng, Tuizi; Zhou, Xuguo; Zhang, Songbai; Zhang, Yu; Cheng, Ju’e; Luo, Yuanhua; Peng, Jing; Zhang, Zhuo; Lu, Xiangyang; Zhang, Deyong; Liu, Yong

    2015-01-01

    Rhodopseudomonas palustris strain JSC-3b isolated from a water canal adjacent to a vegetable field produces a protein that was purified by bioactivity-guided fractionation based on ammonium sulfate precipitation, ion-exchange absorption and size exclusion. The protein was further identified as an endoribonuclease L-PSP (Liver-Perchloric acid-soluble protein) by shotgun mass spectrometry analysis and gene identification, and it is member of YER057c/YjgF/UK114 protein family. Herein, this protein is designated Rhp-PSP. Rhp-PSP exhibited significant inhibitory activities against tobacco mosaic virus (TMV) in vivo and in vitro. To our knowledge, this represents the first report on the antiviral activity of a protein of the YER057c/YjgF/UK114 family and also the first antiviral protein isolated from R. palustris. Our research provides insight into the potential of photosynthetic bacterial resources in biological control of plant virus diseases and sustainable agriculture. PMID:26530252

  10. Characterisation of the LH2 spectral variants produced by the photosynthetic purple sulphur bacterium Allochromatium vinosum.

    PubMed

    Carey, Anne-Marie; Hacking, Kirsty; Picken, Nichola; Honkanen, Suvi; Kelly, Sharon; Niedzwiedzki, Dariusz M; Blankenship, Robert E; Shimizu, Yuuki; Wang-Otomo, Zheng-Yu; Cogdell, Richard J

    2014-11-01

    This study systematically investigated the different types of LH2 produced by Allochromatium (Alc.) vinosum, a photosynthetic purple sulphur bacterium, in response to variations in growth conditions. Three different spectral forms of LH2 were isolated and purified, the B800-820, B800-840 and B800-850 LH2 types, all of which exhibit an unusual split 800 peak in their low temperature absorption spectra. However, it is likely that more forms are also present. Relatively more B800-820 and B800-840 are produced under low light conditions, while relatively more B800-850 is produced under high light conditions. Polypeptide compositions of the three different LH2 types were determined by a combination of HPLC and TOF/MS. The B800-820, B800-840 and B800-850 LH2 types all have a heterogeneous polypeptide composition, containing multiple types of both α and β polypeptides, and differ in their precise polypeptide composition. They all have a mixed carotenoid composition, containing carotenoids of the spirilloxanthin series. In all cases the most abundant carotenoid is rhodopin; however, there is a shift towards carotenoids with a higher conjugation number in LH2 complexes produced under low light conditions. CD spectroscopy, together with the polypeptide analysis, demonstrates that these Alc. vinosum LH2 complexes are more closely related to the LH2 complex from Phs. molischianum than they are to the LH2 complexes from Rps. acidophila. PMID:25111749

  11. Development of a gene cloning system for the hydrogen-producing marine photosynthetic bacterium Rhodopseudomonas sp.

    PubMed Central

    Matsunaga, T; Matsunaga, N; Tsubaki, K; Tanaka, T

    1986-01-01

    Seventy-six strains of marine photosynthetic bacteria were analyzed by agarose gel electrophoresis for plasmid DNA content. Among these strains, 12 carried two to four different plasmids with sizes ranging from 3.1 to 11.0 megadaltons. The marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 had two plasmids, pRD06S and pRD06L. The smaller plasmid, pRD06S, had a molecular weight of 3.8 megadaltons and was cut at a single site by restriction endonucleases SalI, SmaI, PstI, XhoI, and BglII. Moreover, the marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 containing plasmid pRD06 had a satisfactory growth rate (doubling time, 7.5 h), a hydrogen-producing rate of 0.96 mumol/mg (dry weight) of cells per h, and nitrogen fixation capability. Plasmid pRD06S, however, had neither drug resistance nor heavy-metal resistance, and its copy number was less than 10. Therefore, a recombinant plasmid consisting of pRD06S and Escherichia coli cloning vector pUC13 was constructed and cloned in E. coli. The recombinant plasmid was transformed into Rhodopseudomonas sp. NKPB002106. As a result, Rhodopseudomonas sp. NKPB002106 developed ampicillin resistance. Thus, a shuttle vector for gene transfer was constructed for marine photosynthetic bacteria. PMID:3020006

  12. Ratoon stunting disease of sugarcane: isolation of the causal bacterium.

    PubMed

    Davis, M J; Gillaspie, A G; Harris, R W; Lawson, R H

    1980-12-19

    A small coryneform bacterium was consistently isolated from sugarcane with ratoon stunting disease and shown to be the causal agent. A similar bacterium was isolated from Bermuda grass. Both strains multiplied in sugarcane and Bermuda grass, but the Bermuda grass strain did not incite the symptoms of ratoon stunting disease in sugarcane. Shoot growth in Bermuda grass was retarded by both strains. PMID:17817853

  13. Carbon monoxide metabolism by the photosynthetic bacterium Rhodospirillum rubrum

    SciTech Connect

    Ludden, P.W.; Roberts, G.P.

    1991-01-01

    Research continued on carbon monoxide metabolism by Rhodospirillum rubrum. In the past year, progress was made in: (1) the identification and isolation of the physiological electron carrier from monoxide dehydrogenase (CODH) to hydrogenase in R. rubrum; (2) the isolation, sequencing and mutagenesis of the genes encoding the components of the CO oxidation system in R. rubrum, (3) the purification and characterization of the CO-induced hydrogenase activity of R. rubrum; (4) the spectroscopic investigation of the cobalt-substituted form of the enzyme.

  14. Nobel lecture. The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis.

    PubMed Central

    Deisenhofer, J; Michel, H

    1989-01-01

    In our lectures we first describe the history and methods of membrane protein crystallization, before we show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. Then the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure. Sections 1 (crystallization), 4 (conclusions on the structure of photosystem II reaction centre and evolutionary aspects) and 5 (aspects of membrane protein structure) were presented and written by H.M., Sections 2 (determination of the structure) and 3 (structure and function) by J.D. We have arranged the paper in this way in order to facilitate continuous reading. Images PMID:2676514

  15. Cytochromes c biogenesis in a photosynthetic bacterium requires a periplasmic thioredoxin-like protein.

    PubMed Central

    Beckman, D L; Kranz, R G

    1993-01-01

    Rhodobacter capsulatus is a Gram-negative photosynthetic bacterium that requires c-type cytochromes for photosynthetic electron transport. Our studies demonstrate that the gene helX is required for the biogenesis of c-type cytochromes in R. capsulatus. A helX chromosomal deletion mutant cannot grow photosynthetically, due to a deficiency of all c-type cytochromes. The predicted amino acid sequence of the helX gene product (176 residues) is related to that of thioredoxin and shares active-site homology with protein disulfide isomerase. Cytochrome c2-alkaline phosphatase gene fusions are used to show that HelX is not required for the transcription, translation, or secretion of apocytochrome c2. HelX-alkaline phosphatase and HelX-beta-galactosidase gene fusions are used to demonstrate that HelX is a periplasmic protein, which is consistent with the presence of a typical signal sequence in HelX. Based on these results, we propose HelX functions as a periplasmic disulfide oxidoreductase that is essential for cytochromes c biogenesis. This role is in accordance with the observation that both heme and the cysteines of apocytochromes c (Cys-Xaa-Yaa-Cys-His) must be in the reduced state for covalent linkage between the two moieties to occur. PMID:8384715

  16. Auracyanin A from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus represents an unusual class of small blue copper proteins.

    PubMed Central

    Van Driessche, G.; Hu, W.; Van de Werken, G.; Selvaraj, F.; McManus, J. D.; Blankenship, R. E.; Van Beeumen, J. J.

    1999-01-01

    The amino acid sequence of the small copper protein auracyanin A isolated from the thermophilic photosynthetic green bacterium Chloroflexus aurantiacus has been determined to be a polypeptide of 139 residues. His58, Cys123, His128, and Met132 are spaced in a way to be expected if they are the evolutionary conserved metal ligands as in the known small copper proteins plastocyanin and azurin. Secondary structure prediction also indicates that auracyanin has a general beta-barrel structure similar to that of azurin from Pseudomonas aeruginosa and plastocyanin from poplar leaves. However, auracyanin appears to have sequence characteristics of both small copper protein sequence classes. The overall similarity with a consensus sequence of azurin is roughly the same as that with a consensus sequence of plastocyanin, namely 30.5%. We suggest that auracyanin A, together with the B forms, is the first example of a new class of small copper proteins that may be descendants of an ancestral sequence to both the azurin proteins occurring in prokaryotic nonphotosynthetic bacteria and the plastocyanin proteins occurring in both prokaryotic cyanobacteria and eukaryotic algae and plants. The N-terminal sequence region 1-18 of auracyanin is remarkably rich in glycine and hydroxy amino acids, and required mass spectrometric analysis to be determined. The nature of the blocking group X is not yet known, although its mass has been determined to be 220 Da. The auracyanins are the first small blue copper proteins found and studied in anoxygenic photosynthetic bacteria and are likely to mediate electron transfer between the cytochrome bc1 complex and the photosynthetic reaction center. PMID:10338005

  17. Decoherence dynamics of coherent electronic excited states in the photosynthetic purple bacterium Rhodobacter sphaeroides

    NASA Astrophysics Data System (ADS)

    Liang, Xian-Ting; Zhang, Wei-Min; Zhuo, Yi-Zhong

    2010-01-01

    In this paper, we present a theoretical description to the quantum coherence and decoherence phenomena of energy transfer in photosynthesis observed in a recent experiment [Science 316, 1462 (2007)]. As a successive two-color laser pulses with selected frequencies cast on a sample of the photosynthetic purple bacterium Rb. sphaeroides two resonant excitations of electrons in chromophores can be generated. However, this effective two-level subsystem will interact with its protein environment and decoherence is inevitable. We describe this subsystem coupled with its environment as a dynamical spin-boson model. The non-Markovian decoherence dynamics is described using a quasiadiabatic propagator path integral (QUAPI) approach. With the photon-induced effective time-dependent level splitting energy and level flip coupling coefficient between the two excited states and the environment-induced non-Markovian decoherence dynamics, our theoretical result is in good agreement with the experimental data.

  18. Purification and characterization of the alternative nitrogenase from the photosynthetic bacterium Rhodospirillum rubrum.

    PubMed Central

    Davis, R; Lehman, L; Petrovich, R; Shah, V K; Roberts, G P; Ludden, P W

    1996-01-01

    The alternative nitrogenase from a nifH mutant of the photosynthetic bacterium Rhodospirillum rubrum has been purified and characterized. The dinitrogenase protein (ANF1) contains three subunits in an apparent alpha2beta2gamma2 structure and contains Fe but no Mo or V. A factor capable of activating apo-dinitrogenase (lacking the FeMo cofactor) from Azotobacter vinelandii was extracted from the alternative dinitrogenase protein with N-methylformamide. The electron paramagnetic resonance (EPR) signal of the dinitrogenase protein is not characteristic of the EPR signals of molybdenum- or vanadium-containing dinitrogenases. The alternative dinitrogenase reductase (ANF2) was purified as an alpha2 dimer containing an Fe4S4 cluster and exhibited an EPR spectrum characteristic of dinitrogenase reductases. The enzyme complex reduces protons to H2 very well but reduces N2 to ammonium poorly. Acetylene is reduced to a mixture of ethylene and ethane. PMID:8631723

  19. Native Mass Spectrometry Characterizes the Photosynthetic Reaction Center Complex from the Purple Bacterium Rhodobacter sphaeroides

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Harrington, Lucas B.; Lu, Yue; Prado, Mindy; Saer, Rafael; Rempel, Don; Blankenship, Robert E.; Gross, Michael L.

    2016-08-01

    Native mass spectrometry (MS) is an emerging approach to study protein complexes in their near-native states and to elucidate their stoichiometry and topology. Here, we report a native MS study of the membrane-embedded reaction center (RC) protein complex from the purple photosynthetic bacterium Rhodobacter sphaeroides. The membrane-embedded RC protein complex is stabilized by detergent micelles in aqueous solution, directly introduced into a mass spectrometer by nano-electrospray (nESI), and freed of detergents and dissociated in the gas phase by collisional activation. As the collision energy is increased, the chlorophyll pigments are gradually released from the RC complex, suggesting that native MS introduces a near-native structure that continues to bind pigments. Two bacteriochlorophyll a pigments remain tightly bound to the RC protein at the highest collision energy. The order of pigment release and their resistance to release by gas-phase activation indicates the strength of pigment interaction in the RC complex. This investigation sets the stage for future native MS studies of membrane-embedded photosynthetic pigment-protein and related complexes.

  20. A cambialistic superoxide dismutase in the thermophilic photosynthetic bacterium Chloroflexus aurantiacus.

    PubMed

    Lancaster, Vanessa L; LoBrutto, Russell; Selvaraj, Fabiyola M; Blankenship, Robert E

    2004-06-01

    Superoxide dismutase from the thermophilic anoxygenic photosynthetic bacterium Chloroflexus aurantiacus was cloned, purified, and characterized. This protein is in the manganese- and iron-containing family of superoxide dismutases and is able to use both manganese and iron catalytically. This appears to be the only soluble superoxide dismutase in C. aurantiacus. Iron and manganese cofactors were identified by using electron paramagnetic resonance spectroscopy and were quantified by atomic absorption spectroscopy. By metal enrichment of growth media and by performing metal fidelity studies, the enzyme was found to be most efficient with manganese incorporated, yet up to 30% of the activity was retained with iron. Assimilation of iron or manganese ions into superoxide dismutase was also found to be affected by the growth conditions. This enzyme was also found to be remarkably thermostable and was resistant to H2O2 at concentrations up to 80 mM. Reactive oxygen defense mechanisms have not been previously characterized in the organisms belonging to the phylum Chloroflexi. These systems are of interest in C. aurantiacus since this bacterium lives in a hyperoxic environment and is subject to high UV radiation fluxes. PMID:15150226

  1. CsmA Protein is Associated with BChl a in the Baseplate Subantenna of Chlorosomes of the Photosynthetic Green Filamentous Bacterium Oscillochloris trichoides belonging to the Family Oscillochloridaceae

    PubMed Central

    Zobova, Anastasiya; Taisova, Alexandra; Lukashev, Eugeny; Fedorova, Nataliya; Baratova, Ludmila; Fetisova, Zoya

    2011-01-01

    The baseplate subantenna in chlorosomes of green anoxygenic photosynthetic bacteria, belonging to the families Chloroflexaceae and Chlorobiaceae, is known to represent a complex of bacteriochlorophyll (BChl) a with the ~6 kDa CsmA proteins. Earlier, we showed the existence of a similar BChl a subantenna in chlorosomes of the photosynthetic green bacterium Oscillochloris trichoides, member of Oscillochloridaceae, the third family of green photosynthetic bacteria. However, this BChl a subantenna was not visually identified in absorption spectra of isolated Osc. trichoides chlorosomes in contrast to those of Chloroflexaceae and Chlorobiaceae. In this work, using room and low-temperature absorbance and fluorescence spectroscopy and sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis of alkaline-treated and untreated chlorosomes of Osc. trichoides, we showed that the baseplate BChl a subantenna does exist in Oscillochloridaceae chlorosomes as a complex of BChl a with the 5.7 kDa CsmA protein. The present results support the idea that the baseplate subantenna, representing a complex of BChl a with a ~6 kDa CsmA protein, is a universal interface between the BChl c subantenna of chlorosomes and the nearest light-harvesting BChl a subantenna in all three known families of green anoxygenic photosynthetic bacteria. PMID:21941538

  2. Production of polyhydroxybutyrate by the marine photosynthetic bacterium Rhodovulum sulfidophilum P5

    NASA Astrophysics Data System (ADS)

    Cai, Jinling; Wei, Ying; Zhao, Yupeng; Pan, Guanghua; Wang, Guangce

    2012-07-01

    The effects of different NaCl concentrations, nitrogen sources, carbon sources, and carbon to nitrogen molar ratios on biomass accumulation and polyhydroxybutyrate (PHB) production were studied in batch cultures of the marine photosynthetic bacterium Rhodovulum sulfidophilum P5 under aerobic-dark conditions. The results show that the accumulation of PHB in strain P5 is a growth-associated process. Strain P5 had maximum biomass and PHB accumulation at 2%-3% NaCl, suggesting that the bacterium can maintain growth and potentially produce PHB at natural seawater salinity. In the nitrogen source test, the maximum biomass accumulation (8.10±0.09 g/L) and PHB production (1.11±0.13 g/L and 14.62%±2.2 of the cell dry weight) were observed when peptone and ammonium chloride were used as the sole nitrogen source. NH{4/+}-N was better for PHB production than other nitrogen sources. In the carbon source test, the maximum biomass concentration (7.65±0.05 g/L) was obtained with malic acid as the sole carbon source, whereas the maximum yield of PHB (5.03±0.18 g/L and 66.93%±1.69% of the cell dry weight) was obtained with sodium pyruvate as the sole carbon source. In the carbon to nitrogen ratios test, sodium pyruvate and ammonium chloride were selected as the carbon and nitrogen sources, respectively. The best carbon to nitrogen molar ratio for biomass accumulation (8.77±0.58 g/L) and PHB production (6.07±0.25 g/L and 69.25%±2.05% of the cell dry weight) was 25. The results provide valuable data on the production of PHB by R. sulfidophilum P5 and further studies are on-going for best cell growth and PHB yield.

  3. The Protective Roles of the Antioxidant Enzymes Superoxide Dismutase and Catalase in the Green Photosynthetic Bacterium Chloroflexus Aurantiacus

    NASA Technical Reports Server (NTRS)

    Blankenship, Robert E.; Rothschild, Lynn (Technical Monitor)

    2004-01-01

    The purpose of this study was to examine the biochemical response of the green thermophilic photosynthetic bacterium Chloroflexus aurantiacus to oxidative stress. Lab experiments focused primarily on characterizing the antioxidant enzyme superoxide dismutase and the response of this organism to oxidative stress. Experiments in the field at the hotsprings in Yellowstone National Park focused on the changes in the level of these enzymes during the day in response to oxidants and to the different types of ultraviolet radiation.

  4. Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacterium.

    PubMed

    Moskvin, Oleg V; Bolotin, Dmitry; Wang, Andrew; Ivanov, Pavel S; Gomelsky, Mark

    2011-02-01

    We present Rhodobase, a web-based meta-analytical tool for analysis of transcriptional regulation in a model anoxygenic photosynthetic bacterium, Rhodobacter sphaeroides. The gene association meta-analysis is based on the pooled data from 100 of R. sphaeroides whole-genome DNA microarrays. Gene-centric regulatory networks were visualized using the StarNet approach (Jupiter, D.C., VanBuren, V., 2008. A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PLoS ONE 3, e1717) with several modifications. We developed a means to identify and visualize operons and superoperons. We designed a framework for the cross-genome search for transcription factor binding sites that takes into account high GC-content and oligonucleotide usage profile characteristic of the R. sphaeroides genome. To facilitate reconstruction of directional relationships between co-regulated genes, we screened upstream sequences (-400 to +20bp from start codons) of all genes for putative binding sites of bacterial transcription factors using a self-optimizing search method developed here. To test performance of the meta-analysis tools and transcription factor site predictions, we reconstructed selected nodes of the R. sphaeroides transcription factor-centric regulatory matrix. The test revealed regulatory relationships that correlate well with the experimentally derived data. The database of transcriptional profile correlations, the network visualization engine and the optimized search engine for transcription factor binding sites analysis are available at http://rhodobase.org. PMID:21070832

  5. Isolation of a bacterium capable of degrading peanut hull lignin

    SciTech Connect

    Kerr, T.A.; Kerr, R.D.; Benner, R.

    1983-11-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter species, was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled (/sup 14/C) lignin-labeled lignocellulose and (/sup 14/C)cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade (/sup 14/C) Kraft lignin from slash pine. After 10 days of incubation with (/sup 14/C) cellulose-labeled lignocellulose or (/sup 14/C) lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. (Refs. 24).

  6. Production and Consumption of Hydrogen in Hot Spring Microbial Mats Dominated by a Filamentous Anoxygenic Photosynthetic Bacterium

    PubMed Central

    Otaki, Hiroyo; Everroad, R. Craig; Matsuura, Katsumi; Haruta, Shin

    2012-01-01

    Microbial mats containing the filamentous anoxygenic photosynthetic bacterium Chloroflexus aggregans develop at Nakabusa hot spring in Japan. Under anaerobic conditions in these mats, interspecies interaction between sulfate-reducing bacteria as sulfide producers and C. aggregans as a sulfide consumer has been proposed to constitute a sulfur cycle; however, the electron donor utilized for microbial sulfide production at Nakabusa remains to be identified. In order to determine this electron donor and its source, ex situ experimental incubation of mats was explored. In the presence of molybdate, which inhibits biological sulfate reduction, hydrogen gas was released from mat samples, indicating that this hydrogen is normally consumed as an electron donor by sulfate-reducing bacteria. Hydrogen production decreased under illumination, indicating that C. aggregans also functions as a hydrogen consumer. Small amounts of hydrogen may have also been consumed for sulfur reduction. Clone library analysis of 16S rRNA genes amplified from the mats indicated the existence of several species of hydrogen-producing fermentative bacteria. Among them, the most dominant fermenter, Fervidobacterium sp., was successfully isolated. This isolate produced hydrogen through the fermentation of organic carbon. Dispersion of microbial cells in the mats resulted in hydrogen production without the addition of molybdate, suggesting that simultaneous production and consumption of hydrogen in the mats requires dense packing of cells. We propose a cyclic electron flow within the microbial mats, i.e., electron flow occurs through three elements: S (elemental sulfur, sulfide, sulfate), C (carbon dioxide, organic carbon) and H (di-hydrogen, protons). PMID:22446313

  7. Isolation and Characterization of a Chlorinated-Pyridinol-Degrading Bacterium

    PubMed Central

    Feng, Y.; Racke, K. D.; Bollag, J.

    1997-01-01

    The isolation of a pure culture of bacteria able to use 3,5,6-trichloro-2-pyridinol (TCP) as a sole source of carbon and energy under aerobic conditions was achieved for the first time. The bacterium was identified as a Pseudomonas sp. and designated ATCC 700113. [2,6-(sup14)C]TCP degradation yielded (sup14)CO(inf2), chloride, and unidentified polar metabolites. PMID:16535719

  8. Isolation and characterization of luminescent bacterium for sludge biodegradation.

    PubMed

    Zahaba, Maryam; Halmi, Mohd Izuan Effendi; Ahmad, Siti Aqlima; Shukor, Mohd Yunus; Syed, Mohd Arif

    2015-11-01

    Microtox is based on the inhibition of luminescence of the bacterium Vibrio fischeri by the toxicants. This technique has been accepted by the USEPA (United States Environmental Protection Agency) as a biomonitoring tool for remediation of toxicants such as hydrocarbon sludge. In the present study, a luminescent bacterium was isolated from yellow striped scad (Selaroides leptolepis) and was tentatively identified as Vibrio sp. isolate MZ. This aerobic isolate showed high luminescence activity in a broad range of temperature from 25 to 35 °C. In addition, optimal conditions for high bioluminescence activity in range of pH 7.5 to 8.5 and 10 gl(-1) of sodium chloride, 10 gl(-1) of peptone and 10 gl(-1) of sucrose as carbon source. Bench scale biodegradation 1% sludge (w/v) was set up and degradation was determined using gas chromatography with flame ionised detector (GC-FID). In this study, Rhodococcus sp. strain AQ5NOL2 was used to degrade the sludge. Based on the preliminary results obtained, Vibrio sp. isolate MZwas able to monitor the biodegradation of sludge. Therefore, Vibrio sp. isolate MZ has the potential to be used as a biomonitoring agent for biomonitoring of sludge biodegradation particularly in the tropical ranged environment. PMID:26688958

  9. Induction and anisotropy of fluorescence of reaction center from photosynthetic bacterium Rhodobacter sphaeroides.

    PubMed

    Sipka, Gábor; Maróti, Péter

    2016-01-01

    Submillisecond dark-light changes of the yield (induction) and anisotropy of fluorescence under laser diode excitation were measured in the photosynthetic reaction center of the purple bacterium Rhodobacter sphaeroides. Narrow band (1-2 nm) laser diodes emitting at 808 and 865 nm were used to selectively excite the accessory bacteriochlorophyll (B, 800 nm) or the upper excitonic state of the bacteriochlorophyll dimer (P-, 810 nm) and the lower excitonic state of the dimer (P+, 865 nm), respectively. The fluorescence spectrum of the wild type showed two bands centered at 850 nm (B) and 910 nm (P-). While the monotonous decay of the fluorescence yield at 910 nm tracked the light-induced oxidation of the dimer, the kinetics of the fluorescence yield at 850 nm showed an initial rise before a decrease. The anisotropy of the fluorescence excited at 865 nm (P-) was very close to the limiting value (0.4) across the whole spectral range. The excitation of both B and P- at 808 nm resulted in wavelength-dependent depolarization of the fluorescence from 0.35 to 0.24 in the wild type and from 0.30 to 0.24 in the reaction center of triple mutant (L131LH-M160LH-M197FH). The additivity law of the anisotropies of the fluorescence species accounts for the wavelength dependence of the anisotropy. The measured fluorescence yields and anisotropies are interpreted in terms of very fast energy transfer from (1)B* to (1)P- (either directly or indirectly by internal conversion from (1)P+) and to the oxidized dimer. PMID:25698106

  10. High-level production of the industrial product lycopene by the photosynthetic bacterium Rhodospirillum rubrum.

    PubMed

    Wang, Guo-Shu; Grammel, Hartmut; Abou-Aisha, Khaled; Sägesser, Rudolf; Ghosh, Robin

    2012-10-01

    The biosynthesis of the major carotenoid spirilloxanthin by the purple nonsulfur bacterium Rhodospirillum rubrum is thought to occur via a linear pathway proceeding through phytoene and, later, lycopene as intermediates. This assumption is based solely on early chemical evidence (B. H. Davies, Biochem. J. 116:93-99, 1970). In most purple bacteria, the desaturation of phytoene, catalyzed by the enzyme phytoene desaturase (CrtI), leads to neurosporene, involving only three dehydrogenation steps and not four as in the case of lycopene. We show here that the chromosomal insertion of a kanamycin resistance cassette into the crtC-crtD region of the partial carotenoid gene cluster, whose gene products are responsible for the downstream processing of lycopene, leads to the accumulation of the latter as the major carotenoid. We provide spectroscopic and biochemical evidence that in vivo, lycopene is incorporated into the light-harvesting complex 1 as efficiently as the methoxylated carotenoids spirilloxanthin (in the wild type) and 3,4,3',4'-tetrahydrospirilloxanthin (in a crtD mutant), both under semiaerobic, chemoheterotrophic, and photosynthetic, anaerobic conditions. Quantitative growth experiments conducted in dark, semiaerobic conditions, using a growth medium for high cell density and high intracellular membrane levels, which are suitable for the conventional industrial production in the absence of light, yielded lycopene at up to 2 mg/g (dry weight) of cells or up to 15 mg/liter of culture. These values are comparable to those of many previously described Escherichia coli strains engineered for lycopene production. This study provides the first genetic proof that the R. rubrum CrtI produces lycopene exclusively as an end product. PMID:22865070

  11. High-Level Production of the Industrial Product Lycopene by the Photosynthetic Bacterium Rhodospirillum rubrum

    PubMed Central

    Wang, Guo-Shu; Grammel, Hartmut; Abou-Aisha, Khaled; Sägesser, Rudolf

    2012-01-01

    The biosynthesis of the major carotenoid spirilloxanthin by the purple nonsulfur bacterium Rhodospirillum rubrum is thought to occur via a linear pathway proceeding through phytoene and, later, lycopene as intermediates. This assumption is based solely on early chemical evidence (B. H. Davies, Biochem. J. 116:93–99, 1970). In most purple bacteria, the desaturation of phytoene, catalyzed by the enzyme phytoene desaturase (CrtI), leads to neurosporene, involving only three dehydrogenation steps and not four as in the case of lycopene. We show here that the chromosomal insertion of a kanamycin resistance cassette into the crtC-crtD region of the partial carotenoid gene cluster, whose gene products are responsible for the downstream processing of lycopene, leads to the accumulation of the latter as the major carotenoid. We provide spectroscopic and biochemical evidence that in vivo, lycopene is incorporated into the light-harvesting complex 1 as efficiently as the methoxylated carotenoids spirilloxanthin (in the wild type) and 3,4,3′,4′-tetrahydrospirilloxanthin (in a crtD mutant), both under semiaerobic, chemoheterotrophic, and photosynthetic, anaerobic conditions. Quantitative growth experiments conducted in dark, semiaerobic conditions, using a growth medium for high cell density and high intracellular membrane levels, which are suitable for the conventional industrial production in the absence of light, yielded lycopene at up to 2 mg/g (dry weight) of cells or up to 15 mg/liter of culture. These values are comparable to those of many previously described Escherichia coli strains engineered for lycopene production. This study provides the first genetic proof that the R. rubrum CrtI produces lycopene exclusively as an end product. PMID:22865070

  12. Structural and conformational study of the O-polysaccharide produced by the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris strain BisA53.

    PubMed

    Silipo, Alba; Di Lorenzo, Flaviana; De Felice, Antonia; Vanacore, Adele; De Castro, Cristina; Gully, Djamel; Lanzetta, Rosa; Parrilli, Michelangelo; Giraud, Eric; Molinaro, Antonio

    2014-12-19

    Rhodopseudomonas palustris is a purple photosynthetic bacterium characterized by a versatile nature and a remarkable ability to adapt to various environments. In this work, we focused our attention to its membrane characteristics and defined the structural and conformational features of the O-chain polysaccharide of LPS isolated from R. palustris strain BisA53. This strain produces a polymer with a trisaccharide repeating unit characterized by d-rhamnose, 3-deoxy-d-lyxo-2-heptulosaric acid (Dha), and a novel C-branched monosaccharide, a 4-amino-4,6-dideoxy-3-C-methyl-2-O-methyl-α-l-glucopyranose whose absolute configuration has been determined by a combination of 2D NMR spectroscopy and molecular mechanic and dynamic simulation. PMID:25263905

  13. Isotope effects associated with the anaerobic oxidation of sulfite and thiosulfate by the photosynthetic bacterium, Chromatium vinosum

    NASA Technical Reports Server (NTRS)

    Fry, B.; Gest, H.; Hayes, J. M.

    1985-01-01

    The purple photosynthetic bacterium Chromatium vinosum, strain D, catalyzes several oxidations of reduced sulfur compounds under anaerobic conditions in the light: e.g., sulfide --> sulfur --> sulfate, sulfite --> sulfate, and thiosulfate --> sulfur + sulfate. Here it is shown that no sulfur isotope effect is associated with the last of these processes; isotopic compositions of the sulfur and sulfate produced can differ, however, if the sulfane and sulfonate positions within the thiosulfate have different isotopic compositions. In the second process, an observed change from an inverse to a normal isotope effect during oxidation of sulfite may indicate the operation of 2 enzymatic pathways. In contrast to heterotrophic anaerobic reduction of oxidized sulfur compounds, anaerobic oxidations of inorganic sulfur compounds by photosynthetic bacteria are characterized by relatively small isotope effects.

  14. Biosynthesis of unnatural bacteriochlorophyll c derivatives esterified with α,ω-diols in the green sulfur photosynthetic bacterium Chlorobaculum tepidum.

    PubMed

    Nishimori, Risato; Mizoguchi, Tadashi; Tamiaki, Hitoshi; Kashimura, Shigenori; Saga, Yoshitaka

    2011-09-13

    Unnatural bacteriochlorophyll (BChl) c derivatives possessing a hydroxy group at the terminus of a hydrocarbon chain at the 17-propionate were biosynthesized in the green sulfur photosynthetic bacterium Chlorobaculum tepidum. Addition of exogenous 1,8-octanediol, 1,12-dodecanediol, and 1,16-hexadecanediol in acetone to liquid cultures resulted in accumulation of BChl c monoesterified with the corresponding diols. The relative ratios of the novel BChl c derivatives esterified with 1,8-, 1,12-, and 1,16-diols to totally producing BChl c were 8.2, 50.2, and 57.6% in the cells grown with additive α,ω-diols at concentrations of 1.5, 0.06, and 0.06 mM, respectively, at the final concentration. The homologue composition of BChl c derivatives esterified with these α,ω-diols was similar to that of original, coexisting BChl c esterified with farnesol (BChl c(F)), suggesting that esterification of α,ω-diols occurred at the last step of the BChl c biosynthetic pathway by BChl c synthase, BchK, in the same manner as in BChl c(F). Chlorosomes, which were isolated from cells grown in the presence of exogenous α,ω-diols, contained a ratio and a composition of BChl c derivatives esterified with the diols similar to those in the whole cells, indicating that these BChl c derivatives were actually present in chlorosomes. Q(y) absorption bands of C. tepidum cells containing the novel BChl c derivatives were shifted to a shorter wavelength, although their bandwidths were analogous to those of cells obtained by normal cultivation. Circular dichroism spectra of cells that had BChl c derivatives esterified with α,ω-diols exhibited S-shaped signals in the Q(y) region, whose polarities were the reverse of those of cells grown in the normal medium and by supplementation with neat acetone as a control experiment. These spectral features of C. tepidum possessing BChl c derivatives esterified with α,ω-diols imply that the novel BChl c derivatives possessing a hydroxy group at the

  15. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene

    SciTech Connect

    Maymo-Gatell, X.; Chien, Yueh-tyng; Zinder, S.H.

    1997-06-06

    Tetrachloroethene is a prominent groundwater pollutant that can be reductively dechlorinated by mixed anaerobic microbial populations to the nontoxic product ethene. Strain 195, a coccoid bacterium that dechlorinates tetrachlorethene to ethene, was isolated and characterized. Growth of strain 195 with H{sub 2} and tetrachloroethene as the electron donor and acceptor pair required extracts from mixed microbial cultures. Growth of strain 195 was resistant to ampicillin and vancomycin; its cell wall did not react with a peptidoglycan-specific lectin and its ultrastructure resembled S-layers of Archaea. Analysis of the 16S ribosomal DNA sequence of strain 195 indicated that it is a eubacterium without close affiliation to any known groups. 24 refs., 4 figs., 1 tab.

  16. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    PubMed

    Oh, Young Joon; Lee, Hae-Won; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Jang, Ja-Young; Park, Hae Woong; Nam, Young-Do; Seo, Myung-Ji; Choi, Hak-Jong

    2016-09-01

    A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)). PMID:27572507

  17. IN SITU RT-PCR WITH A SULFATE-REDUCING BACTERIUM ISOLATED FROM SEAGRASS ROOTS

    EPA Science Inventory

    Bacteria considered to be obligate anaerobes internally colonize roots of the submerged macrophyte Halodule wrightii. A sulfate reducing bacterium, Summer lac 1, was isolated on lactate from H. wrightii roots. The isolate has physiological characteristics typical of Desulfovibri...

  18. Breakdown of food waste by anaerobic fermentation and non-oxygen producing photosynthesis using a photosynthetic bacterium.

    PubMed

    Mekjinda, N; Ritchie, R J

    2015-01-01

    Large volumes of food waste are produced by restaurants, hotels, etc generating problems in its collection, processing and disposal. Disposal as garbage increases the organic matter in landfills and leachates. The photosynthetic bacterium Rhodopseudomonas palustris (CGA 009) easily broke down food waste. R. palustris produces H2 under anaerobic conditions and digests a very wide range of organic compounds. R. palustris reduced BOD by ≈70% and COD by ≈33%, starch, ammonia, nitrate, was removed but had little effect on reducing sugar or the total phosphorus, lipid, protein, total solid in a 7-day incubation. R. palustris produced a maximum of 80ml H2/g COD/day. A two-stage anaerobic digestion using yeast as the first stage, followed by a R. palustris digestion was tested but production of H2 was low. PMID:25465509

  19. A new isolation method for labyrinthulids using a bacterium, Psychrobacter phenylpyruvicus.

    PubMed

    Yokochi, T; Nakahara, T; Higashihara, T; Yamaoka, M; Kurane, R

    2001-01-01

    A new isolation method for labyrinthulids, marine microbes with spindle-shaped vegetative cells and gliding movement, is presented. The method for isolating labyrinthulids has been found to be more difficult and less reproducible than that for thraustochytrids, classified in the same order. So far serum seawater agar fortified with antibiotics has been proposed to be the best for isolation of labyrinthulids. The method presented here involves placing plant samples on an agar medium on which a marine bacterium, Psychrobacter phenylpyruvicus, has been grown. The new method, which utilizes fallen mangrove leaves as source material, was more than twice as effective as isolation agar medium without the bacterium. The increased effectiveness appears to derive partly from the bacterial colonies' delaying extension of fungal mycelium. The bacterium was more effective for the isolation of labyrinthulids than either the bacterium Shewanella sp. or the yeast Rhodotorula rubra. PMID:14961392

  20. Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil.

    PubMed

    Wang, Yuanli; Chen, Wei; He, Linyan; Wang, Qi; Sheng, Xia-Fang

    2016-01-01

    Ensifer adhaerens M78, a bacterium isolated from soil, can weather potash feldspar and release Fe, Si, and Al from rock under nutrient-poor conditions. Here, we report the draft genome sequence of strain M78, which may facilitate a better understanding of the molecular mechanism involved in mineral weathering by the bacterium. PMID:27609930

  1. Jeongeupia chitinilytica sp. nov., a chitinolytic bacterium isolated from soil.

    PubMed

    Chen, Wen-Ming; Chang, Rey-Chang; Cheng, Chih-Yu; Shiau, Yu-Wen; Sheu, Shih-Yi

    2013-03-01

    A novel bacterium, designated strain Jchi(T), was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain Jchi(T) were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20-37 °C (optimum between 25 and 30 °C), at pH 6.0-8.0 (optimum between pH 7.0 and pH 8.0) and with 0-2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Jchi(T) belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2(T) (98.0 % sequence similarity). The major fatty acids (>10 %) of strain Jchi(T) were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA-DNA relatedness value between strain Jchi(T) and J. naejangsanensis BIO-TAS4-2(T) was about 41.0 %. On the basis of the genotypic and phenotypic data, strain Jchi(T) represents a novel species in the genus Jeongeupia, for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is Jchi(T) ( = BCRC 80367(T)  = KCTC 23701(T)). PMID:22659500

  2. Excitation energy transfer in the green photosynthetic bacterium Chloroflexus aurantiacus: A specific effect of 1-hexanol on the optical properties of baseplate and energy transfer processes.

    PubMed

    Mimuro, M; Nishimura, Y; Yamazaki, I; Kobayashi, M; Wang, Z Y; Nozawa, T; Shimada, K; Matsuura, K

    1996-05-01

    The effect of 1-hexanol on spectral properties and the processes of energy transfer of the green gliding photosynthetic bacterium Chloroflexus aurantiacus was investigated with reference to the baseplate region. On addition of 1-hexanol to a cell suspension in a concentration of one-fourth saturation, a specific change in the baseplate region was induced: that is, a bleach of the 793-nm component, and an increase in absorption of the 813-nm component. This result was also confirmed by fluorescence spectra of whole cells and isolated chlorosomes. The processes of energy transfer were affected in the overall transfer efficiency but not kinetically, indicating that 1-hexanol suppressed the flux of energy flow from the baseplate to the B806-866 complexes in the cytoplasmic membranes. The fluorescence excitation spectrum suggests a specific site of interaction between bacteriochlorophyll (BChl) c with a maximum at 771 nm in the rod elements and BChl a with a maximum at 793 nm in the baseplate, which is a funnel for a fast transfer of energy to the B806-866 complexes in the membranes. The absorption spectrum of chlorosomes was resolved to components consistently on the basis, including circular dichroism and magnetic circular dichroism spectra; besides two major BChl c forms, bands corresponding to tetramer, dimer, and monomer were also discernible, which are supposed to be intermediary components for a higher order structure. A tentative model for the antenna system of C. aurantiacus is proposed. PMID:24271307

  3. Light-enhanced bioaccumulation of molybdenum by nitrogen-deprived recombinant anoxygenic photosynthetic bacterium Rhodopseudomonas palustris.

    PubMed

    Naito, Taki; Sachuronggui; Ueki, Masayoshi; Maeda, Isamu

    2016-01-01

    As molybdenum (Mo) is an indispensable metal for plant nitrogen metabolisms, accumulation of dissolved Mo into bacterial cells may connect to the development of bacterial fertilizers that promote plant growth. In order to enhance Mo bioaccumulation, nitrogen removal and light illumination were examined in anoxygenic photosynthetic bacteria (APB) because APB possess Mo nitrogenase whose synthesis is strictly regulated by ammonium ion concentration. In addition, an APB, Rhodopseudomonas palustris, transformed with a gene encoding Mo-responsive transcriptional regulator ModE was constructed. Mo content was most markedly enhanced by the removal of ammonium ion from medium and light illumination while their effects on other metal contents were limited. Increases in contents of trace metals including Mo by the genetic modification were observed. Thus, these results demonstrated an effective way to enrich Mo in the bacterial cells by the culture conditions and genetic modification. PMID:26376718

  4. Triplet excited state spectra and dynamics of carotenoids from the thermophilic purple photosynthetic bacterium Thermochromatium tepidum

    SciTech Connect

    Niedzwiedzki, Dariusz; Kobayashi, Masayuki; Blankenship, R. E.

    2011-01-13

    Light-harvesting complex 2 from the anoxygenic phototrophic purple bacterium Thermochromatium tepidum was purified and studied by steady-state absorption, fluorescence and flash photolysis spectroscopy. Steady-state absorption and fluorescence measurements show that carotenoids play a negligible role as supportive energy donors and transfer excitation to bacteriochlorophyll-a with low energy transfer efficiency of ~30%. HPLC analysis determined that the dominant carotenoids in the complex are rhodopin and spirilloxanthin. Carotenoid excited triplet state formation upon direct (carotenoid) or indirect (bacteriochlorophyll-a Q{sub x} band) excitation shows that carotenoid triplets are mostly localized on spirilloxanthin. In addition, no triplet excitation transfer between carotenoids was observed. Such specific carotenoid composition and spectroscopic results strongly suggest that this organism optimized carotenoid composition in the light-harvesting complex 2 in order to maximize photoprotective capabilities of carotenoids but subsequently drastically suppressed their supporting role in light-harvesting process.

  5. Pathways of energy flow through the light-harvesting antenna of the photosynthetic purple bacterium rhodobacter sphaeroides

    PubMed Central

    Zhang, Fu Geng; van Grondelle, Rienk; Sundström, Villy

    1992-01-01

    Using low intensity picosecond absorption spectroscopy with independently tunable excitation and probing infrared pulses, we have studied the pathways of energy transport through the light-harvesting antenna pigments of the photosynthetic purple bacterium Rhodobacter sphaeroides. From the observed excited-state rise time of the red-most pigment B896 as a function of excitation wavelength it is concluded that the B850 pigment of LH2 is spectrally heterogeneous. For excitations originating in the B850 pigment this results in a fast channel (9 ps) that is mainly excited in the peak of the B850 absorption band, and a slow channel (35 ps) that is predominantly excited at ∼840 nm. Upon excitation of B800, more than 90% of the excitations follow the fast path. From the observed kinetics it is concluded that the majority of the LH2 → LH1 energy transfer takes place within at most a few picoseconds. The rate-limiting step in the whole energy transfer sequence appears to be the B896 → reaction center transfer. The origin of the B850 heterogeneity and the slow 35-ps component is at the moment unclear. Possibly it represents a highly extended form of LH2 in which transfer to LH1 takes a relatively long time, due to a large number of transfer steps. PMID:19431825

  6. Inhibitor-complexed Structures of the Cytochrome bc[subscript 1] from the Photosynthetic Bacterium Rhodobacter sphaeroides

    SciTech Connect

    Esser, Lothar; Elberry, Maria; Zhou, Fei; Yu, Chang-An; Yu, Linda; Xia, Di

    2008-06-30

    The cytochrome bc{sub 1} complex (bc{sub 1}) is a major contributor to the proton motive force across the membrane by coupling electron transfer to proton translocation. The crystal structures of wild type and mutant bc{sub 1} complexes from the photosynthetic purple bacterium Rhodobacter sphaeroides (Rsbc{sub 1}), stabilized with the quinol oxidation (Q{sub P}) site inhibitor stigmatellin alone or in combination with the quinone reduction (Q{sub N}) site inhibitor antimycin, were determined. The high quality electron density permitted assignments of a new metal-binding site to the cytochrome c1 subunit and a number of lipid and detergent molecules. Structural differences between Rsbc{sub 1} and its mitochondrial counterparts are mostly extra membranous and provide a basis for understanding the function of the predominantly longer sequences in the bacterial subunits. Functional implications for the bc{sub 1} complex are derived from analyses of 10 independent molecules in various crystal forms and from comparisons with mitochondrial complexes.

  7. Femtosecond spectroscopy of excitation energy transfer and initial charge separation in the reaction center of the photosynthetic bacterium Rhodopseudomonas viridis

    PubMed Central

    Breton, J.; Martin, J.-L.; Migus, A.; Antonetti, A.; Orszag, A.

    1986-01-01

    Reaction centers from the photosynthetic bacterium Rhodopseudomonas viridis have been excited within the near-infrared absorption bands of the dimeric primary donor (P), of the “accessory” bacteriochlorophylls (B), and of the bacteriopheophytins (H) by using laser pulses of 150-fsec duration. The transfer of excitation energy between H, B, and P occurs in slightly less than 100 fsec and leads to the ultrafast formation of an excited state of P. This state is characterized by a broad absorption spectrum and exhibits stimulated emission. It decays in 2.8 ± 0.2 psec with the simultaneous oxidation of the primary donor and reduction of the bacteriopheophytin acceptor, which have been monitored at 545, 675, 815, 830, and 1310 nm. Although a transient bleaching relaxing in 400 ± 100 fsec is specifically observed upon excitation and observation in the 830-nm absorption band, we have found no indication that an accessory bacteriochlorophyll is involved as a resolvable intermediary acceptor in the primary electron transfer process. PMID:16593728

  8. Extracellular production of tellurium nanoparticles by the photosynthetic bacterium Rhodobacter capsulatus.

    PubMed

    Borghese, Roberto; Brucale, Marco; Fortunato, Gianuario; Lanzi, Massimiliano; Mezzi, Alessio; Valle, Francesco; Cavallini, Massimiliano; Zannoni, Davide

    2016-05-15

    The toxic oxyanion tellurite (TeO3(2-)) is acquired by cells of Rhodobacter capsulatus grown anaerobically in the light, via acetate permease ActP2 and then reduced to Te(0) in the cytoplasm as needle-like black precipitates. Interestingly, photosynthetic cultures of R. capsulatus can also generate Te(0) nanoprecipitates (TeNPs) outside the cells upon addition of the redox mediator lawsone (2-hydroxy-1,4-naphtoquinone). TeNPs generation kinetics were monitored to define the optimal conditions to produce TeNPs as a function of various carbon sources and lawsone concentration. We report that growing cultures over a 10 days period with daily additions of 1mM tellurite led to the accumulation in the growth medium of TeNPs with dimensions from 200 up to 600-700 nm in length as determined by atomic force microscopy (AFM). This result suggests that nucleation of TeNPs takes place over the entire cell growth period although the addition of new tellurium Te(0) to pre-formed TeNPs is the main strategy used by R. capsulatus to generate TeNPs outside the cells. Finally, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FT-IR) analysis of TeNPs indicate they are coated with an organic material which keeps the particles in solution in aqueous solvents. PMID:26894294

  9. Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil

    PubMed Central

    Chan, Kok-Gan; Yaakop, Amira Suriaty; Chan, Chia Sing; Ee, Robson; Tan, Wen-Si; Gan, Han Ming

    2015-01-01

    Jeotgalibacillus soli, a bacterium capable of degrading N-acyl homoserine lactone, was isolated from a soil sample in Portugal. J. soli constitutes the only Jeotgalibacillus species isolated from a non-marine source. Here, the draft genome, several interesting glycosyl hydrolases, and its putative N-acyl homoserine lactonases are presented. PMID:25999554

  10. Transcriptional Control of Expression of Genes for Photosynthetic Reaction Center and Light-Harvesting Proteins in the Purple Bacterium Rhodovulum sulfidophilum

    PubMed Central

    Masuda, Shinji; Nagashima, Kenji V. P.; Shimada, Keizo; Matsuura, Katsumi

    2000-01-01

    The purple photosynthetic bacterium Rhodovulum sulfidophilum synthesizes photosynthetic apparatus even under highly aerated conditions in the dark. To understand the oxygen-independent expression of photosynthetic genes, the expression of the puf operon coding for the light-harvesting 1 and reaction center proteins was analyzed. Northern blot hybridization analysis showed that puf mRNA synthesis was not significantly repressed by oxygen in this bacterium. High-resolution 5′ mapping of the puf mRNA transcriptional initiation sites and DNA sequence analysis of the puf upstream regulatory region indicated that there are three possible promoters for the puf operon expression, two of which have a high degree of sequence similarity with those of Rhodobacter capsulatus, which shows a high level of oxygen repression of photosystem synthesis. Deletion analysis showed that the third promoter is oxygen independent, but the activity of this promoter was not enough to explain the aerobic level of mRNA. The posttranscriptional puf mRNA degradation is not significantly influenced by oxygen in R. sulfidophilum. From these results, we conclude that puf operon expression in R. sulfidophilum is weakly repressed by oxygen, perhaps as a result of the following: (i) there are three promoters for puf operon transcription, at least one of which is oxygen independent; (ii) readthrough transcripts which may not be affected by oxygen may be significant in maintaining the puf mRNA levels; and (iii) the puf mRNA is fairly stable even under aerobic conditions. PMID:10781546

  11. Isolation and identification of antifungal peptides from Bacillus BH072, a novel bacterium isolated from honey.

    PubMed

    Zhao, Xin; Zhou, Zhi-jiang; Han, Ye; Wang, Zhan-zhong; Fan, Jie; Xiao, Hua-zhi

    2013-11-01

    A bacterial strain BH072 isolated from a honey sample showed antifungal activity against mold. Based on morphological, biochemical, physiological tests, and analysis of 16S rDNA sequence, the strain was identified to be a new subspecies of Bacillus sp. It had a broad spectrum of antifungal activity against various mold, such as Aspergillus niger, Pythium, and Botrytis cinerea. Six pairs of antifungal genes primers were designed and synthesized, and ituA, hag, tasA genes were detected by PCR analysis. The remarkable antifungal activity could be associated with the co-production of these three peptides. One of them was purified by 30-40% ammonium sulfate precipitation, Sephadex G-75 gel filtration and anion exchange chromatography on D201 resin. The purified peptide was estimated to be 35.615 kDa and identified to be flagellin by micrOTOF-Q II. By using methanol extraction, another substance was isolated from fermentation liquor, and determined to be iturin with liquid chromatography-mass spectrometry (LC-MS) method. The third possible peptide encoded by tasA was not isolated in this study. The culture liquor displayed antifungal activity in a wide pH range (5.0-9.0) and at 40-100°C. The result of the present work suggested that Bacillus BH072 might be a bio-control bacterium of research value. PMID:23545354

  12. Oceanobacillus-like bacterium isolated from Vyhna travertine spring.

    PubMed

    Pristas, P; Cunderlikova, M; Judova, J

    2014-03-01

    During characterization of autochthonic Vyhna travertine source microflora, several bacterial strains were isolated and characterised. Isolate T6, a halotolerant, moderately alkaliphilic and thermophilic bacterial isolate, was further characterised based on physiological, microbiological and biochemical tests and phylogenetic 16S rRNA analysis. On the basis of the results obtained, the T6 isolate should be placed in the genus Oceanobacillus, and it is probably a prototype of a novel bacterial species. Characterization of the T6 isolate broadens our knowledge on variability of halophilic bacteria of Oceanobacillus genus and expands data on travertine-associated bacterial communities. PMID:24022266

  13. Five New Amicoumacins Isolated from a Marine-Derived Bacterium Bacillus subtilis

    PubMed Central

    Li, Yongxin; Xu, Ying; Liu, Lingli; Han, Zhuang; Lai, Pok Yui; Guo, Xiangrong; Zhang, Xixiang; Lin, Wenhan; Qian, Pei-Yuan

    2012-01-01

    Four novel amicoumacins, namely lipoamicoumacins A–D (1–4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. PMID:22412803

  14. Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan

    PubMed Central

    Onodera, Takefumi; Omoso, Kota; Takeda-Yano, Kiyoko; Katayama, Takeshi; Oono, Yutaka; Narumi, Issay

    2016-01-01

    Deinococcus grandis is a radioresistant bacterium isolated from freshwater fish in Japan. Here we reported the draft genome sequence of D. grandis (4.1 Mb), which will be useful for elucidating the common principles of radioresistance in Deinococcus species through the comparative analysis of genomic sequences. PMID:26868384

  15. "Ihubacter massiliensis": a new bacterium isolated from the human gut.

    PubMed

    Ndongo, S; Lagier, J-C; Fournier, P-E; Raoult, D; Khelaifia, S

    2016-09-01

    We report here the main characteristics of "Ihubacter massiliensis," strain Marseille-P2843(T) (CSUR P2843), a new genus of the Clostridiales family isolated from a stool sample from a healthy 29-year-old woman. PMID:27579171

  16. Structure analysis and comparative characterization of the cytochrome c' and flavocytochrome c from thermophilic purple photosynthetic bacterium Thermochromatium tepidum.

    PubMed

    Hirano, Yu; Kimura, Yukihiro; Suzuki, Hideaki; Miki, Kunio; Wang, Zheng-Yu

    2012-08-21

    The thermodynamic and spectroscopic properties of two soluble electron transport proteins, cytochrome (Cyt) c' and flavocytochrome c, isolated from thermophilic purple sulfur bacterium Thermochromatium (Tch.) tepidum were examined and compared with those of the corresponding proteins from a closely related mesophilic bacterium Allochromatium (Alc.) vinosum. These proteins share sequence identities of 82% for the cytochromes c' and 86% for the flavocytochromes c. Crystal structures of the two proteins have been determined at high resolutions. Differential scanning calorimetry and denaturing experiments show that both proteins from Tch. tepidum are thermally and structurally much more stable than their mesophilic counterparts. The denaturation temperature of Tch. tepidum Cyt c' was 22 °C higher than that of Alc. vinosum Cyt c', and the midpoints of denaturation using guanidine hydrochloride were 2.0 and 1.2 M for the Tch. tepidum and Alc. vinosum flavocytochromes c, respectively. The enhanced stabilities can be interpreted on the basis of the structural and sequence information obtained in this study: increased number of hydrogen bonds formed between main chain nitrogen and oxygen atoms, more compact structures and reduced number of glycine residues. Many residues with large side chains in Alc. vinosum Cyt c' are substituted by alanines in Tch. tepidum Cyt c'. Both proteins from Tch. tepidum exhibit high structural similarities to their counterparts from Alc. vinosum, and the different residues between the corresponding proteins are mainly located on the surface and exposed to the solvent. Water molecules are found in the heme vicinity of Tch. tepidum Cyt c' and form hydrogen bonds with the heme ligand and C-terminal charged residues. Similar bound waters are also found in the vicinity of one heme group in the diheme subunit of Tch. tepidum flavocytochrome c. Electron density map of the Tch. tepidum flavocytochrome c clearly revealed the presence of disulfur atoms

  17. Isolation of the Paenibacillus phoenicis, a Spore-Forming Bacterium

    NASA Technical Reports Server (NTRS)

    Benardini, James N.; Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Osman, Shariff; Satomi, Masataka

    2010-01-01

    A microorganism was isolated from the surfaces of the cleanroom facility in which the Phoenix lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Paenibacillus and represents a novel species. Bacillus spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Spores of Bacillus species are of particular concern to planetary protection due to the extreme resistance of some members of the genus to space environmental conditions such as UV and gamma radiation, vacuum, oxidation, and temperature fluctuation. These resistive spore phenotypes have enhanced potential for transfer, and subsequent proliferation, of terrestrial microbes on another solar body. Due to decreased nutrient conditions within spacecraft assembly facility clean rooms, the vegetative cells of Bacillus species and other spore-forming Paenibacillus species are induced to sporulate, thereby enhancing their survivability of bioreduction

  18. Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream

    PubMed Central

    Lee, Sang-Jae; Lee, Yong-Jik; Park, Gun-Seok; Kim, Byoung-Chan; Lee, Sang Jun; Shin, Jae-Ho

    2013-01-01

    Caldanaerobacter yonseiensis is a strictly anaerobic, thermophilic, spore-forming bacterium, which was isolated from a geothermal hot stream in Indonesia. This bacterium utilizes xylose and produces a variety of proteases. Here, we report the draft genome sequence of C. yonseiensis, which reveals insights into the pentose phosphate pathway and protein degradation metabolism in thermophilic microorganisms. PMID:24201201

  19. Isolation and biological characteristics of aerobic marine magnetotactic bacterium YSC-1

    NASA Astrophysics Data System (ADS)

    Gao, Jun; Pan, Hongmiao; Yue, Haidong; Song, Tao; Zhao, Yong; Chen, Guanjun; Wu, Longfei; Xiao, Tian

    2006-12-01

    Magnetotactic bacteria have become a hot spot of research in microbiology attracting intensive interest of researchers in multiple disciplinary fields. However, the studies were limited in few fastidious bacteria. The objective of this study aims at isolating new marine magnetic bacteria and better comprehension of magnetotactic bacteria. In this study, an aerobic magnetotactic bacterium YSC-1 was isolated from sediments in the Yellow Sea Cold Water Mass (YSCWM). In TEM, magnetic cells have one or several circular magnetosomes in diameter of 100nm, and consist of Fe and Co shown on energy dispersive X-ray spectrum. The biological and physiological characteristics of this bacterium were also described. The colour of YSC-1 colony is white in small rod. The gram stain is negative. Results showed that Strain YSC-1 differs from microaerophile magnetotactic bacteria MS-1 and WD-1 in biology.

  20. Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil.

    PubMed

    Ghosh, A; Bhardwaj, M; Satyanarayana, T; Khurana, M; Mayilraj, S; Jain, R K

    2007-02-01

    A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Bacillus. Growth was observed at pH 7.0-11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was with Bacillus oshimensis JCM 12663T (98.8 %). However, DNA-DNA hybridization experiments indicated low levels of genomic relatedness with the type strains of B. oshimensis (62 %), Bacillus patagoniensis (55 %), Bacillus clausii (51 %) and Bacillus gibsonii (34 %), the species with which strain MLB2T formed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species of Bacillus, for which the name Bacillus lehensis sp. nov. is proposed. The type strain is MLB2T (=MTCC 7633T=JCM 13820T). PMID:17267957

  1. Massilia sp. BS-1, a novel violacein-producing bacterium isolated from soil.

    PubMed

    Agematu, Hitosi; Suzuki, Kazuya; Tsuya, Hiroaki

    2011-01-01

    A novel bacterium, Massilia sp. BS-1, producing violacein and deoxyviolacein was isolated from a soil sample collected from Akita Prefecture, Japan. The 16S ribosomal DNA of strain BS-1 displayed 93% homology with its nearest violacein-producing neighbor, Janthinobacterium lividum. Strain BS-1 grew well in a synthetic medium, but required both L-tryptophan and a small amount of L-histidine to produce violacein. PMID:21979084

  2. Chryseomicrobium aureum sp. nov., a bacterium isolated from activated sludge.

    PubMed

    Deng, Shi-Kai; Ye, Xiao-Mei; Chu, Cui-Wei; Jiang, Jin; He, Jian; Zhang, Jun; Li, Shun-Peng

    2014-08-01

    A Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, aerobic bacterial strain, designated BUT-2(T), was isolated from activated sludge of one herbicide-manufacturing wastewater-treatment facility in Kunshan, Jiangsu province, China, and subjected to polyphasic taxonomic studies. Analysis of the 16S rRNA gene sequence indicated that strain BUT-2(T) shared the highest similarity with Chryseomicrobium amylolyticum (98.98%), followed by Chryseomicrobium imtechense (98.88%), with less than 96% similarlity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain BUT-2(T) clustered with C. amylolyticum JC16(T) and C. imtechense MW10(T), occupying a distinct phylogenetic position. The major fatty acid (>10% of total fatty acids) type of strain BUT-2(T) was iso-C(15 : 0). The quinone system comprised menaquinone MK-7 (77.8%), MK-6 (11.9%) and MK-8 (10.3%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and some unidentified phospholipids. The cell-wall peptidoglycan type of strain BUT-2(T) was L-Orn-D-Glu. The genomic DNA G+C content of strain BUT-2(T) was 48.5 mol%. Furthermore, the DNA-DNA relatedness in hybridization experiments against the reference strain was lower than 70%, confirming that strain BUT-2(T) did not belong to previously described species of the genus Chryseomicrobium. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strain BUT-2(T) is considered to represent a novel species of the genus Chryseomicrobium, for which the name Chryseomicrobium aureum sp. nov. is proposed. The type strain is BUT-2(T) ( = CCTCC AB2013082(T) = KACC 17219(T)). PMID:24827708

  3. Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine.

    PubMed

    Megaw, Julianne; Gilmore, Brendan F

    2016-01-01

    Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This moderately halophilic bacterium was isolated from the surface of a halite sample obtained from a Triassic salt mine. PMID:27284152

  4. Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine

    PubMed Central

    Gilmore, Brendan F.

    2016-01-01

    Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This moderately halophilic bacterium was isolated from the surface of a halite sample obtained from a Triassic salt mine. PMID:27284152

  5. Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed.

    PubMed

    Fang, Yunxia; Lin, Haiyan; Wu, Liwen; Ren, Deyong; Ye, Weijun; Dong, Guojun; Zhu, Li; Guo, Longbiao

    2015-07-20

    Xanthomonas sacchari, was first identified as a pathogenic bacterium isolated from diseased sugarcane in Guadeloupe. In this study, R1 was first isolated from rice seed samples from Philippines in 2002. The antagonistic ability against several rice pathogens raises our attention. The genomic feature of this strain was described in this paper. The total genome size of X. sacchari R1 is 5,000,479 bp with 4315 coding sequences (CDS), 59 tRNAs, 2rRNAs and one plasmid. PMID:25931193

  6. Solid state photosensitive devices which employ isolated photosynthetic complexes

    DOEpatents

    Peumans, Peter; Forrest, Stephen R.

    2009-09-22

    Solid state photosensitive devices including photovoltaic devices are provided which comprise a first electrode and a second electrode in superposed relation; and at least one isolated Light Harvesting Complex (LHC) between the electrodes. Preferred photosensitive devices comprise an electron transport layer formed of a first photoconductive organic semiconductor material, adjacent to the LHC, disposed between the first electrode and the LHC; and a hole transport layer formed of a second photoconductive organic semiconductor material, adjacent to the LHC, disposed between the second electrode and the LHC. Solid state photosensitive devices of the present invention may comprise at least one additional layer of photoconductive organic semiconductor material disposed between the first electrode and the electron transport layer; and at least one additional layer of photoconductive organic semiconductor material, disposed between the second electrode and the hole transport layer. Methods of generating photocurrent are provided which comprise exposing a photovoltaic device of the present invention to light. Electronic devices are provided which comprise a solid state photosensitive device of the present invention.

  7. Effect of algal extract on H2 production by a photosynthetic bacterium Rhodobium marinum A-501: analysis of stimulating effect using a kinetic model.

    PubMed

    Kawaguchi, Hideo; Nagase, Hiroyasu; Hashimoto, Kyoko; Kimata, Shiho; Doi, Mikio; Hirata, Kazumasa; Miyamoto, Kazuhisa

    2002-01-01

    We have established a system for hydrogen (H2) production from algal starch via lactic acid using a mixed culture of a lactic acid bacterium, Lactobacillus amylovorus, and a photosynthetic bacterium, Rhodobium marinum A-501. We found that the H2 production from lactate was stimulated in the presence of algal extract, which was obtained from algal biomass homogenate used as a substrate in the system by removing settleable solids including starch. To analyze the stimulating effect of algal extract on H2 production, we developed a kinetic model for H2 production by R. marinum A-501. The model revealed that approximately 20% of lactate was consumed for cell mass production, and the remaining portion was a source of reducing power to drive hydrogen production or other cellular processes. In the presence of algal extract, the model indicated that the conversion efficiency from lactate to the reducing power increased from 0.56 to 0.80 and nitrogenase activity increased up to twofold, resulting in the increase in yield of hydrogen from lactate from 29% to 48%. These results suggest that algal extract can attenuate the limitation process in lactate catabolism by which the supplementation of reducing power to drive H2 production was suppressed. PMID:16233271

  8. Measurement of soil bacterial colony temperatures and isolation of a high heat-producing bacterium

    PubMed Central

    2013-01-01

    Background The cellular temperatures of microorganisms are considered to be the same as those of their surroundings because the cellular volume is too small to maintain a cellular temperature that is different from the ambient temperature. However, by forming a colony or a biofilm, microorganisms may be able to maintain a cellular temperature that is different from the ambient temperature. In this study, we measured the temperatures of bacterial colonies isolated from soils using an infrared imager and investigated the thermogenesis by a bacterium that increases its colony temperature. Results The temperatures of some colonies were higher or lower than that of the surrounding medium. A bacterial isolate with the highest colony temperature was identified as Pseudomonas putida. This bacterial isolate had an increased colony temperature when it grew at a temperature suboptimal for its growth. Measurements of heat production using a microcalorimeter showed that the temperature of this extraordinary, microcalorimetrically determined thermogenesis corresponded with the thermographically observed increase in bacterial colony temperature. When investigating the effects of the energy source on this thermal behavior, we found that heat production by this bacterium increased without additional biomass production at a temperature suboptimal for its growth. Conclusions We found that heat production by bacteria affected the bacterial colony temperature and that a bacterium identified as Pseudomonas putida could maintain a cellular temperature different from the ambient temperature, particularly at a sub-optimal growth temperature. The bacterial isolate P. putida KT1401 increased its colony temperature by an energy-spilling reaction when the incubation temperature limited its growth. PMID:23497132

  9. Deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from Mumbai, India.

    PubMed

    Shashidhar, Ravindranath; Bandekar, Jayant R

    2006-01-01

    A radiation-resistant, Gram-negative and pleomorphic bacterium (CON-1) was isolated from a contaminated tryptone glucose yeast extract agar plate in the laboratory. It was red pigmented, nonmotile, nonsporulating, and aerobic, and contained MK-8 as respiratory quinone. The cell wall of this bacterium contained ornithine. The major fatty acids were C16:0, C16:1, C17:0, C18:1 and iso C18:0. The DNA of CON-1 had a G+C content of 70 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that CON-1 exhibited a maximum similarity (94.72%) with Deinococcus grandis. Based on the genotypic, phenotypic and chemotaxonomic characteristics, the bacterium CON-1 was identified as a new species of the genus Deinococcus, for which the name Deinococcus mumbaiensis sp. nov. is proposed. The type strain of D. mumbaiensis is CON-1 (MTCC 7297(T)=DSM 17424(T)). PMID:16445756

  10. Purification and Characterization of Haloalkaline, Organic Solvent Stable Xylanase from Newly Isolated Halophilic Bacterium-OKH

    PubMed Central

    Sanghvi, Gaurav; Jivrajani, Mehul; Patel, Nirav; Jivrajani, Heta; Bhaskara, Govinal Badiger; Patel, Shivani

    2014-01-01

    A novel, alkali-tolerant halophilic bacterium-OKH with an ability to produce extracellular halophilic, alkali-tolerant, organic solvent stable, and moderately thermostable xylanase was isolated from salt salterns of Mithapur region, Gujarat, India. Identification of the bacterium was done based upon biochemical tests and 16S rRNA sequence. Maximum xylanase production was achieved at pH 9.0 and 37°C temperature in the medium containing 15% NaCl and 1% (w/v) corn cobs. Sugarcane bagasse and wheat straw also induce xylanase production when used as carbon source. The enzyme was active over a range of 0–25% sodium chloride examined in culture broth. The optimum xylanase activity was observed at 5% sodium chloride. Xylanase was purified with 25.81%-fold purification and 17.1% yield. Kinetic properties such as Km and Vmax were 4.2 mg/mL and 0.31 μmol/min/mL, respectively. The enzyme was stable at pH 6.0 and 50°C with 60% activity after 8 hours of incubation. Enzyme activity was enhanced by Ca2+, Mn2+, and Mg2+ but strongly inhibited by heavy metals such as Hg2+, Fe3+, Ni2+, and Zn2+. Xylanase was found to be stable in organic solvents like glutaraldehyde and isopropanol. The purified enzyme hydrolysed lignocellulosic substrates. Xylanase, purified from the halophilic bacterium-OKH, has potential biotechnological applications. PMID:27350996

  11. Isolation and Characterization of Strain MMB-1 (CECT 4803), a Novel Melanogenic Marine Bacterium.

    PubMed

    Solano, F; Garcia, E; Perez, D; Sanchez-Amat, A

    1997-09-01

    A novel marine melanogenic bacterium, strain MMB-1, was isolated from the Mediterranean Sea. The taxonomic characterization of this strain indicated that it belongs to the genus Alteromonas. Under in vivo conditions, L-tyrosine was the specific monophenolic precursor for melanin synthesis. This bacterium contained all types of activities associated with polyphenol oxidases (PPOs), cresolase (EC 1.18.14.1), catecholase (EC 1.10.3.1), and laccase (EC 1.10.3.2). These activities were due to the presence of two different PPOs. The first one showed all the enzymatic activities, but it was not involved in melanogenesis in vivo, since amelanogenic mutant strains obtained by nitrosoguanidine treatment contained levels of this PPO similar to that of the wild-type MMB-1 strain. The second PPO showed cresolase and catecholase activities but no laccase, and it was involved in melanogenesis, since this enzyme was lost in amelanogenic mutant strains. This PPO was strongly activated by sodium dodecyl sulfate below the critical micelle concentration, and it is a tyrosinase-like enzyme showing a lag period in its tyrosine hydroxylase activity that could be avoided by small amounts of L-dopa. This is the first report of a bacterium that contains two PPOs and also the first report of a pluripotent PPO showing all types of oxidase activities. The bacterium and the pluripotent PPO may be useful models for exploring the roles of PPOs in cellular physiology, aside from melanin formation. On the other hand, the high oxidizing capacity of the PPO for a wide range of substrates could make possible its application in phenolic biotransformations, food processing, or the cosmetic industry, where fungal and plant PPOs are being used. PMID:16535688

  12. Isolation and Characterization of Strain MMB-1 (CECT 4803), a Novel Melanogenic Marine Bacterium

    PubMed Central

    Solano, F.; Garcia, E.; Perez, De; Sanchez-Amat, A.

    1997-01-01

    A novel marine melanogenic bacterium, strain MMB-1, was isolated from the Mediterranean Sea. The taxonomic characterization of this strain indicated that it belongs to the genus Alteromonas. Under in vivo conditions, L-tyrosine was the specific monophenolic precursor for melanin synthesis. This bacterium contained all types of activities associated with polyphenol oxidases (PPOs), cresolase (EC 1.18.14.1), catecholase (EC 1.10.3.1), and laccase (EC 1.10.3.2). These activities were due to the presence of two different PPOs. The first one showed all the enzymatic activities, but it was not involved in melanogenesis in vivo, since amelanogenic mutant strains obtained by nitrosoguanidine treatment contained levels of this PPO similar to that of the wild-type MMB-1 strain. The second PPO showed cresolase and catecholase activities but no laccase, and it was involved in melanogenesis, since this enzyme was lost in amelanogenic mutant strains. This PPO was strongly activated by sodium dodecyl sulfate below the critical micelle concentration, and it is a tyrosinase-like enzyme showing a lag period in its tyrosine hydroxylase activity that could be avoided by small amounts of L-dopa. This is the first report of a bacterium that contains two PPOs and also the first report of a pluripotent PPO showing all types of oxidase activities. The bacterium and the pluripotent PPO may be useful models for exploring the roles of PPOs in cellular physiology, aside from melanin formation. On the other hand, the high oxidizing capacity of the PPO for a wide range of substrates could make possible its application in phenolic biotransformations, food processing, or the cosmetic industry, where fungal and plant PPOs are being used. PMID:16535688

  13. Cadmium resistance and uptake by bacterium, Salmonella enterica 43C, isolated from industrial effluent.

    PubMed

    Khan, Zaman; Rehman, Abdul; Hussain, Syed Z; Nisar, Muhammad A; Zulfiqar, Soumble; Shakoori, Abdul R

    2016-12-01

    Cadmium resistant bacterium, isolated from industrial wastewater, was characterized as Salmonella enterica 43C on the basis of biochemical and 16S rRNA ribotyping. It is first ever reported S. enterica 43C bared extreme resistance against heavy metal consortia in order of Pb(2+)>Cd(2+)>As(3+)>Zn(2+)>Cr(6+)>Cu(2+)>Hg(2+). Cd(2+) stress altered growth pattern of the bacterium in time dependent manner. It could remove nearly 57 % Cd(2+) from the medium over a period of 8 days. Kinetic and thermodynamic studies based on various adsorption isotherm models (Langmuir and Freundlich) depicted the Cd(2+) biosorption as spontaneous, feasible and endothermic in nature. Interestingly, the bacterium followed pseudo first order kinetics, making it a good biosorbent for heavy metal ions. The S. enterica 43C Cd(2+) processivity was significantly influenced by temperature, pH, initial Cd(2+) concentration, biomass dosage and co-metal ions. FTIR analysis of the bacterium revealed the active participation of amide and carbonyl moieties in Cd(2+) adsorption confirmed by EDX analysis. Electron micrographs beckoned further surface adsorption and increased bacterial size due to intracellular Cd(2+) accumulation. An overwhelming increase in glutathione and other non-protein thiols levels played a significant role in thriving oxidative stress generated by metal cations. Presence of metallothionein clearly depicted the role of such proteins in bacterial metal resistance mechanism. The present study results clearly declare S. enterica 43C a suitable candidate for green chemistry to bioremediate environmental Cd(2+). PMID:27491862

  14. Niveispirillum cyanobacteriorum sp. nov., a nitrogen-fixing bacterium isolated from cyanobacterial aggregates in a eutrophic lake.

    PubMed

    Cai, Haiyuan; Wang, Yanan; Xu, Huacheng; Yan, Zaisheng; Jia, Bin; Majid Maszenan, Abdul; Jiang, Helong

    2015-08-01

    A Gram-stain-negative, slightly curved rod-shaped, non-spore-forming diazotrophic bacterium, designated strain TH16T, was isolated from cyanobacterial aggregates taken from eutrophic Lake Taihu, Jiangsu Province, China. The pH range for growth was 5-9 (optimum at pH 7.0), salinity range was 0-2% (w/v) NaCl (optimum 0%) and temperature range was 20-37 °C (optimum 30 °C) in nutrient broth. Phylogenetic analysis indicated that strain TH16T clusters near and is closely related to the genus Niveispirillum within the family Rhodospirillaceae of the class Alphaproteobacteria. Within the genus Niveispirillum, strain TH16T was related most closely to Niveispirillum irakense KBC1T (98.1% 16S rRNA gene sequence similarity) and Niveispirillum fermenti CC-LY736T (97.0 %). The DNA G+C content of strain TH16T was 64 mol%. DNA-DNA relatedness between strain TH16T and the type strains of N. irakense and N. fermenti was 39.6 and 30.1%, respectively. The major respiratory quinone was ubiquinone Q-10.The major fatty acids (>10%) were C18  :  1ω6c/C18  :  1ω7c, C18  :  1 2-OH and C16  :  0 3-OH. Genes in the puf operon, encoding proteins of the photosynthetic reaction centre and core light-harvesting complexes, were also present. Based on morphological, chemotaxonomic and phylogenetic data, strain TH16T represents a novel species within the genus Niveispirillum, for which the name Niveispirillum cyanobacteriorum sp. nov. is proposed. The type strain is TH16T ( = CGMCC 1.12958T = LMG 28334T). PMID:25944809

  15. A light-dependent mechanism for massive accumulation of manganese in the photosynthetic bacterium Synechocystis sp. PCC 6803.

    PubMed

    Keren, Nir; Kidd, Matthew J; Penner-Hahn, James E; Pakrasi, Himadri B

    2002-12-17

    Manganese is an essential micronutrient for many organisms. Because of its unique role in the water oxidizing activity of photosystem II, manganese is required for photosynthetic growth in plants and cyanobacteria. Here we report on the mechanism of manganese uptake in the cyanobacterium Synechocystis sp. PCC 6803. Cells grown in 9 microM manganese-containing medium accumulate up to 1 x 10(8) manganese atoms/cell, bound to the outer membrane (pool A). This pool could be released by EDTA treatment. Accumulation of manganese in pool A was energized by photosynthetic electron flow. Moreover, collapsing the membrane potential resulted in the immediate release of this manganese pool. The manganese in this pool is mainly Mn(II) in a six-coordinate distorted environment. A distinctly different pool of manganese, pool B ( approximately 1.5 x 10(6) atoms/cell), could not be extracted by EDTA. Transport into pool B was light-independent and could be detected only under limiting manganese concentrations (1 nM). Evidently, manganese uptake in Synechocystis 6803 cells occurs in two steps. First, manganese accumulates in the outer membrane (pool A) in a membrane potential-dependent process. Next, manganese is transported through the inner membrane into pool B. We propose that pool A serves as a store that allows the cells to overcome transient limitations in manganese in the environment. PMID:12475258

  16. Draft Genome Sequence of Bacillus murimartini LMG 21005T, an Alkalitolerant Bacterium Isolated from a Church Wall Mural in Germany

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai; Ge, Ci-bin

    2015-01-01

    Bacillus murimartini LMG 21005T is a Gram-positive, spore-forming, and alkalitolerant bacterium isolated from a church wall mural. Here, we report the 4.17-Mb genome sequence of B. murimartini LMG 21005T, which will accelerate the application of this alkalitolerant bacterium and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26494676

  17. Exciton interactions in reaction centers of the photosynthetic bacterium Rhodopseudomonas viridis probed by optical triplet-minus-singlet polarization spectroscopy at 1.2 K monitored through absorbance-detected magnetic resonance.

    PubMed

    Lous, E J; Hoff, A J

    1987-09-01

    Linear dichroic triplet-minus-singlet [LD-(T - S)] spectra of isolated reaction centers of the photosynthetic bacterium Rhodopseudomonas viridis have been measured at 1.2 K with the linear dichroic absorbance-detected magnetic resonance (LD-ADMR) technique for two mutually perpendicular directions of the preferred axis. The LD-(T - S) spectra have been calibrated with respect to the corresponding (T - S) spectra as a function of applied microwave power and quantitatively interpreted using the formalism of photoselection. The transition moment of the optical transition at 1007 nm makes angles of 72 degrees +/- 5 degrees and 15 degrees +/- 5 degrees with the triplet x and y spin axes, respectively. The experimental spectra have been simulated employing exciton theory and using the atomic coordinates of the resolved crystal structure of the reaction center. The spectral interpretation yields the angles between the transition moments of the various absorption bands of the (T - S) spectra and the triplet axes, and between the moments themselves, with the triplet state of the primary donor (3)P localized on the P-bacteriochlorophyll b in the "active" (L) chain. PMID:16578814

  18. Enrichment, isolation and characterization of pentachlorophenol degrading bacterium Acinetobacter sp. ISTPCP-3 from effluent discharge site.

    PubMed

    Sharma, Ashwani; Thakur, Indu Shekhar; Dureja, Prem

    2009-09-01

    Three pentachlorophenol (PCP) degrading bacterial strains were isolated from sediment core of pulp and paper mill effluent discharge site. The strains were continuously enriched in mineral salts medium supplemented with PCP as sole source of carbon and energy. One of the acclimated strains with relatively high PCP degradation capability was selected and characterized in this study. Based on morphology, biochemical tests, 16S rDNA sequence analysis and phylogenetic characteristics, the strains showed greatest similarity with Acinetobacter spp. The strain was identified as Acinetobacter sp. ISTPCP-3. The physiological characteristics and optimum growth conditions of the bacterial strain were investigated. The results of optimum growth temperature revealed that it was a mesophile. The optimum growth temperature for the strain was 30 degrees C. The preferential initial pH for the strain was ranging at 6.5-7.5, the optimum pH was 7. The bacterium was able to tolerate and degrade PCP up to a concentration of 200 mg/l. Increase in PCP concentration had a negative effect on biodegradation rate and PCP concentration above 250 mg/l was inhibitory to its growth. Acinetobacter sp. ISTPCP-3 was able to utilize PCP through an oxidative route with ortho ring-cleavage with the formation of 2,3,5,6-tetrachlorohydroquinone and 2-chloro-1,4-benzenediol, identified using gas chromatograph-mass spectrometric (GC-MS) analysis. The degradation pathway followed by isolated bacterium is different from previously characterized pathway. PMID:19214760

  19. Removal of arsenic from groundwater by using a native isolated arsenite-oxidizing bacterium.

    PubMed

    Kao, An-Chieh; Chu, Yu-Ju; Hsu, Fu-Lan; Liao, Vivian Hsiu-Chuan

    2013-12-01

    Arsenic (As) contamination of groundwater is a significant public health concern. In this study, the removal of arsenic from groundwater using biological processes was investigated. The efficiency of arsenite (As(III)) bacterial oxidation and subsequent arsenate (As(V)) removal from contaminated groundwater using bacterial biomass was examined. A novel As(III)-oxidizing bacterium (As7325) was isolated from the aquifer in the blackfoot disease (BFD) endemic area in Taiwan. As7325 oxidized 2300μg/l As(III) using in situ As(III)-contaminated groundwater under aerobic conditions within 1d. After the oxidation of As(III) to As(V), As(V) removal was further examined using As7325 cell pellets. The results showed that As(V) could be adsorbed efficiently by lyophilized As7325 cell pellets, the efficiency of which was related to lyophilized cell pellet concentration. Our study conducted the examination of an alternative technology for the removal of As(III) and As(V) from groundwater, indicating that the oxidation of As(III)-contaminated groundwater by native isolated bacterium, followed by As(V) removal using bacterial biomass is a potentially effective technology for the treatment of As(III)-contaminated groundwater. PMID:24096199

  20. Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque.

    PubMed

    Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

    2016-01-01

    Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium. PMID:26860259

  1. Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque

    PubMed Central

    Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

    2016-01-01

    Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium. PMID:26860259

  2. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage

    PubMed Central

    Mehboob, Farrakh; van Gelder, Antonie H.; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Stams, Alfons J. M.

    2010-01-01

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5–0.8 μm in diameter, and 2–8 μm in length, growing as single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H2/CO2 to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO2. The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts. PMID:20680263

  3. Ultrafast time-resolved spectroscopy of the light-harvesting complex 2 (LH2) from the photosynthetic bacterium Thermochromatium tepidum

    SciTech Connect

    Niedzwiedzki, Dariusz M.; Fuciman, Marcel; Kobayashi, Masayuki; Frank, Harry A.; Blankenship, Robert E.

    2011-10-08

    The light-harvesting complex 2 from the thermophilic purple bacterium Thermochromatium tepidum was purified and studied by steady-state absorption and fluorescence, sub-nanosecond-time-resolved fluorescence and femtosecond time-resolved transient absorption spectroscopy. The measurements were performed at room temperature and at 10 K. The combination of both ultrafast and steady-state optical spectroscopy methods at ambient and cryogenic temperatures allowed the detailed study of carotenoid (Car)-to-bacteriochlorophyll (BChl) as well BChl-to-BChl excitation energy transfer in the complex. The studies show that the dominant Cars rhodopin (N = 11) and spirilloxanthin (N = 13) do not play a significant role as supportive energy donors for BChl a. This is related with their photophysical properties regulated by long π-electron conjugation. On the other hand, such properties favor some of the Cars, particularly spirilloxanthin (N = 13) to play the role of the direct quencher of the excited singlet state of BChl.

  4. Mageeibacillus indolicus gen. nov., sp. nov.: a novel bacterium isolated from the female genital tract.

    PubMed

    Austin, Michele N; Rabe, Lorna K; Srinivasan, Sujatha; Fredricks, David N; Wiesenfeld, Harold C; Hillier, Sharon L

    2015-04-01

    Three isolates of a bacterium recovered from human endometrium using conventional culture methods were characterized biochemically and subjected to 16S rRNA gene sequencing and phylogenetic analysis. Isolates were non-motile, obligately anaerobic, non-spore forming, asaccharolytic, non-cellulolytic, indole positive, Gram positive rods. Cell wall fatty acid profiling revealed C14:0, C16:0, C18:2 ω6, 9c, C18:1 ω9c and C18:0 to be the major fatty acid composition. The DNA mol % G+C was determined to be 44.2%. 16S rRNA gene sequence analysis revealed only 91% sequence similarity with the closest cultivated bacterial isolate, Saccharofermentans acetigenes. Based on genotypic and phenotypic data, all three isolates are considered to be members of the same species and data suggest it represents a novel genus and species in the order Clostridiales with an association with Clostridium rRNA cluster III within the family Ruminococcaceae. We propose the name, Mageeibacillus indolicus gen. nov., sp. nov. The type strain is BAA-2120(T) and CCUG 59143(T). PMID:25482717

  5. Roseovarius aquimarinus sp. nov., a slightly halophilic bacterium isolated from seawater.

    PubMed

    Kang, Hyeonji; Kim, Jong-Hwa; Jeon, Che Ok; Yoon, Jung-Hoon; Kim, Wonyong

    2015-12-01

    A Gram-stain-negative, non-spore-forming, rod-shaped, motile, facultatively anaerobic bacterium, designated CAU 1059T, was isolated from a seawater sample from Jeju Island, Republic of Korea. The bacterium grew optimally at 37 °C, at pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1059T belonged to the genus Roseovarius. It exhibited only 91.5-96.9 % sequence similarity to the type strains of recognized Roseovarius species. Similar to other species of the genus Roseovarius, strain CAU 1059T had ubiquinone-10 (Q-10) as the predominant ubiquinone and C16 : 0 and summed feature 8 (C18 : 1ω7c/ω6c) as the major fatty acids. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine; three unidentified phospholipids, two aminolipids, an aminophospholipid and nine other lipids were also found. The G+C content of the genomic DNA was 61.9 mol%. On the basis of the data provided, strain CAU 1059T should be classified as representing a novel species of the genus Roseovarius, for which the name Roseovarius aquimarinus sp. nov. is proposed. The type strain is CAU 1059T ( = KCTC 32014T = CCUG 64792T). PMID:26374629

  6. Isolation, cloning and characterization of an azoreductase from the halophilic bacterium Halomonas elongata.

    PubMed

    Eslami, Maryam; Amoozegar, Mohammad Ali; Asad, Sedigheh

    2016-04-01

    Azo dyes are a major class of colorants used in various industries including textile, paper and food. These dyes are regarded as pollutant since they are not readily reduced under aerobic conditions. Halomonas elongata, a halophilic bacterium, has the ability to decolorize different mono and di-azo dyes in anoxic conditions. In this study the putative azoreductase gene of H. elongata, formerly annotated as acp, was isolated, heterologously expressed in Escherichia coli, purified and characterized. The gene product, AzoH, was found to have a molecular mass of 22 kDa. The enzyme requires NADH, as an electron donor for its activity. The apparent Km was 63 μM for NADH and 12 μM for methyl red as a mono-azo dye substrate. The specific activity for methyl red was 0.27 μmol min(-1)mg(-1). The optimum enzyme activity was achieved in 50mM sodium phosphate buffer at pH 6. Although increased salinity resulted in reduced activity, AzoH could decolorize azo dye at NaCl concentrations up to 15% (w/v). The enzyme was also shown to be able to decolorize remazol black B as a representative of di-azo dyes. This is the first report describing the sequence and activity of an azo-reducing enzyme from a halophilic bacterium. PMID:26724685

  7. Biogenesis of antibacterial silver nanoparticles using the endophytic bacterium Bacillus cereus isolated from Garcinia xanthochymus

    PubMed Central

    Sunkar, Swetha; Nachiyar, C Valli

    2012-01-01

    Objective To synthesize the ecofriendly nanoparticles, which is viewed as an alternative to the chemical method which initiated the use of microbes like bacteria and fungi in their synthesis. Methods The current study uses the endophytic bacterium Bacillus cereus isolated from the Garcinia xanthochymus to synthesize the silver nanoparticles (AgNPs). The AgNPs were synthesized by reduction of silver nitrate solution by the endophytic bacterium after incubation for 3-5 d at room temperature. The synthesis was initially observed by colour change from pale white to brown which was confirmed by UV-Vis spectroscopy. The AgNPs were further characterized using FTIR, SEM-EDX and TEM analyses. Results The synthesized nanoparticles were found to be spherical with the size in the range of 20-40 nm which showed a slight aggregation. The energy-dispersive spectra of the nanoparticle dispersion confirmed the presence of elemental silver. The AgNPs were found to have antibacterial activity against a few pathogenic bacteria like Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi and Klebsiella pneumoniae. Conclusions The endophytic bacteria identified as Bacillus cereus was able to synthesize silver nanoparticles with potential antibacterial activity. PMID:23593575

  8. Novel detoxification of the trichothecene mycotoxin deoxynivalenol by a soil bacterium isolated by enrichment culture.

    PubMed Central

    Shima, J; Takase, S; Takahashi, Y; Iwai, Y; Fujimoto, H; Yamazaki, M; Ochi, K

    1997-01-01

    A mixed microbial culture capable of metabolizing deoxynivalenol was obtained from soil samples by an enrichment culture procedure. A bacterium (strain E3-39) isolated from the enrichment culture completely removed exogenously supplied deoxynivalenol from culture medium after incubation for 1 day. On the basis of morphological, physiological, and phylogenetic studies, strain E3-39 was classified as a bacterium belonging to the Agrobacterium-Rhizobium group. Thin-layer chromatographic analysis indicated the presence of one major and two minor metabolites of deoxynivalenol in ethyl acetate extracts of the E3-39 culture filtrates. The main metabolite was identified as 3-keto-4-deoxynivalenol by mass spectroscopy and 1H and 13C nuclear magnetic resonance analysis. The immunosuppressive toxicity of 3-keto-4-deoxynivalenol was evaluated by means of a bioassay based on the mitogen-induced and mitogen-free proliferations of mouse spleen lymphocytes. This compound exhibited a remarkably decreased (to less than one tenth) immunosuppressive toxicity relative to deoxynivalenol, indicating that the 3-OH group in deoxynivalenol is likely to be involved in exerting its immunosuppressive toxicity. Strain E3-39 was also capable of transforming 3-acetyldeoxynivalenol but not nivalenol and fusarenon-X. PMID:9327545

  9. Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA.

    PubMed

    Simbahan, Jessica; Drijber, Rhae; Blum, Paul

    2004-09-01

    A thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35-65 degrees C (optimum 55 degrees C) and at pH 2.0-6.0 (optimum 4.0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97.8 % identity) and Alicyclobacillus sendaiensis (96.9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96.1-96.5 %) and Alicyclobacillus genomic species FR-6 (96.3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of omega-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA-DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T = DSM 16176T). PMID:15388732

  10. Isolation, Identification and Characteristics of an Endophytic Quinclorac Degrading Bacterium Bacillus megaterium Q3

    PubMed Central

    Wang, Yunsheng; Zeng, Aiping; Zhou, Xiaomao; Luo, Feng; Bai, Lianyang

    2014-01-01

    In this study, we isolated an endophytic quinclorac-degrading bacterium strain Q3 from the root of tobacco grown in quinclorac contaminated soil. Based on morphological characteristics, Biolog identification, and 16S rDNA sequence analysis, we identified strain Q3 as Bacillus megaterium. We investigated the effects of temperature, pH, inoculation size, and initial quinclorac concentration on growth and degrading efficiency of Q3. Under the optimal degrading condition, Q3 could degrade 93% of quinclorac from the initial concentration of 20 mg/L in seven days. We analyzed the degradation products of quinclorac using liquid chromatography–tandem mass spectrometry (LC-MS/MS). The major degradation products by Q3 were different from those of previously identified quinclorac degrading strains, which suggests that Q3 may employ new pathways for quinclorac degradation. Our indoor pot experiments demonstrated that Q3 can effectively alleviate the quinclorac phytotoxicity in tobacco. As the first endophytic microbial that is capable of degrading quinclorac, Q3 can be a good bioremediation bacterium for quinclorac phytotoxicity. PMID:25244184

  11. Aerobic Reduction of Arsenate by a Bacterium Isolated From Activated Sludge

    NASA Astrophysics Data System (ADS)

    Kozai, N.; Ohnuki, T.; Hanada, S.; Nakamura, K.; Francis, A. J.

    2006-12-01

    Microlunatus phosphovorus strain NM-1 is a polyphosphate-accumulating bacterium isolated from activated sludge. This bacterium takes up a large amount of polyphosphate under aerobic conditions and release phosphate ions by hydrolysis of polyphosphate to orthophosphate under anaerobic conditions to derive energy for taking up substrates. To understand the nature of this strain, especially, influence of potential contaminants in sewage and wastewater on growth, we have been investigating behavior of this bacterium in media containing arsenic. The present paper mainly reports reduction of arsenate by this bacterium under aerobic conditions. The strain NM-1 (JCM 9379) was aerobically cultured at 30 °C in a nutrient medium containing 2.5 g/l peptone, 0.5 g/l glucose, 1.5 g/l yeast extract, and arsenic [Na2HAsO4 (As(V)) or Na3AsO3 (As(III))] at concentrations between 0 and 50 mM. The cells collected from arsenic-free media were dispersed in buffer solutions containing 2mM HEPES, 10mM NaCl, prescribed concentrations of As(V), and 0-0.2 percent glucose. Then, this cell suspension was kept at 20 °C under aerobic or anaerobic conditions. The speciation of arsenic was carried out by ion chromatography and ICP-MS. The growth of the strain under aerobic conditions was enhanced by the addition of As(V) at the concentration between 1 and 10 mM. The maximum optical density of the culture in the medium containing 5mM As(V) was 1.4 times greater than that of the control culture. Below the As(V) concentration of 10mM, most of the As(V) was reduced to As(III). The growth of the strain under anaerobic conditions has not been observed so far. The cells in the buffer solutions reduced As(V) under aerobic condition. The reduction was enhanced by the addition of glucose. However, the cell did not reduce As(V) under anaerobic conditions. The strain NM-1 showed high resistance to As(V) and As(III). The maximum optical density of the culture grown in a medium containing 50 mM As(V) was only

  12. Carbon monoxide metabolism by the photosynthetic bacterium Rhodospirillum rubrum. Progress report, November 15, 1990--November 15, 1991

    SciTech Connect

    Ludden, P.W.; Roberts, G.P.

    1991-12-31

    Research continued on carbon monoxide metabolism by Rhodospirillum rubrum. In the past year, progress was made in: (1) the identification and isolation of the physiological electron carrier from monoxide dehydrogenase (CODH) to hydrogenase in R. rubrum; (2) the isolation, sequencing and mutagenesis of the genes encoding the components of the CO oxidation system in R. rubrum, (3) the purification and characterization of the CO-induced hydrogenase activity of R. rubrum; (4) the spectroscopic investigation of the cobalt-substituted form of the enzyme.

  13. Loktanella spp. Gb03 as an algicidal bacterium, isolated from the culture of Dinoflagellate Gambierdiscus belizeanus

    PubMed Central

    Bloh, Anmar Hameed; Usup, Gires; Ahmad, Asmat

    2016-01-01

    Aim: Bacteria associated with harmful algal blooms can play a crucial role in regulating algal blooms in the environment. This study aimed at isolating and identifying algicidal bacteria in Dinoflagellate culture and to determine the optimum growth requirement of the algicidal bacteria, Loktanella sp. Gb-03. Materials and Methods: The Dinoflagellate culture used in this study was supplied by Professor Gires Usup's Laboratory, School of Environmental and Natural Resources Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, Malaysia. The culture was used for the isolation of Loktanella sp., using biochemical tests, API 20 ONE kits. The fatty acid content of the isolates and the algicidal activity were further evaluated, and the phenotype was determined through the phylogenetic tree. Results: Gram-negative, non-motile, non-spore-forming, short rod-shaped, aerobic bacteria (Gb01, Gb02, Gb03, Gb04, Gb05, and Gb06) were isolated from the Dinoflagellate culture. The colonies were pink in color, convex with a smooth surface and entire edge. The optimum growth temperature for the Loktanella sp. Gb03 isolate was determined to be 30°C, in 1% of NaCl and pH7. Phylogenetic analysis based on 16S rRNA gene sequences showed that the bacterium belonged to the genus Loktanella of the class Alphaproteobacteria and formed a tight cluster with the type strain of Loktanella pyoseonensis (97.0% sequence similarity). Conclusion: On the basis of phenotypic, phylogenetic data and genetic distinctiveness, strain Gb-03, were placed in the genus Loktanella as the type strain of species. Moreover, it has algicidal activity against seven toxic Dinoflagellate. The algicidal property of the isolated Loktanella is vital, especially where biological control is needed to mitigate algal bloom or targeted Dinoflagellates. PMID:27051199

  14. Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium

    PubMed Central

    Arif, Mohammad; Busot, Grethel Y.; Mann, Rachel; Rodoni, Brendan; Liu, Sanzhen; Stack, James P.

    2016-01-01

    Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of isolation was determined for isolates collected over a forty-year period. Discriminant analyses of recently collected and archived isolates using Multi-Locus Sequence Typing (MLST) and Inter-Simple Sequence Repeats (ISSR) identified three populations of R. toxicus; RT-I and RT-II from South Australia and RT-III from Western Australia. Population RT-I, detected in 2013 and 2014 from the Yorke Peninsula in South Australia, is a newly emerged population of R. toxicus not previously reported. Commonly used housekeeping genes failed to discriminate among the R. toxicus isolates. However, strategically selected and genome-dispersed MLST genes representing an array of cellular functions from chromosome replication, antibiotic resistance and biosynthetic pathways to bacterial acquired immunity were discriminative. Genetic variation among isolates within the RT-I population was less than the within-population variation for the previously reported RT-II and RT-III populations. The lower relative genetic variation within the RT-I population and its absence from sampling over the past 40 years suggest its recent emergence. RT-I was the dominant population on the Yorke Peninsula during the 2013–2014 sampling period perhaps indicating a competitive advantage over the previously detected RT-II population. The potential for introduction of this bacterial plant pathogen into new geographic areas provide a rationale for understanding the ecological and evolutionary trajectories of R. toxicus

  15. Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium.

    PubMed

    Arif, Mohammad; Busot, Grethel Y; Mann, Rachel; Rodoni, Brendan; Liu, Sanzhen; Stack, James P

    2016-01-01

    Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of isolation was determined for isolates collected over a forty-year period. Discriminant analyses of recently collected and archived isolates using Multi-Locus Sequence Typing (MLST) and Inter-Simple Sequence Repeats (ISSR) identified three populations of R. toxicus; RT-I and RT-II from South Australia and RT-III from Western Australia. Population RT-I, detected in 2013 and 2014 from the Yorke Peninsula in South Australia, is a newly emerged population of R. toxicus not previously reported. Commonly used housekeeping genes failed to discriminate among the R. toxicus isolates. However, strategically selected and genome-dispersed MLST genes representing an array of cellular functions from chromosome replication, antibiotic resistance and biosynthetic pathways to bacterial acquired immunity were discriminative. Genetic variation among isolates within the RT-I population was less than the within-population variation for the previously reported RT-II and RT-III populations. The lower relative genetic variation within the RT-I population and its absence from sampling over the past 40 years suggest its recent emergence. RT-I was the dominant population on the Yorke Peninsula during the 2013-2014 sampling period perhaps indicating a competitive advantage over the previously detected RT-II population. The potential for introduction of this bacterial plant pathogen into new geographic areas provide a rationale for understanding the ecological and evolutionary trajectories of R. toxicus

  16. Isolation and characterization of bacterium producing lipid from short-chain fatty acids.

    PubMed

    Okamura, Yoshiko; Nakai, Shota; Ohkawachi, Masahiko; Suemitsu, Masahiro; Takahashi, Hirokazu; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Nakashimada, Yutaka; Matsumoto, Mitsufumi

    2016-02-01

    Anaerobic fermentation generates propionic acid, which inhibits microbial growth and accumulates in wastewater containing increased amounts of organic matter. We therefore isolated a propionic acid-assimilating bacterium that could produce triacylglycerol, for use in wastewater treatment. Nitratireductor sp. strain OM-1 can proliferate in medium containing propionic, acetic, butyric, and valeric acids as well as glycerol, and produces triacylglycerol when both propionic and acetic acids or glycerol are present. In composite model wastewater containing acetic acid, propionic acid and glycerol, this strain shows an even higher conversion rate, suggesting that it is suitable for wastewater treatment. Further, nitrogen depletion in medium containing an acetic-propionic acid mixture resulted in the production of the light oil 2-butenoic acid 1-methylethyl ester, but not triacylglycerol. Collectively, our data indicate that strain OM-1 has the potential to reduce accumulation of activated sludge in wastewater treatment and may contribute to the production of biodiesel. PMID:26649900

  17. Bioethanol production from mannitol by a newly isolated bacterium, Enterobacter sp. JMP3.

    PubMed

    Wang, Jing; Kim, Young Mi; Rhee, Hong Soon; Lee, Min Woo; Park, Jong Moon

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation. PMID:23186687

  18. Isolation and characterization of an anaerobic ruminal bacterium capable of degrading hydrolyzable tannins.

    PubMed Central

    Nelson, K E; Pell, A N; Schofield, P; Zinder, S

    1995-01-01

    An anaerobic diplococcoid bacterium able to degrade hydrolyzable tannins was isolated from the ruminal fluid of a goat fed desmodium (Desmodium ovalifolium), a tropical legume which contains levels as high as 17% condensed tannins. This strain grew under anaerobic conditions in the presence of up to 30 g of tannic acid per liter and tolerated a range of phenolic monomers, including gallic, ferulic, and p-coumaric acids. The predominant fermentation product from tannic acid breakdown was pyrogallol, as detected by high-performance liquid chromatography and mass spectrometry. Tannic acid degradation was dependent on the presence of a sugar such as glucose, fructose, arabinose, sucrose, galactose, cellobiose, or soluble starch as an added carbon and energy source. The strain also demonstrated resistance to condensed tannins up to a level of 4 g/liter. PMID:7574640

  19. Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax

    PubMed Central

    Wang, Guangli; Zhang, Ji; Wang, Li; Liang, Bin; Chen, Kai; Li, Shunpeng; Jiang, Jiandong

    2010-01-01

    Microbial degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) is the most promising way to clean up DDT residues found in the environment. In this paper, a bacterium designated as wax, which was capable of co-metabolizing DDT with other carbon sources, was isolated from a long-term DDT-contaminated soil sample by an enrichment culture technique. The new isolate was identified as a member of the Pseudoxanthomonas sp., based on its morphological, physiological and biochemical properties, as well as by 16S rRNA gene analysis. In the presence of 100 mg l-1 glucose, the wax strain could degrade over 95% of the total DDT, at a concentration of 20 mg l-1, in 72 hours, and could degrade over 60% of the total DDT, at a concentration of 100 mg l-1, in 144 hours. The wax strain had the highest degradation efficiency among all of the documented DDT-degrading bacteria. The wax strain could efficiently degrade DDT at temperatures ranging from 20 to 37°C, and with initial pH values ranging from 7 to 9. The bacterium could also simultaneously co-metabolize 1,1-dichloro-2,2-bis(p-chlorophenyl)ethane (DDD), 2,2-bis(p-chlorophenyl)-1,1-dichlorethylene (DDE), and other organochlorine compounds. The wax strain could also completely remove 20 mg kg-1 of DDT from both sterile and non-sterile soils in 20 days. This study demonstrates the significant potential use of Pseudoxanthomonas sp. wax for the bioremediation of DDT in the environment. PMID:24031514

  20. Luteimonas arsenica sp. nov., an arsenic-tolerant bacterium isolated from arsenic-contaminated soil.

    PubMed

    Mu, Yao; Pan, Yunfan; Shi, Wanxia; Liu, Lan; Jiang, Zhao; Luo, Xuesong; Zeng, Xian-Chun; Li, Wen-Jun

    2016-06-01

    A Gram-stain-negative, rod-shaped bacterium that formed yellow and viscous colonies was isolated from arsenic-contaminated soil of the Jianghan plain, Hubei Province, China, and it was designated 26-35T. This strain was capable of resisting arsenate and arsenite with MICs of 40 and 20 mM, respectively. The 16S rRNA gene of the novel isolate displayed 96.7-94.2 % sequence similarities to those of other known species of the genus Luteimonas. The respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content was 71.4 mol%. The predominant cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0, iso-C11 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic and physiological analysis indicated that the isolate represents a novel species of the genus Luteimonas, for which the name Luteimonas arsenica sp. nov. is proposed. The type strain is 26-35T (=KCTC 42824T=CCTCC AB 2014326T). PMID:26978245

  1. Paenibacillus pini sp. nov., a cellulolytic bacterium isolated from the rhizosphere of pine tree.

    PubMed

    Kim, Byung-Chun; Lee, Kang Hyun; Kim, Mi Na; Kim, Eun-Mi; Min, Sung Ran; Kim, Hyun Soon; Shin, Kee-Sun

    2009-12-01

    Strain S22(T), a novel cellulolytic bacterium was isolated from the rhizosphere of pine trees. This isolate was Gram-reaction positive, motile and rods, and formed terminal or subterminal ellipsoidal spores. S22(T) represented positive activity for catalase, oxidase, esterase (C4), esterase lipase (C8), beta-galactosidase, leucine arylamidase, and hydrolysis of esculin. It contained meso-diaminopimelic acid as the diagnostic dia-mino acid in the cell-wall. The predominant isoprenoid quinone was menaquinone 7 (MK-7), and the major cellular fatty acids were anteiso-C(15:0) (52.9%), iso-Ci(16:0) (11.3%), and iso-C(15:0) (10.0%). The DNA G+C content was 43.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this isolate belonged to the family Paenibacillaceae. S22(T) exhibited less than 97.0% 16S rRNA gene similarity with all relative type strains in the genus Paenibacillus, and the most closely related strains were Paenibacillus anaericanus MH21(T) and Paenibacillus ginsengisoli Gsoil 1638(T), with equal similarities of 95.8%. This polyphasic evidence suggested that strain S22(T) should be considered a novel species in the genus Paenibacillus, for which the name, Paenibacillus pini sp. nov., is proposed. The type strain is S22(T) (=KCTC 13694(T) =KACC 14198(T) =JCM 16418(T)). PMID:20127462

  2. Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment.

    PubMed

    Wu, Wen-Jie; Liu, Qian-Qian; Chen, Guan-Jun; Du, Zong-Jun

    2015-07-01

    A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08(T), was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5-8.0 and with 2-3% (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88-90% sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08(T) ( = KCTC 42261(T) = CICC 10901(T)). PMID:25866024

  3. Degradation of Reactive Black 5 dye by a newly isolated bacterium Pseudomonas entomophila BS1.

    PubMed

    Khan, Sana; Malik, Abdul

    2016-03-01

    The textile and dye industries are considered as one of the major sources of environmental pollution. The present study was conducted to investigate the degradation of the azo dye Reactive Black 5 (RB 5) using a bacterium isolated from soil samples collected around a textile industry. The bacterial strain BS1 capable of degrading RB 5 was isolated and identified as Pseudomonas entomophila on the basis of 16S rDNA sequencing. The effects of different parameters on the degradation of RB 5 were studied to find out the optimal conditions required for maximum degradation, which was 93% after 120 h of incubation. Static conditions with pH in the range of 5-9 and a temperature of 37 °C were found to be optimum for degrading RB 5. Enzyme assays demonstrated that P. entomophila possessed azoreductase, which played an important role in degradation. The enzyme was dependent on flavin mononucleotide and NADH for its activity. Furthermore, a possible degradation pathway of the dye was proposed through gas chromatography - mass spectrometry analysis, which revealed that the metabolic products were naphthalene-1,2-diamine and 4-(methylsulfonyl) aniline. Thus the ability of this indigenous bacterial isolate for simultaneous decolorization and degradation of the azo dye signifies its potential application for treatment of industrial wastewaters containing azo dyes. PMID:26911309

  4. Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates

    SciTech Connect

    Jeffrey, W.H.; Paul, J.H. )

    1990-05-01

    One assumption made in bacterial production estimates from ({sup 3}H)thymidine incorporation is that all heterotrophic bacteria can incorporate exogenous thymidine into DNA. Heterotrophic marine bacterium isolates from Tampa Bay, Fla., Chesapeake Bay, Md., and a coral surface microlayer were examined for thymidine uptake (transport), thymidine incorporation, the presence of thymidine kinase genes, and thymidine kinase enzyme activity. Of the 41 isolates tested, 37 were capable of thymidine incorporation into DNA. The four organisms that could not incorporate thymidine also transported the thymidine poorly and lacked thymidine kinase activity. Attempts to detect thymidine kinase genes in the marine isolates by molecular probing with gene probes made from Escherichia coli and herpes simplex virus thymidine kinase genes proved unsuccessful. To determine if the inability to incorporate thymidine was due to the lack of thymidine kinase, one organism, Vibro sp. strain DI9, was transformed with a plasmid (pGQ3) that contained an E. coli thymidine kinase gene. Although enzyme assays indicated high levels of thymidine kinase activity in transformants, these cells still failed to incorporate exogenous thymidine into DNA or to transport thymidine into cells. These results indicate that the inability of certain marine bacteria to incorporate thymidine may not be solely due to the lack of thymidine kinase activity but may also be due to the absence of thymidine transport systems.

  5. Draft Genome Sequence of the Polyhydroxyalkanoate-Producing Bacterium Burkholderia sacchari LMG 19450 Isolated from Brazilian Sugarcane Plantation Soil

    PubMed Central

    Alexandrino, Paulo Moises Raduan; Mendonça, Thatiane Teixeira; Guamán Bautista, Linda Priscila; Cherix, Juliano; Lozano-Sakalauskas, Gabriela Cazonato; Fujita, André; Ramos Filho, Edmar; Long, Paul; Padilla, Gabriel; Taciro, Marilda Keico; Gomez, José Gregório Cabrera

    2015-01-01

    Burkholderia sacchari LMG 19450, isolated from the soil of a sugarcane plantation in Brazil, accumulates large amounts of polyhydroxyalkanoates from sucrose, xylose, other carbohydrates, and organic acids. We present the draft genome sequence of this industrially relevant bacterium, which is 7.2 Mb in size and has a G+C content of 64%. PMID:25953171

  6. Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil.

    PubMed

    Tonomura, Mimori; Ehara, Ayaka; Suzuki, Haruo; Amachi, Seigo

    2015-01-01

    Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified. PMID:25977440

  7. Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil

    PubMed Central

    Tonomura, Mimori; Ehara, Ayaka; Suzuki, Haruo

    2015-01-01

    Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified. PMID:25977440

  8. Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China.

    PubMed

    Peng, Zixin; Wang, Wei; Hu, Yujie; Li, Fengqin

    2016-01-01

    Daptomycin-resistant Enterococcus hirae R17 was isolated from retail pork sold at a free-trade market in Beijing, China. The complete genome sequence of R17 contains a circular 2,886,481-bp chromosome and a circular 73,574-bp plasmid. Genes involved in cell envelope homeostasis of this bacterium were identified by whole-genome analysis. PMID:27340071

  9. A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

    PubMed

    Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

    2016-01-01

    Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS. PMID:26826831

  10. Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea.

    PubMed

    Hwangbo, Kyeong; Um, Yurry; Chung, Hee; Yoo, Jemin; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min; Lee, Yi

    2016-01-01

    Dyella thiooxydans ATSB10 (KACC 12756(T) = LMG 24673(T)) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sunflower plants. In this study, we completely sequenced the genome of D. thiooxydans ATSB10 and identified the genes involved in thiosulfate oxidation and the metabolism of aromatic intermediates. PMID:27340060

  11. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment.

    PubMed

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M P

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. PMID:25838495

  12. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment

    PubMed Central

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant’Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. PMID:25838495

  13. Complete genome sequence of Agarivorans gilvus WH0801(T), an agarase-producing bacterium isolated from seaweed.

    PubMed

    Zhang, Pujuan; Rui, Junpeng; Du, Zongjun; Xue, Changhu; Li, Xiangzhen; Mao, Xiangzhao

    2016-02-10

    Agarivorans gilvus WH0801(T), an agarase-producing bacterium, was isolated from the surface of seaweed. Here, we present the complete genome sequence, which consists of one circular chromosome of 4,416,600 bp with a GC content of 45.9%. This genetic information will provide insight into biotechnological applications of producing agar for food and industry. PMID:26689482

  14. Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa

    PubMed Central

    Chen, Mingyue; Lin, Li; Zhang, Yanming; Sun, Li

    2013-01-01

    Klebsiella oxytoca strain SA2 is an endophytic nitrogen-fixing bacterium isolated from the pioneer grass Psammochloa villosa, which grows in the moving sand dunes of Ordos Plateau, China. The SA2 genome sequence provides the genetic background for understanding its endophytic lifestyle and survival in association with grass in nitrogen-poor environments. PMID:23950120

  15. Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa.

    PubMed

    Chen, Mingyue; Lin, Li; Zhang, Yanming; Sun, Li; An, Qianli

    2013-01-01

    Klebsiella oxytoca strain SA2 is an endophytic nitrogen-fixing bacterium isolated from the pioneer grass Psammochloa villosa, which grows in the moving sand dunes of Ordos Plateau, China. The SA2 genome sequence provides the genetic background for understanding its endophytic lifestyle and survival in association with grass in nitrogen-poor environments. PMID:23950120

  16. Complete genome sequence of a keratin-degrading bacterium Chryseobacterium gallinarum strain DSM 27622(T) isolated from chicken.

    PubMed

    Park, Gun-Seok; Hong, Sung-Jun; Jung, Byung Kwon; Khan, Abdur Rahim; Park, Yeong-Jun; Park, Chang Eon; Lee, Ara; Kwak, Yunyoung; Lee, Yong-Jik; Lee, Dong-Woo; Lee, Changhee; Park, Choi Kyu; Shin, Jae-Ho

    2015-10-10

    Chryseobacterium gallinarum strain DSM 27622(T) is a keratin-degrading bacterium belonging to the class Flavobacteriia, which was isolated from chicken. Here, we report the 4633,632bp complete genome sequence of the strain DSM 27622(T) with 4161 genes. PMID:26209507

  17. Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste.

    PubMed

    Park, Gun-Seok; Hong, Sung-Jun; Lee, Chang-Hyun; Khan, Abdur Rahim; Ullah, Ihsan; Jung, Byung Kwon; Choi, JungBae; Kwak, Yunyoung; Back, Chang-Gi; Jung, Hee-Young; Shin, Jae-Ho

    2014-01-01

    Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes. PMID:25428979

  18. Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site.

    PubMed

    Lim, Yan-Lue; Ee, Robson; Yong, Delicia; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

    2015-11-20

    Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens. PMID:26393955

  19. Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese

    PubMed Central

    Velly, H.; Abraham, A.-L.; Loux, V.; Delacroix-Buchet, A.; Fonseca, F.; Bouix, M.

    2014-01-01

    Lactococcus lactis is a lactic acid bacterium used in the production of many fermented foods, such as dairy products. Here, we report the genome sequence of L. lactis subsp. lactis TOMSC161, isolated from nonscalded curd pressed cheese. This genome sequence provides information in relation to dairy environment adaptation. PMID:25377704

  20. Complete Genome Sequence of Raoultella ornithinolytica Strain S12, a Lignin-Degrading Bacterium Isolated from Forest Soil.

    PubMed

    Bao, Wenying; Zhou, Yun; Jiang, Jingwei; Xu, Zhihui; Hou, Liyuan; Leung, Frederick Chi-Ching

    2015-01-01

    We report the complete genome sequence of Raoultella ornithinolytica strain S12, isolated from a soil sample collected from areas bordering rotten wood and wet soil on Mt. Zijin, Nanjing. The complete genome of this bacterium may contribute toward the discovery of efficient lignin-degrading pathways. PMID:25792045

  1. Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China

    PubMed Central

    Peng, Zixin; Wang, Wei; Hu, Yujie

    2016-01-01

    Daptomycin-resistant Enterococcus hirae R17 was isolated from retail pork sold at a free-trade market in Beijing, China. The complete genome sequence of R17 contains a circular 2,886,481-bp chromosome and a circular 73,574-bp plasmid. Genes involved in cell envelope homeostasis of this bacterium were identified by whole-genome analysis. PMID:27340071

  2. Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea

    PubMed Central

    Hwangbo, Kyeong; Um, Yurry; Chung, Hee; Yoo, Jemin; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min

    2016-01-01

    Dyella thiooxydans ATSB10 (KACC 12756T = LMG 24673T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sunflower plants. In this study, we completely sequenced the genome of D. thiooxydans ATSB10 and identified the genes involved in thiosulfate oxidation and the metabolism of aromatic intermediates. PMID:27340060

  3. Introduction of perfluoroalkyl chain into the esterifying moiety of bacteriochlorophyll c in the green sulfur photosynthetic bacterium Chlorobaculum tepidum by pigment biosynthesis.

    PubMed

    Saga, Yoshitaka; Yamashita, Hayato; Hirota, Keiya

    2016-09-15

    The green sulfur photosynthetic bacterium Chlorobaculum (Cba.) tepidum was grown in liquid cultures containing perfluoro-1-decanol, 1H,1H,2H,2H-heptadecafluoro-1-decanol [CF3(CF2)7(CH2)2OH] or 1H,1H-nonadecafluoro-1-decanol [CF3(CF2)8CH2OH], to introduce rigid and fluorophilic chains into the esterifying moiety of light-harvesting bacteriochlorophyll (BChl) c. Exogenous 1H,1H,2H,2H-heptadecafluoro-1-decanol was successfully attached to the 17(2)-carboxy group of bacteriochlorophyllide (BChlide) c in vivo: the relative ratio of the unnatural BChl c esterified with this perfluoroalcohol over the total BChl c was 10.3%. Heat treatment of the liquid medium containing 1H,1H,2H,2H-heptadecafluoro-1-decanol with β-cyclodextrin before inoculation increased the relative ratio of the BChl c derivative esterified with this alcohol in the total BChl c in Cba. tepidum. In a while, 1H,1H-nonadecafluoro-1-decanol was not attached to BChlide c in Cba. tepidum, which was grown by its supplementation. These results suggest that the rigidity close to the hydroxy group of the esterifying alcohol is not suitable for the recognition by the BChl c synthase called BchK in Cba. tepidum. The unnatural BChl c esterified with 1H,1H,2H,2H-heptadecafluoro-1-decanol participated in BChl c self-aggregates in chlorosomes. PMID:27427396

  4. Thermosipho activus sp. nov., a thermophilic, anaerobic, hydrolytic bacterium isolated from a deep-sea sample.

    PubMed

    Podosokorskaya, Olga A; Bonch-Osmolovskaya, Elizaveta A; Godfroy, Anne; Gavrilov, Sergey N; Beskorovaynaya, Daria A; Sokolova, Tatyana G; Kolganova, Tatyana V; Toshchakov, Stepan V; Kublanov, Ilya V

    2014-09-01

    A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift-s3(T), was isolated from a deep-sea sample containing Riftia pachyptila sheath from Guaymas Basin, Gulf of California. Cells of the novel isolate were rods, 0.3-0.8 µm in width and 1.5-10 µm in length, surrounded by a sheath-like structure (toga). Strain Rift-s3(T) grew at temperatures ranging from 44 to 75 °C, at pH 5.5 to 8.0, and with NaCl concentrations of 3 to 60 g l(-1). Under optimum conditions (65 °C, pH 6.0, NaCl 25 g l(-1)), the doubling time was 30 min. The isolate was able to ferment mono-, oligo- and polysaccharides including cellulose, chitin, xylan and pectin, and proteins including β-keratins, casein and gelatin. Acetate, hydrogen and carbon dioxide were the main products of glucose fermentation. The G+C content of the DNA was 30 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed the affiliation of strain Rift-s3(T) with the genus Thermosipho, with Thermosipho atlanticus Ob7(T) as the closest relative (96.5 % 16S rRNA gene sequence similarity). Based on the phylogenetic analysis and physiological properties of the novel isolate we propose a novel species of the genus Thermosipho, Thermosipho activus sp. nov., with Rift-s3(T) ( = DSM 26467(T) = VKM B-2803(T)) as the type strain. PMID:24994778

  5. Alkaline Anaerobic Respiration: Isolation and Characterization of a Novel Alkaliphilic and Metal-Reducing Bacterium

    PubMed Central

    Ye, Qi; Roh, Yul; Carroll, Susan L.; Blair, Benjamin; Zhou, Jizhong; Zhang, Chuanlun L.; Fields, Matthew W.

    2004-01-01

    Iron-reducing enrichments were obtained from leachate ponds at the U.S. Borax Company in Boron, Calif. Based on partial small-subunit (SSU) rRNA gene sequences (approximately 500 nucleotides), six isolates shared 98.9% nucleotide identity. As a representative, the isolate QYMF was selected for further analysis. QYMF could be grown with Fe(III)-citrate, Fe(III)-EDTA, Co(III)-EDTA, or Cr(VI) as electron acceptors, and yeast extract and lactate could serve as electron donors. Growth during iron reduction occurred over the pH range of 7.5 to 11.0 (optimum, pH 9.5), a sodium chloride range of 0 to 80 g/liter (optimum, 20 g/liter), and a temperature range of 4 to 45°C (optimum, approximately 35°C), and iron precipitates were formed. QYMF was a strict anaerobe that could be grown in the presence of borax, and the cells were straight rods that produced endospores. Sodium chloride and yeast extract stimulated growth. Phylogenetic analysis of the SSU rRNA gene indicated that the bacterium was a low-G+C gram-positive microorganism and had 96 and 92% nucleotide identity with Alkaliphilus transvaalensis and Alkaliphilus crotonatoxidans, respectively. The major phospholipid fatty acids were 14:1, 16:1ω7c, and 16:0, which were different from those of other alkaliphiles but similar to those of reported iron-reducing bacteria. The results demonstrated that the isolate might represent a novel metal-reducing alkaliphilic species. The name Alkaliphilus metalliredigens sp. nov. is proposed. The isolation and activity of metal-reducing bacteria from borax-contaminated leachate ponds suggest that bioremediation of metal-contaminated alkaline environments may be feasible and have implications for alkaline anaerobic respiration. PMID:15345448

  6. Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake.

    PubMed

    Dimitriu, Pedro A; Shukla, Sanjay K; Conradt, Jennifer; Márquez, M Carmen; Ventosa, Antonio; Maglia, Anne; Peyton, Brent M; Pinkart, Holly C; Mormile, Melanie R

    2005-11-01

    A novel alkaliphilic bacterium, strain 4CAT, was isolated from decomposing wood taken from the shore of Soap Lake, a saline, alkaline lake in Grant County, WA, USA. Cells of the isolate were Gram-negative, asporogenous, short, motile rods that utilized only a limited range of organic acids as sole carbon and energy sources. In addition to oxygen, the strain possessed the ability to reduce in the presence of acetate. Strain 4CAT was oxidase- and catalase-positive; it degraded Tween 60, but not DNA, urea, gelatin or starch. It grew at pH values from 7.5 to 11.0, with optimum growth occurring at pH 9.0, and growth was observed in NaCl concentrations of 0.2-1.3 M, with optimum growth at 0.8 M NaCl. The optimum temperature for growth was 37 degrees C. Strain 4CAT was resistant to erythromycin, bacitracin, novobiocin, polymyxin B, neomycin, gentamicin, streptomycin, carbenicillin, rifampicin and tetracycline, and was susceptible to nalidixic acid, chloramphenicol, ampicillin and penicillin. The isolate's 16S rRNA gene sequence indicated that it belonged to the gamma-Proteobacteria, showing 90-94 % similarity to its closest relatives. Maximum-likelihood phylogenetic inferences placed strain 4CAT within a novel lineage related to the marine bacterial genera Neptunomonas and Marinobacterium. The DNA G+C content of the isolate was 47.4 mol%. On the basis of genotypic and phenotypic characterization, it was concluded that strain 4CAT should be placed in a separate taxon as a novel genus and species, with the proposed name Nitrincola lacisaponensis gen. nov., sp. nov. The type strain is 4CAT (=ATCC BAA-920T=DSM 16316T). PMID:16280482

  7. Isolation and characterization of the homoacetogenic thermophilic bacterium Moorella glycerini sp. nov.

    SciTech Connect

    Slobodkin, A.; Wiegel, J.; Reysenbach, A.L.

    1997-10-01

    A thermophilic, anaerobic, spore-forming bacterium (strain JW/AS-Y6) was isolated from a mixed sediment-water sample from a hot spring (Calcite Spring area) at Yellowstone National Park. The vegetative cells of this organism were straight rods, 0.5 to 0.6 by 3.0 to 6.5 {mu}m. Cells occurred singly and exhibited a slight tumbling motility. They formed round refractile endospores in terminal swollen sporangia. Cells stained gram positive. The temperature range for growth at pH 6.8 was 43 to 65{degrees}C, with optimum growth at 58{degrees}C. The range for growth at 60{degrees}C (pH{sup 60C}; with the pH meter calibrated at 60{degrees}C) was 5.9 to 7.8, with an optimum pH{sub 60C} of 6.3 to 6.5. The substrates utilized included glycerol, glucose, fructose, mannose, galactose, xylose, lactate, glycerate, pyruvate, and yeast extract. In the presence of CO{sub 2}, acetate was the only organic product from glyerol and carbohydrate fermentation. No H{sub 2} was produced during growth. The strain was not able to grow chemolithotrophically at the expense of H{sub 2}-CO{sub 2}; however, suspensions of cells in the exponential growth phase consumed H{sub 2}. The bacterium reduced fumarate to succinate and thiosulfate to elemental sulfur. Growth was exhibited by ampicillin, chloramphenicol, erythromycin, rifampin, and tetracycline, but not by streptomycin. The G+C content of the DNA was 54.5 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolate in the Gram type-positive Bacillus-Clostridium subphylum. On the basis of physiological properties and phylogenetic analysis we propose that the isolated strain constitutes a new species, Moorella glycerini; the type strain is JW/AS-Y6 (= DSM 11254 = ATCC 700316).

  8. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium.

    PubMed Central

    Beller, H R; Spormann, A M; Sharma, P K; Cole, J R; Reinhard, M

    1996-01-01

    A novel sulfate-reducing bacterium isolated from fuel-contaminated subsurface soil, strain PRTOL1, mineralizes toluene as the sole electron donor and carbon source under strictly anaerobic conditions. The mineralization of 80% of toluene carbon to CO2 was demonstrated in experiments with [ring-U-14C]toluene; 15% of toluene carbon was converted to biomass and nonvolatile metabolic by-products, primarily the former. The observed stoichiometric ratio of moles of sulfate consumed per mole of toluene consumed was consistent with the theoretical ratio for mineralization of toluene coupled with the reduction of sulfate to hydrogen sulfide. Strain PRTOL1 also transforms o- and p-xylene to metabolic products when grown with toluene. However, xylene transformation by PRTOL1 is slow relative to toluene degradation and cannot be sustained over time. Stable isotope-labeled substrates were used in conjunction with gas chromatography-mass spectrometry to investigate the by-products of toluene and xylene metabolism. The predominant by-products from toluene, o-xylene, and p-xylene were benzylsuccinic acid, (2-methylbenzyl)succinic acid, and 4-methylbenzoic acid (or p-toluic acid), respectively. Metabolic by-products accounted for nearly all of the o-xylene consumed. Enzyme assays indicated that acetyl coenzyme A oxidation proceeded via the carbon monoxide dehydrogenase pathway. Compared with the only other reported toluene-degrading, sulfate-reducing bacterium, strain PRTOL1 is distinct in that it has a novel 16S rRNA gene sequence and was derived from a freshwater rather than marine environment. PMID:8919780

  9. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal

    NASA Astrophysics Data System (ADS)

    Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W.

    2000-10-01

    Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10 9.

  10. Isolation of Aureimonas altamirensis, a Brucella canis-like bacterium, from an edematous canine testicle.

    PubMed

    Reilly, Thomas J; Calcutt, Michael J; Wennerdahl, Laura A; Williams, Fred; Evans, Tim J; Ganjam, Irene K; Bowman, Jesse W; Fales, William H

    2014-11-01

    Microbiological and histological analysis of a sample from a swollen testicle of a 2-year-old Border Collie dog revealed a mixed infection of the fungus Blastomyces dermatitidis and the Gram-negative bacterium Aureimonas altamirensis. When subjected to an automated microbial identification system, the latter isolate was provisionally identified as Psychrobacter phenylpyruvicus, but the organism shared several biochemical features with Brucella canis and exhibited agglutination, albeit weakly, with anti-B. canis antiserum. Unequivocal identification of the organism was only achieved by 16S ribosomal RNA gene sequencing, ultimately establishing the identity as A. altamirensis. Since its first description in 2006, this organism has been isolated infrequently from human clinical samples, but, to the authors' knowledge, has not been reported from a veterinary clinical sample. While of unknown clinical significance with respect to the pathology observed for the polymicrobial infection described herein, it highlights the critical importance to unambiguously identify the microbe for diagnostic, epidemiological, infection control, and public health purposes. PMID:25292192

  11. Isolation and Identification of a Red Pigment from the Antarctic Bacterium Shewanella frigidimarina.

    PubMed

    Martín-Cerezo, Maria Luisa; García-López, Eva; Cid, Cristina

    2015-01-01

    The present study dealt with the isolation, identification and characterization of pigments from red snow samples of the Quito coastal front glacier (S 62º 27,217', W 059º 45,960') in Greenwich, Archipelago South Shetland, Antarctica, during summer 2013. As a strain of Shewanella was found to be the most common and abundant species with maximum red color production, the pigment -contained in the protein fraction- was isolated and characterized by high performance liquid chromatography (HPLC), two-dimensional fluorescence Difference Gel Electrophoresis (2-D DIGE) and matrix- assisted laser desorption/ionization-time of flight mass spectrometry (MALDI/TOF/TOF). The identified pigment is a cytochrome c3 with apparent molecular weight of 10 kDa and apparent pI around 4.5. The maximum pigment concentration was produced at warm temperatures, 28ºC, and with increasing exposure time to UV radiation. Here we demonstrate that the synthesis of cytochrome c3 by the Antarctic bacterium is due to thermal adaptation and/or adaptation to radiation. Further, pigments such as cytochrome c3 enable this bacterial species to use an anaerobic and ferric metabolism. In addition, this study draws attention to the relevance of adaptation investigations; to the study of in vivo monitoring of environmental warming and UV radiation due to global warming; and to the study of the potential habitability of other worlds in the Solar System and beyond. PMID:26369950

  12. Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces.

    PubMed

    Velázquez, Encarna; de Miguel, Trinidad; Poza, Margarita; Rivas, Raúl; Rosselló-Mora, Ramón; Villa, Tomás G

    2004-01-01

    During a search for xylan-degrading micro-organisms, a sporulated bacterium was recovered from recent and old cow dung and rectal samples. The isolates were identified as members of a novel species of the genus Paenibacillus, based on 16S rRNA gene sequences. According to the results of phylogenetic analysis, the most closely related species was Paenibacillus azoreducens. Phenotypic and chemotaxonomic analyses and DNA-DNA hybridization experiments also showed that the isolates belonged to a novel species of the genus Paenibacillus. The novel species is a facultatively anaerobic, motile, Gram-variable, sporulated rod. The spores of this rod-shaped micro-organism occur in slightly swollen sporangia and are honeycomb-shaped. The main fatty acid is anteiso-branched C(15:0). Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. The novel species produces a wide variety of hydrolytic enzymes, such as xylanases, cellulases, amylases, gelatinase, urease and beta-galactosidase. On the contrary, it does not produce caseinase, phenylalanine deaminase or lysine decarboxylase. According to the data obtained in this work, the strains belong to a novel species, for which the name Paenibacillus favisporus sp. nov. is proposed (type strain, GMP01T=LMG 20987T=CECT 5760T). PMID:14742459

  13. Biodegradation of the neonicotinoid insecticide Acetamiprid by bacterium Pigmentiphaga sp. strain AAP-1 isolated from soil.

    PubMed

    Wang, Guangli; Yue, Wenlong; Liu, Yuan; Li, Feng; Xiong, Minhua; Zhang, Hui

    2013-06-01

    The Acetamiprid-degrading bacterium AAP-1 was isolated from contaminated soil, and identified as Pigmentiphaga sp. combined traditionary categorization method with modern molecule method. The strain could utilize Acetamiprid as the sole carbon, nitrogen and energy source for growth and metabolized 100 mgL(-1) Acetamiprid within 2.5h. During the degradation of Acetamiprid, one N-deacetylation metabolite, was characterized by FT-IR, GC-MS and NMR analysis. A novel microbial biodegradation pathway for Acetamiprid was proposed on the basis of the metabolite. Compared with uninoculated soils, the addition of the AAP-1 strain into soils treated with Acetamiprid gained a higher degradation rate, and the bacteria community analysis by T-RFLP in contaminated soil recovered after inoculation of the AAP-1 strain. On the basis of these results, strain AAP-1 has the potential to be used in the bioremediation of Acetamiprid-contaminated environments. This is the first report of Acetamiprid-degrading isolate from the genus of Pigmentiphaga. PMID:23624055

  14. Isolation and characterization of an Enterococcus-like bacterium causing muscle necrosis and mortality in Macrobrachium rosenbergii in Taiwan.

    PubMed

    Cheng, W; Chen, J C

    1998-10-01

    A Gram-positive, ovoid, diplococoid bacterium tentatively identified as Enterococcus-like was isolated from diseased Macrobrachium rosenbergii in Taiwanese aquaculture ponds. The diseased prawns displayed poor growth, anorexia, inactivity, opaque and whitish musculature, and mortality. In histological preparations, melanized hemocytic granulomas were seen in the connective tissue around hemal sinuses together with hemocytic aggregation in necrotic musculature. Five isolates of diplococci were collected from diseased prawns at 4 farms and these were evaluated for 93 characteristics including morphology, physiology, biochemistry and sensitivity to antibiotics. The results indicated that the isolates belonged to a single species. They grew in 0.5 to 6.0% NaCl, at 10 to 40 degrees C, at pH 9.6 and on bile esculin medium, gave positive pyrrolidonylarylamidase, arginine dehydrolase and Voges-Proskauer tests, were resistant to bacitracin and SXT, and were CAMP-negative and non-hemolytic on sheep blood agar. These findings indicated an Enterococcus-like bacterium closely related to Enterococcus seriolicida (recently reduced to synonymy with Lactococcus garvieae). Experimental injection of 3 x 10(5) cells of strain KM002 of this Enterococcus-like bacterium into the ventral sinus of the prawn cephalothorax caused 100% mortality in 11 d, and induced muscular necrosis and hepatopancreatitis, gross signs and histopathology similar to those observed in the naturally infected prawns. It was concluded that this Enterococcus-like bacterium was the etiological agent associated with mortality of the farmed, diseased prawns. PMID:9828405

  15. Lentibacillus amyloliquefaciens sp. nov., a halophilic bacterium isolated from saline sediment sample.

    PubMed

    Wang, Jing-Li; Ma, Ke-Dong; Wang, Yan-Wei; Wang, Hui-Min; Li, Yan-Bin; Zhou, Shan; Chen, Xiao-Rong; Kong, De-Long; Guo, Xiang; He, Ming-Xiong; Ruan, Zhi-Yong

    2016-02-01

    A Gram-stain positive, non-motile, non-sporogenous, aerobic, rod-shaped and halophilic bacterium, designated LAM0015(T), was isolated from a saline sediment sample collected from Yantai City in China. The isolate was found to be able to grow at NaCl concentrations of 5-25 % (w/v) (optimum: 7-12 %), 15-45 °C (optimum: 35 °C) and pH 5.0-9.0 (optimum: 7.0). The major fatty acids were determined to be anteiso-C15:0 and anteiso-C17:0. The predominant respiratory quinone was identified as MK-7. The cell wall peptidoglycan was determined to contain meso-diaminopimelic acid. The polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, five phospholipids and one glycolipid. The DNA G+C content was 43.1 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate belongs within the genus Lentibacillus and is closely related to Lentibacillus persicus DSM 22530(T), Lentibacillus salicampi JCM 11462(T) and Lentibacillus jeotgali JCM 15795(T) with 97.3, 96.7 and 96.4 % sequence similarity, respectively. The DNA-DNA hybridization value between LAM0015(T) and L. persicus DSM 22530(T) was 51.2 ± 1.4 %. Based on its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0015(T) is concluded to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus amyloliquefaciens sp. nov. is proposed. The type strain is LAM0015(T) (=ACCC 06401(T) = JCM 19838(T)). PMID:26545789

  16. Draft Genome Sequence of the Endophytic Strain Rhodococcus kyotonensis KB10, a Potential Biodegrading and Antibacterial Bacterium Isolated from Arabidopsis thaliana

    PubMed Central

    Hong, Chi Eun; Jo, Sung Hee

    2016-01-01

    Rhodococcus kyotonensis KB10 is an endophytic bacterium isolated from Arabidopsis thaliana. The organism showed mild antibacterial activity against the phytopathogen Pseudomonas syringae pv. tomato DC3000. This study reports the genome sequence of R. kyotonensis KB10. This bacterium contains an ectoine biosynthesis gene cluster and has the potential to degrade nitroaromatic compounds. The identified bacterium may be a suitable biocontrol agent and degrader of environmental pollutants. PMID:27389269

  17. Draft Genome Sequence of the Endophytic Strain Rhodococcus kyotonensis KB10, a Potential Biodegrading and Antibacterial Bacterium Isolated from Arabidopsis thaliana.

    PubMed

    Hong, Chi Eun; Jo, Sung Hee; Jeong, Haeyoung; Park, Jeong Mee

    2016-01-01

    Rhodococcus kyotonensis KB10 is an endophytic bacterium isolated from Arabidopsis thaliana The organism showed mild antibacterial activity against the phytopathogen Pseudomonas syringae pv. tomato DC3000. This study reports the genome sequence of R. kyotonensis KB10. This bacterium contains an ectoine biosynthesis gene cluster and has the potential to degrade nitroaromatic compounds. The identified bacterium may be a suitable biocontrol agent and degrader of environmental pollutants. PMID:27389269

  18. Isolation and characterization of a novel poly(vinyl alcohol)-degrading bacterium, Sphingopyxis sp. PVA3.

    PubMed

    Yamatsu, Atsushi; Matsumi, Rie; Atomi, Haruyuki; Imanaka, Tadayuki

    2006-10-01

    We have isolated a poly(vinyl alcohol) (PVA)-degrading bacterium from an activated sludge sample obtained from the drainage of a dyeing factory. Enrichment cultures were performed in media containing PVA as the sole or major carbon source. After several rounds of cultivation on liquid and solid media, we were able to isolate a single colony with PVA-degrading ability (strain PVA3). The bacterium could degrade PVA in the absence of symbionts or cofactors such as pyrroloquinoline quinone (PQQ). Over 90% of PVA, at an initial concentration of 0.1%, was degraded within a 6-day cultivation. Degradation was confirmed by both iodometric methods and gel permeation chromatography. Examination of the PVA attached to the cells revealed a large increase in carbonyl groups, suggesting the oxidation of hydroxyl groups of the polymer on the surfaces of cells. Addition of PQQ to the culture medium did not enhance the growth and the PVA-degrading rates of strain PVA3. Furthermore, we found that cells grown on PVA generated hydrogen peroxide upon the addition of PVA. The results strongly suggest that the initial oxidation of PVA is mediated via a PVA oxidase, and not a PQQ-dependent dehydrogenase. A biochemical and phylogenetic characterization of the bacterium was performed. The sequence of the 16S ribosomal RNA gene of the bacterium indicated a phylogenetic position of the strain within the genus Sphingopyxis, and the strain was therefore designated Sphingopyxis sp. PVA3. PMID:16583228

  19. Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice.

    PubMed

    Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

    2015-09-01

    A Gram-stain-negative, rod-shaped, orange bacterium (strain MDB1-A(T)) was isolated from ice samples collected from Midui glacier in Tibet, south-west China. Cells were aerobic and psychrotolerant (growth occurred at 0-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that it was a member of the genus Sphingomonas, with its closest relative being Sphingomonas glacialis C16y(T) (98.9% similarity). Q-10 was the predominant ubiquinone. C17 : 1ω6c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) were the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The polyamines detected were sym-homospermidine, spermidine and spermine. The G+C content of the genomic DNA was 63.6%. Based on data from this polyphasic analysis, strain MDB1-A(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas psychrolutea sp. nov. is proposed. The type strain is MDB1-A(T) ( = CGMCC 1.10106(T) = NBRC 109639(T)). PMID:26025946

  20. Degradation of polyester polyurethane by a newly isolated soil bacterium, Bacillus subtilis strain MZA-75.

    PubMed

    Shah, Ziaullah; Krumholz, Lee; Aktas, Deniz Fulya; Hasan, Fariha; Khattak, Mutiullah; Shah, Aamer Ali

    2013-11-01

    A polyurethane (PU) degrading bacterial strain MZA-75 was isolated from soil through enrichment technique. The bacterium was identified through 16S rRNA gene sequencing, the phylogenetic analysis indicated the strain MZA-75 belonged to genus Bacillus having maximum similarity with Bacillus subtilis strain JBE0016. The degradation of PU films by strain MZA-75 in mineral salt medium (MSM) was analyzed by scanning electron microscopy (SEM), fourier transform infra-red spectroscopy (FT-IR) and gel permeation chromatography (GPC). SEM revealed the appearance of widespread cracks on the surface. FTIR spectrum showed decrease in ester functional group. Increase in polydispersity index was observed in GPC, which indicates chain scission as a result of microbial treatment. CO2 evolution and cell growth increased when PU was used as carbon source in MSM in Sturm test. Increase in both cell associated and extracellular esterases was observed in the presence of PU indicated by p-Nitrophenyl acetate (pNPA) hydrolysis assay. Analysis of cell free supernatant by gas chromatography-mass spectrometry (GC-MS) revealed that 1,4-butanediol and adipic acid monomers were produced. Bacillus subtilis strain MZA-75 can degrade the soft segment of polyester polyurethane, unfortunately no information about the fate of hard segment could be obtained. Growth of strain MZA-75 in the presence of these metabolites indicated mineralization of ester hydrolysis products into CO2 and H2O. PMID:23536219

  1. Deinococcus puniceus sp. nov., a bacterium isolated from soil-irradiated gamma radiation.

    PubMed

    Lee, Jae-Jin; Srinivasan, Sathiyaraj; Lim, Sangyong; Joe, Minho; Im, Seonghun; Kim, Myung Kyum

    2015-04-01

    A Gram-positive, coccus-shaped, crimson-color-pigmented bacterium was isolated from soil irradiated with 5 kGy gamma radiation and was designated strain DY1(T). Cells showed growth at 10-30 °C and pH 7-11 and were oxidase-negative and catalase-positive. Phylogenetic analyses of the 16S rRNA gene showed that the strain DY1(T) belonged to the genus Deinococcus with sequence similarities to Deinococcus aquatilis CCUG 53370(T) (96.2 %) and Deinococcus navajonensis KR-114(T) (94.1 %). Strain DY1(T) showed low level of DNA relatedness with D. aquatilis CCUG 53370(T) (41.3 ± 3.9 %). The DNA G + C content of DY1(T) was 58.7 mol%. Predominant fatty acids were summed feature 3 (C16:1 ω7c/ω6c), C16:0, and C17:0. The major amino acids were D-alanine, L-glutamic acid, glycine, and L-ornithine in the peptidoglycan. The major polar lipids were unknown phosphoglycolipids (PGL). Strain DY1(T) has resistance to gamma radiation and was found to be a novel species. Therefore, the strain was designated as DY1(T) (=KCTC 33027(T) = JCM 18576(T)), and the name Deinococcus puniceus sp. nov. is herein proposed. PMID:25477066

  2. Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost.

    PubMed

    Kang, Myung-Suk; Im, Wan-Taek; Jung, Hae-Min; Kim, Myung Kyum; Goodfellow, Michael; Kim, Kwang Kyu; Yang, Hee-Chan; An, Dong-Shan; Lee, Sung-Taik

    2007-06-01

    A bacterial strain, TR7-06(T), which has cellulase and beta-glucosidase activities, was isolated from compost at a cattle farm near Daejeon, Republic of Korea. It was a Gram-positive, aerobic or facultatively anaerobic, non-motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas, with highest sequence similarity to Cellulomonas uda DSM 20107(T) (98.5 %). Cell wall analysis revealed the presence of type A4beta, L-orn-D-Glu peptidoglycan. The cell-wall sugars detected were mannose and glucose. The predominant menaquinone was MK-9(H(4)); MK-8(H(4)) was detected in smaller quantities. The major fatty acids were anteiso-C(15 : 0), C(16 : 0), C(14 : 0) and C(18 : 0). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that TR7-06(T) represents a novel species. The combined genotypic and phenotypic data show that strain TR7-06(T) (=KCTC 19030(T)=NBRC 100758(T)) merits description as the type strain of a novel Cellulomonas species, Cellulomonas composti sp. nov. PMID:17551039

  3. Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater.

    PubMed

    Zhang, Wen-wu; Fang, Ming-xu; Tan, Hai-qin; Zhang, Xin-qi; Wu, Min; Zhu, Xu-fen

    2012-09-01

    A novel Gram-negative, non-spore-forming, strictly anaerobic, heterotrophic bacterium, strain TY(T), was isolated from salty pickle wastewater. Cells were rod-shaped with comb-like flagella, slightly curved and very variable in length. Optimal growth occurred at 28 °C and pH 6.5. Cells were resistant to up to 50 g NaCl l(-1). Strain TY(T) produced acid from glycerol, sucrose, glucose, fructose and mannitol. The main fermentation products from glucose were acetic and propionic acids. Tests for acid phosphatase and naphthol-AS-BI-phosphohydrolase activities were positive. The major fatty acids were C(14 : 0) DMA (18.7 %), C(15 : 0) (15.4 %), anteiso-C(18 : 1) (15.2 %), C(11 : 0) (13.3 %) and summed feature 5 (C(17 : 1)ω7c and/or C(17 : 2)) (11.0 %). The DNA G+C content was 35.9 mol%. 16S rRNA gene sequence-based phylogenetic analysis indicated that strain TY(T) represented a novel species of the genus Pectinatus (sequence similarity to other members of the genus ranged from 93.2 to 94.8 %). Based on its phenotypic, genotypic and phylogenetic characteristics, strain TY(T) is proposed to represent a novel species, named Pectinatus brassicae sp. nov. (type strain TY(T) = JCM 17499(T) = DSM 24661(T)). PMID:22058316

  4. Colwellia asteriadis sp. nov., a marine bacterium isolated from the starfish Asterias amurensis.

    PubMed

    Choi, Eun Ju; Kwon, Hak Cheol; Koh, Hye Yeon; Kim, Young Sug; Yang, Hyun Ok

    2010-08-01

    A marine bacterial strain, KMD 002T, was isolated from an Amur starfish, Asterias amurensis, collected in the East Sea of Korea. Strain KMD 002T was a Gram-negative, beige-pigmented, rod-shaped bacterium. The strain was capable of growth at relatively low temperatures (4-25 degrees C) and over a broad pH range (pH 4.0-10.0). The major fatty acids were C16:1omega7c and/or iso-C15:0 2-OH and C16:0 and the predominant isoprenoid quinone was Q-8. The DNA G+C content of strain KMD 002T was 40.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain KMD 002T belonged to the genus Colwellia. However, various phenotypic properties as well as low 16S rRNA gene sequence similarities to members of the genus Colwellia (94.1-96.7%) suggested that strain KMD 002T is a representative of a novel species, for which the name Colwellia asteriadis sp. nov. is proposed. The type strain is KMD 002T (=KCCM 90077T =JCM 15608T). PMID:19801395

  5. Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine.

    PubMed

    Santini, Joanne M; Streimann, Illo C A; vanden Hoven, Rachel N

    2004-11-01

    A strictly anaerobic arsenate-respiring bacterium isolated from a gold mine in Bendigo, Victoria, Australia, belonging to the genus Bacillus is described. Cells are Gram-positive, motile rods capable of respiring with arsenate and nitrate as terminal electron acceptors using a variety of substrates, including acetate as the electron donor. Reduction of arsenate to arsenite is catalysed by a membrane-bound arsenate reductase that displays activity over a broad pH range. Synthesis of the enzyme is regulated; maximal activity is obtained when the organism is grown with arsenate as the terminal electron acceptor and no activity is detectable when it is grown with nitrate. Mass of the catalytic subunit was determined to be approximately 87 kDa based on ingel activity stains. The closest phylogenetic relative, based on 16S rRNA gene sequence analysis, is Bacillus arseniciselenatis, but DNA-DNA hybridization experiments clearly show that strain JMM-4(T) represents a novel Bacillus species, for which the name Bacillus macyae sp. nov. is proposed. The type strain is JMM-4(T) (=DSM 16346(T)=JCM 12340(T)). PMID:15545465

  6. Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat

    NASA Technical Reports Server (NTRS)

    Madigan, M. T.; Jung, D. O.; Woese, C. R.; Achenbach, L. A.

    2000-01-01

    A new species of purple nonsulfur bacteria isolated from an Antarctic microbial mat is described. The organism, designated strain ANT.BR, was mildly psychrophilic, growing optimally at 15-18 degrees C with a growth temperature range of 0-25 degrees C. Cells of strain ANT.BR were highly motile curved rods and spirals, contained bacteriochlorophyll a, and showed a multicomponent in vivo absorption spectrum. A specific phylogenetic relationship was observed between strain ANT.BR and the purple bacterium Rhodoferax fermentans FR2T, and the two organisms shared several physiological and other phenotypic properties, with the notable exception of growth temperature optimum. Tests of genomic DNA hybridization, however, showed Rfx. fermentans FR2T and strain ANT.BR to be genetically distinct bacteria. Because of its unique set of properties, especially its requirement for low growth temperatures, we propose to recognize strain ANT.BR as a new species of the genus Rhodoferax, Rhodoferax antarcticus, named for its known habitat, the Antarctic.

  7. Dysgonomonas alginatilytica sp. nov., an alginate-degrading bacterium isolated from a microbial consortium.

    PubMed

    Kita, Akihisa; Miura, Toyokazu; Okamura, Yoshiko; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Kato, Junichi; Nakashimada, Yutaka

    2015-10-01

    Gram-stain-negative, facultatively anaerobic, non-motile, non-spore-forming, rod-shaped bacterium, designated strain HUA-2T, was isolated from an alginate-degrading microbial consortium. Strain HUA-2T was related to Dysgonomonas capnocytophagoides JCM 16697T, Dysgonomonas macrotermitis JCM 19375T and Dysgonomonas mossii CCUG 43457T with 95.1 %, 94.1 % and 92.1 % 16S rRNA gene sequence similarity, respectively. The optimal growth temperature and pH for strain HUA-2T were 35 °C and pH 8.0, respectively. Enzyme production, major fermentation products from glucose, and the major cellular fatty acids were different from those of D. capnocytophagoides CCUG 17966T or other members of the genus Dysgonomonas. Therefore, strain HUA-2T is proposed to represent a novel species of the genus Dysgonomonas, for which we propose the name Dysgonomonas alginatilytica sp. nov. The type strain is HUA-2T ( = DSM 100214T = HUT 8134T). PMID:26297040

  8. Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea.

    PubMed

    Machado, Henrique; Giubergia, Sonia; Mateiu, Ramona Valentina; Gram, Lone

    2015-12-01

    A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic differences, strain S2753T is considered to represent a novel species of the genus Photobacterium. Furthermore, whole genome sequence analysis comparing S2753T and type-strains of closely related species of the genus Photobacterium also demonstrated that the strain is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T). PMID:26374506

  9. Marinobacter piscensis sp. nov., a moderately halophilic bacterium isolated from salty food in Tunisia.

    PubMed

    Hedi, Abdeljabbar; Cayol, Jean Luc; Sadfi, Najla; Fardeau, Marie-Laure

    2015-04-01

    An aerobic, Gram-negative, moderately halophilic bacterium, oxidase, and catalase positive-designated Abdou3(T), was isolated from salted traditional foods (Anchovies) in Tunisia. Cells were rod-shaped, non-spore-forming and motile. Growth occurred at 15-45 °C (optimum, 37 °C), pH 5.5-8.75 (optimum, 7.3), and in the presence of 1-15 % NaCl (optimum, 10 %). Strain Abdou3(T) used glucose, D-arabinose, and sucrose. Strain Abdou3(T) had Q9 as the major respiratory quinone and C18:1 ω9c and C16:0 as predominant fatty acids. The DNA G+C content was 55.2 mol%. Phylogenetic analysis of the small-subunit ribosomal RNA (rRNA) gene sequence indicated that strain Abdou3(T) had as its closest relative Marinobacter maritimus (identity of 96 %). Based on phenotypic, phylogenetic, and taxonomic characteristics, strain Abdou3(T) is proposed as a novel species of the genus Marinobacter within the order Alteromonadales, for which the name M. piscensis sp. nov. is proposed. The type strain is Abdou3(T) (=DSM 26804(T)). PMID:25510172

  10. Bacillus haikouensis sp. nov., a facultatively anaerobic halotolerant bacterium isolated from a paddy soil.

    PubMed

    Li, Jibing; Yang, Guiqin; Lu, Qin; Zhao, Yong; Zhou, Shungui

    2014-10-01

    A Gram-stain positive, rod-shaped, endospore-forming and facultatively anaerobic halotolerant bacterium, designated as C-89(T), was isolated from a paddy field soil in Haikou, Hainan Province, People's Republic of China. Optimal growth was observed at 37 °C and pH 7.0 in the presence of 4% NaCl (w/v). The predominant menaquinone was identified as MK-7, the major cellular fatty acids were identified as anteiso-C(15:0) and iso-C(15:0), and the major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unknown phospholipids. The peptidoglycan type was determined to be based on meso-DAP. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relatives were identified as Bacillus vietnamensis JCM 11124(T) (98.8% sequence similarity), Bacillus aquimaris JCM 11545(T) (98.6%) and Bacillus marisflavi JCM 11544(T) (98.5%). The DNA G+C content of strain C-89(T) was determined to be 45.4 mol%. The DNA-DNA relatedness values of strain C-89(T) with its closest relatives were below 18%. Therefore, on the basis of phylogenetic, chemotaxonomic, and phenotypic results, strain C-89(T) can be considered to represent a novel species within the genus Bacillus, for which the name Bacillus haikouensis sp. nov., is proposed. The type strain is C-89(T) (=KCTC 33545(T) = CCTCC AB 2014076(T)). PMID:25100188

  11. Chlorhexidine resistance in a Gram-negative bacterium isolated from an aquatic source.

    PubMed

    Sekavec, Jeffrey G; Moore, William T; Gillock, Eric T

    2013-01-01

    Aeromonas hydrophila is a Gram-negative bacterium of considerable importance in both clinical, especially nosocomial infections, and zoonotic respects, both aquatic and terrestrial infections. In addition to the ability to thrive in a wide range of conditions, A. hydrophila is resistant to numerous antibiotics and antimicrobials. In conjunction with Kansas State University and the Kansas Water Office, water samples from various locations within Kansas were screened for organisms resistant to chlorhexidine. Chlorhexidine is the active agent in many surgical scrubs, prescription mouthwashes, and other bactericidal and bacteriostatic substances. Aeromonas hydrophila capable of growth in therapeutic levels of chlorhexidine was detected in one of the water samples. The isolate was determined not to be harboring a plasmid, lending to a course of inquiry founded on the premise that the source of chlorhexidine resistance resides within the chromosome. Investigation into efflux pumps (EP) is underway with select resistance-nodulation-cell division (RND) pumps, especially the AheABC EP, being exculpated of responsibility for chlorhexidine resistance following testing with a select EP inhibitor. Inquiry into the major facilitator superfamily (MFS) EPs is underway with specific examination of the EmrB/QacA EPs, as chlorhexidine resistance in Staphylococcus aureus carrying the QacA gene has been observed. PMID:24007437

  12. Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil.

    PubMed

    Zhou, Shungui; Yang, Guiqin; Lu, Qin; Wu, Min

    2014-11-01

    A novel Fe(III)-reducing bacterium, designated GSS01(T), was isolated from a forest soil sample using a liquid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS01(T) were strictly anaerobic, Gram-stain-negative, motile, non-spore-forming and slightly curved rod-shaped. Growth occurred at 16-40 °C and optimally at 30 °C. The DNA G+C content was 60.9 mol%. The major respiratory quinone was MK-8. The major fatty acids were C(16:0), C(18:0) and C(16:1)ω7c/C(16:1)ω6c. Strain GSS01(T) was able to grow with ferrihydrite, Fe(III) citrate, Mn(IV), sulfur, nitrate or anthraquinone-2,6-disulfonate, but not with fumarate, as sole electron acceptor when acetate was the sole electron donor. The isolate was able to utilize acetate, ethanol, glucose, lactate, butyrate, pyruvate, benzoate, benzaldehyde, m-cresol and phenol but not toluene, p-cresol, propionate, malate or succinate as sole electron donor when ferrihydrite was the sole electron acceptor. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSS01(T) was most closely related to Geobacter sulfurreducens PCA(T) (98.3% sequence similarity) and exhibited low similarities (94.9-91.8%) to the type strains of other species of the genus Geobacter. The DNA-DNA relatedness between strain GSS01(T) and G. sulfurreducens PCA(T) was 41.4 ± 1.1%. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS01(T) is believed to represent a novel species of the genus Geobacter, and the name Geobacter soli sp. nov. is proposed. The type strain is GSS01(T) ( =KCTC 4545(T) =MCCC 1K00269(T)). PMID:25139417

  13. Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal.

    PubMed

    Chang, Chi-huan; Chen, Yi-sheng; Lee, Tzu-tai; Chang, Yu-chung; Yu, Bi

    2015-01-01

    A Gram-reaction-positive, catalase-negative, facultatively anaerobic, rod-shaped lactic acid bacterium, designated strain S215(T), was isolated from fermented soybean meal. The organism produced d-lactic acid from glucose without gas formation. 16S rRNA gene sequencing results showed that strain S215(T) had 98.74-99.60 % sequence similarity to the type strains of three species of the genus Lactobacillus (Lactobacillus farciminis BCRC 14043(T), Lactobacillus futsaii BCRC 80278(T) and Lactobacillus crustorum JCM 15951(T)). A comparison of two housekeeping genes, rpoA and pheS, revealed that strain S215(T) was well separated from the reference strains of species of the genus Lactobacillus. DNA-DNA hybridization results indicated that strain S215(T) had DNA related to the three type strains of species of the genus Lactobacillus (33-66 % relatedness). The DNA G+C content of strain S215(T) was 36.2 mol%. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type and the major fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 cyclo ω10c/C19 : 1ω6c. Phenotypic and genotypic features demonstrated that the isolate represents a novel species of the genus Lactobacillus, for which the name Lactobacillus formosensis sp. nov. is proposed. The type strain is S215(T) ( = NBRC 109509(T) = BCRC 80582(T)). PMID:25281727

  14. Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample.

    PubMed

    Chen, Wei; Zhao, Ying-Liang; Cheng, Juan; Zhou, Xing-Kui; Salam, Nimaichand; Fang, Bao-Zhu; Li, Qing-Qing; Hozzein, Wael N; Li, Wen-Jun

    2016-07-01

    A Gram-staining negative, aerobic, rod-shaped bacterium, designated YIM C01544(T), was isolated from a soil sample collected from Sigangli Cave, Yunnan province, South-West China. The strain was able to grow over a range of temperatures (4-30 °C), pH (6.0-10.0) and NaCl concentration (0-2 %, w/v). Comparative 16S rRNA gene sequence analysis revealed that strain YIM C01544(T) should be a member of the genus Lysobacter. The strain is closely related to Lysobacter niastensis GH41-7(T) (97.6 %), Lysobacter soli DCY21(T) (97.5 %), Lysobacter enzymogenes DSM 2043(T) (97.3 %), Lysobacter antibioticus DSM 2044(T) (97.1 %) and Lysobacter panacisoli CJ29(T) (97.1 %). The genomic DNA relatedness values (<47 %) as indicated by DNA-DNA hybridization studies were below the threshold limit for characterization of new bacterial species. The chemotaxonomic features of the new isolate include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and two unidentified polar lipids as its characteristic polar lipids and Q-8 as the only quinone. The major fatty acids detected were iso-C15:0 and iso-C17:1 ω9c. The DNA G + C content of the strain was determined to be 64.9 mol %. Based on the data from phenotypic, chemotaxonomic and molecular studies, strain YIM C01544(T) merits recognition as novel species in the genus Lysobacter for which the name Lysobacter cavernae sp. nov. is proposed. The type strain of Lysobacter cavernae is YIM C01544(T) (= KCTC 42875(T) = DSM 101561(T) = CPCC 100816(T)). PMID:27180096

  15. Chryseobacterium formosus sp. nov., a bacterium isolated from an ancient tree trunk.

    PubMed

    Akter, Shahina; NGO, Hien T T; Du, Juan; Won, KyungHwa; Singh, Hina; Yin, Chang Shik; Kook, MooChang; Yi, Tae-Hoo

    2015-10-01

    A Gram-reaction-negative, non-motile and rod-shaped bacterium, designated as THG-DN3.6(T), was isolated from an ancient tree trunk from Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain THG-DN3.6(T) was shown to belong to the genus Chryseobacterium and the highest similarity to Chryseobacterium indoltheticum LMG 4025(T) (97.2%) and the closest phylogenetic relatives were Chryseobacterium scophthalmum (96.8%), Chryseobacterium piscium (96.7%) and Chryseobacterium balustinum KCTC 2903(T) (96.3%). The DNA G + C content of the isolate was 33.2 mol%. The predominant isoprenoid quinone was menaquinone-6. The major fatty acids were iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω7t and/or iso-C15:0 2-OH), iso-C17:1 ω9c and iso-C17:0 3-OH. The major polar lipids of strain THG-DN3.6(T) were phosphatidylethanolamine. The mean DNA-DNA relatedness of strain THG-DN3.6(T) to C. indoltheticum LMG 4025(T) was 52 ± 0.5%. Based on the results of polyphasic characterization, strain THG-DN3.6(T) represented a novel species within the genus Chryseobacterium, for which the name Chryseobacterium formosus sp. nov. is proposed. The type strain is THG-DN3.6(T) (=KCTC 42606 = CCTCC AB 2015118). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain THG-DN3.6(T) is KM035938. PMID:26210236

  16. Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China.

    PubMed

    Zhang, Lei; Wang, Yang; Dai, Jun; Tang, Yali; Yang, Qiao; Luo, Xuesong; Fang, Chengxiang

    2009-07-01

    A Gram-positive-staining, rod-shaped, motile, spore-forming and moderately halotolerant bacterium, designated ZLC-26(T), was isolated from a sand soil sample collected from Xinjiang Province, China, and was characterized by using a polyphasic taxonomic approach. This isolate grew optimally at 30-37 degrees C and pH 7-8. It grew with 0-8% NaCl (optimum, 0-2 %). Comparative 16S rRNA gene sequence analysis showed that strain ZLC-26(T) was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarities to Bacillus nealsonii DSM 15077(T) (97.1 %), B. shackletonii LMG 18435(T) (97.0 %), B. siralis 171544(T) (97.0 %), B. circulans IAM 12462(T) (96.7 %) and B. pocheonensis Gsoil 420(T) (96.7 %). Strain ZLC-26(T) contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)omega11c and anteiso-C(15 : 0). The DNA G+C content was 38.2 mol%. These chemotaxonomic results supported the affiliation of strain ZLC-26(T) to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLC-26(T) from recognized Bacillus species. On the basis of the evidence presented, strain ZLC-26(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus korlensis sp. nov. is proposed. The type strain is ZLC-26(T) (=CCTCC AB 207172(T)=NRRL B-51302(T)). PMID:19542113

  17. Fusibacter fontis sp. nov., a sulfur-reducing, anaerobic bacterium isolated from a mesothermic Tunisian spring.

    PubMed

    Fadhlaoui, Khaled; Ben Hania, Wajdi; Postec, Anne; Fauque, Guy; Hamdi, Moktar; Ollivier, Bernard; Fardeau, Marie-Laure

    2015-10-01

    Strain KhalAKB1T, a mesophilic, anaerobic, rod-shaped bacterium, was isolated from water collected from a mesothermic Tunisian spring. Cells were Gram-staining-positive rods, occurring singly or in pairs and motile by one lateral flagellum. Strain KhalAKB1T grew at 15-45 °C (optimum 30 °C), at pH 5.5-8.5 (optimum pH 7.0) and in the presence of 0-35 g NaCl l- 1 (optimum 1 g NaCl l- 1). It fermented yeast extract and a wide range of carbohydrates including cellobiose, d-glucose, d-ribose, sucrose, d-xylose, maltose, d-galactose and starch as electron donors. Acetate, ethanol, CO2 and H2 were end products of glucose metabolism. It reduced elemental sulfur, but not sulfate, thiosulfate or sulfite, into sulfide. The DNA G+C content was 37.6 mol%. The predominant cellular fatty acids were C14 : 0 and C16 : 0. Phylogenetic analysis of the 16S rRNA gene sequence suggested Fusibacter bizertensis as the closest relative of this isolate (identity of 97.2 % to the type strain). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain KhalAKB1T is proposed to be assigned to a novel species within the genus Fusibacter, order Clostridiales, Fusibacter fontis sp. nov. The type strain is KhalAKB1T ( = DSM 28450T = JCM 19912T). PMID:26296995

  18. Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring.

    PubMed

    Bouanane-Darenfed, Amel; Ben Hania, Wajdi; Hacene, Hocine; Cayol, Jean-Luc; Ollivier, Bernard; Fardeau, Marie-Laure

    2013-06-01

    A hyperthermophilic anaerobic bacterium, designated D2C22(T), was isolated from the hydrothermal hot spring of Guelma in north-east Algeria. The isolate was a Gram-stain-positive, non-sporulating, non-motile rod, appearing singly or in pairs (0.3-0.4 × 8.0-9.0 µm). Strain D2C22(T) grew anaerobically at 45-85 °C (optimum 65 °C), at pH 5-9 (optimum pH 6.8) and with 0-20 g NaCl l(-1). Strain D2C22(T) used glucose, galactose, lactose, fructose, ribose, xylose, arabinose, maltose, cellobiose, mannose, melibiose, sucrose, xylan and pyruvate (only in the presence of yeast extract or biotrypticase) as electron donors. The end products from glucose fermentation were acetate, lactate, CO2 and H2. Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate and sulfite were not used as electron acceptors. The predominant cellular fatty acids were iso-C15:0 and iso-C17:0. The DNA G+C content was 41.6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain D2C22(T) was most closely related to Caldicoprobacter oshimai JW/HY-331(T), Caldicoprobacter algeriensis TH7C1(T) and Acetomicrobium faecale DSM 20678(T) (95.5, 95.5 and 95.3% 16S rRNA gene sequence similarity, respectively). Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain D2C22(T) is proposed to be a representative of a novel species of the genus Caldicoprobacter within the order Clostridiales, for which the name Caldicoprobacter guelmensis sp. nov. is proposed. The type strain is D2C22(T) (=DSM 24605(T)=JCM 17646(T)). PMID:23041645

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

    PubMed

    Zhu, Lingfang; Long, Mingxiu; Si, Meiru; Wei, Linfang; Li, Changfu; Zhao, Liang; Shen, Xihui; Wang, Yao; Zhang, Lei

    2014-12-01

    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)). PMID:25205798

  20. Halomonas xinjiangensis sp. nov., a halotolerant bacterium isolated from a salt lake.

    PubMed

    Guan, Tong-Wei; Xiao, Jing; Zhao, Ke; Luo, Xiao-Xia; Zhang, Xiao-Ping; Zhang, Li-Li

    2010-02-01

    A novel bacterium, TRM 0175(T), belonging to the genus Halomonas, was isolated from a soil sample taken from a salt lake in Xinjiang Province, north-west China. The isolate was Gram-negative, aerobic, rod-shaped and motile by means of peritrichous flagella. It was catalase-positive and oxidase-negative. Growth occurred at NaCl concentrations of 0-20 % (optimum at 10-13 %), at 15-50 degrees C (optimum at 37 degrees C) and at pH 6.0-9.0 (optimum at pH 7.0). Metabolism was respiratory with oxygen as terminal electron acceptor. Acid was produced from D-ribose, D- and L-arabinose, D-xylose, D-galactose, D-mannose, L-rhamnose, cellobiose, maltose, trehalose and D- and L-fucose and was produced weakly from aesculin. The predominant ubiquinone was Q-9. The major fatty acids were C(18 : 1)omega7c and C(19 : 0) cyclo omega8c. The G+C content of the genomic DNA was 60.0 mol%. The affiliation of strain TRM 0175(T) with the genus Halomonas was confirmed by 16S rRNA gene sequence comparisons. The most closely related species was Halomonas anticariensis; 16S rRNA gene sequence similarity between H. anticariensis FP35(T) and strain TRM 0175(T) was 95.3 %. Phenotypically, some characteristics of TRM 0175(T) differed from those of H. anticariensis. On the basis of data from this polyphasic study, strain TRM 0175(T) represents a novel species of the genus Halomonas, for which the name Halomonas xinjiangensis sp. nov. is proposed; the type strain is TRM 0175(T) (=CCTCC AB 208329(T) =KCTC 22608(T)). PMID:19651733

  1. Dichloromethane dehalogenase with improved catalytic activity isolated from a fast-growing dichloromethane-utilizing bacterium

    SciTech Connect

    Scholtz, R.; Egli, C.; Cook, A.M.; Leisinger, T. ); Wackett, L.P. )

    1988-12-01

    A methylotrophic bacterium, denoted strain DM11, was isolated from groundwater and shown to utilize dichloromethane or dibromomethane as the sole carbon and energy source. The new isolate grew at the high rate of 0.22 h{sup {minus}1} compared with 11 previously characterized dichloromethane-utilizing bacteria ({mu}{sub max}, 0.08 h{sup {minus}1}). The dichloromethane dehalogenase from strain DM11 (group B enzyme) was purified by anion-exchange chromatography. It was shown to be substantially different from the set of dichloromethane dehalogenases from the 11 slow-growing strains (group A enzymes) that had previously been demonstrated to be identical. The V{sub max} for the group B enzyme was 97 mkat/kg of protein, some 5.6-fold higher than that of the group A enzymes. The group A dehalogenases showed hyperbolic saturation with the cosubstrate glutathione, whereas the group B enzyme showed positive cooperativity in glutathione binding. Only 1 of 15 amino acids occupied common positions at the N termini, and amino acid contents were substantially different in group A and group B dehalogenases. Immunological assays demonstrated weak cross-reactivity between the two enzymes. Despite the observed structural and kinetic differences, there is potentially evolutionary relatedness between group A and group B enzymes, as indicated by (i) hybridization of DM11 DNA with a gene probe of the group A enzyme, (ii) a common requirement for glutathione in catalysis, and (iii) similar subunit molecular weights of about 34,000.

  2. Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj

    2014-02-01

    A pink-pigmented, Gram negative, aerobic, facultatively methylotrophic bacterium, strain BL44(T), was isolated from bamboo leaves and identified as a member of the genus Methylobacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed similarity values of 98.7-97.0 % with closely related type strains and showed highest similarity to Methylobacterium zatmanii DSM 5688(T) (98.7 %) and Methylobacterium thiocyanatum DSM 11490(T) (98.7 %). Methylotrophic metabolism in this strain was confirmed by PCR amplification and sequencing of the mxaF gene coding for the α-subunit of methanol dehydrogenase. Strain BL44(T) produced three known quorum sensing signal molecules with similar retention time to C8, C10 and C12-HSLs when characterized by GC-MS. The fatty acid profiles contained major amounts of C18:1 ω7c, iso-3OH C17:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH), which supported the grouping of the isolate in the genus Methylobacterium. The DNA G+C content was 66.9 mol%. DNA relatedness of the strain BL44(T) to its most closely related strains ranged from 12-43.3 %. On the basis of the phenotypic, phylogenetic and DNA-DNA hybridization data, strain BL44(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium pseudosasae sp. nov. is proposed (type strain BL44(T) = NBRC 105205(T) = ICMP 17622(T)). PMID:24297603

  3. Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.

    PubMed

    Lei, Zuchao; Qiu, Peng; Ye, Renyuan; Tian, Jiewei; Liu, Yang; Wang, Lei; Tang, Shu-Kun; Li, Wen-Jun; Tian, Yongqiang

    2014-01-01

    A moderately halophilic bacterium, strain HNA-14(T), was isolated from a saline-alkali soil sample collected in Shache County, Xinjiang Province. On the basis of the polyphasic taxonomic data, the isolate was considered to be a member of the genus Bacillus. The organism grew optimally at 30 °C and pH 8.0. It was moderately halophilic and its optimum growth occurred at 5-10% NaCl. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. The G+C content of the genomic DNA was 48.6 mol%. Strain HNA-14(T) exhibited a low 16S rRNA gene sequence similarity of 96% with its nearest neighbors [Bacillus clausii KSM-K16 (96.5%), Bacillus xiaoxiensis DSM 21943(T)(96.2%), Bacillus clausii DSM 8716(T) (96.1%), Bacillus patagoniensis PAT05(T) (96.1%), Bacillus lehensis MLB-2(T) (96.0%), Bacillus oshimensis K11(T) (95.9%) and Bacillus hunanensis DSM 23008(T) (95.8%)] and the phenotypic characteristics indicate that strain HNA-14(T) can be distinguished from them. Therefore, a novel species of the genus Bacillus, Bacillus shacheensis sp. nov. (type strain, HNA-14(T) = KCTC 33145 = DSM 26902) is proposed. PMID:25008165

  4. Mycoavidus cysteinexigens gen. nov., sp. nov., an endohyphal bacterium isolated from a soil isolate of the fungus Mortierella elongata.

    PubMed

    Ohshima, Shoko; Sato, Yoshinori; Fujimura, Reiko; Takashima, Yusuke; Hamada, Moriyuki; Nishizawa, Tomoyasu; Narisawa, Kazuhiko; Ohta, Hiroyuki

    2016-05-01

    An endohyphal bacterium (strain B1-EBT) living in association with the fungus Mortierella elongata FMR23-6 I-B1 was isolated from a fungal cell homogenate and studied for its taxonomic allocation. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, non-motile, and negative for oxidase and catalase. Strain B1-EBT required cysteine for growth and grew at temperatures between 4 and 35 °C. A comparative analysis of 16S rRNA gene sequences revealed that strain B1-EBT forms a distinct clade in the family Burkholderiaceae, encompassing a group of endosymbionts associated with several soil isolates of M. elongata. The most closely related genus is 'Candidatus Glomeribacter gigasporarum', an endosymbiont of the arbuscular mycorrhizal fungus Gigaspora margarita. The major cellular fatty acids of strain B1-EBT were C16 : 0, summed feature 3 (C16 : 1ω7c and C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c or C18 : 1ω6c). Ubiquinone Q-8 was the only quinone detected. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid and two unknown aminolipids. The DNA G+C content was 49.8 mol%. On the basis of phenotypic, chemotaxonomic, and phylogenetic characteristics, strain B1-EBT represents a novel genus and novel species in the family Burkholderiaceae, for which the name Mycoavidus cysteinexigens gen. nov., sp. nov. is proposed. The type strain is B1-EBT ( = JCM 30646T = LMG 28693T = NBRC 110909T). PMID:26920389

  5. Genome Assembly of Chryseobacterium polytrichastri ERMR1:04, a Psychrotolerant Bacterium with Cold Active Proteases, Isolated from East Rathong Glacier in India.

    PubMed

    Kumar, Rakshak; Singh, Dharam; Swarnkar, Mohit Kumar; Singh, Anil Kumar; Kumar, Sanjay

    2015-01-01

    We report here the genome assembly of a psychrotolerant bacterium, Chryseobacterium polytrichastri ERMR1:04, which secretes cold-active proteases. The bacterium was isolated from a pristine location, the East Rathong Glacier in the Sikkim Himalaya. The 5.53-Mb genome provides insight into the cold-active industrial enzyme and adaptation in the cold environment. PMID:26543128

  6. Genome Assembly of Chryseobacterium polytrichastri ERMR1:04, a Psychrotolerant Bacterium with Cold Active Proteases, Isolated from East Rathong Glacier in India

    PubMed Central

    Singh, Dharam; Swarnkar, Mohit Kumar; Singh, Anil Kumar; Kumar, Sanjay

    2015-01-01

    We report here the genome assembly of a psychrotolerant bacterium, Chryseobacterium polytrichastri ERMR1:04, which secretes cold-active proteases. The bacterium was isolated from a pristine location, the East Rathong Glacier in the Sikkim Himalaya. The 5.53-Mb genome provides insight into the cold-active industrial enzyme and adaptation in the cold environment. PMID:26543128

  7. Complete Genome Sequence of the Unclassified Iron-Oxidizing, Chemolithoautotrophic Burkholderiales Bacterium GJ-E10, Isolated from an Acidic River

    PubMed Central

    Tojo, Fuyumi; Asano, Ryoki; Kobayashi, Yayoi; Shimura, Yoichiro; Okano, Kunihiro; Miyata, Naoyuki

    2015-01-01

    Burkholderiales bacterium GJ-E10, isolated from the Tamagawa River in Akita Prefecture, Japan, is an unclassified, iron-oxidizing chemolithoautotrophic bacterium. Its single circular genome, consisting of 3,276,549 bp, was sequenced by using three types of next-generation sequencers and the sequences were then confirmed by PCR-based Sanger sequencing. PMID:25657271

  8. Halomonas urumqiensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkaline lake.

    PubMed

    Zhang, Shanshan; Pan, Jiao; Lu, Weidong; Yan, Yanchun; Wang, Haisheng; Wiegel, Jurgen; Zhao, Baisuo

    2016-05-01

    A moderately halophilic, aerobic bacterium, strain BZ-SZ-XJ27T, belonging to the genus Halomonas, was isolated from a saline-alkaline lake in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences and a multilocus sequence analysis using the 16S rRNA, gyrB and rpoD genes demonstrated that strain BZ-SZ-XJ27T represents a member of the genus Halomonas. On the basis of 16S rRNA gene sequence similarity, the closest relatives were Halomonas campaniensis 5AGT, H. fontilapidosi 5CRT, H. korlensis XK1T and H. sinaiensis ALO SharmT, with similarities of 96.2-97.2 %. DNA-DNA hybridization with H. korlensis CGMCC 1.6981T (the nearest phylogenetic neighbour) and H. campaniensis DSM 15293T (the highest 16S rRNA gene sequence similarity) showed relatedness values of 53 and 38 %, respectively, demonstrating the separateness of the three taxa. The bacterium stained Gram-negative and the cells were motile and rod-shaped. The strain formed creamy-white colonies and grew under optimal conditions of 1.42 M Na+ (range 0.22-4.32 M Na+), pH 8.0-8.5 (range pH 6.0-10.0) and 39 °C (range 4-43 °C). The dominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 36.6 %), C16 : 0 (25.9 %) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 21.2 %). The dominant polar lipids were two unknown phospholipids, phosphatidylethanolamine and phosphatidylglycerol, and the main respiratory quinones were ubiquinone 9 (Q-9; 89 %) and ubiquinone 8 (Q-8; 10 %). The genomic DNA G+C content was 61.7 ± 0.8 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ27T is proposed to represent a novel species, Halomonas urumqiensis sp. nov., within the genus Halomonas of the family Halomonadaceae. The type strain is BZ-SZ-XJ27T ( = JCM 30202T = CGMCC 1.12917T). PMID:26873696

  9. Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil

    PubMed Central

    Ehara, Ayaka; Suzuki, Haruo

    2015-01-01

    Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring bacterium isolated from Japanese paddy soil. It contained two distinct arsenic islands, one including genes for a respiratory arsenate reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB) and the second containing only genes for arsenic resistance. PMID:25635012

  10. Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil.

    PubMed

    Ehara, Ayaka; Suzuki, Haruo; Amachi, Seigo

    2015-01-01

    Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring bacterium isolated from Japanese paddy soil. It contained two distinct arsenic islands, one including genes for a respiratory arsenate reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB) and the second containing only genes for arsenic resistance. PMID:25635012

  11. Isolation and identification of berberine and berberrubine metabolites by berberine-utilizing bacterium Rhodococcus sp. strain BD7100.

    PubMed

    Ishikawa, Kazuki; Takeda, Hisashi; Wakana, Daigo; Sato, Fumihiko; Hosoe, Tomoo

    2016-05-01

    Based on the finding of a novel berberine (BBR)-utilizing bacterium, Rhodococcus sp. strain BD7100, we investigated the degradation of BBR and its analog berberrubine (BRU). Resting cells of BD7100 demethylenated BBR and BRU, yielding benzeneacetic acid analogs. Isolation of benzeneacetic acid analogs suggested that BD7100 degraded the isoquinoline ring of the protoberberine skeleton. This work represents the first report of cleavage of protoberberine skeleton by a microorganism. PMID:26882131

  12. Draft Genome Sequence of Strain P7-3-5, a New Flavobacteriaceae Bacterium Isolated from Intertidal Sand

    PubMed Central

    Zhang, Xi-Ying; Qin, Qi-Long; Liu, Ang; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2012-01-01

    The Flavobacteriaceae bacterium strain P7-3-5 was isolated from intertidal sand of the Yellow Sea, China. Analysis of the 16S rRNA gene sequences showed that strain P7-3-5 formed a distinct phylogenetic lineage within the family Flavobacteriaceae. The genome of strain P7-3-5 was sequenced to facilitate the physiological, ecological, and evolutionary studies of the bacteria within the family Flavobacteriaceae. PMID:23144387

  13. A Novel Mycobacterium cosmeticum-Like Bacterium Isolated from the Ear Swab of a Patient with Otitis Externa

    PubMed Central

    Teo, Jeanette W. P.; Cheng, Janet W. S.; Jureen, Roland; Lin, Raymond T. P.

    2015-01-01

    We describe the identification and characterization of a novel nontuberculous mycobacterium (NTM), isolated from an ear swab of an adult male patient with chronic otitis externa. Genetically, the bacterium is most closely related to Mycobacterium cosmeticum; however, growth and biochemical features indicate that it is distinctly different. Here, we highlight for the first time an unusual NTM that is a probable cause of ear infection. PMID:25866687

  14. Draft Genome Sequence of Phosphate-Solubilizing Bacterium Paraburkholderia tropica Strain P-31 Isolated from Pomegranate (Punica granatum) Rhizosphere

    PubMed Central

    Selvakumar, Govindan; Ganeshamurthy, Arakalgud Nanjundiah

    2016-01-01

    We report the 8.9 Mb draft genome sequence of phosphate-solubilizing bacterium Paraburkholderia tropica strain P-31, isolated from pomegranate (Punica granatum) rhizosphere. The draft genome sequence of Paraburkholderia tropica strain P-31 consists of 8,881,246 bp with a G+C content of 64.7%, 8,039 protein-coding genes, and 49 RNAs. PMID:27540068

  15. Draft Genome Sequence of Phosphate-Solubilizing Bacterium Paraburkholderia tropica Strain P-31 Isolated from Pomegranate (Punica granatum) Rhizosphere.

    PubMed

    Kaur, Chandandeep; Selvakumar, Govindan; Ganeshamurthy, Arakalgud Nanjundiah

    2016-01-01

    We report the 8.9 Mb draft genome sequence of phosphate-solubilizing bacterium Paraburkholderia tropica strain P-31, isolated from pomegranate (Punica granatum) rhizosphere. The draft genome sequence of Paraburkholderia tropica strain P-31 consists of 8,881,246 bp with a G+C content of 64.7%, 8,039 protein-coding genes, and 49 RNAs. PMID:27540068

  16. Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments.

    PubMed

    Florentino, Anna P; Brienza, Claudio; Stams, Alfons J M; Sánchez-Andrea, Irene

    2016-03-01

    A novel acidotolerant and moderately thermophilic sulfur-reducing bacterium was isolated from sediments of the Tinto River (Spain), an extremely acidic environment. Strain TR1T stained Gram-negative, and was obligately anaerobic, non-spore-forming and motile. Cells were short rods (1.5-2 × 0.5-0.7 μm), appearing singly or in pairs. Strain TR1T was catalase-negative and slightly oxidase-positive. Urease activity and indole formation were absent, but gelatin hydrolysis was present. Growth was observed at 20-52 °C with an optimum close to 50 °C, and a pH range of 3-7 with optimum between pH 6 and 6.5. Yeast extract was essential for growth, but extra vitamins were not required. In the presence of sulfur, strain TR1T grew with acetate, formate, lactate, pyruvate, stearate, arginine and H2/CO2. All substrates were completely oxidized and H2S and CO2 were the only metabolic products detected. Besides elemental sulfur, thiosulfate was used as an electron acceptor. The isolate also grew by disproportionation of elemental sulfur. The predominant cellular fatty acids were saturated components: C16 : 0, anteiso-C17 : 0 and C18 : 0. The only quinone component detected was menaquinone MK-7(H2). The G+C content of the genomic DNA was 34 mol%. The isolate is affiliated to the genus Desulfurella of the class Deltaproteobacteria, sharing 97 % 16S rRNA gene sequence similarity with the four species described in the genus Desulfurella. Considering the distinct physiological and phylogenetic characteristics, strain TR1T represents a novel species within the genus Desulfurella, for which the name Desulfurella amilsii sp. nov. is proposed. The type strain is TR1T ( = DSM 29984T = JCM 30680T). PMID:26704766

  17. Anoxybacillus calidus sp. nov., a thermophilic bacterium isolated from soil near a thermal power plant.

    PubMed

    Cihan, Arzu Coleri; Cokmus, Cumhur; Koc, Melih; Ozcan, Birgul

    2014-01-01

    A novel thermophilic, Gram-stain-positive, facultatively anaerobic, endospore-forming, motile, rod-shaped bacterium, strain C161ab(T), was isolated from a soil sample collected near Kizildere, Saraykoy-Buharkent power plant in Denizli. The isolate could grow at temperatures between 35 and 70 °C (optimum 55 °C), at pH 6.5-9.0 (optimum pH 8.0-8.5) and with 0-2.5 % NaCl (optimum 0.5 %, w/v). The strain formed cream-coloured, circular colonies and tolerated up to 70 mM boron. Its DNA G+C content was 37.8 mol%. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. Strain C161ab(T) contained menaquinones MK-7 (96 %) and MK-6 (4 %). The major cellular fatty acids were iso-branched fatty acids: iso-C15 : 0 (52.2 %) and iso-C17 : 0 (28.0 %,) with small amounts of C16 : 0 (7.4 %). Phylogenetic analysis based on the 16S rRNA gene revealed 94.6-96.8 % sequence similarity with all recognized species of the genus Anoxybacillus. Strain C161ab(T) showed the greatest sequence similarity to Anoxybacillus rupiensis DSM 17127(T) and Anoxybacillus voinovskiensis DSM 17075(T), both had 96.8 % similarity to strain C161ab(T), as well as to Anoxybacillus caldiproteolyticus DSM 15730(T) (96.6 %). DNA-DNA hybridization revealed low levels of relatedness with the closest relatives of strain C161ab(T), A. rupiensis (21.2 %) and A. voinovskiensis (16.5 %). On the basis of the results obtained from phenotypic, chemotaxonomic, genomic fingerprinting, phylogenetic and hybridization analyses, the isolate is proposed to represent a novel species, Anoxybacillus calidus sp. nov. (type strain C161ab(T) = DSM 25520(T) = NCIMB 14851(T)). PMID:24052627

  18. Isolation, sequence analysis, and comparison of two plasmids (28 and 29 kilobases) from the biomining bacterium Leptospirillum ferrooxidans ATCC 49879.

    PubMed

    Coram, Nicolette J; van Zyl, Leonardo J; Rawlings, Douglas E

    2005-11-01

    Two plasmids, of 28,878 bp and 28,012 bp, were isolated from Leptospirillum ferrooxidans ATCC 49879. Altogether, a total of 67 open reading frames (ORFs) were identified on both plasmids, of which 32 had predicted products with high homology to proteins of known function, while 11 ORFs had predicted products with homology to previously identified proteins of unknown function. Twenty-four ORFs had products with no homologues in the GenBank/NCBI database. An analysis of the ORFs and other features of the two plasmids, the first to be isolated from a bacterium of the genus Leptospirillum, is presented. PMID:16269793

  19. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water.

    PubMed

    Albert, Richard A; Waas, Nancy E; Pavlons, Shawn C; Pearson, Jamie L; Ketelboeter, Laura; Rosselló-Móra, Ramon; Busse, Hans-Jürgen

    2013-03-01

    A psychrophilic, Gram-negative bacterium, designated MOL-1(T), was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1(T) has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of Sphingobacterium shayense HS39(T), S. lactis WCC 4512(T), S. composti T5-12(T), S. daejeonense TR6-04(T), S. bambusae IBFC2009(T) and S. alimentarium WCC 4521(T). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1(T) represents a novel Sphingobacterium species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1(T) ( = NRRL B-59232(T)  = DSM 22418(T)). PMID:22659507

  20. Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water.

    PubMed

    Vaidya, Bhumika; Kumar, Ravinder; Korpole, Suresh; Tanuku, Naga Radha Srinivas; Pinnaka, Anil Kumar

    2015-07-01

    A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21(T), was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, L-proline arylamidase and tyrosine arylamidase activities. The predominant fatty acids were C12:0, C12:0 3-OH, C16:0, C16:1ω9c, C18:1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, two unidentified phospholipids and one unidentified lipid. Q-10 was the predominant respiratory quinone. The DNA G+C content of the strain was 54.6 mol%. 16S rRNA gene sequence analysis indicated that strain AK21(T) was a member of the genus Marinobacter and was closely related to Marinobacter xestospongiae, with pairwise sequence similarity of 97.2% to the type strain, with similarity to other members of the genus of 94.0-96.8%. The mean DNA-DNA relatedness of strain AK21(T) with M. xestospongiae JCM 17469(T) was 34.5%, and relatedness with Marinobacter mobilis JCM 15154(T) was 40.5%. Phylogenetic analysis showed that strain AK21(T) clustered with the type strains of M. xestospongiae and M. mobilis at distances of 2.9 and 2.8% (97.1 and 97.2% similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain AK21(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter nitratireducens sp. nov. is proposed. The type strain of Marinobacter nitratireducens is AK21(T) ( = MTCC 11704(T ) = JCM 18428(T)). PMID:25835026

  1. Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora

    NASA Astrophysics Data System (ADS)

    Genicot, Sabine; Groisillier, Agnès; Rogniaux, Hélène; Meslet-Cladière, Laurence; Barbeyron, Tristan; Helbert, William

    2014-08-01

    Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ?-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40°C ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ?-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ?-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ?-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes.

  2. Shewanella algicola sp. nov., a marine bacterium isolated from brown algae.

    PubMed

    Kim, Ji-Young; Yoo, Han-Su; Lee, Dong-Heon; Park, So-Hyun; Kim, Young-Ju; Oh, Duck-Chul

    2016-06-01

    A Gram-stain-negative, aerobic, rod-shaped bacterium motile by means of a single polar flagella, strain ST-6T, was isolated from a brown alga (Sargassum thunbergii) collected in Jeju, Republic of Korea. Strain ST-6T was psychrotolerant, growing at 4-30 °C (optimum 20 °C). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that strain ST-6T belonged to a distinct lineage in the genus Shewanella. Strain ST-6T was related most closely to Shewanella basaltis J83T, S. gaetbuli TF-27T, S. arctica IT12T, S. vesiculosa M7T and S. aestuarii SC18T, showing 96-97 % and 85-70 % 16S rRNA and gyrB gene sequences similarities, respectively. DNA-DNA relatedness values between strain ST-6T and the type strains of two species of the genus Shewanella were <22.6 %. The major cellular fatty acids (>5 %) were summed feature 3 (comprising C16:1ω7c and/ or iso-C15:0 2-OH), C16:0, iso-C13:0 and C17:1ω8c. The DNA G+C content of strain ST-6Twas 42.4 mol%, and the predominant isoprenoid quinones were menaquinone MK-7 and ubiquinones Q-7 and Q-8. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain ST-6T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella algicola sp. nov. is proposed. The type strain is ST-6T (= KCTC 23253T = JCM 31091T). PMID:26962005

  3. Marinococcus tarijensis sp. nov., a moderately halophilic bacterium isolated from a salt mine.

    PubMed

    Balderrama-Subieta, Andrea; Guzmán, Daniel; Minegishi, Hiroaki; Echigo, Akinobu; Shimane, Yasuhiro; Hatada, Yuji; Quillaguamán, Jorge

    2013-09-01

    A Gram-stain-positive, coccoid-shaped, halophilic bacterium, strain SR-1(T), was isolated from a salt crystal obtained from a mine located in Tarija, Bolivia. The strain was investigated using a polyphasic approach. The optimum conditions for growth of strain SR-1(T) were reached at 5% (w/v) NaCl, pH 7.6 and 37-40 °C. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone was MK-7. The major cellular fatty acids of strain SR-1(T) were anteiso-C(15:0), anteiso-C(17:0) and iso-C(16:0). The DNA G+C content of strain SR-1(T) was 48.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed a close relationship between strain SR-1(T) and Marinococcus halophilus JCM 2479(T) (99.7% 16S rRNA gene sequence similarity), Marinococcus halotolerans KCTC 19045(T) (99.4%) and Marinococcus luteus KCTC 13214(T) (99.8%). However, strain SR-1(T) also showed low levels of DNA-DNA relatedness with these reference strains (47, 61 and 58%, respectively). On the basis of phenotypic differences and DNA-DNA hybridization results, strain SR-1(T) is considered to represent a novel species of the genus Marinococcus, for which the name Marinococcus tarijensis sp. nov. is proposed. The type strain is SR-1(T) ( =LMG 26930(T) =CECT 8130(T)). PMID:23504966

  4. Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge.

    PubMed

    Sun, Le-Ni; Wang, Dao-Sheng; Yang, En-Dong; Fang, Lian-Cheng; Chen, Yi-Fei; Tang, Xin-Yun; Hua, Ri-Mao

    2016-06-01

    A Gram-stain-negative, aerobic, coccoid to small rod-shaped bacterium, designated X1T, was isolated from sludge collected from the vicinity of a pesticide manufacturer in Nantong, Jiangsu Province, China. Based on 16S rRNA gene sequence analysis, strain X1T belonged to the genus Cupriavidus, and was most closely related to Cupriavidus taiwanensis LMG 19424T (99.1 % 16S rRNA gene sequence similarity) and Cupriavidus alkaliphilus LMG 26294T (98.9 %). Strain X1T showed 16S rRNA gene sequence similarities of 97.2-98.2 % with other species of the genus Cupriavidus. The major cellular fatty acids of strain X1T were C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), C18 : 1ω7c and C17 : 0 cyclo, and the major respiratory quinone was ubiquinone Q-8. The major polar lipids of strain X1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phospholipid and hydroxyphosphatidylethanolamine. The DNA G+C content was 66.6 mol%. The DNA-DNA relatedness values of strain X1T with the five reference strains C. taiwanensis LMG 19424T, C. alkaliphilus LMG 26294T, Cupriavidus necator LMG 8453T, Cupriavidus gilardii LMG 5886T and 'Cupriavidus yeoncheonense' KCTC 42053 were lower than 70 %. The results obtained from phylogenetic analysis, phenotypic characterization and DNA-DNA hybridization indicated that strain X1T should be proposed to represent a novel species of the genus Cupriavidus, for which the name Cupriavidus nantongensis sp. nov. is proposed. The type strain is X1T (=KCTC 42909T=LMG 29218T). PMID:27001671

  5. Gordonibacter urolithinfaciens sp. nov., a urolithin-producing bacterium isolated from the human gut.

    PubMed

    Selma, María V; Tomás-Barberán, Francisco A; Beltrán, David; García-Villalba, Rocio; Espín, Juan C

    2014-07-01

    Urolithins are dibenzopyranone metabolites that exert anti-inflammatory activity in vivo and are produced by the gut microbiota from the dietary polyphenols ellagic acid (EA) and ellagitannins. However, the bacteria involved in this process remain unknown. We report here a novel bacterium, strain CEBAS 1/15P(T), capable of metabolizing EA to urolithins, that was isolated from healthy human faeces and characterized by determining phenotypic, biochemical and molecular methods. The strain was related to Gordonibacter pamelaeae 7-10-1-b(T), the type and only reported strain of the only species of the genus Gordonibacter, with about 97% 16S rRNA gene sequence similarity; they were both obligately anaerobic, non-spore-forming, Gram-stain-positive, short-rods/coccobacilli and metabolized only small numbers of carbon sources. L-Fucose, D-fructose, turanose, D-galacturonic acid and α-ketobutyric acid were metabolized by strain CEBAS 1/15P(T), while G. pamelaeae was negative for metabolism of these compounds. The whole-cell fatty acids consisted predominantly of saturated fatty acids (70%); strain CEBAS 1/15P(T) differed significantly from G. pamelaeae in the major fatty acid, which was C18 : 1ω9c, while anteiso-C15 : 0 was the major component for G. pamelaeae. The presence of a number of different fatty acid peaks, especially C19 : 0 cyclo and C18 : 1ω6c, was also indicative of distinct species. Six glycolipids (GL1-6) were recognized, while, in G. pamelaeae, only four glycolipids were described. On the basis of these data, the novel species Gordonibacter urolithinfaciens sp. nov. is described, with strain CEBAS 1/15P(T) ( = DSM 27213(T) = CCUG 64261(T)) as the type strain. PMID:24744017

  6. Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.

    PubMed

    Zhang, Shi-Ying; Xiao, Wei; Xia, Yun-Sheng; Wang, Yong-Xia; Cui, Xiao-Long; Zhang, Nai-Ming

    2015-05-01

    A Gram-stain negative, aerobic, rod-shaped bacterial strain, YN2-31A(T), was isolated from rice-field soil, Taoyuan Village, Yunnan province of China. The bacterium was observed to grow at 20-45 °C (optimum 28 °C), at pH 5.0-10.0 (optimum 7.0), and in the presence of 0-2% (w/v) NaCl (optimum 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2-31A(T) is most closely related to Arenimonas daejeonensis DSM 18060(T) (96.1%), Arenimonas malthae DSM 21305(T) (95.9%), Arenimonas donghaensis DSM 18148(T) (95.1%), Arenimonas composti DSM 18010(T) (94.8%) and Arenimonas maotaiensis JCM 19710(T) (94.8%). The major cellular fatty acids (>10%) were found to be iso-C(18:1) ω9c, iso-C(15:0), Sum In Feature 3 (C(16:1) ω7c/C(16:1) ω6c), and C(16:0). The major ubiquinone was identified as Q-8 and the major cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The genomic DNA G+C content was determined to be 72.3 mol%. The results of the phylogenetic, genetic, phenotypic and chemotaxonomic analyses suggest that strain YN2-31A(T) represents a novel species of the genus Arenimonas, for which the name Arenimonas taoyuanensis sp. nov. is proposed. The type strain is YN2-31A(T) (=DSM 26777(T) = CCTCC AB2012964(T)). PMID:25731739

  7. Paenibacillus populi sp. nov., a novel bacterium isolated from the rhizosphere of Populus alba.

    PubMed

    Han, Tong-Yan; Tong, Xiao-Mei; Wang, Yan-Wei; Wang, Hui-Min; Chen, Xiao-Rong; Kong, De-Long; Guo, Xiang; Ruan, Zhi-Yong

    2015-09-01

    A novel aerobic bacterium, designated strain LAM0705(T), was isolated from the rhizosphere of Populus alba in the Peking University Third Hospital. Cells of strain LAM0705(T) were observed to be Gram-stain positive, motile, spore-forming and rod-shaped. The optimal temperature and pH for growth were found to be 30 °C and pH 7.5, respectively. Strain LAM0705(T) was found to be able to grow in the presence 0-5 % NaCl (w/v) (optimum 1.0 %). The major fatty acids of strain LAM0705(T) were identified as anteiso-C15:0, C16:0 and iso-C16:0. The dominant polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The cell wall peptidoglycan of strain LAM0705(T) was found to contain meso-diaminopimelic acid. The predominant menaquinone was identified as MK-7. The G+C content of genomic DNA was found to be 48 mol% when determined by the T m method. The 16S rRNA gene sequence similarity analysis indicated that strain LAM0705(T) is closely related to Paenibacillus agaridevorans DSM 1355(T) and Paenibacillus thailandensis KCTC 13043(T) with 97.8 and 96.1 % sequence similarity, respectively. The DNA-DNA hybridization value between strain LAM0705(T) and P. agaridevorans DSM 1355(T) was 47 ± 0.8 %. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0705(T) is concluded to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus populi sp. nov. is proposed. The type strain is LAM0705(T) (=ACCC 06427(T) = JCM 19843(T)). PMID:26133115

  8. Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil.

    PubMed

    Li, Qin-Fen; Sun, Li-Na; Kwon, Soon-Wo; Chen, Qing; He, Jian; Li, Shun-Peng; Zhang, Jun

    2014-06-01

    A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)). PMID:24585373

  9. Bacillus nitroreducens sp. nov., a humus-reducing bacterium isolated from a compost.

    PubMed

    Guo, Junhui; Wang, Yue Qiang; Yang, Guiqin; Chen, Yunqi; Zhou, Shungui; Zhao, Yong; Zhuang, Li

    2016-05-01

    A Gram-staining-positive, facultative anaerobic, motile and rod-shaped bacterium, designated GSS08(T), was isolated from a windrow compost pile and characterized by means of a polyphasic approach. Growth occurred with 0-4 % (w/v) NaCl (optimum 1 %), at pH 6.5-9.5 (optimum pH 7.5) and at 20-45 °C (optimum 37 °C). Anaerobic growth occurred with anthraquinone-2,6-disulphonate, fumarate and NO3 (-) as electron acceptor. The main respiratory quinone was MK-7. The predominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>5 %) were iso-C15:0 (43.1 %), anteiso-C15:0 (27.4 %) and iso-C16:0 (8.3 %). The DNA G + C content was 39.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GSS08(T) formed a phyletic lineage with the type strain of Bacillus humi DSM 16318(T) with a high sequence similarity of 97.5 %, but it displayed low sequence similarity with other valid species in the genus Bacillus (<96.0 %). The DNA-DNA relatedness between strains GSS08(T) and B. humi DSM 16318(T) was 50.8 %. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS08(T) represents a novel species, for which the name Bacillus nitroreducens sp. nov. is proposed. The type strain is GSS08(T) (=KCTC 33699(T) = MCCC 1K01091(T)). PMID:26832132

  10. Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora

    PubMed Central

    Genicot, Sabine M.; Groisillier, Agnès; Rogniaux, Hélène; Meslet-Cladière, Laurence; Barbeyron, Tristan; Helbert, William

    2014-01-01

    Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ι-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40 ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ι-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ι-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ι-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes. PMID:25207269

  11. Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots.

    PubMed

    Zhang, Lei; Gao, Ju-Sheng; Kim, Song-Gun; Zhang, Cai-Wen; Jiang, Ju-Quan; Ma, Xiao-Tong; Zhang, Jun; Zhang, Xiao-Xia

    2016-01-01

    A novel endophytic bacterium, strain ZYY112T, isolated from rice roots, was characterized by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, ZYY112T showed highest sequence similarity to Novosphingobium sediminicola HU1-AH51T (97.2 %) and less than 97 % similarity with respect to other Novosphingobium species with validly published names. The DNA G+C content of strain ZYY112T was 60.8 mol%. The level of DNA-DNA relatedness between strain ZYY112T and N. sediminicola DSM 27057T was 33.7 % (reciprocal 5.2 %), which supported the suggestion that ZYY112T represented a novel species of the genus Novosphingobium. Ubiquinone Q-10 was the unique respiratory quinone (100 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unknown aminolipid and an unknown phospholipid. The major fatty acids of strain ZYY112T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c), C14 : 0 2-OH and C16 : 0. The major polyamine of ZYY112T was spermidine, which is a characteristic trait of the genus Novosphingobium. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain ZYY112T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium oryzae sp. nov. is proposed. The type strain is ZYY112T ( = ACCC 06131T = JCM 30537T). PMID:26514117

  12. Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring.

    PubMed

    Díaz-Cárdenas, C; López, G; Patel, B K C; Baena, S

    2010-04-01

    A mesophilic, strictly anaerobic, slightly halophilic bacterium, designated strain USBA 82(T), was isolated from a terrestrial saline spring in the Colombian Andes. The non-spore-forming curved rods (5-7 x 1.3 microm) with pointed or rounded ends, stained Gram-negative and were motile by means of laterally inserted flagella. The strain grew optimally at 30 degrees C (growth range 20-40 degrees C), pH 7.3 (growth range pH 5.5-8.5) and 2 % (w/v) NaCl (growth range 0.1-7 % NaCl). The strain fermented peptides, amino acids and a few organic acids, but growth was not observed on carbohydrates, alcohols or fatty acids. The strain reduced thiosulfate and sulfur to sulfide. Sulfate, sulfite, nitrate and nitrite were not used as electron acceptors. On peptone alone, acetate, succinate, propionate and traces of ethanol were formed, but in the presence of thiosulfate, acetate and succinate were formed. The G+C content of the chromosomal DNA was 52 mol% (T(m)). 16S rRNA gene sequence analysis indicated that strain USBA 82(T) was affiliated to Dethiosulfovibrio peptidovorans within the phylum Synergistetes with a similarity value of approximately 93 %. Based on the differences between the new strain and the type species of the genus Dethiosulfovibrio, we suggest that strain USBA 82(T) represents a novel species of the genus for which the name Dethiosulfovibrio salsuginis sp. nov. is proposed. The type strain is USBA 82(T) (=DSM 21565(T)=KCTC 5659(T)). PMID:19661517

  13. Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil.

    PubMed

    Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

    2016-01-01

    A Gram-stain-negative, rod-shaped, red-pigmented bacterium (MDT1-10-3T) was isolated from Midui glacier in Tibet, China. Cells were aerobic and psychrotolerant (growth occurred at 4-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was a member of the genus Rufibacter, with Rufibacter immobilis MCC P1T (96.7 % similarity) as its closest phylogenetic relative. MK-7 was the predominant respiratory menaquinone. The major cellular fatty acids were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C17 : 1ω6c, iso-C16 : 0, iso-C15 : 0 and C16 : 1ω5c. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids, one glycolipid and four unidentified lipids. The G+C content of the genomic DNA was 49 mol%. On the basis of the phenotypic characteristics and phylogenetic analysis, strain MDT1-10-3T represents a novel species of the genus Rufibacter, for which the name Rufibacter glacialis sp. nov. is proposed. The type strain is MDT1-10-3T ( = CGMCC 1.9789T = NBRC 109705T). PMID:26510965

  14. Zooshikella marina sp. nov. a cycloprodigiosin- and prodigiosin-producing marine bacterium isolated from beach sand.

    PubMed

    Ramaprasad, E V V; Bharti, Dave; Sasikala, Ch; Ramana, Ch V

    2015-12-01

    A red-pigmented bacterium producing a metallic green sheen, designated strain JC333T, was isolated from a sand sample collected from Shivrajpur-Kachigad beach, Gujarat, India. Phylogenetic analyses based on the 16S rRNA gene sequence of strain JC333T showed highest sequence similarity to Zooshikella ganghwensis JC2044T (99.24 %) and less than 91.94 % similarity with other members of the class Gammaproteobacteria. DNA-DNA hybridizations between JC333T and Z. ganghwensis JC2044T showed low relatedness values of 19 ± 1.3 % (reciprocal 21 ± 2.2 %). The major respiratory quinone was ubiquinone-9 (Q9) and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The presence of C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C18 : 1ω7c and C12 : 0 as major fatty acids supported the affiliation of strain JC333T to the genus Zooshikella. Prodigiosin, cycloprodigiosin and eight other prodigiosin analogues were the pigments of JC333T. Characterization based on 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, and polar lipid and fatty acid compositions revealed that JC333T represents a novel species of the genus Zooshikella, for which the name Zooshikella marina sp. nov. is proposed. The type strain is JC333T ( = KCTC 42659T = LMG 28823T). PMID:26409875

  15. Ferrovibrio xuzhouensis sp. nov., a cyhalothrin-degrading bacterium isolated from cyhalothrin contaminated wastewater.

    PubMed

    Song, Man; Zhang, Long; Sun, Bin; Zhang, Hao; Ding, Hui; Li, Qiang; Guo, Suhui; Huang, Xing

    2015-08-01

    A novel cyhalothrin-degrading strain, designated as LM-6(T), was isolated from a cyhalothrin contaminated wastewater sample. The bacterium was found to be Gram stain-negative, non-spore-forming, vibrio-shaped, and motile with a single polar flagellum. Strain LM-6(T) was observed to grow optimally at 28-30 °C, pH 6.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain LM-6(T) is a member of the genus Ferrovibrio, and showed the highest sequence similarity with Ferrovibrio denitrificans Sp-1(T) (97.7 %), followed by Taonella mepensis H1(T) (93.3 %). The major fatty acids of strain LM-6(T) (>5 %) were determined to be C18:1 ω7c and/or C18:1 ω6c, C16:0, C18:1 2-OH and C17:1 iso I and/or anteiso B. The major polar lipids were identified to be phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmethylethanolamine. The major respiratory quinone was determined to be ubiquinone-10. The genomic DNA G+C content of strain LM-6(T) is 66.5 mol %. Strain LM-6(T) showed low DNA-DNA relatedness with F. denitrificans Sp-1(T) (53.1 ± 0.5 %). On the basis of phylogenetic, genomic, phenotypic and chemotaxonomic data, strain LM-6(T) is considered to represent a novel species of the genus Ferrovibrio, for which the name Ferrovibrio xuzhouensis sp. nov. is proposed. The type strain is Ferrovibrio xuzhouensis LM-6(T) (=KCTC 42182(T) = ACCC 19710(T)). PMID:26002076

  16. Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India.

    PubMed

    Saha, P; Mondal, A K; Mayilraj, S; Krishnamurthi, S; Bhattacharya, A; Chakrabarti, T

    2005-11-01

    A polyphasic approach was used to characterize a bacterium, GPTSA 11(T), isolated from a warm spring located in a reserve forest in Assam, India. The cells are Gram-variable, strictly aerobic, sporulating motile rods. The major fatty acids of the strain are C(15 : 0) anteiso (48.42 %), C(16 : 0) iso (11.59 %), C(16 : 1)omega11c (6.16 %), C(15 : 0) iso (6.03 %), C(17 : 0) anteiso (5.68 %) and C(16 : 1)omega7c alcohol (5.01 %). The presence of the fatty acid C(16 : 1)omega7c alcohol distinguishes this strain from other closely related species of the genus Paenibacillus. The strain contains MK-7 as the diagnostic menaquinone. The G+C content of the genomic DNA is 41.2 mol%. Analysis of the 16S rRNA gene sequence (1466 nt) revealed the presence of signature sequences PAEN 515F (5'-GAGTAACTGCTCTCGGAATGACGGTACTTGAGAAGAAAGCCCC-3') and PAEN 862F (5'-TCGATACCCTTGGTGCCGAAGT-3'), which were found in the species of the genus Paenibacillus surveyed by Shida et al. [Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. (1997). Int J Syst Bacteriol 47, 289-298]. The sequence shows closest similarity (95.85 %) to that of Paenibacillus apiarius, followed by Paenibacillus alvei (94.34 %), Paenibacillus cineris (93.87 %), Paenibacillus favisporus (93.80 %), Paenibacillus chibensis (93.47 %) and Paenibacillus azoreducens (93.40 %). Biochemical, physiological, chemotaxonomic and phylogenetic analyses justify placement of the strain in the genus Paenibacillus but not within any existing species. It should, therefore, be considered as representing a novel species, for which the name Paenibacillus assamensis sp. nov. is proposed. The type strain is GPTSA 11T (=MTCC 6934T=JCM 13186T). PMID:16280530

  17. Thermoactinomyces khenchelensis sp. nov., a filamentous bacterium isolated from soil sediment of a terrestrial hot spring.

    PubMed

    Mokrane, Salim; Bouras, Noureddine; Meklat, Atika; Lahoum, Abdelhadi; Zitouni, Abdelghani; Verheecke, Carol; Mathieu, Florence; Schumann, Peter; Spröer, Cathrin; Sabaou, Nasserdine; Klenk, Hans-Peter

    2016-02-01

    A novel thermophilic filamentous bacterium, designated strain T36(T), was isolated from soil sediment sample from a hot spring source collected in Khenchela province, Algeria. Strain T36(T) was identified as a member of the genus Thermoactinomyces by a polyphasic approach. Strain T36(T) was observed to form white aerial mycelium and non-coloured to pale yellow substrate mycelium, both producing endospores, sessile or borne by short sporophores. The optimum growth temperature and pH were found to be 37-55 °C and 7.0-9.0, respectively and the optimum NaCl concentration for growth was found to be 0-7 % (w/v). The diagnostic diamino acid in the cell wall peptidoglycan was identified as meso-diaminopimelic acid. The predominant menaquinone of strain T36(T) was identified as MK-7 (H0). The major fatty acids were found to be iso-C15:0 and iso-C17:0. The phospholipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphoglycolipid. The chemotaxonomic properties of strain T36(T) are consistent with those shared by members of the genus Thermoactinomyces. 16S rRNA gene sequence analysis indicated that the sequence similarities between strain T36(T) and Thermoactinomyces species with validly published names were less than 98 %. Based on the combined genotypic and phenotypic evidence, it is proposed that strain T36(T) should be classified as representative of a novel species, for which the name Thermoactinomyces khenchelensis sp. nov. is proposed. The type strain is T36(T) (=DSM 45951(T) = CECT 8579(T)). PMID:26678783

  18. Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.

    PubMed

    Kämpfer, P; Arun, A B; Rekha, P D; Busse, H-J; Young, C-C; Glaeser, S P

    2013-07-01

    A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2(T), was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157(T), and a lower sequence similarity to all other species of the genus Ruegeria. Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2(T) clustered within the genus Ruegeria. Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2(T) represents a novel species of the genus Ruegeria, for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2(T) ( = CCUG 59209(T) = LMG 25539(T) = CCM 7758(T)). PMID:23243093

  19. Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil.

    PubMed

    Lee, Jae-Chan; Kim, Young-Sook; Yun, Bong-Sik; Whang, Kyung-Sook

    2015-12-01

    A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0-10.8 (optimum, pH 8.5), at 10-55 °C (optimum, 28 °C) and at salinities of 0-23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA-DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T). PMID:26431725

  20. Halomonas heilongjiangensis sp. nov., a novel moderately halophilic bacterium isolated from saline and alkaline soil.

    PubMed

    Dou, Guiming; He, Wei; Liu, Hongcan; Ma, Yuchao

    2015-08-01

    A moderately halophilic bacterium, designated strain 9-2(T), was isolated from saline and alkaline soil collected in Lindian county, Heilongjiang province, China. The strain was observed to be strictly aerobic, Gram-negative, rod-shaped, oxidase-positive, catalase-positive and motile. It was found to require NaCl for growth and to grow at NaCl concentrations of 0.5-14 % (w/v) (optimum, 7-10 %, w/v), at temperatures of 10-45 °C (optimum 25-30 °C) and at pH 5.0-10.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 9-2(T) is a member of the genus Halomonas and is closely related to Halomonas desiderata DSM 9502(T) (96.68 %), Halomonas campaniensis DSM 1293(T) (96.46 %), Halomonas ventosae DSM 15911(T) (96.27 %) and Halomonas kenyensis DSM 17331(T) (96.27 %). The DNA-DNA hybridization value was 38.9 ± 0.66 % between the novel isolate 9-2(T) and H. desiderata DSM 9502(T). The predominant ubiquinones were identified as Q9 (75.1 %) and Q8 (24.9 %). The major fatty acids were identified as C16:0 (22.0 %), Summed feature 8 (C18:1 ω6c/C18:1 ω7c, 19.6 %), Summed feature 3 (C16:1 ω6c/C16:1 ω7c, 12.6 %), C12:0 3-OH (12.0 %) and C10:0 (11.7 %). The DNA G+C content was determined to be 69.7 mol%. On the basis of the evidence presented in this study, strain 9-2(T) is considered to represent a novel species of the genus Halomonas, for which the name Halomonas heilongjiangensis sp. nov. is proposed. The type strain is 9-2(T) (=DSM 26881(T) = CGMCC 1.12467(T)). PMID:26036672

  1. Halobacillus salicampi sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.

    PubMed

    Kim, Su-Jin; Lee, Jae-Chan; Han, Song-Ih; Whang, Kyung-Sook

    2016-05-01

    A Gram-positive, moderately halophilic bacterium, designated strain TGS-15(T), was isolated from the sediment of a solar saltern pond located in Shinan, Korea. Strain TGS-15(T) was found to be a strictly aerobic, non-motile rod which can grow at pH 6.0-10.0 (optimum, pH 9.0), at 20-35 °C (optimum, 28 °C) and at salinities of 1-20 % (w/v) NaCl (optimum, 9 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain TGS-15(T) belongs to the genus Halobacillus, with sequence similarity of 98.5-96.0 % to known type strains, showing high sequence similarity to Halobacillus locisalis MSS-155(T) (98.5 %), Halobacillus faecis IGA7-4(T) (98.2 %) and Halobacillus alkaliphilus FP5(T) (98.0 %), and less than 98.0 % sequence similarity to other currently recognised type strains of the genus. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The cell wall peptidoglycan was found to be based on L-Orn-D-Asp, the predominant isoprenoid quinone was identified as menaquinone-7 (MK-7) and the major fatty acids were identified as anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:1 ω7c alcohol. The DNA G+C content of this novel isolate was determined to be 45.3 mol %. Levels of DNA:DNA relatedness between strain TGS-15(T) and the type strains of 13 other species of the genus ranged from 52 to 9 %. On the basis of the polyphasic analysis conducted in this study, strain TGS-15(T) is concluded to represent a novel species of the genus Halobacillus, for which the name Halobacillus salicampi sp. nov. is proposed. The type strain is TGS-15(T) (=KACC 18264(T) = NBRC 110640(T)). PMID:26942918

  2. Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia

    PubMed Central

    Rahman, Raja Noor Zaliha Raja Abd; Leow, Thean Chor; Salleh, Abu Bakar; Basri, Mahiran

    2007-01-01

    Background Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78°C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5–99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification. Results Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70°C and was also stable up to 60°C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T) and Geobacillus kaustophilus (DSM 7263T). Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T). Conclusion Strain T1T was able to secrete extracellular thermostable lipase into

  3. Tumebacillus flagellatus sp. nov., an α-amylase/pullulanase-producing bacterium isolated from cassava wastewater.

    PubMed

    Wang, Qingyan; Xie, Nengzhong; Qin, Yan; Shen, Naikun; Zhu, Jing; Mi, Huizhi; Huang, Ribo

    2013-09-01

    A novel α-amylase/pullulanase-producing bacterium, designated strain GST4(T), was isolated from samples collected from the wastewater of a cassava starch factory in Nanning, Guangxi Autonomous Region, southern China. Cells of strain GST4(T) were rod-shaped bacilli containing ellipsoidal terminal spores and found to be Gram-reaction-positive, aerobic, motile, oxidase-positive, catalase-negative and formed light yellow colonies on agar plates. Strain GST4(T) was able to grow at pH 4.5-8.5 (optimum at pH 5.5), temperatures ranging from 20 to 42 °C (optimum at 37 °C) and salt concentrations of 0-1% (w/v) NaCl (optimum at 0.5%, w/v) on R2A medium. Strain GST4(T) grew heterotrophically on complex carbon substrates and chemolithoautotrophically on inorganic sulfur compounds, as demonstrated by growth on sodium thiosulfate and sulfite as sole electron donors. It can reduce nitrate and nitrite. Strain GST4(T) contained iso-C(15:0) and anteiso-C(15:0) as the major cellular fatty acids and menaquinone 7 (MK-7) as the major respiratory quinone. The cell-wall peptidoglycan was of type A1γ. The genomic DNA G+C content of strain GST4(T) was 53.7 mol%. Physiological and chemotaxonomic characteristics combined with phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GST4(T) was a member of the genus Tumebacillus and most closely related to Tumebacillus permanentifrigoris DSM 18773(T) and Tumebacillus ginsengisoli DSM 18389(T) with 97.3 and 94.5% sequence similarity, respectively. The DNA-DNA relatedness values between strain GST4(T) and T. permanentifrigoris DSM 18773(T), and strain GST4(T) and T. ginsengisoli DSM 18389(T) were 44.0 and 60.4%, respectively. The new isolate differed from those species of the genus Tumebacillus in that it has peritrichous flagella for motility. Based on the evidence obtained from this study, strain GST4(T) represents a novel species of the genus Tumebacillus, for which the name Tumebacillus flagellatus sp. nov. is proposed

  4. Microbial metabolism of polycyclic aromatic hydrocarbons: Isolation and characterization of a pyrene-degrading bacterium. [Mycobacterium sp

    SciTech Connect

    Heitkamp, M.A.; Franklin, W.; Cerniglia, C.E. )

    1988-10-01

    Microbiological analyses of sediments located near a point source for petrogenic chemicals resulted in the isolation of a pyrene-mineralizing bacterium. This isolate was identified as a Mycobacterium sp. on the basis of its cellular and colony morphology, gram-positive and strong acid-fast reactions, diagnostic biochemical tests, 66.6% G+C content of the DNA, and high-molecular-weight mycolic acids (C{sub 58} to C{sub 64}). The mycobacterium mineralized pyrene when grown in a mineral salts medium supplemented with nutrients but was unable to utilize pyrene as a sole source of carbon and energy. The mycobacterium grew well at 24 and 30{degree}C and minimally at 35{degree}C. No growth was observed at 5 or 42{degree}C. The mycobacterium grew well at salt concentrations up to 4%. Pyrene-induced Mycobacterium cultures mineralized 5% of the pyrene after 6 h and reached a maximum of 48% mineralization within 72 h. Treatment of induced and noninduced cultures with chloramphenicol showed that pyrene-degrading enzymes were inducible in this Mycobacterium sp. This bacterium could also mineralize other polycyclic aromatic hydrocarbons and alkyl- and nitro-substituted polycyclic aromatic hydrocarbons including naphthalene, phenanthrene, fluoranthene, 3-methylcholanthrene, 1-nitropyrene, and 6-nitrochrysene. This is the first report of a bacterium able to extensively mineralize pyrene and other polycyclic aromatic hydrocarbons containing four aromatic rings.

  5. (Per)chlorate Reduction by the Thermophilic Bacterium Moorella perchloratireducens sp. nov., Isolated from Underground Gas Storage▿

    PubMed Central

    Balk, Melike; van Gelder, Ton; Weelink, Sander A.; Stams, Alfons J. M.

    2008-01-01

    A thermophilic bacterium, strain An10, was isolated from underground gas storage with methanol as a substrate and perchlorate as an electron acceptor. Cells were gram-positive straight rods, 0.4 to 0.6 μm in diameter and 2 to 8 μm in length, growing as single cells or in pairs. Spores were terminal with a bulged sporangium. The temperature range for growth was 40 to 70°C, with an optimum at 55 to 60°C. The pH optimum was around 7. The salinity range for growth was between 0 and 40 g NaCl liter−1 with an optimum at 10 g liter−1. Strain An10 was able to grow on CO, methanol, pyruvate, glucose, fructose, cellobiose, mannose, xylose, and pectin. The isolate was able to respire with (per)chlorate, nitrate, thiosulfate, neutralized Fe(III) complexes, and anthraquinone-2,6-disulfonate. The G+C content of the DNA was 57.6 mol%. On the basis of 16S rRNA analysis, strain An10 was most closely related to Moorella thermoacetica and Moorella thermoautotrophica. The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell extracts. Strain An10 is the first thermophilic and gram-positive bacterium with the ability to use (per)chlorate as a terminal electron acceptor. PMID:17981952

  6. Microbial selenite reduction with organic carbon and electrode as sole electron donor by a bacterium isolated from domestic wastewater.

    PubMed

    Nguyen, Van Khanh; Park, Younghyun; Yu, Jaecheul; Lee, Taeho

    2016-07-01

    Selenium is said to be multifaceted element because it is essential at a low concentration but very toxic at an elevated level. For the purpose of screening a potential microorganism for selenite bioremediation, we isolated a bacterium, named strain THL1, which could perform both heterotrophic selenite reduction, using organic carbons such as acetate, lactate, propionate, and butyrate as electron donors under microaerobic condition, and electrotrophic selenite reduction, using an electrode polarized at -0.3V (vs. standard hydrogen electrode) as the sole electron donor under anaerobic condition. This bacterium determined to be a new strain of the genus Cronobacter, could remove selenite with an efficiency of up to 100%. This study is the first demonstration on a pure culture could take up electrons from an electrode to perform selenite reduction. The selenium nanoparticles produced by microbial selenite reduction might be considered for recovery and use in the nanotechnology industry. PMID:27099943

  7. Isolation and characterization of endophytic bacterium LRE07 from cadmium hyperaccumulator Solanum nigrum L. and its potential for remediation.

    PubMed

    Luo, Shenglian; Wan, Yong; Xiao, Xiao; Guo, Hanjun; Chen, Liang; Xi, Qiang; Zeng, Guangming; Liu, Chengbin; Chen, Jueliang

    2011-03-01

    Valuable endophytic strains facilitating plants growth and detoxification of heavy metals are required because the application of plant-endophyte symbiotic system is a promising potential technique to improve efficiency of phytoremediation. In this study, endophytic bacterium LRE07 was isolated from cadmium hyperaccumulator Solanum nigrum L. It was identified as Serratia sp. by 16S rRNA sequence analysis. The endophytic bacterium LRE07 was resistant to the toxic effects of heavy metals, solubilized mineral phosphate, and produced indoleacetic acid and siderophore. The heavy metal detoxification was studied in growing LRE07 cells. The strain bound over 65% of cadmium and 35% of zinc in its growing cells from single metal solutions 72 h after inoculation. Besides the high removal efficiencies in single-ion system, an analogous removal phenomenon was also observed in multi-ions system, indicating that the endophyte possesses specific and remarkable heavy metal remediation abilities. PMID:20953602

  8. Alteromonas infernus sp. nov., a new polysaccharide-producing bacterium isolated from a deep-sea hydrothermal vent.

    PubMed

    Raguénès, G H; Peres, A; Ruimy, R; Pignet, P; Christen, R; Loaec, M; Rougeaux, H; Barbier, G; Guezennec, J G

    1997-04-01

    A deep-sea, aerobic, mesophilic and heterotrophic new bacterium was isolated from a sample of fluid collected among a dense population of Riftia pachyptila, in the vicinity of an active hydrothermal vent of the Southern depression of the Guaymas basin (Gulf of California). On the basis of phenotypic and phylogenetic analyses and DNA/DNA relatedness, the strain GY785 was recognized as a new species of the genus Alteromonas and the name of Alteromonas infernus is proposed. During the stationary phase in batch cultures in the presence of glucose, this bacterium secreted two unusual polysaccharides. The water-soluble exopolysaccharide-1 produced contained glucose, galactose, galacturonic and glucuronic acids as monosaccharides. The gel-forming exopolysaccharide-2 was separated from the bacterial cells by dialysis against distilled water and partially characterized. PMID:9134716

  9. Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment.

    PubMed

    Tsubouchi, Taishi; Shimane, Yasuhiro; Usui, Keiko; Shimamura, Shigeru; Mori, Kozue; Hiraki, Toshiki; Tame, Akihiro; Uematsu, Katsuyuki; Maruyama, Tadashi; Hatada, Yuji

    2013-06-01

    A novel Gram-negative, aerobic, psychrotolerant, alkali-tolerant, heterotrophic and dimorphic prosthecate bacterium, designated strain TAR-001(T), was isolated from deep-sea floor sediment in Japan. Cells of this strain had a dimorphic life cycle and developed an adhesive stalk at a site not coincident with the centre of the cell pole, and the other type of cell, a swarm cell, had a polar flagellum. Colonies were glossy, viscous and yellowish-white in colour. The temperature, pH and salt concentration range for growth were 2-41 °C, pH 6.5-10.0 and 1-4% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-001(T) belongs to the family Caulobacteraceae of the class Alphaproteobacteria, and lies between the genus Brevundimonas and the genus Caulobacter. Levels of similarity between the 16S rRNA gene sequence of strain TAR-001(T) and those of the type strains of Brevundimonas species were 93.3-95.7%; highest sequence similarity was with the type strain of Brevundimonas diminuta. Levels of sequence similarity between those of the type strains of Caulobacter species were 94.9-96.0%; highest sequence similarity was with the type strain of Caulobacter mirabilis. The G+C content of strain TAR-001(T) was 67.6 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18:1ω7c and C16:0, and the presence of 1,2-di-O-acyl-3-O-[D-glucopyranosyl-(1→4)-α-D-glucopyranuronosyl]glycerol suggests strain TAR-001(T) is more closely to the genus Brevundimonas than to the genus Caulobacter. The mean DNA-DNA hybridization levels between strain TAR-001(T) and the type strains of two species of the genus Brevundimonas were higher than that of the genus Caulobacter. On the basis of polyphasic biological features and the 16S rRNA gene sequence comparison presented here, strain TAR-001(T) is considered to represent a novel species of the genus Brevundimonas, for which the name Brevundimonas abyssalis sp. nov. is proposed; the

  10. Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge.

    PubMed

    Chen, Qing; Zhang, Jun; Wang, Cheng-Hong; Jiang, Jin; Kwon, Soon-Wo; Sun, Li-Na; Shen, Wen-Biao; He, Jian

    2014-08-01

    Strain BUT-14(T), a Gram-reaction-negative, non-spore-forming, ellipse-shaped bacterium, was isolated from activated sludge of a chloroacetamide-herbicides-manufacturing wastewater treatment facility. The strain was able to degrade more than 90% of butachlor, acetochlor and alachlor (100 mg l(-1)) within 5 days of incubation. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-14(T) was a member of the genus Novosphingobium and showed the highest sequence similarities to Novosphingobium soli DSM 22821(T) (97.9%), N. naphthalenivorans KACC 15258(T) (97.4%), N. pentaromativorans JCM 12182(T) (97.4%) and N. barchaimii DSM 25411(T) (97.1%) and lower (<97%) sequence similarities to all other species of the genus Novosphingobium. Chemotaxonomic analysis revealed that strain BUT-14(T) possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine and C(18 : 1)ω7c (46.9%), C(17 : 1)ω6c (17.9%), summed feature 3, C(14 : 0) 2-OH (4.4%), C(15 : 0) 2-OH (3.1%) and C(16 : 0) (5.51%) as the major fatty acids. The polar lipids included lipid, glycolipid, phosphatidylglycerol, phospholipid, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phospatidyldimethylethanolamine. Strain BUT-14(T) showed low DNA-DNA relatedness with N. soli DSM 22821(T) (41.5±2.9%), N. naphthalenivorans JCM 12182(T) (49.2±4.2%), N. pentaromativorans KACC 12295(T) (53.2±1.9%) and N. barchaimii DSM 25411 (51.2±4.5%). The DNA G+C content was 66±0.3 mol%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic data and DNA-DNA hybridization supports the suggestion that strain BUT-14(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-14(T) ( = CCTCC AB 2013086(T) = KACC 17147(T) = JCM 19923(T)). PMID

  11. Salipiger nanhaiensis sp. nov., a bacterium isolated from deep sea water.

    PubMed

    Dai, Xiaofeng; Shi, Xiaochong; Gao, Xin; Liang, Jing; Zhang, Xiao-Hua

    2015-04-01

    A Gram-stain-negative, facultatively anaerobic, chemoheterotrophic, moderately halophilic, exopolysaccharide (EPS)-producing, cream, non-motile and rod-shaped bacterium, designated strain ZH114(T), was isolated from deep water of the South China Sea, and was subjected to a polyphasic taxonomic study. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that this strain belongs to the genus Salipiger with the highest sequence similarity to Salipiger mucescens LMG 22090(T) (96.83%), followed by Pseudodonghicola xiamenensis LMG 24574(T) (96.12%). Growth occurred at 4-37 °C (optimum 32 °C), pH 6.0-10.0 (optimum pH 9.0-10.0) and in the presence of 0-19% NaCl (w/v) (optimum 6%, w/v). It did not produce poly-β-hydroxyalkanoate granules or bacteriochlorophyll a. Acid was produced from glycerol, erythrose, ribose, D-xylose, galactose, glucose, fructose, mannitol, cellobiose, maltose, lactose, melibiose, turanose, D-lyxose, D-tagatose, D-fucose, D-arabitol and L-arabitol after inoculating for 24 h and weakly positive results were also detected after 48 h in API 50CH strips with D-arabinose, L-arabinose, L-xylose, adonitol, mannose, aesculin, salicin, sucrose, mycose and L-fucose. The predominant fatty acids were C(18 : 1)ω7c and/or C(18 : 1)ω6c, C(16 : 0), C(18 : 0) and 11-methyl C(18 : 1)ω7c. The major polar lipids of ZH114(T) were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The major respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content of strain ZH114(T) was 63.8 mol%. Based on this phenotypic, chemotaxonomic and phylogenetic analysis, strain ZH114(T) should be classified as a representative of a novel species of the genus Salipiger , for which the name Salipiger nanhaiensis sp. nov. is proposed. The type strain is ZH114(T) ( = JCM 19383(T) = KCTC 32468(T)). PMID:25589735

  12. Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil.

    PubMed

    Gao, Zhao-Ming; Xiao, Jing; Wang, Xing-Na; Ruan, Ling-Wei; Chen, Xiu-Lan; Zhang, Yu-Zhong

    2012-08-01

    A taxonomic study was carried out on a cellulase-producing bacterium, strain G21(T), isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15-40 °C and in 0.5-10% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21(T) belonged to the genus Vibrio and formed a clade with Vibrio furnissii ATCC 350116(T) (97.4% sequence similarity), V. fluvialis LMG 7894(T) (97.1%) and V. ponticus CECT 5869(T) (96.1%). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA-DNA hybridization experiments indicated that the strain was distinct from the closest related Vibrio species. Additionally, strain G21(T) could be differentiated from them phenotypically by the ability to grow in 10% NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA-DNA hybridization analysis, it is concluded that strain G21(T) represents a novel species of the genus Vibrio, for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21(T) ( = DSM 22851(T)  = CGMCC 1.10228(T)). PMID:22039001

  13. Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil.

    PubMed

    Pham, Van Hong Thi; Jeong, Seung-Woo; Kim, Jaisoo

    2015-10-01

    Strain NHI-1T is a Gram-negative, motile, non-spore-forming bacterium isolated from oil-contaminated soil in South Korea. The strain was able to grow by using gasoline, diesel and kerosene as energy and carbon sources. After incubation for 14 days, cells (1 g l- 1) degraded approximately 58 % of oil present at concentration of 1500 p.p.m. at pH 8 and 28 °C. Strain NHI-1T grew well under aerobic conditions, with optimal growth at pH 7-9 and 28 °C-37 °C but grew poorly in the presence of ≥ 0.5 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest relatives of strain NHI-1T were Aquabacterium fontiphilum CS-6T (97.96 % sequence similarity), Aquabacterium parvum B6T (96.39 %), Aquabacterium commune B8T (95.76 %), Aquabacterium limnoticum ABP-4T (95.72 %) and Aquabacterium citratiphilum B4T (95.25 %). DNA-DNA relatedness was 41-53 % between strain NHI-1T and its closest type strains. The major fatty acids present in strain NHI-1T were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c, 44.5 %), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c, 21.5 %) and C16 : 0 (16.2 %), and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol and uncharacterized aminophospholipids. Strain NHI-1T was distinguishable from other members of genus Aquabacterium based on phenotypic, chemotaxonomic and genotypic characteristics. Therefore, strain NHI-1T represents a novel species of the genus Aquabacterium for which the name Aquabacterium olei sp. nov. is proposed. The type strain is NHI-1T ( = KEMB 9005-082T =  KACC 18244T = NBRC 110486T). PMID:26297008

  14. Caloramator quimbayensis sp. nov., an anaerobic, moderately thermophilic bacterium isolated from a terrestrial hot spring.

    PubMed

    Rubiano-Labrador, Carolina; Baena, Sandra; Díaz-Cárdenas, Carolina; Patel, Bharat K C

    2013-04-01

    An anaerobic, moderately thermophilic, terminal-spore-forming bacterium, designated strain USBA A(T), was isolated from a terrestrial hot spring located at an altitude of 2683 m in the Andean region of Colombia (04° 50' 14.0″ N 75° 32' 53.4″ W). Cells of strain USBA A(T) were Gram-stain-positive, straight to slightly curved rods (0.9×2.5 µm), that were arranged singly or in pairs, and were motile by means of flagella. Growth occurred at 37-55 °C and pH 6.0-8.0, with a doubling time of 2 h under the optimal conditions (50 °C and pH 7.0). Glucose fermentation in strain USBA A(T) required yeast extract or peptone (each at 0.2 %, w/v). The novel strain fermented sugars, amino acids, Casamino acids, propanol, propionate, starch and dextrin, but no growth was observed on galactose, lactose, xylose, histidine, serine, threonine, benzoate, butyrate, lactate, pyruvate, succinate, methanol, ethanol, glycerol, casein, gelatin or xylan. The end products of glucose fermentation were formate, acetate, ethanol and lactate. Strain USBA A(T) did not grow autotrophically (with CO2 as carbon source and H2 as electron donor) and did not reduce thiosulfate, sulfate, elemental sulfur, sulfite, vanadium (V) or Fe (III) citrate. Growth of strain USBA A(T) was inhibited by ampicillin, chloramphenicol, kanamycin, penicillin and streptomycin (each at 10 µg ml(-1)). The predominant fatty acids were iso-C15 : 0, C16 : 0 and iso-C17 : 0 and the genomic DNA G+C content was 32.6 mol%. 16S rRNA gene sequence analysis indicated that strain USBA A(T) belonged in the phylum Firmicutes and that its closest relative was Caloramator viterbiensis JW/MS-VS5(T) (95.0 % sequence similarity). A DNA-DNA relatedness value of only 30 % was recorded in hybridization experiments between strain USBA A(T) and Caloramator viterbiensis DSM 13723(T). Based on the phenotypic, chemotaxonomic and phylogenetic evidence and the results of the DNA-DNA hybridization experiments, strain USBA A

  15. Marinobacter halophilus sp. nov., a halophilic bacterium isolated from a salt lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Liu, Hong-Can; Wang, Fang; Zhou, Yu-Guang; Liu, Zhi-Pei

    2015-09-01

    A Gram-staining-negative bacterium, strain XCD-X12(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/w) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X12(T) were non-spore-forming rods, 0.4-0.7 μm wide, 2.1-3.2 μm long and motile with a single polar flagellum. Strain XCD-X12(T) was strictly aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-20.0% (w/v) NaCl (optimum, 4.0-8.0%), at 4-35 °C (optimum, 30 °C) and at pH 6.5-10.5 (optimum, pH 8.5). It contained Q-9 as the predominant respiratory quinone. The major fatty acids (>10.0%) were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and an uncharacterized aminophospholipid. The DNA G+C content was 55.6 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X12(T) was associated with the genus Marinobacter, and showed the highest 16S rRNA gene sequence similarity to Marinobacter hydrocarbonoclasticus ATCC 49840(T) (97.4%), M. vinifirmus FB1(T) (96.8%), M. excellens KMM 3809(T) (96.8%) and M. antarcticus ZS2-30(T) (96.7%). DNA-DNA relatedness of strain XCD-X12(T) to M. hydrocarbonoclasticus CGMCC 1.7683(T) was 34 ± 5%. Based on these data, it is concluded that strain XCD-X12(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter halophilus sp. nov. is proposed. The type strain is XCD-X12(T) ( = CGMCC 1.12481(T)= JCM 30472(T)). PMID:25985830

  16. Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock.

    PubMed

    Fukuda, Wakao; Chino, Yohzo; Araki, Shigeo; Kondo, Yuka; Imanaka, Hiroyuki; Kanai, Tamotsu; Atomi, Haruyuki; Imanaka, Tadayuki

    2014-06-01

    A Gram-stain-negative, non-spore-forming, aerobic, oligotrophic bacterium (strain 262-7(T)) was isolated from a crack of white rock collected in the Skallen region of Antarctica. Strain 262-7(T) grew at temperatures between -4 and 30 °C, with optimal growth at 25 °C. The pH range for growth was between pH 6.0 and 9.0, with optimal growth at approximately pH 7.0. The NaCl concentration range allowing growth was between 0.0 and 1.0%, with an optimum of 0.5%. Strain 262-7(T) showed an unprecedented range of morphological diversity in response to growth conditions. Cells grown in liquid medium were circular or ovoid with smooth surfaces in the lag phase. In the exponential phase, ovoid cells with short projections were observed. Cells in the stationary phase possessed long tentacle-like projections intertwined intricately. By contrast, cells grown on agar plate medium or in liquid media containing organic compounds at low concentration exhibited short- and long-rod-shaped morphology. These projections and morphological variations clearly differ from those of previously described bacteria. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C(17 : 1)ω6c (28.2%), C(16 : 1)ω7c (22.6%), C(18 : 1)ω7c (12.9%) and C(15 : 0) 2-OH (12.3%). The G+C content of genomic DNA was 68.0 mol%. Carotenoids were detected from the cells. Comparative analyses of 16S rRNA gene sequences indicated that strain 262-7(T) belongs to the family Sphingomonadaceae, and that 262-7(T) should be distinguished from known genera in the family Sphingomonadaceae. According to the phylogenetic position, physiological characteristics and unique morphology variations, strain 262-7(T) should be classified as a representative of a novel genus of the family Sphingomonadaceae. Here, a novel genus and species with the name Polymorphobacter multimanifer gen. nov., sp. nov. is proposed (type strain 262-7(T) = JCM 18140(T) = ATCC BAA-2413(T)). The novel species was

  17. Marinobacter aromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from sea sediment.

    PubMed

    Cui, Zhisong; Gao, Wei; Xu, Guangfei; Luan, Xiao; Li, Qian; Yin, Xiaofei; Huang, Deming; Zheng, Li

    2016-01-01

    A rod-shaped, Gram-stain-negative, slightly halotolerant bacterium, designated strain D15-8PT, was isolated from a sediment sample from the South China Sea. The strain could grow in NaCl concentrations ranging from 0.5 % to 10 % (w/v) (optimum 0.5-1.5 %), and could be cultivated at 10-40 °C (optimum 25 °C) and pH 5.5-9.5 (optimum pH 7.0-8.0). The strain was positive for catalase, oxidase, and hydrolysis of Tween 80, but negative for hydrolysis of DNA and gelatin, nitrite reduction, indole production, Voges-Proskauer reaction, and methyl red test. Strain D15-8PT could biodegrade naphthalene, phenanthrene, and anthracene. The major respiratory quinone was Q-9. The main cellular fatty acids were C12 : 0 (11.5 %), C14 : 0 3-methyl (22.0 %), C16 : 0 (19.2 %), C16 : 1ω9c (22.9 %), and C18 : 1ω9c (6.7 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid and an unidentified phospholipid. The DNA G+C content was 56.8 mol%. Phylogenetic analyses based on 16S rRNA genes showed that strain D15-8PT was most closely related to Marinobacter maritimus JCM 12521T (98.5 % 16S rRNA gene sequence similarity), Marinobacter antarcticus CGMCC 1.10835T (98.1 %), Marinobacter lipolyticus DSM 15157T (97.1 %), and Marinobacter guineae CECT 7243T (97.0 %). Results of the gyrB gene analysis and DNA-DNA hybridization were both less than the cut-off values (90 % for gyrB gene sequence similarity and 70 % for DNA-DNA hybridization). On the basis of this taxonomic study using a polyphasic approach, strain D15-8PT represents a novel species of the genus Marinobacter, for which the name Marinobacter aromaticivorans sp. nov. is proposed. The type strain is D15-8PT ( = CGMCC 1.11015T = KCTC 23781T). PMID:26518711

  18. Caulobacter flavus sp. nov., a stalked bacterium isolated from rhizosphere soil.

    PubMed

    Sun, Le-Ni; Yang, En-Dong; Wei, Jie-Chao; Tang, Xin-Yun; Cao, Yuan-Yuan; Han, Guo-Min

    2015-12-01

    A Gram-stain-negative, aerobic, yellow-pigmented and rod-shaped bacterium with a single polar flagellum or a stalk, designated strain RHGG3T, was isolated from rhizosphere soil of cultivated watermelon (Citrullus lanatus) collected from Hefei, China. Optimal growth of strain RHGG3T was observed at pH 7.0 and 28-30 °C. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain RHGG3T belonged to the genus Caulobacter and showed the highest 16S rRNA gene sequence similarities to Caulobacter segnis ATCC 21756T (98.6 %), Caulobacter vibrioides CB51T (98.3 %) and Caulobacter henricii ATCC 15253T (97.2 %). The G+C content of the genomic DNA was 70 mol%. Strain RHGG3T contained Q-10 as the sole ubiquinone and the major fatty acids (>8 %) were 11-methyl C18 : 1ω7c, C18 : 1ω7c, C16 : 0, C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipids were various unknown glycolipids, phosphatidylglycerol and phosphoglycolipids. DNA-DNA relatedness of strain RHGG3T to type strains of the most closely related species (Caulobacter segnis ATCC 21756T, Caulobacter vibrioides DSM 4738 and Caulobacter henricii ATCC 15253T) was 32.4-40.9 %. Based on polyphasic taxonomy analysis (phylogenetic, unique phenotypic traits, chemotaxonomic and DNA-DNA hybridizations), strain RHGG3T represents a novel species of the genus Caulobacter, for which the name Caulobacter flavus sp. nov. is proposed. The type strain is RHGG3T ( = CGMCC 1.15093T = KCTC 42581T = JCM 30763T). PMID:26354335

  19. Isolation and identification of a bacterium from marine shrimp digestive tract: A new degrader of starch and protein

    NASA Astrophysics Data System (ADS)

    Li, Jiqiu; Tan, Beiping; Mai, Kangsen

    2011-09-01

    It is a practical approach to select candidate probiotic bacterial stains on the basis of their special traits. Production of digestive enzyme was used as a trait to select a candidate probiotic bacterial strain in this study. In order to select a bacterium with the ability to degrade both starch and protein, an ideal bacterial strain STE was isolated from marine shrimp ( Litopenaeus vannamei) intestines by using multiple selective media. The selected isolate STE was identified on the basis of its morphological, physiological, and biochemical characteristics as well as molecular analyses. Results of degradation experiments confirmed the ability of the selected isolate to degrade both starch and casein. The isolate STE was aerobic, Gram-negative, rod-shaped, motile and non-spore-forming, and had catalase and oxidase activities but no glucose fermentation activity. Among the tested carbon/nitrogen sources, only Tween40, alanyl-glycine, aspartyl-glycine, and glycyl-l-glutamic acid were utilized by the isolate STE. Results of homology comparison analyses of the 16S rDNA sequences showed that the isolate STE had a high similarity to several Pseudoalteromonas species and, in the phylogenetic tree, grouped with P. ruthenica with maximum bootstrap support (100%). In conclusion, the isolate STE was characterized as a novel strain belonging to the genus Pseudoalteromonas. This study provides a further example of a probiotic bacterial strain with specific characteristics isolated from the host gastrointestinal tract.

  20. Isolation and Characterization of a Subsurface Bacterium Capable of Growth on Toluene, Naphthalene, and Other Aromatic Compounds

    PubMed Central

    Fredrickson, J. K.; Brockman, F. J.; Workman, D. J.; Li, S. W.; Stevens, T. O.

    1991-01-01

    A bacterium, designated F199, utilized toluene, naphthalene, dibenzothiophene, salicylate, benzoate, p-cresol, and all isomers of xylene as a sole carbon and energy source. This bacterium was isolated from Middendorf sediments, a Cretaceous age formation that underlies the Southeast Coastal Plain in South Carolina, at a depth of approximately 410 m. F199 is a gram-positive, irregular-shaped bacterium that has a varied cell morphology that is dependent on culture medium type and growth stage. F199 required microaerobic conditions (40 to 80 μM O2) for growth on hydrocarbons, glucose, acetate, and lactate in mineral salts medium but not for growth on rich media. [14C]naphthalene mineralization by F199 was induced by either naphthalene or toulene; however, [14C]toluene mineralization by this strain was induced by toluene but not naphthalene. F199 was also found to harbor two plasmids larger than 100 kb. Restricted F199 plasmid and genomic DNA did not hybridize with toluene (pWW0) or naphthalene (NAH7) catabolic plasmid DNA probes. The presence in the Middendorf formation of bacteria with the capacity for degrading a variety of aromatic compounds suggests that indigenous microorganisms may have potential for in situ degradation of organic contaminants. Images PMID:16348445

  1. Isolation of an indigenous imidacloprid-degrading bacterium and imidacloprid bioremediation under simulated in situ and ex situ conditions.

    PubMed

    Hu, Guiping; Zhao, Yan; Liu, Bo; Song, Fengqing; You, Minsheng

    2013-11-28

    The Bacterial community structure and its complexity of the enrichment culture during the isolation and screening of imidacloprid-degrading strain were studied using denaturating gradient gel electrophoresis analysis. The dominant bacteria in the original tea rhizosphere soil were uncultured bacteria, Rhizobium sp., Sinorhizobium, Ochrobactrum sp., Alcaligenes, Bacillus sp., Bacterium, Klebsiella sp., and Ensifer adhaerens. The bacterial community structure was altered extensively and its complexity reduced during the enrichment process, and four culturable bacteria, Ochrobactrum sp., Rhizobium sp., Geobacillus stearothermophilus, and Alcaligenes faecalis, remained in the final enrichment. Only one indigenous strain, BCL-1, with imidacloprid-degrading potential, was isolated from the sixth enrichment culture. This isolate was a gram-negative rod-shaped bacterium and identified as the genus Ochrobactrum based on its morphological, physiological, and biochemical properties and its 16S rRNA gene sequence. The degradation test showed that approximately 67.67% of the imidacloprid (50 mg/l) was degraded within 48 h by strain BCL-1. The optimum conditions for degradation were a pH of 8 and 30°C. The simulation of imidacloprid bioremediation by strain BCL-1 in soil demonstrated that the best performance in situ (tea soil) resulted in the degradation of 92.44% of the imidacloprid (100 mg/g) within 20 days, which was better than those observed in the ex situ simulations that were 64.66% (cabbage soil), 41.15% (potato soil), and 54.15% (tomato soil). PMID:23985542

  2. Alcaligenes faecalis subsp. phenolicus subsp. nov. a phenol-degrading, denitrifying bacterium isolated from a graywater bioprocessor.

    PubMed

    Rehfuss, Marc; Urban, James

    2005-07-01

    A Gram (-) coccobacillary bacterium, J(T), was isolated from a graywater bioprocessor. 16S rRNA and biochemical analysis has revealed strain J(T) closely resembles Alcaligenes faecalis ATCC 8750T and A. faecalis subsp. parafaecalis DSM 13975T, but is a distinct, previously uncharacterized isolate. Strain J(T), along with the type strain of A. faecalis and its previously described subspecies share the ability to aerobically degrade phenol. The degradation rates of phenol for strain J(T) and reference phenol degrading bacteria were determined by photometrically measuring the change in optical density when grown on 0.1% phenol as the sole carbon source, followed by addition of Gibb's reagent to measure depletion of substrate. The phenol degradation rates of strain J(T) was found to exceed that of the phenol hydroxylase group III bacterium Pseudomonas pseudoalcaligenes, with isolate J(T) exhibiting a doubling time of 4.5 h. The presence of the large subunit of the multicomponent phenol hydroxylase gene in strain J(T) was confirmed by PCR. The presence of the nirK nitrite reductase gene as demonstrated by PCR as well as results obtained from nitrite media indicated denitrification at least to N2O. Based on phenotypic, phylogenetic, fatty acid analysis and results from DNA DNA hybridization, we propose assigning a novel subspecies of Alcaligenes faecalis, to be named Alcaligenes faecalis subsp. phenolicus with the type strain J(T) (= DSM 16503) (= NRRL B-41076). PMID:16094869

  3. Diaphorobacter nitroreducens gen nov, sp nov, a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge.

    PubMed

    Khan, Shams Tabrez; Hiraishi, Akira

    2002-12-01

    Three denitrifying strains of bacteria capable of degrading poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were isolated from activated sludge and characterized. All of the isolates had almost identical phenotypic characteristics. They were motile gram-negative rods with single polar flagella and grew well with simple organic compounds, as well as with PHB and PHBV, as carbon and energy sources under both aerobic and anaerobic denitrifying conditions. However, none of the sugars tested supported their growth. The cellular fatty acid profiles showed the presence of C16:1omega7cis and C16:0 as the major components and of 3-OH-C10:0 as the sole component of hydroxy fatty acids. Ubiquinone-8 was detected as the major respiratory quinone. A 16S rDNA sequence-based phylogenetic analysis showed that all the isolates belonged to the family Comamonadaceae, a major group of beta-Proteobacteria, but formed no monophyletic cluster with any previously known species of this family. The closest relative to our strains was an unidentified bacterium strain LW1 (=DSM 13225) (99.9% similarity), reported previously as a 1-chloro-4-nitrobenzene degrading bacterium. DNA-DNA hybridization levels among the new isolates were more than 60%, whereas those between our isolates and strain DSM 13225 were less than 50%. The G+C content of genomic DNA of the new strains was 64 to 65 mol%. Based on these results, we concluded that the PHBV-degrading denitrifying isolates should be classified as a new genus and a new species, for which we propose the name Diaphorobacter nitroreducens. The type strain is strain NA10B (=JCM 11421=CIP 107294). We also propose to classify strain DSM 13225 as a genospecies of Diaphorobacter. PMID:12682868

  4. Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes.

    PubMed

    Ghazal, Shimaa; Oshone, Rediet; Simpson, Stephen; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Khalil, Kamal M; Tisa, Louis S

    2016-01-01

    Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a G+C content of 42.4% and containing 4,243 candidate protein-coding genes. PMID:26988056

  5. Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes

    PubMed Central

    Ghazal, Shimaa; Oshone, Rediet; Simpson, Stephen; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W. Kelley; Khalil, Kamal M.

    2016-01-01

    Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a G+C content of 42.4% and containing 4,243 candidate protein-coding genes. PMID:26988056

  6. Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant.

    PubMed

    Tokuyama, Tatsuaki; Mine, Atsusi; Kamiyama, Kaoru; Yabe, Ryuichi; Satoh, Kazuo; Matsumoto, Hirotoshi; Takahashi, Reiji; Itonaga, Koji

    2004-01-01

    An ammonia-oxidizing bacterium (strain YNSRA) was isolated from the rhizoplane of the reed (Phragmites communis) used in an aquaponics plant which is a wastewater treatment plant. Strain YNSRA was identified as Nitrosomonas communis by taxonomic studies. The hydroxylamine-cytochrome c reductase (HCR) of strain YNSRA was found to have a higher activity (25.60 u/mg) than that of Nitrosomonas europaea ATCC25978T (8.94 u/mg). Ribulose-1,5-bisphosphate carboxylase (RubisCO) activity was detected at very low levels in strain YNSRA, whereas strain ATCC25978T had definite activity. PMID:16233712

  7. Aerobic and anaerobic metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium isolated from marine sediments.

    PubMed Central

    Rontani, J F; Gilewicz, M J; Michotey, V D; Zheng, T L; Bonin, P C; Bertrand, J C

    1997-01-01

    This report describes the metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium (Marinobacter sp. strain CAB) isolated from marine sediments. Under aerobic and denitrifying conditions, this strain efficiently degraded this ubiquitous isoprenoid ketone. Several bacterial metabolites, 4,8,12-trimethyl-tridecan-1-ol, 4,8,12-trimethyltridecanal, 4,8,12-trimethyltridecanoic acid, Z-3,7-dimethylocten-2-oic acid, Z-3,7,11-trimethyldodecen-2-oic acid, and 6,10,14-trimethylpentadecan-2-ol, were formally identified, and different pathways were proposed to explain the formation of such isoprenoid compounds. PMID:9023941

  8. Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser, Iceland.

    PubMed

    Gaisin, Vasil A; Ivanov, Timophey M; Kuznetsov, Boris B; Gorlenko, Vladimir M; Grouzdev, Denis S

    2016-01-01

    We report here the draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain isl-2, which was isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C content of 59.65%. The annotated genome sequence offers the genetic basis for understanding the strain's ecological role as a phototrophic bacterium within the bacterial community. PMID:27445390

  9. Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser, Iceland

    PubMed Central

    Gaisin, Vasil A.; Ivanov, Timophey M.; Kuznetsov, Boris B.; Gorlenko, Vladimir M.

    2016-01-01

    We report here the draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain isl-2, which was isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C content of 59.65%. The annotated genome sequence offers the genetic basis for understanding the strain’s ecological role as a phototrophic bacterium within the bacterial community. PMID:27445390

  10. Complete Genome Sequence of Alteromonas stellipolaris LMG 21856, a Budding Brown Pigment-Producing Oligotrophic Bacterium Isolated from the Southern Ocean

    PubMed Central

    Chen, Jigang; Wang, Xing; Zhu, Sidong; Chen, Yong

    2016-01-01

    Here, we report the complete genome sequence of Alteromonas stellipolaris LMG 21856, which was isolated from seawater collected from the Southern Ocean. A. stellipolaris LMG 21856 is a budding, psychrotrophic, brown pigment-producing, and oligotrophic bacterium. The complete genome of this bacterium contains 4,686,200 bp, with a G+C content of 43.6%. PMID:27013039

  11. Draft Genome Sequence of Triclosan-Degrading Bacterium Sphingomonas sp. Strain YL-JM2C, Isolated from a Wastewater Treatment Plant in China

    PubMed Central

    Mulla, Sikandar I.; Xu, Haili

    2015-01-01

    Sphingomonas sp. strain YL-JM2C was isolated from a wastewater treatment plant in Xiamen, China, by enrichment on triclosan. The bacterium is of special interest because of its ability to degrade triclosan. Here, we present a draft genome sequence of the microorganism and its functional annotation. To our best knowledge, this is the first report of a draft genome sequence of a triclosan-degrading bacterium PMID:26044437

  12. Isolation of Aerobic Anoxygenic Photosynthetic Bacteria from Black Smoker Plume Waters of the Juan de Fuca Ridge in the Pacific Ocean

    PubMed Central

    Yurkov, Vladimir; Beatty, J. Thomas

    1998-01-01

    A strain of the aerobic anoxygenic photosynthetic bacteria was isolated from a deep-ocean hydrothermal vent plume environment. The in vivo absorption spectra of cells indicate the presence of bacteriochlorophyll a incorporated into light-harvesting complex I and a reaction center. The general morphological and physiological characteristics of this new isolate are described. PMID:16349490

  13. Isolation of a methanogenic bacterium, Methanosarcina sp. strain FR, for its ability to degrade high concentration of perchloroethylene.

    PubMed

    Cabirol, N; Villemur, R; Perrier, J; Jacob, F; Fouillet, B; Chambon, P

    1998-12-01

    Tetrachloroethylene (PCE) is a toxic compound essentially used as a degreasing and dry-cleaning solvent. A methanogenic and sulfate-reducing consortium that dechlorinates and mineralizes high concentrations of PCE was derived from anaerobically digested sludge obtained from a waste water treatment plant (Bourg-en-Bresse, France). A methanogenic bacterium, strain FR, was isolated from this acclimated consortium. On the basis of morphological and physiological characteristics, strain FR was classified in the genus of Methanosarcina. Phylogeny analysis with the 16S rRNA gene sequence revealed that strain FR is highly related to Methanosarcina mazei and Methanosarcina frisia (99.6 and 99.5% identity, respectively). High concentrations (50-87 microM) of PCE were completely dechlorinated by strain FR cultures at the rate of 76 nM-mg protein(-1).day(-1). PCE dechlorination produced a nonidentified compound. The tracer experiments with [13C]PCE revealed that the product was nonchlorinated. Dechlorination of PCE to trichloroethylene was still active in the presence of boiled cell extract of the strain FR. However, no further dechlorination was observed. This result suggests that a cofactor rather than an enzymatic system is responsible for the first dechlorination of PCE. Dechlorination-active fractions purified from cell extracts on a XAD-4 column revealed the presence of F(420), F(430), and cobamides cofactors. This is the first report of the isolation of a methanogenic bacterium with the ability to dechlorinate high concentrations of PCE to a nonchlorinated product. PMID:10383226

  14. Isolation and identification of methanethiol-utilizing bacterium CZ05 and its application in bio-trickling filter of biogas.

    PubMed

    Zhang, Chao-zheng; Zhang, Wei-jiang; Xu, Jiao

    2013-12-01

    A bacterium capable of methanethiol (MT) degradation was enriched and isolated by employing activated sewage sludge as the inoculum in a mineral medium containing MT. The isolate was identified as Paenibacillus polymyxa CZ05 through a Biolog test and 16S rDNA sequencing. This strain can utilize both organic and inorganic media and thrives at pH 4 to 9. The batch culture showed that the strain can degrade MT better in the No. 4 medium than in the No. 1 medium. A series-operating biotrickling filter with lava stone as the carrier was employed to test the application of P. polymyxa CZ05 in the removal of MT in simulated biogas. Long-term experiments showed that a high concentration of MT (60 ppm) was efficiently removed (99.5%) by the biotrickling filters at EBRT 30 s. The addition of hydrogen sulfide decreased the MT removal rate because the dissolved oxygen competed with MT. PMID:24185035

  15. Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium.

    PubMed

    Tang, M; Chen, C; Li, J; Xiang, W; Wu, H; Wu, J; Dai, S; Wu, H; Li, T; Wang, G

    2016-02-01

    A Gram-stain-negative, red, non-spore-forming, strictly aerobic bacterium, designated strain A4T, was isolated from culture broth of a marine cyanobacterium. Cells were flexible rods with gliding motility. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain A4T formed a coherent cluster with members of the genera Roseivirga and Fabibacter, and represents a distinct lineage in the family Flammeovirgaceae. Thermotolerance and a distinctive cellular fatty acid profile could readily distinguish this isolate from any bacteria of the genera Roseivirga and Fabibacter with a validly published name. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain A4T is suggested to represent a novel species in a novel genus, for which the name Fabivirga thermotolerans gen. nov., sp. nov. is proposed. The type strain is A4T ( = KCTC 42507T = CGMCC 1.15111T). PMID:26652750

  16. Isolation and characterization of bacteriophage SPI1, which infects the activated-sludge-foaming bacterium Skermania piniformis.

    PubMed

    Dyson, Z A; Tucci, J; Seviour, R J; Petrovski, S

    2016-01-01

    Foaming in activated sludge plants is a worldwide problem commonly caused by proliferation of bacteria of the order Corynebacteriales. These include Skermania piniformis, a filamentous bacterium that has been documented to be a major cause of foaming globally, and particularly in Australian treatment plants. Phage SPI1 is the first phage that was isolated and shown to infect this organism. It targets seven of the nine strains of S. piniformis held in our culture collection, but none of the other 73 mycolata strains of different genera, mostly isolated from wastewater, against which it was tested. Phage SPI1 is a member of the family Siphoviridae and has a circularly permuted dsDNA genome of 55,748 bp with a G+C content of 67.8 mol %. It appears to be obligatorily lytic, with no evidence of genes related to a lysogenic mode of existence. PMID:26459285

  17. Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.

    PubMed

    Koeck, Daniela E; Ludwig, Wolfgang; Wanner, Gerhard; Zverlov, Vladimir V; Liebl, Wolfgang; Schwarz, Wolfgang H

    2015-08-01

    Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the family Lachnospiraceae. As a representative of the whole group of isolates, strain T3/55T was further characterized. The closest relative of T3/55T among the taxa with validly published names is Mobilitalea sibirica, sharing 93.9% 16S rRNA gene sequence similarity. Strain T3/55T was catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1%) were 16 : 0 dimethyl acetal, 16 : 0 fatty acid methyl ester and 16 : 0 aldehyde. The DNA G+C content was 36.6 mol%. A novel genus and species, Herbinix hemicellulosilytica gen. nov., sp. nov., is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T ( = DSM 29228T = CECT 8801T), represents the type strain of Herbinix hemicellulosilytica gen. nov., sp. nov. PMID:25872956

  18. Quantitative measurement of the growth rate of the PHA-producing photosynthetic bacterium Rhodocyclus gelatinous CBS-2[PolyHydroxyAlkanoate

    SciTech Connect

    Wolfrum, E.J.; Weaver, P.F.

    1999-07-01

    Researchers at the National Renewable Energy Laboratory (NREL) have been investigating the use of model photosynthetic microorganisms that use sunlight and two-carbon organic substrates (e.g., ethanol, acetate) to produce biodegradable polyhydroxyalkanoate (PHA) copolymers as carbon storage compounds. Use of these biological PHAs in single-use plastics applications, followed by their post-consumer composting or anaerobic digestion, could impact petroleum consumption as well as the overloading of landfills. The large-scale production of PHA polymers by photosynthetic bacteria will require large-scale reactor systems utilizing either sunlight or artificial illumination. The first step in the scale-up process is to quantify the microbial growth rates and the PHA production rates as a function of reaction conditions such as nutrient concentration, temperature, and light quality and intensity.

  19. Isolation of a Sulfur-oxidizing Bacterium That can Grow under Alkaline pH, from Corroded Concrete.

    PubMed

    Maeda, T; Negishi, A; Oshima, Y; Nogami, Y; Kamimura, K; Sugio, T

    1998-01-01

    To study the early stages of concrete corrosion by bacteria, sulfur-oxidizing bacterium strain RO-1, which grows in an alkaline thiosulfate medium (pH 10.0) was isolated from corroded concreate and characterized. Strain RO-1 was a Gram negative, rod-shaped bacterium (0.5-0.6×0.9-1.5 μm). The mean G+C content of the DNA of strain RO-1 was 65.0 mol%. Optimum pH and temperature for growth were 8.0. and 30-37°C, respectively. When grown in thiosulfate medium with pH 10.0, growth rate of the strain was 48% of that observed at the optimum pH for growth. Strain RO-1 used sulfide, thiosulfate, and glucose, but not elemental sulfur or tetrathionate, as a sole energy source. Strain RO-1 grew under anaerobic conditions in pepton-NO3 (-) medium containing sodium nitrate as an electron acceptor, and had enzyme activities that oxidized sulfide, elemental sulfur, thiosulfate, sulfite, and glucose, but not tetrathionate. The bacterium had an activity to assimilate (14)CO2 into the cells when thiosulfate was used as an energy source. These results suggest that strain RO-1 is Thiobacillus versutus. Strain RO-1 exuded Ca(2+) from concrete blocks added to thiosulfate medium with pH 9.0 and the pH of the medium decreased from 9.0 to 5.5 after 22 days of cultivation. In contrast, Thiobacillus thiooxidans strain NB1-3 could not exude Ca(2+) in the same thiosulfate medium, suggesting that strain RO-1, but not T. thiooxidans NB1-3, is involved in the early stage of concrete corrosion because concrete structures just after construction contain calcium hydroxide and have a pH of 12-13. PMID:27388643

  20. Whole-Genome Sequence of Chryseobacterium oranimense, a Colistin-Resistant Bacterium Isolated from a Cystic Fibrosis Patient in France

    PubMed Central

    Sharma, Poonam; Gupta, Sushim Kumar; Diene, Seydina M.

    2015-01-01

    For the first time, we report the whole-genome sequence analysis of Chryseobacterium oranimense G311, a multidrug-resistant bacterium, from a cystic fibrosis patient in France, including resistance to colistin. Whole-genome sequencing of C. oranimense G311 was performed using Ion Torrent PGM, and RAST, the EMBL-EBI server, and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database were used for annotation of all genes, including antibiotic resistance (AR) genes. General features of the C. oranimense G311 draft genome were compared to the other available genomes of Chryseobacterium gleum and Chryseobacterium sp. strain CF314. C. oranimense G311 was found to be resistant to all β-lactams, including imipenem, and to colistin. The genome size of C. oranimense G311 is 4,457,049 bp in length, with 37.70% GC content. We found 27 AR genes in the genome, including β-lactamase genes which showed little similarity to the known β-lactamase genes and could likely be novel. We found the type I polyketide synthase operon followed by a zeaxanthin glycosyltransferase gene in the genome, which could impart the yellow pigmentation of the isolate. We located the O-antigen biosynthesis cluster, and we also discovered a novel capsular polysaccharide biosynthesis cluster. We also found known mutations in the orthologs of the pmrA (E8D), pmrB (L208F and P360Q), and lpxA (G68D) genes. We speculate that the presence of the capsular cluster and mutations in these genes could explain the resistance of this bacterium to colistin. We demonstrate that whole-genome sequencing was successfully applied to decipher the resistome of a multidrug resistance bacterium associated with cystic fibrosis patients. PMID:25583710

  1. Whole-genome sequence of Chryseobacterium oranimense, a colistin-resistant bacterium isolated from a cystic fibrosis patient in France.

    PubMed

    Sharma, Poonam; Gupta, Sushim Kumar; Diene, Seydina M; Rolain, Jean-Marc

    2015-03-01

    For the first time, we report the whole-genome sequence analysis of Chryseobacterium oranimense G311, a multidrug-resistant bacterium, from a cystic fibrosis patient in France, including resistance to colistin. Whole-genome sequencing of C. oranimense G311 was performed using Ion Torrent PGM, and RAST, the EMBL-EBI server, and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database were used for annotation of all genes, including antibiotic resistance (AR) genes. General features of the C. oranimense G311 draft genome were compared to the other available genomes of Chryseobacterium gleum and Chryseobacterium sp. strain CF314. C. oranimense G311 was found to be resistant to all β-lactams, including imipenem, and to colistin. The genome size of C. oranimense G311 is 4,457,049 bp in length, with 37.70% GC content. We found 27 AR genes in the genome, including β-lactamase genes which showed little similarity to the known β-lactamase genes and could likely be novel. We found the type I polyketide synthase operon followed by a zeaxanthin glycosyltransferase gene in the genome, which could impart the yellow pigmentation of the isolate. We located the O-antigen biosynthesis cluster, and we also discovered a novel capsular polysaccharide biosynthesis cluster. We also found known mutations in the orthologs of the pmrA (E8D), pmrB (L208F and P360Q), and lpxA (G68D) genes. We speculate that the presence of the capsular cluster and mutations in these genes could explain the resistance of this bacterium to colistin. We demonstrate that whole-genome sequencing was successfully applied to decipher the resistome of a multidrug resistance bacterium associated with cystic fibrosis patients. PMID:25583710

  2. From metagenomics to pure culture: isolation and characterization of the moderately halophilic bacterium Spiribacter salinus gen. nov., sp. nov.

    PubMed

    León, María José; Fernández, Ana B; Ghai, Rohit; Sánchez-Porro, Cristina; Rodriguez-Valera, Francisco; Ventosa, Antonio

    2014-07-01

    Recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both Euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera Alkalilimnicola and Arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. Here we used several strategies and culture media in order to isolate this organism in pure culture. We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40(T), isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. Morphologically small curved cells (young cultures) with a tendency to form long spiral cells in older cultures were observed in pure cultures. The organism is a Gram-negative, nonmotile bacterium that is strictly aerobic, non-endospore forming, heterotrophic, and moderately halophilic, and it is able to grow at 10 to 25% (wt/vol) NaCl, with optimal growth occurring at 15% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that strain M19-40(T) has a low similarity with other previously described bacteria and shows the closest phylogenetic similarity with species of the genera Alkalilimnicola (94.9 to 94.5%), Alkalispirillum (94.3%), and Arhodomonas (93.9%) within the family Ectothiorhodospiraceae. The phenotypic, genotypic, and chemotaxonomic features of this new bacterium showed that it constitutes a new genus and species, for which the name Spiribacter salinus gen. nov., sp. nov., is proposed, with strain M19-40(T) (= CECT 8282(T) = IBRC-M 10768(T) = LMG 27464(T)) being the type strain. PMID:24747894

  3. From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov.

    PubMed Central

    León, María José; Fernández, Ana B.; Ghai, Rohit; Sánchez-Porro, Cristina; Rodriguez-Valera, Francisco

    2014-01-01

    Recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both Euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera Alkalilimnicola and Arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. Here we used several strategies and culture media in order to isolate this organism in pure culture. We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40T, isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. Morphologically small curved cells (young cultures) with a tendency to form long spiral cells in older cultures were observed in pure cultures. The organism is a Gram-negative, nonmotile bacterium that is strictly aerobic, non-endospore forming, heterotrophic, and moderately halophilic, and it is able to grow at 10 to 25% (wt/vol) NaCl, with optimal growth occurring at 15% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that strain M19-40T has a low similarity with other previously described bacteria and shows the closest phylogenetic similarity with species of the genera Alkalilimnicola (94.9 to 94.5%), Alkalispirillum (94.3%), and Arhodomonas (93.9%) within the family Ectothiorhodospiraceae. The phenotypic, genotypic, and chemotaxonomic features of this new bacterium showed that it constitutes a new genus and species, for which the name Spiribacter salinus gen. nov., sp. nov., is proposed, with strain M19-40T (= CECT 8282T = IBRC-M 10768T = LMG 27464T) being the type strain. PMID:24747894

  4. Isolation of an endosulfan-degrading bacterium from a coffee farm soil: persistence and inhibitory effect on its biological functions.

    PubMed

    Castillo, Jean Manuel; Casas, Jaime; Romero, Esperanza

    2011-12-15

    Endosulfan is a lypophilic persistent organic pollutant (POP) that has caused widespread concern due to its persistence in the environment, toxicity and bioaccumulation in living organisms. The aim of this study is to isolate endosulfan-degrading bacteria taken from five coffee farms historically exposed to this insecticide which could be used in future remediation strategies. The biodegradation capability of the isolated strain as well as endosulfan's impact on some of the strain's biological functions was studied. Endosulfan and its metabolites were analyzed using TLC and GC-MS. The isolated strain, capable of growing in a liquid culture treated with this insecticide as the sole sulfur source rather than a carbon source, was selected for further study. The isolated bacterium is Gram-negative, having the morphological and biochemical characteristics of Azotobacter sp. The remaining concentrations after 6 days, using 2 and 10 mg l(-1) of endosulfan, were 57.6 and 72.3% respectively, and the degradation constants were 0.12 d(-1) and 0.26 d(-1). Four metabolites were detected, one of which was identified as endosulfan ether. Endosulfan reduced nitrogenase activity but had no impact on indole 3-acetic acid production. Thus, these results suggest that this strain has the potential to act as a biocatalyst in endosulfan degradation. PMID:22033355

  5. Isolation, identification, and algicidal activity of aerobic denitrifying bacterium R11 and its effect on Microcystis aeruginosa.

    PubMed

    Su, Jun-Feng; Shao, Si-Cheng; Huang, Ting-Lin; Ma, Fang; Zhang, Kai; Wen, Gang; Zheng, Sheng-Chen

    2016-01-01

    Recently, algicidal bacteria have attracted attention as possible agents for the inhibition of algal water blooms. In this study, an aerobic denitrifying bacterium, R11, with high algicidal activity against the toxic Microcystis aeruginosa was isolated from lake sediments. Based on its physiological characteristics and 16S rRNA gene sequence, it was identified as Raoultella, indicating that the bacterium R11 has a good denitrifying ability at 30 °C and can reduce the concentration of nitrate-N completely within 36 h. Additionally, different algicidal characteristics against Microcystis aeruginosa were tested. The results showed that the initial bacterial cell density and algal cell densities strongly influence the removal rates of chlorophyll a. Algicidal activity increased with an increase in the bacterial cell density. With densities of bacterial culture at over 2.4 × 10(5) cell/mL, algicidal activity of up to 80% was obtained in 4 days. We have demonstrated that, with the low initial algal cell density (OD680 less than 0.220), the algicidal activity reached was higher than 90% after 6 days. PMID:27232395

  6. Partial characterization of xylanase produced by Caldicoprobacter algeriensis, a new thermophilic anaerobic bacterium isolated from an Algerian hot spring.

    PubMed

    Bouacem, Khelifa; Bouanane-Darenfed, Amel; Boucherba, Nawel; Joseph, Manon; Gagaoua, Mohammed; Ben Hania, Wajdi; Kecha, Mouloud; Benallaoua, Said; Hacène, Hocine; Ollivier, Bernard; Fardeau, Marie-Laure

    2014-11-01

    To date, xylanases have expanded their use in many processing industries, such as pulp, paper, food, and textile. This study aimed the production and partial characterization of a thermostable xylanase from a novel thermophilic anaerobic bacterium Caldicoprobacter algeriensis strain TH7C1(T) isolated from a northeast hot spring in Algeria. The obtained results showed that C. algeriensis xylanase seems not to be correlated with the biomass growth profile whereas the maximum enzyme production (140.0 U/ml) was recorded in stationary phase (18 h). The temperature and pH for optimal activities were 70 °C and 11.0, respectively. The enzyme was found to be stable at 50, 60, 70, and 80 °C, with a half-life of 10, 9, 8, and 4 h, respectively. Influence of metal ions on enzyme activity revealed that Ca(+2) enhances greatly the relative activity to 151.3 %; whereas Hg(2+) inhibited significantly the enzyme. At the best of our knowledge, this is the first report on the production of xylanase by the thermophilic bacterium C. algeriensis. This thermo- and alkaline-tolerant xylanase could be used in pulp bleaching process. PMID:25161038

  7. Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India.

    PubMed

    Suresh, K; Prabagaran, S R; Sengupta, S; Shivaji, S

    2004-07-01

    Strain Sd/3T (=MTCC 4374T=DSM 15820T), an arsenic-resistant bacterium, was isolated from a sand sample obtained from an arsenic-contaminated aquifer in Chakdah district in West Bengal, India (23 degrees 3' N 88 degrees 35' E). The bacterium was Gram-positive, rod-shaped, non-motile, endospore-forming and yellowish-orange pigmented. It possessed all the characteristics that conform to the genus Bacillus, such as it had A4beta murein type (L-orn-D-Asp) peptidoglycan variant, MK-7 as the major menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Based on its chemotaxonomic and phylogenetic characteristics, strain Sd/3T was identified as a species of the genus Bacillus. It exhibited maximum similarity (95%) at the 16S rRNA gene level with Bacillus cohnii; however, DNA-DNA similarity with B. cohnii was 60.7%. Strain Sd/3T also exhibited a number of phenotypic differences from B. cohnii (DSM 6307T). These data suggest that Sd/3T represents a novel species of the genus Bacillus. The name Bacillus indicus sp. nov. is proposed. PMID:15280316

  8. Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State

    PubMed Central

    Mormile, Melanie R.

    2014-01-01

    Soap Lake is a meromictic, alkaline (∼pH 9.8) and saline (∼14–140 g liter-1) lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years) and the extremely high sulfide level (∼140 mM) in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment. PMID:25477871

  9. Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State.

    PubMed

    Mormile, Melanie R

    2014-01-01

    Soap Lake is a meromictic, alkaline (∼pH 9.8) and saline (∼14-140 g liter(-1)) lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years) and the extremely high sulfide level (∼140 mM) in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment. PMID:25477871

  10. Complete genome sequence of Hymenobacter sp. strain PAMC26554, an ionizing radiation-resistant bacterium isolated from an Antarctic lichen.

    PubMed

    Oh, Tae-Jin; Han, So-Ra; Ahn, Do-Hwan; Park, Hyun; Kim, Augustine Yonghwi

    2016-06-10

    A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843bp) with two plasmids (199,990bp and 6421bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment. PMID:27063139