Science.gov

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 of a thermotolerant photosynthetic bacterium, Rhodobacter sphaeroides Strain, NAT, and its capacity for oil and chemical oxygen demand removal at high temperatures.

    PubMed

    Yamaoka, Yosuke; Takeno, Kenji; Shinkawa, Hidenori; Noparatnaraporn, Napavarn; Sasaki, Ken

    2008-06-01

    A thermotolerant photosynthetic bacterium NAT identified as Rhodobacter sphaeroides was isolated. When alginate-immobilized cells of strain NAT were used in high-temperature treatment of artificial sewage wastewater containing oil, the chemical oxygen demand (COD) decreased by 80% and 76% of the oil was removed after 96 h of treatment at 55 degrees C. Lipase activity was observed in the culture.

  3. 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.

  4. 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.

  5. 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.

  6. Polarization angle dependence of stark absorption spectra of spirilloxanthin bound to the reconstituted LH1 complexes using LH1-subunits isolated from the purple photosynthetic bacterium Rhodospirillum rubrum.

    PubMed

    Horibe, Tomoko; Nakagawa, Katsunori; Kusumoto, Toshiyuki; Fujii, Ritsuko; Cogdell, Richard J; Nango, Mamoru; Hashimoto, Hideki

    2012-01-01

    Reconstituted LH1 complexes were prepared using the LH1 subunit-type complexes, isolated from the purple photosynthetic bacterium Rhodospirillum (Rs.) rubrum, and purified all-trans spirilloxanthin. Stark absorption spectra of spirilloxanthin bound to both the native and reconstituted LH1 complexes were compared in different polarization angles (χ) against the external electric field. From the polarization angle dependence of the Stark absorption spectra, two angles were determined in reference to the direction of transition dipole moment (m) of spirilloxanthin: one is the change in polarizability upon photoexcitation (Δα), θ(Δα) and the other is the change in static dipole moment upon photoexcitation (Δμ), θ(Δμ). Despite the symmetric molecular structure of all-trans spirilloxanthin, its Stark absorption spectra show pronounced values of Δμ. This large Δμ values essentially caused by the effect of induced dipole moment through Δα both in the cases for native and reconstituted LH1 complexes. However, slightly different values of θ(Δα) and θ(Δμ) observed for the native LH1 complex suggest that spirilloxanthin is asymmetrically distorted when bound to the native LH1 complex and gives rise to intrinsic Δμ value.

  7. Inorganic nitrogen assimilation by the photosynthetic bacterium Rhodopseudomonas capsulata.

    PubMed Central

    Johansson, B C; Gest, H

    1976-01-01

    The photosynthetic bacterium Rhodopseudomonas capsulata lacks glutamate dehydrogenase and normally uses the glutamine synthetase/glutamate synthase sequence of reactions for assimilation of N2 and ammonia. The glutamine synthetase in cell-free extracts of the organism is completely sedimented by centrifugation at 140,000 X g for 2 h, is inhibited by L-alanine but not by adenosine 5'-monophosphate, and exhibits two apparent Km values for ammonia (ca. 13 muM and 1 mM). PMID:10281

  8. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    PubMed Central

    Brown, Alfred E.; Gilbert, Carl W.; Guy, Rachel; Arntzen, Charles J.

    1984-01-01

    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 QB protein of chloroplast membranes. Images PMID:16593520

  9. Nitrogenase from the photosynthetic bacterium Rhodopseudomonas capsulata: purification and molecular properties.

    PubMed Central

    Hallenbeck, P C; Meyer, C M; Vignais, P M

    1982-01-01

    Nitrogenase proteins were isolated from cultures of the photosynthetic bacterium Rhodopseudomonas capsulata grown on a limiting amount of ammonia. Under these conditions, the nitrogenase N2ase A was active in vivo, and nitrogenase activity in vitro was not dependent upon manganese and the activating factor. The nitrogenase proteins were also isolated from nitrogen-limited cultures in which the in vivo nitrogenase activity had been stopped by an ammonia shock. This nitrogenase activity, N2ase R, showed an in vitro requirement for manganese and the activating factor for maximal activity. The Mo-Fe protein (dinitrogenase) was composed of two dissimilar subunits with molecular weights of 55,000 and 59,500; the Fe protein (dinitrogenase reductase), from either type of culture, was composed of a single subunit (molecular weight), 33,500). The metal and acid labile sulfur contents of both nitrogenase proteins were similar to those found for previously isolated nitrogenases. The Fe proteins from both N2ase A and N2ase R contained phosphate and ribose, 2 mol of each per mol of N2ase R Fe protein and about 1 mol of each per mol of N2ase A Fe protein. The greatest difference between the two types of Fe protein was that the N2ase R Fe protein contained about 1 mol per mol of an adenine-like molecule, whereas the N2ase A Fe protein content of this compound was insignificant. These results are compared with various models previously presented for the short-term regulation of nitrogenase activity in the photosynthetic bacteria. PMID:6799495

  10. 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

    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

    2015-11-04

    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.

  11. Secreted protease mediates interspecies interaction and promotes cell aggregation of the photosynthetic bacterium Chloroflexus aggregans.

    PubMed

    Morohoshi, Sho; Matsuura, Katsumi; Haruta, Shin

    2015-01-01

    Interspecies interactions were studied in hot spring microbial mats where diverse species of bacterial cells are densely packed. The anoxygenic photosynthetic bacterium, Chloroflexus aggregans, has been widely found in the microbial mats as a major component in terrestrial hot springs in Japan at the temperature from 50 to 70°C. C. aggregans shows cellular motility to form a microbial mat-like dense cell aggregate. The aggregating ability of C. aggregans was affected by another bacterial species, strain BL55a (related to Bacillus licheniformis) isolated from the microbial mats containing C. aggregans. Cell aggregation rate of C. aggregans was promoted by the addition of culture supernatants of strain BL55a. Similar effects were also detected from other bacterial isolates, specifically Geobacillus sp. and Aeribacillus sp. Protease activity was detected from the culture supernatants from all of these isolates. The promoting effect of strain BL55a was suppressed by a serine protease inhibitor, phenylmethylsulfonyl fluoride. A purified serine protease, subtilisin obtained from B. licheniformis, showed a promoting effect on the cell aggregation. These results suggest that an extracellular protease, secreted from co-existing bacterial species promoted the aggregating motility of C. aggregans. This is the first report that exogenous protease affects bacterial cellular motility.

  12. Hydrogen Production by Co-cultures of Rhizopus oryzae and a Photosynthetic Bacterium, Rhodobacter sphaeroides RV

    NASA Astrophysics Data System (ADS)

    Asada, Yasuo; Ishimi, Katsuhiro; Nagata, Yoko; Wakayama, Tatsuki; Miyake, Jun; Kohno, Hideki

    Hydrogen production with glucose by using co-immobilized cultures of a fungus, Rhizopus oryzae NBRC5384, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. The co-immobilized cultures converted glucose to hydrogen via lactate in a high molar yield of about 8moles of hydrogen per glucose at a maximum under illuminated conditions.

  13. Hydrogen Production by the Photosynthetic Bacterium Rhodospirillum rubrum

    PubMed Central

    Zürrer, Hans; Bachofen, Reinhard

    1979-01-01

    Continuous photosynthetic production of hydrogen by Rhodospirillum rubrum in batch cultures was observed up to 80 days with the hydrogen donor, pure lactate or lactic acid-containing wastes, supplied periodically. Hydrogen was produced at an average rate of 6 ml/h per g (dry weight) of cells with whey as a hydrogen donor. In continuous cultures with glutamate as a growth-limiting nitrogen source and lactate as a hydrogen donor, hydrogen was evolved at a rate of 20 ml/h per g (dry weight). The composition of the gas evolved remained practically constant (70 to 75% H2, 25 to 30% CO2). Photosynthetic bacteria processing specific organic wastes could be an advantage in large-scale production of hydrogen together with food protein of high value, compared to other biological systems. Images PMID:16345375

  14. 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

  15. 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.

  16. Effects of carotenoid inhibition on the photosynthetic RC-LH1 complex in purple sulphur bacterium Thiorhodospira sibirica.

    PubMed

    Moskalenko, A A; Makhneva, Z K; Fiedor, L; Scheer, H

    2005-11-01

    Core complexes (LH1-RC) were isolated using preparative gel electrophoresis from photosynthetic membranes of the purple bacterium, Thiorhodospira sibirica, grown in the absence or presence of the carotenoid biosynthesis inhibitor, diphenylamine. The biosynthesis of carotenoids is affected by diphenylamine both quantitavely and qualitatively: after inhibition, the level of carotenoids in core complexes reaches only 10% of the normal content, as analyzed by HPLC and absorption spectroscopy. The normally grown bacterium biosynthesizes spirilloxanthin, rhodopin, anhydrorhodovibrin and lycopene, whereas after inhibition only neurosporene, zeta-carotene and their derivatives are found in the complexes. There is no concomitant accumulation of appreciable amounts of colorless carotenoid precursors. Interestingly, the main absorption band of the core light harvesting complex isolated from carotenoid-inhibited cells, shows a red shift to 889 nm, instead of a blue shift observed in many carotenoid-deficient species of purple photosynthetic bacteria. The stability of isolated core complexes against n-octyl-beta-D: -glucopyranoside clearly depends on the presence of carotenoids. Subcomplexes resulting from the detergent treatment, were characterized by non-denaturating gel electrophoresis combined with in situ absorption spectroscopy. Core complexes with the native carotenoid complement dissociate into three subcomplexes: (a) LH1 complexes partially depleted of carotenoids, with an unusual spectrum in the NIR region (lambdamax = 791, 818, 847 and 875 nm), (b) reaction centers associated with fragments of LH1, (c) small amounts of a carotenoidless B820 subcomplex. The core complex from the carotenoid-deficient bacterium is much less stable and yields only the two sub-complexes (b) and (c). We conclude that carotenoids contribute critically to stability and interactions of the core complexes with detergents.

  17. Energy transfer and exciton coupling in isolated B800-850 complexes of the photosynthetic purple sulfur bacterium Choromatium tepidum. The effect of structural symmetry on bacteriochlorophyll excited states

    SciTech Connect

    Kennis, J.T.M.; Streltsov, A.M.; Aartsma, T.J.; Amesz, J.; Nozawa, Tsunenori

    1996-02-08

    Energy transfer and exciton coupling in isolated B800-850 complexes from the purple sulfur bacterium Chromatium tepidum were studied by means of spectrally resolved absorbance difference spectroscopy with a time resolution of 200 fs. Energy transfer from bacteriochlorophyll (BChl) 800 to BChl 850 was found to occur with a time constant of 0.8-0.9 ps. Remarkably, the amplitude of the absorbance changes of BChl 850 was 4 times larger than that of BChl 800. By relating this result to the crystal structure of B800-850 complexes of Rhodopseudomonas acidophila, it was concluded that the spectral properties of BChl 850 are mainly determined by strong exciton interactions between BChl 850 molecules in a circular symmetric arrangement, which lead to concentration of the oscillator strength in a few optically allowed transitions, corresponding to delocalized eigenstates. In BChl 850, a rapid red shift of the bleaching was observed. This relaxation process may be ascribed either to vibrational relaxation or exciton scattering. A similar red shift appears to occur in BChl 800. 26 refs., 5 figs.

  18. 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.

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

    SciTech Connect

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

    1986-10-01

    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 ..mu..mol/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.

  20. Efficiency of light harvesting in a photosynthetic bacterium adapted to different levels of light.

    PubMed

    Timpmann, Kõu; Chenchiliyan, Manoop; Jalviste, Erko; Timney, John A; Hunter, C Neil; Freiberg, Arvi

    2014-10-01

    In this study, we use the photosynthetic purple bacterium Rhodobacter sphaeroides to find out how the acclimation of photosynthetic apparatus to growth conditions influences the rates of energy migration toward the reaction center traps and the efficiency of charge separation at the reaction centers. To answer these questions we measured the spectral and picosecond kinetic fluorescence responses as a function of excitation intensity in membranes prepared from cells grown under different illumination conditions. A kinetic model analysis yielded the microscopic rate constants that characterize the energy transfer and trapping inside the photosynthetic unit as well as the dependence of exciton trapping efficiency on the ratio of the peripheral LH2 and core LH1 antenna complexes, and on the wavelength of the excitation light. A high quantum efficiency of trapping over 80% was observed in most cases, which decreased toward shorter excitation wavelengths within the near infrared absorption band. At a fixed excitation wavelength the efficiency declines with the LH2/LH1 ratio. From the perspective of the ecological habitat of the bacteria the higher population of peripheral antenna facilitates growth under dim light even though the energy trapping is slower in low light adapted membranes. The similar values for the trapping efficiencies in all samples imply a robust photosynthetic apparatus that functions effectively at a variety of light intensities.

  1. Synergistic Effect of Photosynthetic Bacteria and Isolated Bacteria in Their Antifungal Activities against Root Rot Fungi.

    PubMed

    Wei, Hongyi; Okunishi, Suguru; Yoshikawa, Takeshi; Kamei, Yuto; Dawwoda, Mahmoud A O; Santander-DE Leon, Sheila Mae S; Nuñal, Sharon Nonato; Maeda, Hiroto

    2016-01-01

    Antifungal bacteria (AB) in root rot fungus (RRF)-contaminated sweet potato farms were isolated, and seven strains were initially chosen as antagonistic candidates. An antagonistic test by using the mycelial disk placement method revealed that one AB strain by itself could inhibit the RRF growth. This AB strain was identified as Bacillus polyfermenticus based on phylogeny of 16S ribosomal RNA genes. Two AB strains (Bacillus aerophilus) displayed high levels of antifungal activity when paired with photosynthetic bacterial strain A (a purple nonsulfur photosynthetic bacterium Rhodopseudomonas faecalis). The results suggest the possible use of the isolates as agents for the biological control of the RRF infection of agricultural products in fields of cultivation.

  2. 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.

  3. Characterization of giant spheroplasts generated from the aerobic anoxygenic photosynthetic marine bacterium Roseobacter litoralis.

    PubMed

    Nojiri, Akane; Ogita, Shinjiro; Isogai, Yasuhiro; Nishida, Hiromi

    2015-01-01

    We generated and characterized giant spheroplasts from the aerobic anoxygenic photosynthetic marine bacterium Roseobacter litoralis. The giant spheroplasts contained vacuole-like structures within the cells, mainly consisting of a single membrane. The in vivo absorption spectrum of the giant spheroplasts did not have peaks typically observed for bacteriochlorophyll a. The culture media pH decreased during the growth of the giant spheroplasts. The change in the pH profile for cells grown under light was no different from that for cells grown in the dark. These results showed that the R. litoralis giant spheroplasts formed lost their photosynthetic apparatus in culture. Most of the giant spheroplasts returned to their original size, likely via filamentous cells. The culture media pH increased during the growth of the filamentous cells. Some filamentous cells had septum-like structures. In such filamentous cells, DNA was separated. Initially, the color of the separated cells was white. Two weeks later, the cells changed to red in the dark, and the in vivo absorption spectrum of the cells had peaks typically observed for bacteriochlorophyll a. Our findings strongly suggest that the giant spheroplasts of R. litoralis can control the genetic information, return to their original cell size, and regain their original functions.

  4. 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.

    2017-01-01

    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.

  5. Excitation dynamics of two spectral forms of the core complexes from photosynthetic bacterium Thermochromatium tepidum.

    PubMed

    Ma, Fei; Kimura, Yukihiro; Zhao, Xiao-Hui; Wu, Yi-Shi; Wang, Peng; Fu, Li-Min; Wang, Zheng-Yu; Zhang, Jian-Ping

    2008-10-01

    The intact core antenna-reaction center (LH1-RC) core complex of thermophilic photosynthetic bacterium Thermochromatium (Tch.) tepidum is peculiar in its long-wavelength LH1-Q(y) absorption (915 nm). We have attempted comparative studies on the excitation dynamics of bacteriochlorophyll (BChl) and carotenoid (Car) between the intact core complex and the EDTA-treated one with the Q(y) absorption at 889 nm. For both spectral forms, the overall Car-to-BChl excitation energy transfer efficiency is determined to be approximately 20%, which is considerably lower than the reported values, e.g., approximately 35%, for other photosynthetic purple bacteria containing the same kind of Car (spirilloxanthin). The RC trapping time constants are found to be 50 approximately 60 ps (170 approximately 200 ps) for RC in open (closed) state irrespective to the spectral forms and the wavelengths of Q(y) excitation. Despite the low-energy LH1-Q(y) absorption, the RC trapping time are comparable to those reported for other photosynthetic bacteria with normal LH1-Q(y) absorption at 880 nm. Selective excitation to Car results in distinct differences in the Q(y)-bleaching dynamics between the two different spectral forms. This, together with the Car band-shift signals in response to Q(y) excitation, reveals the presence of two major groups of BChls in the LH1 of Tch. tepidum with a spectral heterogeneity of approximately 240 cm(-1), as well as an alteration in BChl-Car geometry in the 889-nm preparation with respect to the native one.

  6. 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.

  7. 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.

  8. 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).

  9. 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

  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.

  11. Functional Genomic Analysis of Three Nitrogenase Isozymes in the Photosynthetic Bacterium Rhodopseudomonas palustris‡

    PubMed Central

    Oda, Yasuhiro; Samanta, Sudip K.; Rey, Federico E.; Wu, Liyou; Liu, Xiudan; Yan, Tingfen; Zhou, Jizhong; Harwood, Caroline S.

    2005-01-01

    The photosynthetic bacterium Rhodopseudomonas palustris is one of just a few prokaryotes described so far that has vnf and anf genes for alternative vanadium cofactor (V) and iron cofactor (Fe) nitrogenases in addition to nif genes for a molybdenum cofactor (Mo) nitrogenase. Transcriptome data indicated that the 32 genes in the nif gene cluster, but not the anf or vnf genes, were induced in wild-type and Mo nitrogenase-expressing strains grown under nitrogen-fixing conditions in Mo-containing medium. Strains that were unable to express a functional Mo nitrogenase due to mutations in Mo nitrogenase structural genes synthesized functional V and Fe nitrogenases and expressed vnf and anf genes in nitrogen-fixing growth media that contained Mo and V at concentrations far in excess of those that repress alternative nitrogenase gene expression in other bacteria. Thus, not only does R. palustris have multiple enzymatic options for nitrogen fixation, but in contrast to reports on other nitrogen-fixing bacteria, the expression of its alternative nitrogenases is not repressed by transition metals. Between 95 and 295 genes that are not directly associated with nitrogenase synthesis and assembly were induced under nitrogen-fixing conditions, depending on which nitrogenase was being used by R. palustris. Genes for nitrogen acquisition were expressed at particularly high levels during alternative nitrogenase-dependent growth. This suggests that alternative nitrogenase-expressing cells are relatively starved for nitrogen and raises the possibility that fixed nitrogen availability may be the primary signal that controls the synthesis of the V and Fe nitrogenases. PMID:16267302

  12. 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.

  13. Isolation of an algal morphogenesis inducer from a marine bacterium.

    PubMed

    Matsuo, Yoshihide; Imagawa, Hiroshi; Nishizawa, Mugio; Shizuri, Yoshikazu

    2005-03-11

    Ulva and Enteromorpha are cosmopolitan and familiar marine algal genera. It is well known that these green macroalgae lose their natural morphology during short-term cultivation under aseptic conditions and during long-term cultivation in nutrient-added seawater and adopt an unusual form instead. These phenomena led to the belief that undefined morphogenetic factors that were indispensable to the foliaceous morphology of macroalgae exist throughout the oceans. We characterize a causative factor, named thallusin, isolated from an epiphytic marine bacterium. Thallusin induces normal germination and morphogenesis of green macroalgae.

  14. Rare bacterium of new genus isolated with prolonged enrichment culture.

    PubMed

    Hashizume, Akiko; Fudou, Ryosuke; Jojima, Yasuko; Nakai, Ryohsuke; Hiraishi, Akira; Tabuchi, Akira; Sen, Kikuo; Shibai, Hiroshiro

    2004-01-01

    Dynamic change in microbial flora was monitored with an oxygen electrode. The 1st phase microorganisms, which first grew well in LB medium, were followed by the 2nd phase microorganisms, which supposedly assimilated microbial cells of the 1st phase and their metabolites. In a similar way, a change in microbial flora was observed from the 1st phase to the 4th phase in 84 hr. Based on this observation, prolonged enrichment culture was done for as long as two months to increase the ratio of existence of rare microorganisms. From these culture liquids, four slow-growing bacteria (provisionally named Shinshu-ah1, -ah2, -ah3, and -ah4), which formed scarcely visible small colonies, were isolated. Sequence analysis of their 16S rDNA showed that Shinshu-ah1 had 97% homology with Bradyrhizobium japonicum and uncultured alpha proteobacterium clone blaii 16, Shinshu-ah2 91% with Rasbo bacterium, Alpha proteobacterium 34619, Bradyrhizobium genosp. P, Afipia felis and an unidentified bacterium, Shinshu-ah3 99% with Methylobacterium mesophilicum, and Shinshu-ah4 95% with Agromyces ramosus DSM 43045. Phylogenetic study indicated that Shinshu-ah2 had a possibility to form a new family, Shinshu-ah1 a new genus, and Shinshu-ah4 a new species.

  15. Expressed genes for plant-type ribulose 1,5-bisphosphate carboxylase/oxygenase in the photosynthetic bacterium Chromatium vinosum, which possesses two complete sets of the genes.

    PubMed Central

    Viale, A M; Kobayashi, H; Akazawa, T

    1989-01-01

    Two sets of genes for the large and small subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) were detected in the photosynthetic purple sulfur bacterium Chromatium vinosum by hybridization analysis with RuBisCO gene probes, cloned by using the lambda Fix vector, and designated rbcL-rbcS and rbcA-rbcB. rbcL and rbcA encode the large subunits, and rbcS and rbcB encode the small subunits. rbcL-rbcS was the same as that reported previously (A. M. Viale, H. Kobayashi, T. Takabe, and T. Akazawa, FEBS Lett. 192:283-288, 1985). A DNA fragment bearing rbcA-rbcB was subcloned in plasmid vectors and sequenced. We found that rbcB was located 177 base pairs downstream of the rbcA coding region, and both genes were preceded by plausible procaryotic ribosome-binding sites. rbcA and rbcD encoded polypeptides of 472 and 118 amino acids, respectively. Edman degradation analysis of the subunits of RuBisCO isolated from C. vinosum showed that rbcA-rbcB encoded the enzyme present in this bacterium. The large- and small-subunit polypeptides were posttranslationally processed to remove 2 and 1 amino acid residues from their N-termini, respectively. Among hetero-oligomeric RuBisCOs, the C. vinosum large subunit exhibited higher homology to that from cyanobacteria, eucaryotic algae, and higher plants (71.6 to 74.2%) than to that from the chemolithotrophic bacterium Alcaligenes eutrophus (56.6%). A similar situation has been observed for the C. vinosum small subunit, although the homology among small subunits from different organisms was lower than that among the large subunits. Images PMID:2708310

  16. 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.

  17. 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.

  18. 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...

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

    PubMed Central

    Wang, Yuanli; Chen, Wei; He, Linyan; Wang, Qi

    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

  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

    2016-09-08

    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.

  1. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium

    PubMed Central

    Eisen, Jonathan A.; Nelson, Karen E.; Paulsen, Ian T.; Heidelberg, John F.; Wu, Martin; Dodson, Robert J.; Deboy, Robert; Gwinn, Michelle L.; Nelson, William C.; Haft, Daniel H.; Hickey, Erin K.; Peterson, Jeremy D.; Durkin, A. Scott; Kolonay, James L.; Yang, Fan; Holt, Ingeborg; Umayam, Lowell A.; Mason, Tanya; Brenner, Michael; Shea, Terrance P.; Parksey, Debbie; Nierman, William C.; Feldblyum, Tamara V.; Hansen, Cheryl L.; Craven, M. Brook; Radune, Diana; Vamathevan, Jessica; Khouri, Hoda; White, Owen; Gruber, Tanja M.; Ketchum, Karen A.; Venter, J. Craig; Tettelin, Hervé; Bryant, Donald A.; Fraser, Claire M.

    2002-01-01

    The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are highly conserved among photosynthetic species. Many of these have no assigned function and may play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species. PMID:12093901

  2. 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.

  3. Photosynthetic bacterium Rhodopseudomonas palustris GJ-22 induces systemic resistance against viruses.

    PubMed

    Su, Pin; Tan, Xinqiu; Li, Chenggang; Zhang, Deyong; Cheng, Ju'e; Zhang, Songbai; Zhou, Xuguo; Yan, Qingpin; Peng, Jing; Zhang, Zhuo; Liu, Yong; Lu, Xiangyang

    2017-03-14

    Photosynthetic bacteria (PSB) have been extensively used in agriculture to promote plant growth and to improve crop quality. Their potential application in plant disease management, however, is largely overlooked. In this study, the PSB strain Rhodopseudomonas palustris GJ-22 was investigated for its ability to induce resistance against a plant virus while promoting plant growth. In the field, a foliar spray of GJ-22 suspension protected tobacco plants against tobacco mosaic virus (TMV). Under axenic conditions, GJ-22 colonized the plant phyllosphere and induced resistance against TMV. Additionally, GJ-22 produced two phytohormones, indole-3-acetic acid and 5-aminolevulinic acid, which promote growth and germination in tobacco. Furthermore, GJ-22-inoculated plants elevated their immune response under subsequent TMV infection. This research may give rise to a novel biological agent with a dual function in disease management while promoting plant growth.

  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. 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.

  6. Presence of exclusively bacteriochlorophyll-c containing substrain in the culture of green sulfur photosynthetic bacterium Chlorobium vibrioforme strain NCIB 8327 producing bacteriochlorophyll-d.

    PubMed

    Saga, Yoshitaka; Oh-oka, Hirozo; Hayashi, Takashi; Tamiaki, Hitoshi

    2003-12-01

    The light-dependent composition change of light harvesting bacteriochlorophyll(BChl)s in the present culture of a green sulfur photosynthetic bacterium Chlorobium (Chl.) vibrioforme f. sp. thiosulfatophilum strain NCIB 8327 was investigated by visible absorption spectroscopy and HPLC analyses. When the culture was repeatedly grown in liquid media under a low light condition, both the Soret and Qy absorption bands of the in vivo spectrum were shifted to longer wavelengths. Analysis of the extracted pigments by HPLC revealed that the ratio of the amount of BChl-c to that of BChl-d molecules gradually increased during repeated cultivation. In contrast, when the culture grown under a low light intensity was transferred to a high light condition and continued to be grown, the absorption bands were shifted to shorter wavelengths and the ratio of BChls-c/d decreased finally to the almost original value. Colonies were prepared on solid agar media from the liquid culture containing both BChls-c and d, which was grown under a low light intensity. Each colony obtained was found to contain either BChl-c or d, but not both of them. Two types of cells isolated in this study were derived from the same clone, judged from their genetic analyses. The variation of pigment composition in our liquid culture observed here could be ascribed to the difference of growth rates between two substrains containing BChl-c and BChl-d, respectively, depending on light conditions.

  7. [Screening and identification of a photosynthetic bacterium reducing selenite to red elemental selenium].

    PubMed

    Wang, Dong-liang; Xiao, Min; Qian, Wei; Han, Bo

    2007-02-01

    Selenium is essential element for humans and animals but is very toxic at higher concentrations. In four inorganic states of selenate [SeO4 2- ( VI)], selenite [SeO3 2- (IV)], elemental selenium [Se (0)] and selenide [Se2- (- II )], selenite is well known to be more soluble and higher toxic than other three forms. Many microorganisms have the capacity to reduce selenite to red elemental selenium, which provide the potential to cope with the detoxification of pollution and to use the biological availability of red elemental selenium. Strain S3 that was more resistant to sodium selenite was selected from 20 photosynthetic bacteria preserved in laboratory. The red granule produced by S3 was identified as elemental selenium ( Se) by transmission electron microscopy and Electron-Dispersive X-ray (EDX) analysis. The granule diameter of the red elemental selenium was 5nm - 200nm, similar as the Nano-Se that has bioavailability. Morphology, physiology and photosynthetic pigments analysis results showed that strain S3 was essentially consistent with Rhodobacter azotoformans . The 16S rDNA sequence analysis (GenBank accession number DQ402051) suggested that strain S3 was clustered together with R. azotoformans in phylogenetic tree, with the sequence identity of 99% . Based on all the results of taxonomy, strain S3 was identified as R. azotoformans S3. The effects of selenite on growth kinetics and the ability to resistant selenite of strain S3 were investigated. In contrast to Rhodospirillum rubrum which was reported not to reduce selenite until the end of exponential growth, strain S3 transformed selenite (1.25mmol/L) at the beginning of the growth, suggesting that strain S3 and Rs. rubrum may employ different strategies to reduce selenite. Strain S3 can grow in the presence of up to 125mmol/L sodium selenite, which is much higher than those which could be resisted to by other bacteria such as Escherichia coli ( < 20mmol/L) and Ralstonia metallidurans CH34 ( < 6mmol/L) . It

  8. Melatonin production in an aerobic photosynthetic bacterium: an evolutionarily early association with darkness.

    PubMed

    Tilden, A R; Becker, M A; Amma, L L; Arciniega, J; McGaw, A K

    1997-03-01

    Melatonin was measured in a species of aerobic photosynthetic bacteria, Erythrobacter longus, grown in either constant light or constant dark. A radioimmunoassay was used to quantify melatonin levels and thin-layer chromatography to confirm the identity of melatonin immunoactivity. Melatonin levels were significantly higher (nearly 2.3-fold) in the dark-grown than in the light-grown samples. Also, the homogenates of the dark-grown bacteria retained melatonin-producing enzymatic activity, whereas the light-grown homogenates did not; melatonin levels extracted from the dark-grown homogenates increased with increasing extraction time, reaching as high as 29.2 ng.mg-1 protein at 120 min. Removal of membrane fragments from homogenates did not influence melatonin levels in light-grown homogenate, but this procedure increased melatonin levels in dark-grown homogenate, indicating that at least some of the enzymes in the pathway of melatonin production are not membrane-bound. This study is the second to demonstrate the presence of melatonin at the prokaryotic level, supporting the evidence that melatonin appeared very early in evolution. Its function in prokaryotes has not been determined, but may relate to its antioxidative actions.

  9. 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.

  10. Extraction of extracellular polymeric substances from the photosynthetic bacterium Rhodopseudomonas acidophila.

    PubMed

    Sheng, Guo-Ping; Yu, Han-Qing; Yu, Zhou

    2005-04-01

    Among the four methods for extracting extracellular polymeric substances (EPS) from Rhodopseudomonas acidophila (EDTA, NaOH, H(2)SO(4), heating/centrifugation), EDTA extraction was found to be the most effective. The contents of the major components of EPS from R. acidophila, i.e., carbohydrate, protein and nucleic acid, were 6.5, 58.4 and 5.4 mg g(-1) dry cells, respectively. The optimum extraction time was 1-3 h and the EDTA dosage was approximately 2.8 g g(-1) dry cells. Under these conditions, no cell lysis was observed. The EPS content and the percentage of the three main components were greatly dependent on the extraction method. The intensity of absorption peaks for photosynthetic pigments in the UV-visible spectrum of bacteria remained unchanged prior to and after EDTA extraction; and no pigment peaks appeared in the EPS spectrum. This suggests that few cells were destroyed and lysis did not occur. UV-visible spectrum analysis, an easy and rapid technique, could be used to monitor cell lysis during EPS extraction from R. acidophila.

  11. 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.

  12. In Vitro Enzymatic Activities of Bacteriochlorophyll a Synthase Derived from the Green Sulfur Photosynthetic Bacterium Chlorobaculum tepidum.

    PubMed

    Saga, Yoshitaka; Hirota, Keiya; Harada, Jiro; Tamiaki, Hitoshi

    2015-08-18

    The activity of an enzyme encoded by the CT1610 gene in the green sulfur photosynthetic bacterium Chlorobaculum tepidum, which was annotated as bacteriochlorophyll (BChl) a synthase, BchG (denoted as tepBchG), was examined in vitro using the lysates of Escherichia coli containing the heterologously expressed enzyme. BChl a possessing a geranylgeranyl group at the 17-propionate residue (BChl aGG) was produced from bacteriochlorophyllide (BChlide) a and geranylgeranyl pyrophosphate in the presence of tepBchG. Surprisingly, tepBchG catalyzed the formation of BChl a bearing a farnesyl group (BChl aF) as in the enzymatic production of BChl aGG, indicating loose recognition of isoprenoid pyrophosphates in tepBchG. In contrast to such loose recognition of isoprenoid substrates, BChlide c and chlorophyllide a gave no esterifying product upon being incubated with geranylgeranyl or farnesyl pyrophosphate in the presence of tepBchG. These results confirm that tepBchG undoubtedly acts as the BChl a synthase in Cba. tepidum. The enzymatic activity of tepBchG was higher than that of BchG of Rhodobacter sphaeroides at 45 °C, although the former activity was lower than the latter below 35 °C.

  13. Structural analysis of the homodimeric reaction center complex from the photosynthetic green sulfur bacterium Chlorobaculum tepidum.

    PubMed

    He, Guannan; Zhang, Hao; King, Jeremy D; Blankenship, Robert E

    2014-08-05

    The reaction center (RC) complex of the green sulfur bacterium Chlorobaculum tepidum is composed of the Fenna-Matthews-Olson antenna protein (FMO) and the reaction center core (RCC) complex. The RCC complex has four subunits: PscA, PscB, PscC, and PscD. We studied the FMO/RCC complex by chemically cross-linking the purified sample followed by biochemical and spectroscopic analysis. Blue-native gels showed that there were two types of FMO/RCC complexes, which are consistent with complexes with one copy of FMO per RCC and two copies of FMO per RCC. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the samples after cross-linking showed that all five subunits of the RC can be linked by three different cross-linkers: bissulfosuccinimidyl suberate, disuccinimidyl suberate, and 3,3-dithiobis-sulfosuccinimidyl propionate. The interaction sites of the cross-linked complex were also studied using liquid chromatography coupled to tandem mass spectrometry. The results indicated that FMO, PscB, PscD, and part of PscA are exposed on the cytoplasmic side of the membrane. PscD helps stabilize FMO to the reaction center and may facilitate transfer of the electron from the RC to ferredoxin. The soluble domain of the heme-containing cytochrome subunit PscC and part of the core subunit PscA are located on the periplasmic side of the membrane. There is a close relationship between the periplasmic portions of PscA and PscC, which is needed for the efficient transfer of the electron between PscC and P840.

  14. Characterization of chlorophyll pigments in the mutant lacking 8-vinyl reductase of green photosynthetic bacterium Chlorobaculum tepidum.

    PubMed

    Mizoguchi, Tadashi; Harada, Jiro; Tamiaki, Hitoshi

    2012-12-01

    The mutant lacking the enzyme BciA (renamed CT1063), which catalyzed reduction of the 8-vinyl group of a porphyrinoid-type 3,8-divinyl-(proto)chlorophyllide-a [DV-(P)Chlide-a] in the green sulfur bacterium Chlorobaculum (Cba.) tepidum, was reconstructed on the basis of the previous study reported by Chew and Bryant [J. Biol. Chem.2007, 282, 2967-2975]. Cba. tepidum biosynthesizes the following three different types of chlorophylls (Chls) through their common precursory DV-(P)Chlide-a as its photosynthetically active pigments: bacteriochlorophyll(BChl)-c and Chl-a with the partially reduced 17,18-trans-dihydroporphyrin and BChl-a with the further reduced 7,8-trans-17,18-trans-tetrahydroporphyrin. The structures of Chls thus produced were characterized in detail by various spectroscopic techniques. In the mutant, both BChl-c and Chl-a possessing the alkyl group at the 8-position were exclusively replaced by their 8-vinylated derivatives, whereas BChl-a possessed the original 8-ethyl group. The present observations were inconsistent with the previous report. However, it was apparently confirmed that the enzyme BciA was responsible for the reduction of DV-(P)Chlide-a to produce BChl-c and Chl-a. Noteworthily, exclusive accumulation of the reduced (8-ethylated) form of BChl-a, not its 8-vinylated derivative, in the mutant indicates the presence of another enzyme catalyzing the 8-vinyl reduction as yet unidentified or any other reduction mechanism using a known enzyme to yield BChl-a.

  15. 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

    2013-11-07

    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.

  16. Coupling of cytochrome and quinone turnovers in the photocycle of reaction centers from the photosynthetic bacterium Rhodobacter sphaeroides.

    PubMed Central

    Osváth, S; Maróti, P

    1997-01-01

    A minimal kinetic model of the photocycle, including both quinone (Q-6) reduction at the secondary quinone-binding site and (mammalian) cytochrome c oxidation at the cytochrome docking site of isolated reaction centers from photosynthetic purple bacteria Rhodobacter sphaeroides, was elaborated and tested by cytochrome photooxidation under strong continuous illumination. The typical rate of photochemical excitation by a laser diode at 810 nm was 2.200 s-1, and the rates of stationary turnover of the reaction center (one-half of that of cytochrome photooxidation) were 600 +/- 70 s-1 at pH 6 and 400 +/- 50 s-1 at pH 8. The rate of turnover showed strong pH dependence, indicating the contribution of different rate-limiting processes. The kinetic limitation of the photocycle was attributed to the turnover of the cytochrome c binding site (pH < 6), light intensity and quinone/quinol exchange (6 < pH < 8), and proton-coupled second electron transfer in the quinone acceptor complex (pH > 8). The analysis of the double-reciprocal plot of the rate of turnover versus light intensity has proved useful in determining the light-independent (maximum) turnover rate of the reaction center (445 +/- 50 s-1 at pH 7.8). PMID:9251814

  17. Photosynthetic responses of thalli and isolated protoplasts of Bryopsis hypnoides (Bryopsidales, Chlorophyta) during dehydration

    NASA Astrophysics Data System (ADS)

    Lü, Fang; Wang, Guangce; Jin, Haochen

    2011-03-01

    Bryopsis hypnoides Lamouroux is a unique intertidal siphonous green alga whose extruded protoplasm can aggregate spontaneously in seawater to form numerous new cells that can develop into mature algal thalli. In this study, the photosynthetic responses during dehydration of both the thalli and protoplasts isolated from B. hypnoides were measured using a Dual-PAM (pulse amplitude modulation)-100 fluorometer. The results show that the photosynthetic rates of B. hypnoides thalli were maintained for an initial period, beyond which continued desiccation resulted in reduced rates of PSI and PSII. However, the photosynthetic performances of the isolated protoplasts dehydrated in air (CO2 concentration 600-700 mg/L) showed a slight increase of Y(II) at 20% water loss, but the rates decreased thereafter with declining water content. When protoplasts were dehydrated in CO2 deficient conditions (CO2 concentration 40-80 mg/L), the values of Y(II) declined steadily with increased dehydration without an initial rise. These results indicated that the thalli and isolated protoplasts of this alga can utilize CO2 in ambient air effectively, and the photosynthetic performances of the isolated protoplasts were significantly different from that of the thalli during dehydration. Thus the protoplasts may be an excellent system for the study of stress tolerance.

  18. Complete Genome Sequence of Flavobacteriales Bacterium Strain UJ101 Isolated from a Xanthid Crab

    PubMed Central

    Yang, Jhung-Ahn; Kwon, Kae Kyoung

    2017-01-01

    ABSTRACT Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab species collected from the East Sea of Korea. Here, we report the complete genome sequence of strain UJ101 for the study of major metabolic pathways related to microbial species from marine invertebrate species. PMID:28153900

  19. 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.

  20. Isolation and Characterization of a Bacteriophage Preying an Antifungal Bacterium.

    PubMed

    Rahimi-Midani, Aryan; Kim, Kyoung-Ho; Lee, Seon-Woo; Jung, Sang Bong; Choi, Tae-Jin

    2016-12-01

    Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of 100 ± 5 nm and tail of 200 ± 5 nm, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene). Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food.

  1. Isolation and Characterization of a Bacteriophage Preying an Antifungal Bacterium

    PubMed Central

    Rahimi-Midani, Aryan; Kim, Kyoung-Ho; Lee, Seon-Woo; Jung, Sang Bong; Choi, Tae-Jin

    2016-01-01

    Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of 100 ± 5 nm and tail of 200 ± 5 nm, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene). Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food. PMID:27904467

  2. 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

  3. 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).

  4. "Bacillus hackensackii" sp. nov., a novel carbon dioxide sensitive bacterium isolated from blood culture.

    PubMed

    Hong, Tao; Heibler, Nueda; Tang, Y i-Wei

    2003-02-01

    An endospore-forming, gram-positive bacillus was isolated from a patient's blood culture. This bacillus did not grow in the presence of 5% carbon dioxide although it grew well in ambient air at 37 degrees C. Although the organism thus is an aerobic bacterium, its sensitivity to increased carbon dioxide concentration places it in a distinct category of gaseous atmospheric requirement: capnophobic. Based on its morphology, growth characteristics, biochemical reactions and a complete 16S rRNA gene nucleotide sequence analysis, this microorganism represents a novel Bacillus species. The clinical significance of this isolate is unknown. It is proposed that the bacterium be classified in the genus Bacillus as "Bacillus hackensackii".

  5. 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

  6. 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)).

  7. 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.

  8. Spectroscopic studies of two spectral variants of light-harvesting complex 2 (LH2) from the photosynthetic purple sulfur bacterium Allochromatium vinosum.

    PubMed

    Niedzwiedzki, Dariusz M; Bina, David; Picken, Nichola; Honkanen, Suvi; Blankenship, Robert E; Holten, Dewey; Cogdell, Richard J

    2012-09-01

    Two spectral forms of the peripheral light-harvesting complex (LH2) from the purple sulfur photosynthetic bacterium Allochromatium vinosum were purified and their photophysical properties characterized. The complexes contain bacteriochlorophyll a (BChl a) and multiple species of carotenoids. The composition of carotenoids depends on the light conditions applied during growth of the cultures. In addition, LH2 grown under high light has a noticeable split of the B800 absorption band. The influence of the change of carotenoid distribution as well as the spectral change of the excitonic absorption of the bacteriochlorophylls on the light-harvesting ability was studied using steady-state absorption, fluorescence and femtosecond time-resolved absorption at 77K. The results demonstrate that the change of the distribution of the carotenoids when cells were grown at low light adapts the absorptive properties of the complex to the light conditions and maintains maximum photon-capture performance. In addition, an explanation for the origin of the enigmatic split of the B800 absorption band is provided. This spectral splitting is also observed in LH2 complexes from other photosynthetic sulfur purple bacterial species. According to results obtained from transient absorption spectroscopy, the B800 band split originates from two spectral forms of the associated BChl a monomeric molecules bound within the same complex.

  9. 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

  10. Anaerobranca zavarzinii sp. nov., an anaerobic, alkalithermophilic bacterium isolated from Kamchatka thermal fields.

    PubMed

    Kevbrin, Vadim; Boltyanskaya, Yulia; Garnova, Elena; Wiegel, Juergen

    2008-06-01

    A novel obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from a small and very shallow geothermally heated pool at Pushino (Kamchatka, Far East Russia). The bacterium, designated strain JW/VK-KS5Y(T), was a Gram staining negative, Gram type positive rod. The cells were sometimes branched, with a tendency to grow in long chains, and were non-sporulating and non-motile. The shortest observed doubling time was 28 min when the novel strain was grown at 54-60 degrees C in 120 mM sodium carbonate-containing medium at pH(25 degrees C) 8.5-9.0. The novel bacterium grew on yeast extract and soytone as sole carbon and energy sources but could also use fumarate, thiosulfate and sulfur as electron acceptors. The DNA G+C content was 32.5 mol%. Based on phylogenetic, DNA-DNA hybridization and phenotypic data, it was concluded that isolate JW/VK-KS5Y(T) (=VKM B-2436(T)=DSM 18970(T)) represents the type strain of a novel species, Anaerobranca zavarzinii sp. nov.

  11. Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium.

    PubMed Central

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

    1988-01-01

    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 (C58 to C64). 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 degrees C and minimally at 35 degrees C. No growth was observed at 5 or 42 degrees 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. Images PMID:3202633

  12. Characterization of a copper-resistant symbiotic bacterium isolated from Medicago lupulina growing in mine tailings.

    PubMed

    Fan, Lian-Mei; Ma, Zhan-Qiang; Liang, Jian-Qiang; Li, Hui-Fen; Wang, En-Tao; Wei, Ge-Hong

    2011-01-01

    A root nodule bacterium, Sinorhizobium meliloti CCNWSX0020, resistant to 1.4 mM Cu2+ was isolated from Medicago lupulina growing in mine tailings. In medium supplied with copper, this bacterium showed cell deformation and aggregation due to precipitation of copper on the cell surface. Genes similar to the copper-resistant genes, pcoR and pcoA from Escherichia coli, were amplified by PCR from a 1.4-Mb megaplasmid. Inoculation with S. meliloti CCNWSX0020 increased the biomass of M. lupulina grown in medium added 0 and 100 mg Cu2+ kg(-1) by 45.8% and 78.2%, respectively, and increased the copper concentration inside the plant tissues grown in medium supplied with 100 μM Cu2+ by 39.3%, demonstrating that it is a prospective symbiotic system for bioremediation purposes.

  13. Genome Sequence of Formosa haliotis Strain MA1, a Brown Alga-Degrading Bacterium Isolated from the Gut of Abalone Haliotis gigantea

    PubMed Central

    Mizutani, Yukino; Shibata, Toshiyuki; Miyake, Hideo; Iehata, Shunpei; Mori, Tetsushi; Kuroda, Kouichi; Ueda, Mitsuyoshi

    2016-01-01

    Formosa haliotis is a brown alga-degrading bacterium isolated from the gut of abalone Haliotis gigantea. Here, we report the draft genome sequence of this bacterium and pointed out possible important features related to alginate degradation. PMID:27856598

  14. Rhodococcus sp. Q5, a novel agarolytic bacterium isolated from printing and dyeing wastewater.

    PubMed

    Feng, Zehua; Peng, Lin; Chen, Mei; Li, Mengying

    2012-09-01

    An agar-degrading bacterium, Rhodococcus sp. Q5, was isolated from printing and dyeing wastewater using a mineral salts agar plate containing agar as the sole carbon source. The bacterium grew from pH 4.0 to 9.0, from 15 to 35°C, and in NaCl concentrations of 0-5 %; optimal values were pH 6.0, 30°C, and 1 % NaCl. Maximal agarase production was observed at pH 6.0 and 30°C. The bacterium did not require NaCl for growth or agarase production. The agarase secreted by Q5 was inducible by agar and was repressed by all simple sugars tested except lactose. Strain Q5 could hydrolyze starch but not cellulose or carboxymethyl cellulose. Agarase activity could also be detected in the medium when lactose or starch was the sole source of carbon and energy. Strain Q5 could grow in nitrogen-free mineral media; an organic nitrogen source was more effective than inorganic carbon sources for growth and agarase production. Addition of more organic nitrogen (peptone) to the medium corresponded with reduced agarase activity.

  15. Exoelectrogenic bacterium phylogenetically related to Citrobacter freundii, isolated from anodic biofilm of a microbial fuel cell.

    PubMed

    Huang, Jianjian; Zhu, Nengwu; Cao, Yanlan; Peng, Yue; Wu, Pingxiao; Dong, Wenhao

    2015-02-01

    An electrogenic bacterium, named Citrobacter freundii Z7, was isolated from the anodic biofilm of microbial fuel cell (MFC) inoculated with aerobic sewage sludge. Cyclic voltammetry (CV) analysis exhibited that the strain Z7 had relatively high electrochemical activity. When the strain Z7 was inoculated into MFC, the maximum power density can reach 204.5 mW/m(2) using citrate as electron donor. Series of substrates including glucose, glycerol, lactose, sucrose, and rhammose could be utilized to generate power. CV tests and the addition of anode solution as well as AQDS experiments indicated that the strain Z7 might transfer electrons indirectly via secreted mediators.

  16. 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.

  17. 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.

  18. Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud.

    PubMed

    Viulu, Samson; Nakamura, Kohei; Okada, Yurina; Saitou, Sakiko; Takamizawa, Kazuhiro

    2013-02-01

    A novel species of Fe(III)-reducing bacterium, designated strain OSK6(T), belonging to the genus Geobacter, was isolated from lotus field mud in Japan. Strain OSK6(T) was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, gram-negative, motile, straight rod-shaped bacterium, 0.6-1.9 µm long and 0.2-0.4 µm wide. The growth of the isolate occurred at 20-40 °C with optima of 30-37 °C and pH 6.5-7.5 in the presence of up to 0.5 g NaCl l(-1). The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6(T) was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6(T) is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6(T) is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6(T) ( = DSM 24905(T) = JCM 17780(T)).

  19. Genome Sequence of the Marine Bacterium Vibrio campbellii DS40M4, Isolated from Open Ocean Water

    PubMed Central

    Dias, Graciela M.; Thompson, Cristiane C.; Fishman, Brian; Naka, Hiroaki; Haygood, Margo G.; Crosa, Jorge H.

    2012-01-01

    Vibrio sp. strain DS40M4 is a marine bacterium that was isolated from open ocean water. In this work, using genomic taxonomy, we were able to classify this bacterium as V. campbellii. Our genomic analysis revealed that V. campbellii DS40M4 harbors genes related to iron transport, virulence, and environmental fitness, such as those encoding anguibactin and vanchrobactin biosynthesis proteins, type II, III, IV, and VI secretion systems, and proteorhodopsin. PMID:22275102

  20. [Isolation, identification and degradation characteristics of a quinoline-degrading bacterium Rhodococcus sp QL2].

    PubMed

    Zhu, Shun-ni; Liu, Dong-qi; Fan, Li; Ni, Jin-ren

    2008-02-01

    A quinoline-degrading bacterium QL2, which utilizes quinoline as sole source of carbon, nitrogen and energy, was isolated from activated sludge in a coke-plant wastewater biological treatment system. According to the morphological characteristics, physiological and biochemical characteristics, and sequence analysis of 16S rRNA, the strain was identified as Rhodococcus sp.. The optimal temperature, initial pH, and shaker rotary speed for strain QL2 utilizing quinoline are 35-42 degrees C, pH 8-9, and 150 r/min, respectively. Extra nitrogen sources stimulate the isolate growth on quinoline, and inorganic nitrogen better than organic nitrogen, NH4+ -N better than NO3(-) -N. The degradation reaction of quinoline by strain QL2 can be described with zero order kinetic equation within the initial quinoline concentrations of 60-680 mg/L. When the initial concentration was 150 mg/L, quinoline was degraded completely in 8 hours and TOC removal efficiency was 70% in 14 hours. This bacterium produced pigmented compounds, and ring nitrogen was released into the growth medium as ammonium. The main intermediate in the degradation pathway was 2-hydroxyquinoline by the analysis of HPLC and GC/MS. With a broad range of substrate utilization, the strain can degrade phenol, naphthalene, pyridine, and some other kinds of aromatic compounds.

  1. 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

    2016-02-10

    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.

  2. Isolation and characterization of a prokaryotic cell organelle from the anammox bacterium Kuenenia stuttgartiensis.

    PubMed

    Neumann, Sarah; Wessels, Hans J C T; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Kartal, Boran; Jetten, Mike S M; van Niftrik, Laura

    2014-11-01

    Anaerobic ammonium oxidizing (anammox) bacteria oxidize ammonium with nitrite to nitrogen gas in the absence of oxygen. These microorganisms form a significant sink for fixed nitrogen in the oceans and the anammox process is applied as a cost-effective and environment-friendly nitrogen removal system from wastewater. Anammox bacteria have a compartmentalized cell plan that consists of three separate compartments. Here we report the fractionation of the anammox bacterium Kuenenia stuttgartiensis in order to isolate and analyze the innermost cell compartment called the anammoxosome. The subcellular fractions were microscopically characterized and all membranes in the anammox cell were shown to contain ladderane lipids which are unique for anammox bacteria. Proteome analyses and activity assays with the isolated anammoxosomes showed that these organelles harbor the energy metabolism in anammox cells. Together the experimental data provide the first thorough characterization of a respiratory cell organelle from a bacterium and demonstrate the essential role of the anammoxosome in the production of a major portion of the nitrogen gas in our atmosphere.

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

    NASA Astrophysics Data System (ADS)

    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 2300 μg/l As(III) using in situ As(III)-contaminated groundwater under aerobic conditions within 1 d. 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.

  4. 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

  5. (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

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

    PubMed

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

    2010-09-01

    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 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). 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.

  7. Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803.

    PubMed

    Montagud, Arnau; Zelezniak, Aleksej; Navarro, Emilio; de Córdoba, Pedro Fernández; Urchueguía, Javier F; Patil, Kiran Raosaheb

    2011-03-01

    Synechocystis sp. PCC6803 is a model cyanobacterium capable of producing biofuels with CO(2) as carbon source and with its metabolism fueled by light, for which it stands as a potential production platform of socio-economic importance. Compilation and characterization of Synechocystis genome-scale metabolic model is a pre-requisite toward achieving a proficient photosynthetic cell factory. To this end, we report iSyn811, an upgraded genome-scale metabolic model of Synechocystis sp. PCC6803 consisting of 956 reactions and accounting for 811 genes. To gain insights into the interplay between flux activities and metabolic physiology, flux coupling analysis was performed for iSyn811 under four different growth conditions, viz., autotrophy, mixotrophy, heterotrophy, and light-activated heterotrophy (LH). Initial steps of carbon acquisition and catabolism formed the versatile center of the flux coupling networks, surrounded by a stable core of pathways leading to biomass building blocks. This analysis identified potential bottlenecks for hydrogen and ethanol production. Integration of transcriptomic data with the Synechocystis flux coupling networks lead to identification of reporter flux coupling pairs and reporter flux coupling groups - regulatory hot spots during metabolic shifts triggered by the availability of light. Overall, flux coupling analysis provided insight into the structural organization of Synechocystis sp. PCC6803 metabolic network toward designing of a photosynthesis-based production platform.

  8. Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea.

    PubMed

    Makemson, J C; Fulayfil, N R; Landry, W; Van Ert, L M; Wimpee, C F; Widder, E A; Case, J F

    1997-10-01

    Thirty-four strains of nonfermentative, respiratory, luminous bacteria were isolated from samples of squid ink and seawater from depths of 200 to 300 m in the Alboran Sea. Although these strains had a few properties similar to properties of Shewanella (Alteromonas) hanedai, they did not cluster phenotypically with any previously described bacterium. The nucleotide sequence of a 740-bp segment of luxA was not homologous with other known luxA sequences but clustered with the luxA sequences of Shewanella hanedai, Vibrio logei, Vibrio fischeri, and Photobacterium species. The 16S RNA gene from two strains was sequenced and was found to be most closely related to the S. hanedai 16S RNA gene. Based on the differences observed, we describe the new isolates as members of new species, Shewanella woodyi sp. nov. Strain ATCC 51908 (= MS32) is the type strain of this new species.

  9. Specific Ca2+-binding motif in the LH1 complex from photosynthetic bacterium Thermochromatium tepidum as revealed by optical spectroscopy and structural modeling.

    PubMed

    Ma, Fei; Kimura, Yukihiro; Yu, Long-Jiang; Wang, Peng; Ai, Xi-Cheng; Wang, Zheng-Yu; Zhang, Jian-Ping

    2009-03-01

    Native and Ca(2+)-depleted light-harvesting-reaction center core complexes (LH1-RC) from the photosynthetic bacterium Thermochromatium (Tch.) tepidum exhibit maximal LH1-Q(y) absorption at 915 and 889 nm, respectively. To understand the structural origins of the spectral variation, we performed spectroscopic and structure modeling investigations. For the 889 nm form of LH1-RC, bacteriochlorophyll a (BChl a) in the native form was found by means of near-infrared Fourier-transform Raman spectroscopy, a higher degree of macrocycle distortion and a stronger hydrogen bond with the beta-Trp(-8) residue. SWISS-MODEL structure modeling suggests the presence of a specific coordination motif of Ca(2+) at the C-terminus of the alpha-subunit of LH1, while MODELLER reveals the tilt of alpha- and beta-polypeptides with reference to the structural template, as well as a change in the concentric orientation of BChl a molecules, both of which may be connected to the long-wavelength LH1-Q(y) absorption of the 915 nm form. The carotenoid spirilloxanthin shows a twisted all-trans configuration in both forms of LH1 as evidenced by the resonance Raman spectroscopic results. With regard to the thermal stability, the 915 nm form was shown by the use of temperature-dependent fluorescence spectroscopy to be approximately 20 K more stable than the 889 nm form, which may be ascribed to the specific Ca(2+)-binding motif of LH1.

  10. A Screening Method for the Isolation of Polyhydroxyalkanoate-Producing Purple Non-sulfur Photosynthetic Bacteria from Natural Seawater

    PubMed Central

    Higuchi-Takeuchi, Mieko; Morisaki, Kumiko; Numata, Keiji

    2016-01-01

    Polyhydroxyalkanoates (PHAs) are a family of biopolyesters accumulated by a variety of microorganisms as carbon and energy storage under starvation conditions. We focused on marine purple non-sulfur photosynthetic bacteria as host microorganisms for PHA production and developed a method for their isolation from natural seawater. To identify novel PHA-producing marine purple non-sulfur photosynthetic bacteria, natural seawaters were cultured in nutrient-rich medium for purple non-sulfur photosynthetic bacteria, and twelve pink- or red-pigmented colonies were picked up. Gas chromatography mass spectrometry analysis revealed that four isolates synthesized PHA at levels ranging from 0.5 to 24.4 wt% of cell dry weight. The 16S ribosomal RNA sequence analysis revealed that one isolate (HM2) showed 100% identity to marine purple non-sulfur photosynthetic bacteria. In conclusion, we have demonstrated in this study that PHA-producing marine purple non-sulfur photosynthetic bacteria can be isolated from natural seawater under nutrient-rich conditions. PMID:27708640

  11. A Screening Method for the Isolation of Polyhydroxyalkanoate-Producing Purple Non-sulfur Photosynthetic Bacteria from Natural Seawater.

    PubMed

    Higuchi-Takeuchi, Mieko; Morisaki, Kumiko; Numata, Keiji

    2016-01-01

    Polyhydroxyalkanoates (PHAs) are a family of biopolyesters accumulated by a variety of microorganisms as carbon and energy storage under starvation conditions. We focused on marine purple non-sulfur photosynthetic bacteria as host microorganisms for PHA production and developed a method for their isolation from natural seawater. To identify novel PHA-producing marine purple non-sulfur photosynthetic bacteria, natural seawaters were cultured in nutrient-rich medium for purple non-sulfur photosynthetic bacteria, and twelve pink- or red-pigmented colonies were picked up. Gas chromatography mass spectrometry analysis revealed that four isolates synthesized PHA at levels ranging from 0.5 to 24.4 wt% of cell dry weight. The 16S ribosomal RNA sequence analysis revealed that one isolate (HM2) showed 100% identity to marine purple non-sulfur photosynthetic bacteria. In conclusion, we have demonstrated in this study that PHA-producing marine purple non-sulfur photosynthetic bacteria can be isolated from natural seawater under nutrient-rich conditions.

  12. Anaerobic and aerobic degradation of pyridine by a newly isolated denitrifying bacterium.

    PubMed Central

    Rhee, S K; Lee, G M; Yoon, J H; Park, Y H; Bae, H S; Lee, S T

    1997-01-01

    New denitrifying bacteria that could degrade pyridine under both aerobic and anaerobic conditions were isolated from industrial wastewater. The successful enrichment and isolation of these strains required selenite as a trace element. These isolates appeared to be closely related to Azoarcus species according to the results of 16S rRNA sequence analysis. An isolated strain, pF6, metabolized pyridine through the same pathway under both aerobic and anaerobic conditions. Since pyridine induced NAD-linked glutarate-dialdehyde dehydrogenase and isocitratase activities, it is likely that the mechanism of pyridine degradation in strain pF6 involves N-C-2 ring cleavage. Strain pF6 could degrade pyridine in the presence of nitrate, nitrite, and nitrous oxide as electron acceptors. In a batch culture with 6 mM nitrate, degradation of pyridine and denitrification were not sensitively affected by the redox potential, which gradually decreased from 150 to -200 mV. In a batch culture with the nitrate concentration higher than 6 mM, nitrite transiently accumulated during denitrification significantly inhibited cell growth and pyridine degradation. Growth yield on pyridine decreased slightly under denitrifying conditions from that under aerobic conditions. Furthermore, when the pyridine concentration used was above 12 mM, the specific growth rate under denitrifying conditions was higher than that under aerobic conditions. Considering these characteristics, a newly isolated denitrifying bacterium, strain pF6, has advantages over strictly aerobic bacteria in field applications. PMID:9212408

  13. 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.

  14. Bacillus flexus strain As-12, a new arsenic transformer bacterium isolated from contaminated water resources.

    PubMed

    Jebeli, Mohammad Ahmadi; Maleki, Afshin; Amoozegar, Mohammad Ali; Kalantar, Enayatollah; Izanloo, Hassan; Gharibi, Fardin

    2017-02-01

    A total of 14 arsenic-resistant bacteria were isolated from an arsenic-contaminated travertine spring water in the central district of Qorveh county, Kurdistan Province, Iran. One of strains designated As-12 was selected for further investigation because of its ability to transform arsenic. The strain was identified by cultural, morphological and biochemical tests, and 16S rRNA gene sequencing. Finally, the growth characteristics of the isolate were investigated in a chemically defined medium which included varied ranges of environmental factors such as pH, temperature and salinity. Moreover, the resistance of this strain to some heavy metals was evaluated. The bacterium was a Gram-positive, endospore-forming with all other characteristics of the genus Bacillus. It revealed maximum similarity at the 16S rRNA gene level with Bacillus flexus. The optimum growth of the strain was observed at 38 °C, pH 9 and 2% salinity. This strain was resistant to heavy metals such as zinc, chromium, lead, nickel, copper, mercuric and cadmium at concentrations of 15 mM, 15.5 mM, 11.5 mM, 12 mM, 11 mM, 5.5 mM, and 1 mM, respectively. The isolated bacterium was able to reduce As (V) to As (III) (about 28%) and oxidize As (III) to As (V) (about 45%) after 48 h of incubation at 37 °C. In conclusion, Bacillus flexus strain As-12, was identified as an arsenic transformer, for the first time.

  15. Enhanced carboxymethylcellulase production by a newly isolated marine bacterium, Cellulophaga lytica LBH-14, using rice bran.

    PubMed

    Gao, Wa; Lee, Eun-Jung; Lee, Sang-Un; Li, Jianhong; Chung, Chung-Han; Lee, Jin-Woo

    2012-10-01

    The aim of this work was to establish the optimal conditions for production of carboxymethylcellulase (CMCase) by a newly isolated marine bacterium using response surface methodology (RSM). A microorganism producing CMCase, isolated from seawater, was identified as Cellulophaga lytica based 16S rDNA sequencing and the neighborjoining method. The optimal conditions of rice bran, ammonium chloride, and initial pH of the medium for cell growth were 100.0 g/l, 5.00 g/l, and 7.0, respectively, whereas those for production of CMCase were 79.9 g/l, 8.52 g/l, and 6.1. The optimal concentrations of K2HPO4, NaCl, MgSO4·7H2O, and (NH4)2SO4 for cell growth were 6.25, 0.62, 0.28, and 0.42 g/l, respectively, whereas those for production of CMCase were 3.72, 0.54, 0.70, and 0.34 g/l. The optimal temperature for cell growth and the CMCase production by C. lytica LBH-14 were 35 degrees C and 25 degrees C, respectively. The maximal production of CMCase under optimized condition for 3 days was 110.8 U/ml, which was 5.3 times higher than that before optimization. In this study, rice bran and ammonium chloride were developed as carbon and nitrogen sources for the production of CMCase by C. lytica LBH-14. The time for production of CMCase by a newly isolated marine bacterium with submerged fermentations reduced to 3 days, which resulted in enhanced productivity of CMCase and a decrease in its production cost.

  16. Isolation of a spiral-shaped bacterium from the cat stomach.

    PubMed Central

    Lee, A; Hazell, S L; O'Rourke, J; Kouprach, S

    1988-01-01

    A spiral- or helix-shaped bacterium that colonizes the stomachs of cats has been isolated in pure culture for the first time. The organism is tightly coiled with tufts of 10 to 17 polar flagella positioned slightly off center at the end of the cell. The body of the cell is entwined with unique periplasmic fibrils that usually occur in pairs, although groupings of one and three fibrils were also seen. The organism is strongly urease, catalase, and oxidase positive and is likely to belong to an as yet unclassified group of bacteria that are specifically adapted to the ecological niche provided by gastrointestinal mucus. Isolation of this organism will allow study of the factors influencing colonization of gastric mucosae, information relevant to the association of another mucus colonizer, Campylobacter pylori, with the human stomach. Recent reports of the isolation of other bacteria with the characteristic periplasmic surface structures suggests that the group may be more widespread than was hitherto thought. Bacteria with the morphology of the organisms seen in the cat stomach have been seen in gastric biopsies from humans. The organism whose isolation is reported here has been used in previous serological studies to support the hypothesis that spiral bacteria from animals can colonize the human stomach. Images PMID:3169989

  17. Lysinibacillus tabacifolii sp. nov., a novel endophytic bacterium isolated from Nicotiana tabacum leaves.

    PubMed

    Duan, Yan-Qing; He, Song-Tao; Li, Qing-Qing; Wang, Ming-Feng; Wang, Wen-Yuan; Zhe, Wei; Cao, Yong-Hong; Mo, Ming-He; Zhai, Yu-Long; Li, Wen-Jun

    2013-06-01

    A Gram-positive, catalase- and oxidase-positive, strictly aerobic, endospore-forming rod bacterium, designated K3514(T), was isolated from the leaves of Nicotiana tabacum. The strain was able to grow at temperatures of 8-40°C, pH 5.0-10.0 and NaCl concentrations of 0-7%. The predominant quinones (>30%) of this strain were MK-7(H2) and MK-7. Phylogenetic analysis of 16S rRNA gene sequence showed that strain K3514(T) was affiliated to the genus Lysinibacillus, with its closest relatives being Lysinibacillus mangiferihumi (98.3% sequence similarity), Lysinibacillus sphaericus (97.9% sequence similarity), Lysinibacillus fusiformis (97.4% sequence similarity), and Lysinibacillus xylanilyticus (97.3% sequence similarity). However, low levels of DNA-DNA relatedness values suggested that the isolate was distinct from the other closest Lysinibacillus species. Additionally, based on analysis of morphological, physiological, and biochemical characteristics, the isolate could be differentiated from the closest known relatives. Therefore, based on polyphasic taxonomic data, the novel isolate likely represents a novel species, for which the name Lysinibacillus tabacifolii sp. nov. and the type strain K3514(T) (=KCTC 33042(T) =CCTCC AB 2012050(T)) are proposed.

  18. Quorum Sensing Activity of Aeromonas Caviae Strain YL12, A Bacterium Isolated from Compost

    PubMed Central

    Lim, Yan-Lue; Ee, Robson; Yin, Wai-Fong; Chan, Kok-Gan

    2014-01-01

    Quorum sensing is a well-studied cell-to-cell communication method that involves a cell-density dependent regulation of genes expression mediated by signalling molecules. In this study, a bacterium isolated from a plant material compost pile was found to possess quorum sensing activity based on bioassay screening. Isolate YL12 was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and molecular typing using rpoD gene which identified the isolate as Aeromonas caviae. High resolution tandem mass spectrometry was subsequently employed to identify the N-acyl homoserine lactone profile of Aeromonas caviae YL12 and confirmed that this isolate produced two short chain N-acyl homoserine lactones, namely C4-HSL and C6, and the production was observed to be cell density-dependent. Using the thin layer chromatography (TLC) bioassay, both AHLs were found to activate C. violaceum CV026, whereas only C6-HSL was revealed to induce bioluminescence expression of E. coli [pSB401]. The data presented in this study will be the leading steps in understanding the role of quorum sensing in Aeromonas caviae strain YL12. PMID:24759107

  19. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora.

    PubMed

    Kim, Byung-Chun; Lee, Kang Hyun; Kim, Mi Na; Kim, Eun-Mi; Rhee, Moon-Soo; Kwon, O-Yu; Shin, Kee-Sun

    2009-10-01

    A novel cellulolytic bacterium, strain S23(T), was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase-positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, alpha-galactosidase, and beta-galactosidase activities. The DNA G+C content was 49.5 mol%. The main cellular fatty acids were anteiso-C(15:0) (51.9%), iso-C(16:0) (14.7%), and iso-C(15:0) (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall pepti-doglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23(T) and other Paenibacillus species were between 89.9% and 95.9%, and S23(T) was most closely related to Paenibacillus tarimensis SA-7-6(T). On the basis of phylogenetic and phenotypic properties of strain S23(T), the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23(T) (=KCTC 13695(T) =KACC 14199(T) =JCM 16419(T)).

  20. Streptococcus danieliae sp. nov., a novel bacterium isolated from the caecum of a mouse.

    PubMed

    Clavel, Thomas; Charrier, Cédric; Haller, Dirk

    2013-01-01

    We report the characterization of one novel bacterium, strain ERD01G(T), isolated from the cecum of a TNF(deltaARE) mouse. The strain was found to belong to the genus Streptococcus based on phylogenetic analysis of partial 16S rRNA gene sequences. The bacterial species with standing name in nomenclature that was most closely related to our isolate was Streptococcus alactolyticus (97 %). The two bacteria were characterized by a DNA-DNA hybridization similarity value of 35 %, demonstrating that they belong to different species. The new isolate was negative for acetoin production, esculin hydrolysis, urease, α-galactosidase and β-glucosidase, was able to produce acid from starch and trehalose, grew as beta-hemolytic coccobacilli on blood agar, did not grow at >40 °C, did not survive heat treatment at 60 °C for 20 min and showed negative agglutination in Lancefield tests. On the basis of these characteristics, strain ERD01G(T) differed from the most closely related species S. alactolyticus, Streptococcus gordonii, Streptococcus intermedius and Streptococcus sanguinis. Thus, based on genotypic and phenotypic evidence, we propose that the isolate belongs to a novel bacterial taxon within the genus Streptococcus, for which the name Streptococcus danieliae is proposed. The type strain is ERD01G(T) (= DSM 22233(T) = CCUG 57647(T)).

  1. Isolation and characterization of the dcw cluster from the piezophilic deep-sea bacterium Shewanella violacea.

    PubMed

    Ishii, Akihiro; Nakasone, Kaoru; Sato, Takako; Wachi, Masaaki; Sugai, Motoyuki; Nagai, Kazuo; Kato, Chiaki

    2002-08-01

    The dcw cluster of genes involved in cell division and cell wall synthesis from the piezophilic deep-sea bacterium Shewanella violacea was isolated and characterized. It comprises 15 open reading frames, of which the organization is mraZ-mraW-ftsL-ftsI-murE-murF-mraY-murD-ftsW-murG-murC-ftsQ-ftsA-ftsZ-envA, in that order. To analyze transcription upstream from the ftsZ gene, Northern blot and primer extension analyses were performed. The results showed that gene expression is not pressure dependent. Western blot analysis showed that the FtsZ protein is equally expressed under several pressure conditions in the range of atmospheric (0.1 MPa) to high (50 MPa) pressures. Using immunofluorescence microscopy, the FtsZ ring was observed in the center of cells at pressure conditions of 0.1 to 50 MPa. These results imply that the FtsZ protein function is not affected by elevated pressure in this piezophilic bacterium.

  2. 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).

  3. 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

  4. 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

  5. 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

  6. 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.

  7. Utilization of Phenylpropanoids by Newly Isolated Bacterium Pseudomonas sp. TRMK1.

    PubMed

    T R, Monisha; I, Mukram; B, Kirankumar; Reddy, Pooja V; Nayak, Anand S; Karegoudar, T B

    2017-01-25

    A bacterium Pseudomonas sp. TRMK1 capable of utilizing various phenylpropanoids was isolated from agro-industrial waste by enrichment culture technique. It is gram-negative, motile, aerobic, and able to utilize three different phenolic acids such as p-coumaric, ferulic, and caffeic acids at concentrations of 5, 10, and 15 mM in 18 h of incubation. The residual concentration of phenolic acids was analyzed by HPLC. The catabolic pathway of p-coumaric, ferulic, and caffeic acids is suggested based on the characterization of metabolic intermediates by GC, GC-HRMS, and different enzymatic assays. Further, Pseudomonas sp. TRMK1 utilizes a wide range of mixture of phenolic acids present in the synthetic effluent.

  8. Legionnaires' disease: isolation of a bacterium and demonstration of its role in other respiratory disease.

    PubMed

    McDade, J E; Shepard, C C; Fraser, D W; Tsai, T R; Redus, M A; Dowdle, W R

    1977-12-01

    To identify the etiologic agent of Legionnaire's disease, we examined patients' serum and tissue specimens in a search for toxins, bacteria, fungi, chlamydiae, rickettsiae and viruses. From the lungs of four of six patients we isolated a gram-negative, non-acid-fast bacillus in guinea pigs. The bacillus could be transferred to yolk sacs of embryonated eggs. Classification of this organism is incomplete. We used yolk-sac cultures of the bacillus as antigen to survey suspected serum specimens, employing antihuman-globulin fluorescent antibody. When compared to controls, specimens from 101 to 111 patients meeting clinical criteria of Legionnaires' disease showed diagnostic increases in antibody titers. Diagnostic increases were also found in 54 recent sporadic cases of severe pneumonia and, retrospectively, in stored serum from most patients in two other previously unsolved outbreaks of respiratory disease. We conclude that Legionnaires' disease is caused by a gram-negative bacterium that may be responsible for widespread infection.

  9. [Isolation and characteristic of a moderately halophilic bacterium accumulated ectoine as main compatible solute].

    PubMed

    He, Jian; Wang, Ting; Sun, Ji-Quan; Gu, Li-Feng; Li, Shun-Peng

    2005-12-01

    A moderately halophilic bacterium(designated strain I15) was isolated from lawn soil. Based on the analysis of 16S rDNA (GenBank accession number DQ010162), morphology, physiological and biochemical characteristics, strain I15 was identified as Virgibacillus marismortuii. This strain was capable of growing under 0% approximately 25% NaCl, and exhibited an optimum NaCl concentration of 10% and an optimum temperature of 30 degrees C and an optimum pH of 7.5 - 8.0 for its growth, respectively. Under hyperosmotic stress, strain 115 accumulated ectoine as the main compatible solute. Under 15% NaCl conditions the intracellar ectoine can reach to 1.608 mmol/(g x cdw), accounted for 89.6% of the total compatible solutes. The biosynthesis of ectoine was under the control of osmotic, and the accumulated ectoine synthesized intraceilularly can released under hypoosmotic shocks and resynthesis under hyperosmotic shock rapidly.

  10. A novel and mild isolation procedure of chlorosomes from the green sulfur bacterium Chlorobaculum tepidum.

    PubMed

    Tokita, Seiji; Shimada, Keizo; Watabe, Kazuyuki; Matsuura, Katsumi; Mimuro, Mamoru

    2011-09-01

    In this article, we developed a new and mild procedure for the isolation of chlorosomes from a green sulfur bacterium Chlorobaculum tepidum. In this procedure, Fenna-Matthews-Olson (FMO) protein was released by long cold treatment (6°C) of cells under the presence of a chaotrope (2 M NaSCN) and 0.6 M sucrose. Chlorosomes were released by an osmotic shock of the cold-treated cells after the formation of spheroplasts without mechanical disruption. Chlorosomes were finally purified by a sucrose step-wise density gradient centrifugation. We obtained two samples with different density (20 and 23% sucrose band, respectively) and compared them by SDS-PAGE, absorption spectroscopy at 80 K, fluorescence and CD spectroscopy at room temperature. Cells whose absorption maximum was longer than 750 nm yielded higher amount of the 20% sucrose fraction than those having an absorption maximum shorter than 750 nm.

  11. Psychrobacter fjordensis sp. nov., a psychrotolerant bacterium isolated from an Arctic fjord in Svalbard.

    PubMed

    Zeng, Yin-Xin; Yu, Yong; Li, Hui-Rong; Luo, Wei

    2015-12-01

    A Gram-negative, non-motile, non-spore-forming, psychrotolerant and halotolerant bacterium designated BSw21516B(T), was obtained from seawater in Kongsfjorden, a glacial fjord in the Arctic Svalbard and subjected to taxonomic analysis using a polyphasic approach. This bacterium was observed to optimally grow at 25-29 °C; between at 4 and 34 °C, but not at >35 °C; and in the presence of 0-8 % (w/v) NaCl at an optimum concentration of 2-5 % (w/v) NaCl. Strain BSw21516B(T) was found to contain Ubiquinone-8 (Q-8) as a predominant respiratory lipoquinone and C18:1 ω9c and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) as predominant cellular fatty acids. Phylogenetic analysis of 16S rRNA and gyrB gene sequences showed that this isolate belongs to the genus Psychrobacter and is closely related to Psychrobacter fozii LMG 21280(T), which was isolated from a sediment sample in Antarctica. DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 58.6 %) between strain BSw21516B(T) and its closest relatives. Based on these results a new species Psychrobacter fjordensis sp. nov. is proposed (type strain BSw21516B(T) = KCTC 42279(T) = CCTCC AB 2014020(T)).

  12. 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)).

  13. Structure and organization of a 25 kbp region of the genome of the photosynthetic green sulfur bacterium Chlorobium vibrioforme containing Mg-chelatase encoding genes.

    PubMed

    Petersen, B L; Møller, M G; Stummann, B M; Henningsen, K W

    1998-01-01

    A region comprising approximately 25 kbp of the genome of the strictly anaerobic and obligate photosynthetic green sulfur bacterium Chlorobium vibrioforme has been mapped, subcloned and partly sequenced. Approximately 15 kbp have been sequenced in it's entirety and three genes with significant homology and feature similarity to the bchI, -D and -H genes and the chlI, -D and -H genes of Rhodobacter and Synechocystis strain PCC6803, respectively, which encode magnesium chelatase subunits, have been identified. Magnesium chelatase catalyzes the insertion of Mg2+ into protoporphyrin IX, and is the first enzyme unique to the (bacterio)chlorophyll specific branch of the porphyrin biosynthetic pathway. The organization of the three Mg-chelatase encoding genes is unique to Chlorobium and suggests that the magnesium chelatase of C. vibrioforme is encoded by a single operon. The analyzed 25 kbp region contains five additional open reading frames, two of which display significant homology and feature similarity to genes encoding lipoamide dehydrogenase and genes with function in purine synthesis, and another three display significant homology to open reading frames with unknown function in distantly related bacteria. Putative E. coli sigma 70-like promoter sequences, ribosome binding sequences and rho-independent transcriptional stop signals within the sequenced 15 kbp region are related to the identified genes and orfs. Southern analysis, restriction mapping and partial sequencing of the remaining ca. 10 kbp of the analyzed 25 kbp region have shown that this part includes the hemA, -C, -D and -B genes (MOBERG and AVISSAR 1994), which encode enzymes with function in the early part of the biosynthetic pathway of porphyrins.

  14. A heterogeneous tag-attachment to the homodimeric type 1 photosynthetic reaction center core protein in the green sulfur bacterium Chlorobaculum tepidum.

    PubMed

    Azai, Chihiro; Kim, Kwang; Kondo, Toru; Harada, Jiro; Itoh, Shigeru; Oh-oka, Hirozo

    2011-07-01

    The 6xHis-tag-pscA gene, which was genetically engineered to express N-terminally histidine (His)-tagged PscA, was inserted into a coding region of the recA gene in the green sulfur bacterium Chlorobaculum tepidum (C. tepidum). Although the inactivation of the recA gene strongly suppressed a homologous recombination in C. tepidum genomic DNA, the mutant grew well under normal photosynthetic conditions. The His-tagged reaction center (RC) complex could be obtained simply by Ni(2+)-affinity chromatography after detergent solubilization of chlorosome-containing membranes. The complex consisted of three subunits, PscA, PscB, and PscC, in addition to the Fenna-Matthews-Olson protein, but there was no PscD. Low-temperature EPR spectroscopic studies in combination with transient absorption measurements indicated that the complex contained all intrinsic electron transfer cofactors as detected in the wild-type strain. Furthermore, the LC/MS/MS analysis revealed that the core protein consisted of a mixture of a His-/His-tagged PscA homodimer and a non-/His-tagged PscA heterodimer. The development of the pscA gene duplication method presented here, thus, enables not only a quick and large-scale preparation of the RC complex from C. tepidum but also site-directed mutagenesis experiments on the artificially incorporated 6xHis-tag-pscA gene itself, since the expression of the authentic PscA/PscA homodimeric RC complex could complement any defect in mutated His-tagged PscA. This method would provide an invaluable tool for structural and functional analyses of the homodimeric type 1 RC complex.

  15. Isolation of a Campylobacter lanienae-like bacterium from laboratory chinchillas (Chinchilla laniger).

    PubMed

    Turowski, E E; Shen, Z; Ducore, R M; Parry, N M A; Kirega, A; Dewhirst, F E; Fox, J G

    2014-12-01

    Routine necropsies of 27 asymptomatic juvenile chinchillas revealed a high prevalence of gastric ulcers with microscopic lymphoplasmacytic gastroenteritis and typhlocolitis. Polymerase chain reaction (PCR) analysis using Campylobacter genus-specific partial 16S rRNA primers revealed the presence of Campylobacter spp. DNA in the faeces of 12 of 27 animals (44.4%). Species-specific partial 16S rRNA PCR and sequencing confirmed that these animals were colonized with Campylobacter lanienae, a gram-negative, microaerophilic bacterium that was first identified on routine faecal screening of slaughterhouse employees and subsequently isolated from faeces of livestock. Campylobacter lanienae was isolated from the faeces of six PCR-positive animals and identified with species-specific PCR and full 16S rRNA sequencing. Phylogenetic analysis showed that these isolates clustered with C. lanienae strain NCTC 13004. PCR analysis of DNA extracted from gastrointestinal tissues revealed the presence of C. lanienae DNA in the caecum and colon of these chinchillas. Gastrointestinal lesions were scored and compared between C. lanienae-positive and C. lanienae-negative animals. There was no correlation between colonization status and lesion severity in the stomach, liver, duodenum, or colon. Possible routes of C. lanienae infection in chinchillas could include waterborne transmission and faecal-oral transmission from wild mice and rats or livestock. Based on these findings, the authors conclude that C. lanienae colonizes the lower bowel of chinchillas in the absence of clinical disease. This is the first report of C. lanienae in any rodent species. Campylobacter lanienae isolates from different mammalian species demonstrate heterogeneity by 16S rRNA sequence comparison. Analysis using rpoB suggests that isolates and clones currently identified as C. lanienae may represent multiple species or subspecies.

  16. Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea

    PubMed Central

    Lafi, Feras F.; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.

    2017-01-01

    ABSTRACT Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth–promoting activity and environmental adaption. PMID:28209831

  17. Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil

    PubMed Central

    Kozlowski, Jessica A.; Kits, K. Dimitri

    2016-01-01

    The complete genome sequence of Nitrosomonas communis strain Nm2, a mesophilic betaproteobacterial ammonia oxidizer isolated from Mediterranean soils in Corfu, Greece, is reported here. This is the first genome to describe a cluster 8 Nitrosomonas species and represents an ammonia-oxidizing bacterium commonly found in terrestrial ecosystems. PMID:26769932

  18. Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Stein, Lisa Y; Kozlowski, Jessica; Bollmann, Annette; Klotz, Martin G; Sayavedra-Soto, Luis; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Varghese, Neha; Mikhailova, Natalia; Palaniappan, Krishna; Ivanova, Natalia; Mukherjee, Supratim; Reddy, T B K; Yee Ngan, Chew; Daum, Chris; Kyrpides, Nikos; Woyke, Tanja

    2017-03-16

    Nitrosomonas cryotolerans ATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2 fixation were identified.

  19. Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L.

    PubMed Central

    Hollensteiner, Jacqueline; Granzow, Sandra; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

    2017-01-01

    ABSTRACT Pseudomonas putida GM4FR is an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Functional annotation of the draft genome (7.1 Mb) revealed 6,272 predicted protein-encoding genes. The genome provides insights into the biocontrol and plant growth-promoting potential of P. putida GM4FR. PMID:28360162

  20. 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

  1. 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.

  2. Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost

    PubMed Central

    Tsujimoto, Yoshiyuki; Saito, Ryo; Sahara, Takehiko; Kimura, Nobutada; Tsuruoka, Naoki; Shigeri, Yasushi

    2017-01-01

    ABSTRACT Caenibacillus caldisaponilyticus B157T (= NBRC 111400T = DSM 101100T), in the family Sporolactobacillaceae, was isolated from acidulocompost as a thermophilic and phospholipid-degrading bacterium. Here, we report the 3.36-Mb draft genome sequence, with a G+C content of 51.8%, to provide the genetic information coding for phospholipases. PMID:28360164

  3. Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters

    PubMed Central

    Rice, Marlen C.; Stein, Lisa Y.; Kozlowski, Jessica; Bollmann, Annette; Sayavedra-Soto, Luis; Shapiro, Nicole; Goodwin, Lynne A.; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Varghese, Neha; Mikhailova, Natalia; Palaniappan, Krishna; Ivanova, Natalia; Mukherjee, Supratim; Reddy, T. B. K.; Yee Ngan, Chew; Daum, Chris; Kyrpides, Nikos; Woyke, Tanja

    2017-01-01

    ABSTRACT Nitrosomonas cryotolerans ATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2 fixation were identified. PMID:28302769

  4. 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.

  5. 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.

  6. 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).

  7. Luteimonas padinae sp. nov., an epiphytic bacterium isolated from an intertidal macroalga.

    PubMed

    Verma, Ashish; Ojha, Anup Kumar; Kumari, Parveen; Sundharam, Shiva S; Mayilraj, Shanmugam; Krishnamurthi, Srinivasan

    2016-12-01

    A Gram-stain-negative, rod-shaped bacterium, forming yellow colonies and designated CDR SL 15T, was isolated from the surface of Padina sp., a brown macroalga, which grows in the Western coastal regions of the state of Goa, India. The 16S rRNA gene sequence phylogeny placed the strain in the genus Luteimonas and it showed closest sequence similarity to Luteimonas terricola BZ92rT (97.6 %) and <97.0 % to other species of the genus Luteimonas. Chemotaxonomic features, such as having iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl/iso-C17 : 1ω9c) as the major fatty acids and Q-8 as the only ubiquinone further supported its placement within this genus. There were some critical differences in phenotypic properties between Luteimonas padinae sp. nov. CDR SL 15T and L. terricola DSM 22344T i.e. temperature range for growth and salinity range and optimum for growth (L. terricola is a psychrotolerant bacterium with a lower optimum temperature for growth), acid production and assimilation of substrates, enzyme activities and resistance to certain antibiotics. The DNA-DNA relatedness value of the novel strain with its closest phylogenetic relative was only 40 %, below the 70 % threshold value recommended for species delineation. All these characteristics are consistent with strain CDR SL 15T representing a novel species of the genus Luteimonas, for which the name Luteimonas padinae sp. nov. is proposed. The type strain is CDR SL 15T (=DSM 101536T=KCTC 52403T).

  8. Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

    PubMed

    Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

    2015-09-01

    A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

  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. Identification of a new microcystin-degrading bacterium isolated from Lake Chaohu, China.

    PubMed

    Zhang, Jian; Shi, Hui; Liu, Aimin; Cao, Zhengyu; Hao, Jiasheng; Gong, Renmin

    2015-05-01

    A microcystin-LR (MC-LR)-degrading bacterium was isolated from Lake Chaohu, a eutrophic freshwater lake containing toxic cyanobacterial blooms. Based on the analysis of 16S rDNA gene sequence and physiobiochemical characteristics, the isolated strain, most likely belongs to the genus Bacillus with the highest sequence similarity value with Bacillus nanhaiencis strain K-W39 (JQ799091.1), was named B. nanhaiencis strain JZ-2013. The strain JZ-2013 could grow on mineral salt medium supplied with MC-LR as sole carbon and nitrogen sources. The optimal temperature and pH for strain JZ-2013 growth and MC-LR biodegradation were 30°C and 8.0, respectively. The MC-LR with the initial concentration of 15 mg/L could be consumed 80 % by strain JZ-2013 within 9 days. The existence of exogenous carbon and nitrogen sources could significantly increase the removal efficiency of MC-LR. The strain JZ-2013 can efficiently removed MC-LR of low concentration in real water sample.

  11. Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater.

    PubMed

    Zhu, Lang; Liu, Qing; Liu, Hongcan; Zhang, Jianli; Dong, Xiuzhu; Zhou, Yuguang; Xin, Yuhua

    2013-06-01

    A non-motile, Gram-stain-negative bacterium, designated R-HLS-17(T), was isolated from the meltwater of Hailuogou Glacier located in Sichuan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Flavobacterium, with the closest relatives being Flavobacterium antarcticum JCM 12383(T) (95.5% 16S rRNA gene sequence similarity), F. omnivorum JCM 11313(T) (95.0%) and F. fryxellicola LMG 22022(T) (95.2%). Growth occurred at 0-29 °C (optimum, 10-20 °C) and pH 6.0-8.5 (optimum, 7.0-8.0). The DNA G+C content was 46.5 mol%. The major cellular fatty acids were iso-C15:0, iso-C15:1 G, summed feature 9 (comprising iso-C17:1ω9c and/or 10-methyl C16:0), iso-C17:0 3-OH and iso-C15:0 3-OH. The predominant menaquinone was MK-6. Based on the genotypic and phenotypic characteristics, we propose that strain R-HLS-17(T) represents a novel species of the genus Flavobacterium, Flavobacterium noncentrifugens sp. nov. The type strain is R-HLS-17(T) (=CGMCC 1.10076(T)=NBRC 108844(T)).

  12. Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.

    PubMed

    Miwa, Hiroki; Ahmed, Iftikhar; Yoon, Jaewoo; Yokota, Akira; Fujiwara, Toru

    2008-01-01

    A non-spore-forming, Gram-negative, motile, rod-shaped, boron-accumulating bacterium isolated from soil was characterized by polyphasic taxonomy. The strain, designated BAM-48(T), was positive for catalase and oxidase activities and grew at 4-37 degrees C, 0-1% NaCl and pH 5-9. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate BAM-48(T) was closely related to Variovorax paradoxus IAM 12373(T) (99.3% sequence similarity), Variovorax soli GH9-3(T) (98.3%) and Variovorax dokdonensis DS-43(T) (97.0%). DNA-DNA hybridization values between strain BAM-48(T) and V. paradoxus NBRC 15149(T), V. soli KACC 11579(T) and V. dokdonensis KCTC 12544(T) were only 49.1, 25.4 and 24.6%, respectively. The major respiratory quinone was ubiquinone 8 (Q-8). The DNA G+C content was 71.2 mol%. Strain BAM-48(T) contained C(16:0) (36.1%), C(16:1)omega7c (21.4%) and C(17:0) cyclo (19.0%) as the major fatty acids. Based on phenotypic, chemotaxonomic and phylogenetic data, strain BAM-48(T) should be classified as a member of a novel species in the genus Variovorax, for which the name Variovorax boronicumulans sp. nov. is proposed. The type strain is BAM-48(T) (=NBRC 103145(T) =KCTC 22010(T)).

  13. Haloimpatiens lingqiaonensis gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater.

    PubMed

    Wu, Dildar; Zhang, Nai-Fang; Sun, Cong; Zhang, Wen-Wu; Han, Shuai-Bo; Pan, Jie; Wu, Min; Th, Dilbar; Zhu, Xu-Fen

    2015-11-11

    An anaerobic bacterium, strain ZC-CMC3T, was isolated from a wastewater sample in Zhejiang, China. Cells were Gram-positive, peritrichous, non-spore-forming and rod-shaped (0.6-1.2 × 2.9-5.1 μm). Strain ZC-CMC3T was able to grow at 25-48 °C (optimum 43 °C), and pH 5.5-8.0 (optimum pH 7.0). NaCl concentration range of growth was 0-3 % (w/v) with the optimum 0 %. Catalase- and Oxidase- negative. The major polar lipids of the isolate were diphosphatidylglycerol, phosphatidylglycerol, several phospholipids and glycolipids. Main fermentation products from PYG medium were formate, acetate, lactate and ethanol. Substrates which could be utilized were peptone, tryptone, yeast extract and beef extract. No respiratory quinone was detected. The mainly fatty acids were C14:0, C16:0, C16:1 cis 7 and C16:1 cis 9. The DNA G+C content was 30.0 mol%. The 16S rRNA gene sequence analysis revealed that the isolate belonged to the family Clostridiaceae. The most closely phylogenetic related species was Oceanirhabdus sediminicola NH-JN4T (with 92.8 % sequence similarity) and Clostridium tepidiprofundi SG 508T (with 92.6 % sequence similarity). On the basis of phylogenetic, chemotaxonomic and phenotypic characteristics, we propose that strain ZC-CMC3T as a novel species of a novel genus in the family Clostridiaceae, for which the name Haloimpatiens lingqiaonensis gen. nov., sp. nov. is proposed. The type strain of type species is ZC-CMC3T (KCTC 15321T = JCM 19210T= CCTCC AB 2013104T).

  14. Fibrinolytic enzyme from newly isolated marine bacterium Bacillus subtilis ICTF-1: media optimization, purification and characterization.

    PubMed

    Mahajan, Prafulla M; Nayak, Shubhada; Lele, Smita S

    2012-03-01

    Fibrinolytic enzymes are important in treatment of cardiovascular diseases. The present work reports isolation, screening and identification of marine cultures for production of fibrinolytic enzymes. A potent fibrinolytic enzyme-producing bacterium was isolated from marine niches and identified as Bacillus subtilis ICTF-1 on the basis of the 16S rRNA gene sequencing and biochemical properties. Further, media optimization using L(18)-orthogonal array method resulted in enhanced production of fibrinolytic enzyme (8814 U/mL) which was 2.6 fold higher than in unoptimized medium (3420 U/mL). In vitro assays revealed that the enzyme could catalyze blood clot lysis effectively, indicating that this enzyme could be a useful thrombolytic agent. A fibrinolytic enzyme was purified from the culture supernatant to homogeneity by three step procedures with a 34.42-fold increase in specific activity and 7.5% recovery. This purified fibrinolytic enzyme had molecular mass of 28 kDa, optimal temperature and pH at 50 °C and 9, respectively. It was stable at pH 5.0-11.0 and temperature of 25-37 °C. The enzyme activity was activated by Ca(2+) and obviously inhibited by Zn(2+), Fe(3)(+), Hg(2+) and PMSF. The purified fibrinolytic enzyme showed high stability towards various surfactants and was relatively stable towards oxidizing agent. Considering these properties purified fibrinolytic enzyme also finds potential application in laundry detergents in addition to thrombolytic agent. The gene encoding fibrinolytic enzyme was isolated and its DNA sequence was determined. Compared the full DNA sequence with those in NCBI, it was considered to be a subtilisin like serine-protease.

  15. Thiobaca trueperi gen. nov., sp. nov., a phototrophic purple sulfur bacterium isolated from freshwater lake sediment.

    PubMed

    Rees, Gavin N; Harfoot, Christopher G; Janssen, Peter H; Schoenborn, Liesbeth; Kuever, Jan; Lünsdorf, Heinrich

    2002-03-01

    Two strains of a novel species of phototrophic micro-organism were isolated from the sediments of a shallow, freshwater, eutrophic lake. Both strains grew photolithoheterotrophically with sulfide as an electron donor, transiently accumulating intracellular sulfur globules. Photolithoautotrophic growth was not observed. One strain was designated BCH(T) (the type strain) and was studied in most detail. Cells contained bacteriochlorophyll a, and the dominant carotenoid was lycopene. Cell suspensions were brown. The photosynthetic membranes had a vesicular arrangement. Acetate, propionate, pyruvate, succinate and fumarate were each used as electron donors and carbon sources in the presence of sulfide and bicarbonate. In the presence of light, growth did not occur with hydrogen, thiosulfate or iron(II). The optimum temperature for growth was between 25 and 30 degrees C, the maximum being 36 degrees C. The G+C content of the genomic DNA of strain BCH(T) was 63 mol%. Analysis of the 16S RNA genes showed that both strains belonged to the gamma-subclass of the Proteobacteria but were phylogenetically distinct from any described phototrophic organisms within the Chromatiaceae. On the basis of phylogenetic and physiological differences from other phototrophic microorganisms, strain BCH(T) is described as a novel species of a new genus, Thiobaca trueperi gen. nov., sp. nov.

  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. Aurantibacter crassamenti gen. nov., sp. nov., a bacterium isolated from marine sediment.

    PubMed

    Yoon, Jaewoo; Kasai, Hiroaki

    2017-01-01

    A Gram-stain-negative, strictly aerobic, orange-colored, rod-shaped, chemoheterotrophic bacterium, designated HG732(T), was isolated from marine sediment in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (94.1 %) sequence similarity with Kriegella aquimaris KMM 3665(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. Major fatty acids of strain HG732(T) were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, three unidentidied aminolipids and two unidentified lipids. The DNA G+C content of the strain was determined to be 35.2 mol%, and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Aurantibacter crassamenti gen. nov., sp. nov. is proposed. The type strain of A. crassamenti gen. nov., sp. nov. is HG732(T) (= KCTC 52207(T) = NBRC 112211(T)).

  18. Marinomonas arctica sp. nov., a psychrotolerant bacterium isolated from the Arctic.

    PubMed

    Zhang, De-Chao; Li, Hui-Rong; Xin, Yu-Hua; Liu, Hong-Can; Chen, Bo; Chi, Zhen-Ming; Zhou, Pei-Jin; Yu, Yong

    2008-07-01

    A novel psychrotolerant, Gram-negative, motile bacterium, designated strain 328(T), was isolated from sea-ice samples collected off the Canadian Basin of the Arctic Ocean (7 degrees 23' 14'' N 14 degrees 06' 55'' W). Strain 328(T) was able to grow at 0-37 degrees C, with optimum growth at 25-27 degrees C. It possessed phosphatidylethanolamine and phosphatidylglycerol as major phospholipids and C(10 : 0) 3-OH (31.78 %), C(18 : 1)omega7c (27.50 %) and iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (19.22 %) as predominant cellular fatty acids. The DNA G+C content of strain 328(T) was 45.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 328(T) was a member of the genus Marinomonas (92.7-96.0 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain 328(T) was considered to represent a novel species of the genus Marinomonas. The name Marinomonas arctica sp. nov. is proposed, with strain 328(T) (=CGMCC 1.6498(T)=JCM 14976(T)) as the type strain.

  19. Sporosarcina antarctica sp. nov., a psychrophilic bacterium isolated from the Antarctic.

    PubMed

    Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Chen, Bo; Sheng, Jun; Chi, Zhen-Ming; Zhou, Pei-Jin; Zhang, De-Chao

    2008-09-01

    A Gram-positive, psychrophilic, rod-shaped bacterium, designated strain N-05(T), was isolated from soil samples collected off King George Island, west Antarctica (6 degrees 13' 31'' S 5 degrees 57' 08'' W). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N-05(T) was related to members of the genus Sporosarcina and had highest 16S rRNA gene sequence similarity with the type strain of Sporosarcina macmurdoensis (98.0%). The temperature range for growth of strain N-05(T) was 0-23 degrees C, with optimum growth occurring at 17-18 degrees C and approximately pH 6.0-8.0. Strain N-05(T) had MK-7 as the major menaquinone and anteiso-C(15:0) and C(16:1)omega7c alcohol as major fatty acids. The genomic DNA G+C content was 39.2 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain N-05(T) is considered to represent a novel species of the genus Sporosarcina, for which the name Sporosarcina antarctica is proposed. The type strain is N-05(T) (=CGMCC 1.6503(T)=JCM 14646(T)).

  20. 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)).

  1. A serine hydroxymethyltransferase from marine bacterium Shewanella algae: Isolation, purification, characterization and l-serine production.

    PubMed

    Jiang, Wei; Xia, Bingzhao; Liu, Ziduo

    2013-10-01

    Currently, l-serine is mainly produced by enzymatic conversion, in which serine hydroxymethyltransferase (SHMT) is the key enzyme, suggesting the importance of searching for a SHMT with high activity. Shewanella algae, a methanol-utilizing marine bacterium showing high SHMT activity, was selected based on screening bacterial strains and comparison of the activities of SHMTs. A glyA was isolated from the S. algae through thermal asymmetric interlaced PCR (TAIL-PCR) and it encoded a 417 amino acid polypeptide. The SaSHMT, encoded by the glyA, showed the optimal activity at 50°C and pH 7.0, and retained over 45% of its maximal activity after incubation at 40°C for 3h. The enzyme showed better stability under alkaline environment (pH 6.5-9.0) than Hyphomicrobium methylovorum GM2's SHMT (pH 6.0-7.5). The SaSHMT can produce 77.76mM of l-serine by enzymatic conversion, with the molecular conversion rate in catalyzing glycine to l-serine being 1.41-fold higher than that of Escherichia coli. Therefore, the SaSHMT has the potential for industrial applications due to its tolerance of alkaline environment and a relatively high enzymatic conversion rate.

  2. Sequential production of amylolytic and lipolytic enzymes by bacterium strain isolated from petroleum contaminated soil.

    PubMed

    Carvalho, Nayara Bezerra; de Souza, Ranyere Lucena; de Castro, Heizir F; Zanin, Gisella M; Lima, Alvaro Silva; Soares, Cleide M F

    2008-07-01

    Amylases and lipases are highly demanded industrial enzymes in various sectors such as food, pharmaceuticals, textiles, and detergents. Amylases are of ubiquitous occurrence and hold the maximum market share of enzyme sales. Lipases are the most versatile biocatalyst and bring about a range of bioconversion reactions such as hydrolysis, inter-esterification, esterification, alcoholysis, acidolysis, and aminolysis. The objective of this work was to study the feasibility for amylolitic and lipolytic production using a bacterium strain isolated from petroleum contaminated soil in the same submerged fermentation. This was a sequential process based on starch and vegetable oils feedstocks. Run were performed in batchwise using 2% starch supplemented with suitable nutrients and different vegetable oils as a lipase inducers. Fermentation conditions were pH 5.0; 30 degrees C, and stirred speed (200 rpm). Maxima activities for amyloglucosidase and lipase were, respectively, 0.18 and 1,150 U/ml. These results showed a promising methodology to obtain both enzymes using industrial waste resources containing vegetable oils.

  3. 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).

  4. 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.

  5. Enterobacter siamensis sp. nov., a transglutaminase-producing bacterium isolated from seafood processing wastewater in Thailand.

    PubMed

    Khunthongpan, Suwannee; Bourneow, Chaiwut; H-Kittikun, Aran; Tanasupawat, Somboon; Benjakul, Soottawat; Sumpavapol, Punnanee

    2013-01-01

    A novel strain of Enterobacter, C2361(T), a Gram-negative, non-spore-forming, rod-shaped and facultative anaerobic bacterium with the capability to produce transglutaminase, was isolated from seafood processing wastewater collected from a treatment pond of a seafood factory in Songkhla Province, Thailand. Phylogenetic analyses and phenotypic characteristics, including chemotaxonomic characteristics, showed that the strain was a member of the genus Enterobacter. The 16S rRNA gene sequence similarities between strain C2361(T) and Enterobacter cloacae subsp. cloacae ATCC 13047(T) and Enterobacter cloacae subsp. dissolvens LMG 2683(T) were 97.5 and 97.5%, respectively. Strain C2361(T) showed a low DNA-DNA relatedness with the above-mentioned species. The major fatty acids were C16:0, C17:0cyclo and C14:0. The DNA G+C content was 53.0 mol%. On the basis of the polyphasic evidence gathered in this study, it should be classified as a novel species of the genus Enterobacter for which the name Enterobacter siamensis sp. nov. is proposed. The type strain is C2361(T) (= KCTC 23282(T) = NBRC 107138(T)).

  6. Isolation and characterization of comprehensive polychlorinated biphenyl degrading bacterium, Enterobacter sp. LY402.

    PubMed

    Jia, Ling-Yun; Zheng, Ai-Ping; Xu, Li; Huang, Xiao-Dong; Zhang, Qing; Yang, Feng-Lin

    2008-05-01

    A Gram-negative bacterium, named LY402, was isolated from contaminated soil. 16S rDNA sequencing and measurement of the physiological and biochemical characteristics identified it as belonging to the genus Enterobacter. Degradation experiments showed that LY402 had the ability to aerobically transform 79 of the 91 major congeners of Aroclor 1242, 1254, and 1260. However, more interestingly, the strain readily degraded certain highly chlorinated and recalcitrant polychlorinated biphenyls (PCBs). Almost all the tri- and tetra-chlorobiphenyls (CBs), except for 3,4,3',4'-CB, were degraded in 3 days, whereas 73% of 3,4,3',4'-, 92% of the penta-, 76% of the hexa-, and 37% of the hepta-CBs were transformed after 6 days. In addition, among 12 octa-CBs, 2,2',3,3',5,5',6,6- CB was obviously degraded, and 2,2',3,3',4,5,6,6'- and 2,2',3,3',4,5,5',6'-CB were slightly transformed. In a metabolite analysis, mono- and di-chlorobenzoic acids (CBAs) were identified, and parts of them were also transformed by strain LY402. Analysis of PCB degradation indicated that strain LY402 could effectively degrade PCB congeners with chlorine substitutions in both ortho- and para-positions. Consequently, this is the first report of an Enterobacteria that can efficiently degrade both low and highly chlorinated PCBs under aerobic conditions.

  7. Asticcacaulis taihuensis sp. nov., a novel stalked bacterium isolated from Taihu Lake, China.

    PubMed

    Liu, Zhi-Pei; Wang, Bao-Jun; Liu, Shuang-Jiang; Liu, Ying-Hao

    2005-05-01

    A novel stalked bacterium, designated strain T3-B7(T), was isolated from sediment of Taihu Lake, Jiangsu Province, China, and its taxonomy was studied by using a polyphasic approach. Cell morphology, physiological and biochemical properties, and polar lipids indicated that strain T3-B7(T) represented a member of the genus Asticcacaulis. Based on 16S rRNA gene sequence similarity analysis, strain T3-B7(T) was found to be phylogenetically related to Asticcacaulis biprosthecium DSM 4723(T) (98.5 %) and Asticcacaulis excentricus DSM 4724(T) (95.0 %), but could be differentiated from these two species on the basis of the number and position of prosthecae, assimilation of sugars, nitrate reduction and tolerance to NaCl. Levels of DNA-DNA relatedness of strain T3-B7(T) to A. biprosthecium DSM 4723(T) and A. excentricus DSM 4724(T) were 37.1 and 18.0 %, respectively. The G + C content of strain T3-B7(T) was 59 mol% (T(m)). It is concluded that strain T3-B7(T) represents a novel species of the genus Asticcacaulis, for which the name of Asticcacaulis taihuensis sp. nov. is proposed. The type strain is T3-B7(T) (=AS 1.3431(T) = JCM 12463(T)).

  8. Paenibacillus puernese sp. nov., a β-glucosidase-producing bacterium isolated from Pu'er tea.

    PubMed

    Wang, Dan-Dan; Kim, Yeon-Ju; Hoang, Van-An; Nguyen, Ngoc-Lan; Singh, Priyanka; Wang, Chao; Chun-Yang, Deok

    2016-04-01

    A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)).

  9. Brassicibacter thermophilus sp. nov., a thermophilic bacterium isolated from coastal sediment.

    PubMed

    Wang, Bing; Ji, Shi-Qi; Tian, Xin-Xin; Qu, Ling-Yun; Li, Fu-Li

    2015-09-01

    A novel thermophilic, obligately anaerobic bacterium, strain Cel2f(T), was isolated from a cellulolytic community enriched from coastal marine sediment. Cells were Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Optimal growth temperature and pH of strain Cel2f(T) were 55 °C and pH 7.0, respectively. NaCl was essential for the growth of strain Cel2f(T) and the strain showed enhanced growth in the presence of sea salt; the optimum sea salt concentration for growth was 7% (w/v). Thiosulfate, sulfate and sulfite were potential electron acceptors. The major fatty acids of strain Cel2f(T) were iso-C15 : 0, C16 : 0, and C18 : 0. Polar lipid analysis indicated the presence of phosphatidylethanolamine and phosphatidylglycerol. Strain Cel2f(T) contained menaquinone MK-7 as the isoprenoid quinone, and the DNA G+C content was 31.3 mol%. Phylogenetic analysis revealed that the nearest relative of strain Cel2f(T) was Brassicibacter mesophilus BM(T) with 93.8% 16S rRNA gene sequence similarity. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain Cel2f(T) represents a novel species of genus Brassicibacter, for which the name Brassicibacter thermophilus sp. nov. is proposed. The type strain is Cel2f(T) ( = JCM 30480(T) = CGMCC 1.5200(T)).

  10. Arthrobacter nitrophenolicus sp. nov. a new 2-chloro-4-nitrophenol degrading bacterium isolated from contaminated soil.

    PubMed

    Arora, Pankaj Kumar; Jain, Rakesh Kumar

    2013-02-01

    Strain SJCon(T), a 2-chloro-4-nitrophenol (2C4NP) degrading bacterium, was isolated from soil collected from a pesticide-contaminated site in Punjab, India. The strain, which stained Gram positive, displayed a rod-coccus life cycle, and possessed a type A3α peptidoglycan (L-Lys-L-Ala3), MK-9(H2) as the major menaquinone, anteiso-C15 and iso-C15:0 as the major cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and a glycolipid as the major polar lipids, showed morphological and chemotaxonomic properties consistent with those reported for members of the genus Arthrobacter. Phylogenetic analysis of the 16S rRNA gene sequence of strain SJCon(T) confirmed that it was a member of this genus with Arthrobacter globiformis DSM 20124(T) being the closest relative (sequence similarity of 97 %). The DNA G + C content of strain SJCon(T) was 69 ± 1 mol% and DNA homology with A. globiformis DSM 20124(T) was 45 %, suggesting that strain SJCon(T) represented a novel species of the genus Arthrobacter, which we have named Arthrobacter nitrophenolicus sp. nov The type strain is SJCon(T) (=MTCC 10104(T) =DSM 23165(T)).

  11. Isolation and Characterization of a Novel Electrogenic Bacterium, Dietzia sp. RNV-4

    PubMed Central

    Sacco, Natalia J.; Bonetto, M. Celina; Cortón, Eduardo

    2017-01-01

    Electrogenic bacteria are organisms that can transfer electrons to extracellular electron acceptors and have the potential to be used in devices such as bioelectrochemical systems (BES). In this study, Dietzia sp. RNV-4 bacterium has been isolated and identified based on its biochemical, physiological and morphological characteristics, as well as by its 16S rRNA sequence analysis. Furthermore, the current density production and electron transfer mechanisms were investigated using bioelectrochemical methods. The chronoamperometric data showed that the biofilm of Dietzia sp. RNV-4 grew as the current increased with time, reaching a maximum of 176.6 ± 66.1 mA/m2 at the end of the experiment (7 d); this highly suggests that the current was generated by the biofilm. The main electron transfer mechanism, indicated by the cyclic voltammograms, was due to secreted redox mediators. By high performance liquid chromatography, canthaxanthin was identified as the main compound involved in charge transfer between the bacteria and the solid electrodes. Dietzia sp. RNV-4 was used as biological material in a microbial fuel cell (MFC) and the current density production was 299.4 ± 40.2 mA/m2. This is the first time that Dietzia sp. RNV-4 has been electrochemically characterized and identified as a new electrogenic strain. PMID:28192491

  12. Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Baek, Sang-Hoon; Im, Wan-Taek; Oh, Hyun Woo; Lee, Jung-Sook; Oh, Hee-Mock; Lee, Sung-Taik

    2006-11-01

    A Gram-positive, rod-shaped, spore-forming bacterium, Gsoil 3088T, was isolated from soil from a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 3088T was shown to belong to the family Paenibacillaceae, being related to Brevibacillus centrosporus (96.6%), Brevibacillus borstelensis (96.3%), Brevibacillus parabrevis (96.1%), Brevibacillus formosus (96.1%), Brevibacillus brevis (96.1%) and Brevibacillus laterosporus (96.0%). The phylogenetic distances from other validly described species within the genus Brevibacillus were greater than 4.0% (i.e. there was less than 96.0% similarity). The G+C content of the genomic DNA was 52.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; fatty acid profile, iso-C15:0, iso-C14:0 and anteiso-C15:0) supported the affiliation of strain Gsoil 3088T to the genus Brevibacillus. The results of physiological and biochemical tests allowed strain Gsoil 3088T to be distinguished genotypically and phenotypically from Brevibacillus species with validly published names. Strain Gsoil 3088T, therefore, represents a novel species of the genus Brevibacillus, for which the name Brevibacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3088T (=KCTC 13938T=LMG 23403T).

  13. Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Im, Wan-Taek; Liu, Qing-Mei; Lee, Kang-Jin; Kim, Se-Young; Lee, Sung-Taik; Yi, Tae-Hoo

    2010-07-01

    A Gram-negative, aerobic or facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium (strain Gsoil 3165(T)) was isolated from soil of a ginseng field in Pocheon, South Korea. Its taxonomic position was determined by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 3165(T) was shown to belong to the family Comamonadaceae, class Betaproteobacteria, and was related most closely to the type strains of Variovorax boronicumulans (98.9 % similarity), Variovorax paradoxus (98.3 %), Variovorax soli (98.2 %) and Variovorax dokdonensis (96.6 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 3165(T) and the type strains of other species in the family Comamonadaceae were less than 97.0 %. The G+C content of the genomic DNA of strain Gsoil 3165(T) was 66 mol%. Phenotypic and chemotaxonomic data (Q-8 as the major ubiquinone; C(16 : 0) and C(17 : 0) cyclo as major fatty acids) supported the affiliation of strain Gsoil 3165(T) to the genus Variovorax. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 3165(T) from recognized Variovorax species. Gsoil 3165(T) is therefore considered to represent a novel species of the genus Variovorax, for which the name Variovorax ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3165(T) (=KCTC 12583(T) =LMG 23392(T)).

  14. 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.

  15. Marinospirillum celere sp. nov., a novel haloalkaliphilic, helical bacterium isolated from Mono Lake.

    PubMed

    Namsaraev, Zorigto; Akimov, Vladimir; Tsapin, Alexandre; Barinova, Ekaterina; Nealson, Kenneth; Gorlenko, Vladimir

    2009-09-01

    Two strains of a Gram-negative, helical, haloalkaliphilic bacterium were isolated from Mono Lake (USA). Both strains were mesophilic and grew between 13 and 55 degrees C, with optimum growth at 35-45 degrees C. The optimum pH for growth was 9.5. Growth was observed at NaCl concentrations of 0.5-12% (w/v), with optimum growth at 2% NaCl. Both isolates were motile by means of bipolar tuft flagella, coccoid body-forming and strictly aerobic. It was concluded that they belong to the same species, based on DNA-DNA hybridization values (95% DNA relatedness). DNA G+C contents of the novel strains were 52.1 and 52.3 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were shown to be related closely to the members of the genus Marinospirillum (family Oceanospirillaceae, class Gammaproteobacteria). Sequence similarity of strain v1c_Sn-redT to the type strains of Marinospirillum alkaliphilum, Marinospirillum minutulum, Marinospirillum megaterium and Marinospirillum insulare was 95.0, 92.7, 91.8 and 91.8%, respectively. Chemotaxonomic data [major ubiquinone, Q8; major fatty acids, C18:1(n-7) and C16:0] and physiological and biochemical tests supported the affiliation of the novel strains to the genus Marinospirillum as members of a novel species, for which the name Marinospirillum celere sp. nov. is proposed, with the type strain v1c_Sn-redT (=LMG 24610T=VKM 2416T).

  16. 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)).

  17. Cyclobacterium halophilum sp. nov., a marine bacterium isolated from a coastal-marine wetland.

    PubMed

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Sepahy, Abbas Akhavan; Schumann, Peter; Ventosa, Antonio

    2014-03-01

    A novel Gram-stain-negative, slightly halophilic bacterium, designated strain GASx41(T), was isolated from soil of the coastal-marine wetland Gomishan in Iran. Cells of strain GASx41(T) were curved, ring-like or horseshoe-shaped rods and non-motile. Strain GASx41(T) was strictly aerobic, and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 1-10% (w/v), with optimum growth occurring at 2.5-3% (w/v) NaCl. The optimum temperature and pH for growth were 25-30 °C and pH 7.5-8.0. On the basis of 16S rRNA gene sequence analysis, strain GASx41(T) was shown to belong to the genus Cyclobacterium within the phylum Bacteroidetes and showed closest phylogenetic similarity to 'Cyclobacterium jeungdonense' HMD3055 (98.0%). The DNA G+C content of strain GASx41(T) was 48.1 mol%. The major cellular fatty acids of strain GASx41(T) were iso-C15 : 0, summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0 2-OH, anteiso-C15 : 0 and iso-C17 : 0 3-OH, and its polar lipid pattern consisted of phosphatidylethanolamine, phosphatidylcholine and 12 unknown lipids. The only quinone present was menaquinone 7 (MK-7). All these features confirmed the placement of isolate GASx41(T) within the genus Cyclobacterium. On the basis of evidence from this study, a novel species of the genus Cyclobacterium, Cyclobacterium halophilum sp. nov., is proposed, with strain GASx41(T) ( = IBRC-M 10761(T) = CECT 8341(T)) as the type strain.

  18. Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil.

    PubMed

    Ahmed, Iftikhar; Yokota, Akira; Fujiwara, Toru

    2007-04-01

    A motile, Gram-positive, boron-tolerant and moderately halotolerant rod-shaped bacterium was isolated from a soil naturally high in boron minerals found in the Hisarcik area of Turkey. The novel isolate, designated T-16X(T), produced spherical or ellipsoidal endospores in a non-bulging or slightly swollen sporangium in a terminal position and survived in a medium containing up to 450 mM boron. Whereas it tolerated 11 % (w/v) NaCl, it also grew without NaCl or boron. The temperature range for growth was 16-37 degrees C (optimum 25-28 degrees C) and the pH range for growth was 6.0-10.0 (optimum pH 7.5-8.5). The DNA G+C content was 35.8 mol% and the major cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0) at 18.2 and 45.7 % of the total fatty acids, respectively. MK-7 (90 %) was the predominant respiratory quinone system and meso-diaminopimelic acid was the predominant diamino acid of the cell-wall peptidoglycan. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the novel strain is closely related to the type strains of Gracilibacillus orientalis (96.7 % similarity), G. halotolerans (95.5 %) and G. dipsosauri (95.4 %). However, the maximum DNA hybridization value for this strain with these closely related strains was less than 26.2 %. On the basis of 16S rRNA gene sequence data and chemotaxonomic and physiological features, the organism T-16X(T) (=DSM 17256(T)=IAM 15263(T)=ATCC BAA-1190(T)) is proposed to be a member of the genus Gracilibacillus as the type strain of the novel species Gracilibacillus boraciitolerans sp. nov.

  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)).

  20. Mobilisporobacter senegalensis gen. nov., sp. nov., an anaerobic bacterium isolated from tropical shea cake.

    PubMed

    Mbengue, Malick; Thioye, Abdoulaye; Labat, Marc; Casalot, Laurence; Joseph, Manon; Samb, Abdoulaye; Ben Ali Gam, Zouhaier

    2016-01-08

    A new Gram-stain positive, endospore-forming, strictly anaerobic bacterium, designated strain Gal1T was isolated from shea cake, a waste material from the production of shea-butter originating from Saraya, Senegal. The cells were rod-shaped slightly curved, motile with peritrichous flagella. The strain is oxidase negative and catalase-negative. Growth was observed at temperatures ranging from 15 to 45 °C (optimum 30 °C) and at pH 6.5-9.3 (optimum pH 7.8). The salinity range for growth was 0-3.5% of NaCl (optimum 1%). Yeast extract is required for growth. Strain Gal1T fermented various carbohydrates such as mannose, mannitol, arabinose, cellobiose, fructose, glucose, maltose, sucrose, trehalose and lactose as positive reactions and the major end products were ethanol and acetate. The only major cellular fatty acid was C16:0 (19.5%). The DNA base G+C content of strain Gal1T was 33.8 mol%. Analysis of the 16S rRNA gene sequence of the isolate indicated that this strain was related respectively to Mobilitalea sibirica DSM 26468T with 94.27% similarity, Clostridium populeti ATTC 3225T with 93.94%, Clostridium aminovalericum DSM 1283T and Anaerosporobacter mobilis DSM 15930T with 93.63%. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain Gal1T was clearly distinguished from closely related genera, and the strain Gal1T can be assigned to a new genus for which the name Mobilisporobacter senegalensis gen. nov., sp. nov. is proposed. The type strain is Gal1T (= DSM 26537T, = JCM 18753T).

  1. 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)).

  2. Cecembia rubra sp. nov., a thermophilic bacterium isolated from a hot spring sediment.

    PubMed

    Duan, Yan-Yan; Ming, Hong; Dong, Lei; Yin, Yi-Rui; Meng, Xiao-Lin; Zhou, En-Min; Zhang, Jian-Xin; Nie, Guo-Xing; Li, Wen-Jun

    2015-07-01

    A Gram-staining negative, rod-shaped bacterium, designated strain YIM 78110(T), was isolated from a sediment sample collected from Hehua hot spring in Tengchong, Yunnan province, south-west China. The taxonomic status of strain YIM 78110(T) was confirmed by a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain YIM 78110(T) belongs to the genus Cecembia, displaying 96.8% and 94.7% sequence similarity with the two most closely related type strains, Cecembia calidifontis RQ-33(T) and Cecembia lonarensis LW9T, respectively. The low value of DNA-DNA hybridization (52.3 ± 2.3%) between strain YIM 78110(T) and its closest neighbour, Cecembia calidifontis RQ-33(T), indicated that this new isolate represented a different genomic species in the genus Cecembia. The temperature for growth ranged from 30 to 50 °C. The pH for growth ranged from pH 4.0 to 10.0, with NaCl tolerance of 0.5-6.0% (w/v). The predominant menaquinone of strain YIM 78110(T) was MK-7 and the major polar lipid was phosphatidylethanolamine. The major fatty acids were iso-C15:0 and C15:0. The DNA G+C content was 47.1 mol%. On the basis of physiological, biochemical and phylogenetic analyses, it is proposed that strain YIM 78110(T) represents a novel species of the genus Cecembia, for which the name Cecembia rubra sp. nov. is proposed. The type strain is YIM 78110(T) ( = CCTCC AB2013287(T) = DSM 28057(T)).

  3. Saccharofermentans acetigenes gen. nov., sp. nov., an anaerobic bacterium isolated from sludge treating brewery wastewater.

    PubMed

    Chen, Shuangya; Niu, Lili; Zhang, Yongxiang

    2010-12-01

    A spore-forming anaerobic bacterium, designated strain P6(T), was isolated from the sludge of an up-flow anaerobic sludge blanket reactor treating brewery wastewater. Cells were Gram-positive, oval and 0.6-0.9 μm by 1.2-1.8 μm in size. Growth was observed at 20-42 °C and at pH 5.0-7.5. It fermented several hexoses, polysaccharides and alcohols. Sucrose and aesculin could also be fermented. The main end products of fermentation from glucose were acetate, lactate and fumarate; trace CO(2) and H(2) were also produced. The DNA G+C content of strain P6(T) was 55.6 mol%. The major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0) and iso-C(14 : 0) 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain P6(T) represented a novel phyletic sublineage in clostridial cluster III, and showed <91 % similarity to the type strains of recognized species in this cluster. Phenotypically, the new isolate was distinguished from its phylogenetic relatives (e.g. Clostridium straminisolvens, Clostridium thermocellum, Acetivibrio cellulolyticus and Clostridium aldrichii) by producing acid from glucose and its inability to degrade cellulose. On the basis of evidence from this polyphasic study, strain P6(T) is considered to represent a novel species of a new genus, for which the name Saccharofermentans acetigenes gen. nov., sp. nov. is proposed. The type strain of Saccharofermentans acetigenes is P6(T) (=JCM 14006(T) =AS 1.5064(T)).

  4. 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).

  5. 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)).

  6. Brassicibacter mesophilus gen. nov., sp. nov., a strictly anaerobic bacterium isolated from food industry wastewater.

    PubMed

    Fang, Ming-Xu; Zhang, Wen-Wu; Zhang, Yan-Zhou; Tan, Hai-Qin; Zhang, Xin-Qi; Wu, Min; Zhu, Xu-Fen

    2012-12-01

    A novel mesophilic, strictly anaerobic bacterium, strain BM(T), was isolated from food industry wastewater. The cells were motile, non-spore-forming rods and stained Gram-negative. Growth of strain BM(T) was observed at 16-44 °C (optimum 37 °C) and pH 6.0-9.0 (optimum pH 7.5). The NaCl concentration range for growth was 0-8% (optimum 1.5%, w/v). Strain BM(T) was chemo-organotrophic, using a few sugars and amino acids as sole carbon and energy sources. The fermentation products from peptone-yeast extract broth were propionate, formate, acetate, ethanol and isovalerate. Indole, NH(3) and H(2)S were produced from peptone. No respiratory quinones could be detected. The major fatty acids were iso-C(15:0) (39.3%), iso-C(15:0) dimethyl acetal (10.1%), anteiso-C(15:0) (7.6%), C(14:0) (6.1%) and C(16:0) (5.6%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a number of unidentified aminoglycolipids, glycolipids and phospholipids. The DNA G+C content was 28.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain BM(T) was related to various genera of the family Clostridiaceae, and its closest relatives were Sporosalibacterium faouarense SOL3f37(T) (94.3% 16S rRNA gene sequence similarity), Proteiniborus ethanoligenes GW(T) (92.1%) and Clostridiisalibacter paucivorans 37HS60(T) (92.0%). In recognition of its distinct phenotypic and genotypic characteristics, isolate BM(T) is proposed to represent a novel species of a new genus, Brassicibacter mesophilus gen. nov., sp. nov. The type strain of Brassicibacter mesophilus is BM(T) ( = JCM 16868(T)  = DSM 24659(T)).

  7. 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

  8. 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.

  9. 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)).

  10. Thermal Inactivation of a Deep-Sea Barophilic Bacterium, Isolate CNPT-3

    PubMed Central

    Yayanos, A. Aristides; Dietz, Allan S.

    1982-01-01

    The barophilic deep-sea bacterium, isolate CNPT-3, was inactivated by exposures to temperatures between 10 and 32°C at atmospheric pressure. Inactivation in samples from warmed cell suspensions was measured as the loss of colonyforming ability (CFA) at 10°C and 587 bars. At atmospheric pressure, there was a slow loss of CFA even at 10°C. The loss of CFA was rapid above 20°C and only slightly affected by high pressures. The first-order rate constants for thermal inactivation fit the Arrhenius equation with an activation energy of 43 kcal (ca. 179.9 kJ)/mol. Light microscopy and scanning transmission electron microscopy revealed morphological changes due to warming of the cells. The changes ensued the loss of CFA. The results supported the hypothesis from an earlier work that indigenous (autochthonous) deep-sea bacteria from cold deep seas are both barophilic and psychrophilic. If ultimately sustained, these characteristics may be useful in designing experiments to assess the relative importance of the autochthonous and allochthonous bacteria in the deep sea. The data were used to evaluate how barophilic bacteria may have been missed in many investigations because of warming of the cells during sample retrieval from the sea or during cultivation in the laboratory. The evaluation revealed the need for temperature and pressure data during retrieval of samples and cultivation in the laboratory. Most deep-ocean microbiology may be possible with thermally insulated equipment for retrieval from the sea and with high-pressure vessels for laboratory incubations. Images PMID:16346041

  11. Bacillus salitolerans sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China.

    PubMed

    Zhang, Wei-Yan; Hu, Jing; Zhang, Xin-Qi; Zhu, Xu-Fen; Wu, Min

    2015-08-01

    A novel aerobic bacterium, KC1(T), was isolated from a salt mine in Kuche county, Xinjiang province, China. Cells were observed to be Gram-positive, rod-shaped, endospore-forming and motile with flagella. Strain KC1(T) was found to grow at 25-45 °C (optimum 37 °C), pH 6.5-9.0 (optimum 8.0) and NaCl 0-10 % (v/v) (optimum 4 %). The major fatty acids were identified as anteiso-C15:0 and anteiso-C17:0. Menaquinone-7 (MK-7) was found to be the predominant isoprenoid quinone. The cell-wall diamino acid was found to be meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol and a glycolipid. The 16S rRNA gene sequence of strain KC1(T) showed low similarity (<96 %) to other validly named species. The phylogenetic trees showed that strain KC1(T) is closely related to Bacillus azotoformans DSM 1046(T) and Bacillus methanolicus DSM 16454(T). Both these type strains showed 95.4 % 16S rRNA gene sequence similarity to strain KC1(T). The DNA G+C content of strain KC1(T) was determined to be 39.0 mol%. On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain KC1(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus salitolerans sp. nov. is proposed. The type strain is KC1(T) (=JCM 19760(T) = CGMCC 1.12810(T)).

  12. 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)).

  13. 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)).

  14. Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces.

    PubMed

    Ouwerkerk, Janneke P; Aalvink, Steven; Belzer, Clara; de Vos, Willem M

    2016-11-01

    A Gram-stain-negative, non-motile, strictly anaerobic, oval-shaped, non-spore-forming bacterium (strain PytT) was isolated from reticulated python faeces. Strain PytT was capable of using mucin as sole carbon, energy and nitrogen source. Cells could grow singly, in pairs, and were also found to aggregate. Scanning electron microscopy revealed the presence of filamentous structures connecting individual bacterial cells. Strain PytT could grow on a limited number of single sugars, including N-acetylglucosamine, N-acetylgalactosamine, glucose, lactose and galactose, but only when a plentiful protein source was provided. Phylogenetic analysis based on 16S rRNA gene sequencing showed strain PytT to belong to the Verrucomicrobiae class I, family Akkermansiaceae, genus Akkermansia, with Akkermansia muciniphila MucT as the closest relative (94.4 % sequence similarity). DNA-DNA hybridization revealed low relatedness of 28.3 % with A. muciniphila MucT. The G+C content of DNA from strain PytT was 58.2 mol%. The average nucleotide identity (ANI) of the genome of strain PytT compared to the genome of strain MucT was 79.7 %. Chemotaxonomic data supported the affiliation of strain PytT to the genus Akkermansia. Based on phenotypic, phylogenetic and genetic characteristics, strain PytT represents a novel species of the genus Akkermansia, for which the name Akkermansia glycaniphila sp. nov. is proposed. The type strain is PytT (=DSM 100705T=CIP 110913T).

  15. 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).

  16. Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove.

    PubMed

    Vashist, Poonam; Nogi, Yuichi; Ghadi, Sanjeev C; Verma, Pankaj; Shouche, Yogesh S

    2013-07-01

    A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13(T), was isolated from the mangrove ecosystem of Goa, India. Strain DD-13(T) degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13(T) was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13(T) formed a coherent cluster with species of the genus Microbulbifer. Strain DD-13(T) exhibited 16S rRNA gene sequence similarity levels of 98.9-97.1 % with Microbulbifer hydrolyticus IRE-31(T), Microbulbifer salipaludis JCM 11542(T), Microbulbifer agarilyticus JAMB A3(T), Microbulbifer celer KCTC 12973(T) and Microbulbifer elongatus DSM 6810(T). However, the level of DNA-DNA relatedness between strain DD-13(T) and the five type strains of these species of the genus Microbulbifer were in the range of 26-33 %. Additionally, strain DD-13(T) demonstrates several phenotypic differences from these type strains of species of the genus Microbulbifer. Thus strain DD-13(T) represents a novel species of the genus Microbulbifer, for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13(T) ( = KCTC 23483(T) = JCM 17729(T)).

  17. Halobacillus mangrovi sp. nov., a moderately halophilic bacterium isolated from the black mangrove Avicennia germinans.

    PubMed

    Soto-Ramírez, Nelís; Sánchez-Porro, Cristina; Rosas-Padilla, Soniris; Almodóvar, Karinna; Jiménez, Gina; Machado-Rodríguez, Marlene; Zapata, Magaly; Ventosa, Antonio; Montalvo-Rodríguez, Rafael

    2008-01-01

    A moderately halophilic, spore-forming, Gram-positive, short-rod-shaped bacterium, designated strain MS10(T), was isolated from the surface of leaves of the black mangrove Avicennia germinans and was subjected to a polyphasic taxonomic study. Strain MS10(T) was able to grow at NaCl concentrations in the range 5-20% (w/v) with optimum growth at 10% (w/v) NaCl. Growth occurred at temperatures of 10-50 degrees C (optimal growth at 33-35 degrees C) and pH 6.0-9.0 (optimal growth at pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MS10(T) fell within the branch encompassing members of the genus Halobacillus and was most closely related to Halobacillus dabanensis JCM 12772(T) (99.2% 16S rRNA gene sequence similarity). The DNA G+C content of strain MS10(T) was 45.7 mol%, the major respiratory isoprenoid quinone was MK-7 and the cell-wall peptidoglycan was of the L-Orn-D-Asp type, characteristics consistent with its affiliation to the genus Halobacillus. Strain MS10(T) showed a level of DNA-DNA hybridization with H. dabanensis JCM 12772(T) of 29% and levels below 70% were also obtained with respect to other recognized members of the genus Halobacillus. The major fatty acids of strain MS10(T) were iso-C(16:0), anteiso-C(15:0), iso-C(14:0) and iso-C(15:0). Overall, the phenotypic, genotypic and phylogenetic results presented in this study demonstrate that strain MS10(T) represents a novel species of the genus Halobacillus, for which the name Halobacillus mangrovi sp. nov. is proposed. The type strain is MS10(T) (=CECT 7206(T)=CCM 7397(T)).

  18. Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.

    PubMed

    Miao, Chaohua; Jia, Fangfang; Wan, Yusong; Zhang, Wei; Lin, Min; Jin, Wujun

    2014-03-01

    A novel, Gram-stain-negative, aerobic, rod-shaped, non-motile and moderately halophilic bacterium, designated strain BJGMM-B45(T), was isolated from a saline-alkali soil collected from Shandong Province, China. Growth of strain BJGMM-B45(T) occurred at 10-45 °C (optimum, 30 °C) and pH 5.0-12.0 (optimum, pH 7.0) on Luria-Bertani agar medium with 1-20 % (w/v) NaCl (optimum, 7-10 %). The predominant respiratory quinone was Q-9. The major cellular fatty acids (>5 %) were C18 : 1ω7c, C16 : 0, C19 : 0 cyclo ω8c, summed feature 3, C12 : 0 3-OH and C12 : 0. The genomic DNA G+C content was 57.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BJGMM-B45(T) belonged to the genus Halomonas in the class Gammaproteobacteria. The closest relatives were Halomonas cupida DSM 4740(T) (98.2 % 16S rRNA gene sequence similarity) and Halomonas denitrificans M29(T) (97.8 %). Levels of DNA-DNA relatedness between strain BJGMM-B45(T) and Halomonas cupida CGMCC 1.2312(T) and Halomonas denitrificans DSM 18045(T) were 57.0 and 58.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BJGMM-B45(T) is considered to represent a novel species of the genus Halomonas, for which the name Halomonas huangheensis sp. nov. is proposed. The type strain is BJGMM-B45(T) ( = ACCC 05850(T) = KCTC 32409(T)).

  19. Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.

    PubMed

    Song, Geun Cheol; Yasir, Muhammad; Bibi, Fehmida; Chung, Eu Jin; Jeon, Che Ok; Chung, Young Ryun

    2011-01-01

    A Gram-staining-positive, coccoid to rod-shaped bacterium, designated strain YC6903(T), was isolated from a halophytic plant (Carex scabrifolia Steud.) collected from sand dunes at Namhae Island, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC6903(T) grew optimally at 30 °C and at pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6903(T) belongs to the genus Nocardioides in the family Nocardioidaceae. Strain YC6903(T) was related most closely to Nocardioides pyridinolyticus OS4(T) (97.0 % 16S rRNA gene sequence similarity), Nocardioides dokdonensis FR1436(T) (96.6 %), Nocardioides aquiterrae GW-9(T) (96.6 %) and Nocardioides hankookensis DS-30(T) (96.6 %). The cell-wall peptidoglycan contained LL-diaminopimelic acid and MK-8(H(4)) was the major respiratory quinone. The mean (±SD) level of DNA-DNA relatedness between strain YC6903(T) and N. pyridinolyticus OS4(T) was 53.5±5.5 %. The predominant cellular fatty acid of strain YC6903(T) was iso-C(16 : 0) (28.9 %). The DNA G+C content was 71.7 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YC6903(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides caricicola sp. nov. is proposed. The type strain is YC6903(T) (=KACC 13778(T) =DSM 22177(T)).

  20. 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

  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. Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima.

    PubMed

    Chung, Eu Jin; Park, Jeong Ae; Pramanik, Prabhat; Bibi, Fehmida; Jeon, Che Ok; Chung, Young Ryun

    2013-06-01

    A Gram-negative, aerobic, short rod-shaped bacterium, designated strain YC6898(T), was isolated from the surface-sterilized root of a halophyte (Suaeda maritima) inhabiting tidal flat of Namhae Island, Korea. Strain YC6898(T) grew optimally at 30-37 °C and pH 6.5-7.5. The strain inhibited mycelial growth of Pythium ultimum and Phytophthora capsici. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YC6898(T) belongs to the genus Hoeflea in the family Phyllobacteriaceae. Its closest relatives were Hoeflea alexandrii AM1V30(T) (96.7% 16S rRNA gene sequence similarity), Hoeflea anabaenae WH2K(T) (95.7%), Hoeflea phototrophica DFL-43(T) (95.5%) and Hoeflea marina LMG 128(T) (94.8%). Strain YC6898(T) contained Q-10 as the major ubiquinone. The major fatty acids of strain YC6898(T) were C18:1ω7c (61.1%), C16:0 (11.9%), 11-methyl C18:1ω7c (9.6%) and C19:0 cyclo ω8c (8.0%). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unknown lipids and an unknown glycolipid. The total genomic DNA G+C content was 53.7 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain YC6898(T) represents a novel species of the genus Hoeflea, for which the name Hoeflea suaedae sp. nov. is proposed. The type strain is YC6898(T) (=KACC 14911(T)=NBRC 107700(T)).

  3. 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.

  4. Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil.

    PubMed

    Lin, Shih-Yao; Hameed, Asif; Liu, You-Cheng; Hsu, Yi-Han; Lai, Wei-An; Chen, Wen-Ming; Shen, Fo-Ting; Young, Chiu-Chung

    2013-07-01

    An aerobic, Gram-stain-negative, rod-shaped bacterium with a single polar flagellum, designated CC-OPY-1(T), was isolated from an oil-contaminated site in Taiwan. CC-OPY-1(T) produces siderophores, and can grow at temperatures of 25-37 °C and pH 5.0-9.0 and tolerate <5 % (w/v) NaCl. The 16S rRNA gene sequence analysis of CC-OPY-1(T) showed high pairwise sequence similarity to Pseudomonas alcaligenes BCRC 11893(T) (97.1 %), Pseudomonas. alcaliphila DSM 17744(T) (97.1 %), Pseudomonas tuomuerensis JCM 14085(T) (97.1 %), Pseudomonas toyotomiensis JCM 15604(T) (96.9 %) and lower sequence similarity to remaining species of the genus Pseudomonas. The phylogenetic trees reconstructed based on gyrB and rpoB gene sequences supported the classification of CC-OPY-1(T) as a novel member of the genus Pseudomonas. The predominant quinone system of strain CC-OPY-1T was ubiquinone (Q-9) and the DNA G+C content was 68.4 ± 0.3 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0 cyclo and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC) and two unknown phospholipids (PL1-2). Due to distinct phylogenetic, phenotypic and chemotaxonomic features, CC-OPY-1(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas sagittaria sp. nov. is proposed. The type strain is CC-OPY-1(T) ( = BCRC 80399(T) = JCM 18195(T)).

  5. 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).

  6. Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake.

    PubMed

    Chen, Wen-Ming; Yang, Shwu-Harn; Huang, Wei-Cheng; Cheng, Chih-Yu; Sheu, Shih-Yi

    2012-05-01

    A facultatively anaerobic, chitinolytic bacterium, strain KL-9(T), was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9(T) were gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15-40 °C (optimum, 30-37 °C), at pH 7.0-9.0 (optimum, pH 8.0) and with 0-1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9(T) was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9(T) formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria, being most closely related to members of the genera Leeia, Chitinimonas, Silvimonas and Andreprevotia. Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9(T) is thus considered to represent a novel species of a new genus within the class Betaproteobacteria, for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9(T) ( = BCRC 80168(T) = LMG 25530(T)).

  7. Burkholderia susongensis sp. nov., a mineral-weathering bacterium isolated from weathered rock surface.

    PubMed

    Gu, Jia-Yu; Zang, Sheng-Gang; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi; Wang, Qi

    2015-03-01

    A novel type of mineral-weathering bacterium was isolated from the weathered surface of rock (mica schist) collected from Susong (Anhui, China). Cells of strain L226(T) were Gram-stain-negative. The strain grew optimally at 30 °C, with 1 % (w/v) NaCl and at pH 7.0 in trypticase soy broth. On the basis of 16S rRNA gene phylogeny, strain L226(T) was shown to belong to the genus Burkholderia and the closest phylogenetic relatives were Burkholderia sprentiae WSM5005(T) (98.3 %), Burkholderia acidipaludis NBRC 101816(T) (98.2 %), Burkholderia tuberum STM678(T) (97.2 %) and Burkholderia diazotrophica JPY461(T) (97.1 %). The DNA G+C content was 63.5 mol% and the respiratory quinone was Q-8. The major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The polar lipid profile of strain L226(T) consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, unknown lipids and unidentified aminophospholipids. Based on the low level of DNA-DNA relatedness (ranging from 25.8 % to 34.4 %) to the tested type strains of species of the genus Burkholderia and unique phenotypic characteristics, it is suggested that strain L226(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia susongensis sp. nov., is proposed. The type strain is L226(T) ( = CCTCC AB2014142(T) = JCM 30231(T)).

  8. Anaeromicrobium sediminis gen. nov., sp. nov., a fermentative bacterium isolated from deep-sea sediment.

    PubMed

    Zhang, Xiaobo; Zeng, Xiang; Li, Xi; Alain, Karine; Jebbar, Mohamed; Shao, Zongze

    2016-12-14

    A novel anaerobic, mesophilic,heterotrophic bacterium, designated strain DY2726DT, was isolated from West Pacific Ocean sediments. Cells were long rods (0.5-0.8 μm wide,4-15 μm long),Gram-positive and motile by means of flagella. The temperature and pH ranges for growth were 25-40 °C and pH 6.5-9.0,while optimal growth occurred at 37 °C and pH 7.5, with a generation time 76 minutes. The strain required sea salts for growth from 10 to 30 g L-1 (optimum at 20 g L-1). Substrates used as carbon sources were yeast extract, tryptone, glucose, cellobiose, starch, gelatin, dextrin, fructose, fucose, galactose, galacturonic acid, gentiobiose, glucosaminic acid, mannose, melibiose, palatinose and rhamnose. Products of fermentation were carbon dioxide, acetic acid and butyric acid. Strain DY2726DT was able to reduce amorphous iron hydroxide, goethite, amorphous iron oxides, AQDS and crotonate, but did not reduce sulfur, sulfate, thiosulfate, sulfite and nitrate. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain DY2726DT was affiliated to the family Clostridiaceae and is most closely related to Alkaliphilus transvaalensis (90.0% similarity), Alkaliphilus oremlandii (89.6%). The genomic DNA G + C content, was 33.4 mol%. The major cellular fatty acids of strain DY2726DT were C16:1, C14:0 and C16:0. On the basis of its phenotypic and genotypic properties, strain DY2726DT is suggested to represent a novel species of a new genus in the family Clostridiaceae, for which the name Anaeromicrobium sediminis gen. nov., sp. nov. is proposed. The type strain of Anaeromicrobium sediminis is DY2726DT (=JCM 30224T =MCCC 1A00776T).

  9. Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater.

    PubMed

    Bhumika, V; Srinivas, T N R; Kumar, P Anil

    2013-07-01

    A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1(T), was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate reduction and ornithine decarboxylase activities and negative for citrate utilization, urease, oxidase, catalase and DNase activities. The predominant fatty acids were C16 : 0 3-OH, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, anteiso-C15 : 0, C16 : 0, C15 : 0 3-OH, and C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3). Strain N1(T) contained menaquinone 6 (MK-6) as the sole respiratory quinone. The only polyamine was homospermidine and the major polar lipids were phosphatidylethanolamine (PE), three unidentified aminolipids (AL1-AL3) and two unidentified lipids (L1, L2). The DNA G+C content of the strain was 36.3 mol%. 16S rRNA gene sequence analysis indicated that strain N1(T) was a member of the genus Flavobacterium and closely related to Flavobacterium resistens with pairwise sequence similarity of 96.5 %. Phylogenetic analysis showed that strain N1(T) clustered with Flavobacterium glycines and Flavobacterium daejeonense with a distance of 4.8 and 6.0 % (95.2 and 94.0 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, strain N1(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium nitratireducens sp. nov. is proposed. The type strain is N1(T) ( = MTCC 11155(T) = JCM 17678(T)).

  10. 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).

  11. Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

    USGS Publications Warehouse

    Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

    2016-01-01

    The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

  12. Genome sequence of Pseudomonas parafulva CRS01-1, an antagonistic bacterium isolated from rice field.

    PubMed

    Liu, Qunen; Zhang, Yingxin; Yu, Ning; Bi, Zhenzhen; Zhu, Aike; Zhan, Xiaodeng; Wu, Weixun; Yu, Ping; Chen, Daibo; Cheng, Shihua; Cao, Liyong

    2015-07-20

    Pseudomonas parafulva (formerly known as Pseudomonas fulva) is an antagonistic bacterium against several rice bacterial and fungal diseases. The total genome size of P. parafulva CRS01-1 is 5,087,619 bp with 4389 coding sequences (CDSs), 77 tRNAs, and 7 rRNAs. The annotated full genome sequence of the P. parafulva CRS01-1 strain might shed light on its role as an antagonistic bacterium.

  13. Bacillusurumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake.

    PubMed

    Zhang, Shanshan; Li, Zhaojun; Yan, Yanchun; Zhang, Chuanlun; Li, Jun; Zhao, Baisuo

    2016-06-01

    A Gram-stain-positive, rod-shaped, aerobic and moderately haloalkaliphilic bacterium, designated BZ-SZ-XJ18T, was isolated from the mixed water and sediment of a saline-alkaline lake located in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BZ-SZ-XJ18T was a member of the genus Bacillus. The closest phylogenetic relatives were Bacillus saliphilus 6AGT (96.7 % 16S rRNA gene sequence similarity), 'Bacillusdaqingensis' X10-1 (96.6 %), Bacillus luteus JC167T (96.5 %), Bacillus daliensis DLS13T (96.2 %), Bacillus chagannorensis CG-15T (95.2 %) and Bacillus polygoni YN-1T (95.0 %). DNA-DNA relatedness between strain BZ-SZ-XJ18T and the reference type strains of the related species of the genus Bacillus was lower than 27 %. The isolate formed yellow pigment and grew in the presence of 0.22-4.32 M Na+ (equivalent to 1.3-25.3 %, w/v, NaCl) (optimum 1.08 M Na+, equivalent to 6.3 %, w/v, NaCl), at pH 6.5-10.0 (optimum pH 8.5-9.5) and at 8-41 ºC (optimum 37 ºC). The major cellular fatty acids were anteiso-C15:0 (43.0 %), C16:0 (18.1 %), iso-C15:0 (11.3 %), anteiso-C17:0 (8.0 %) and iso-C16:0 (7.0 %). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The main respiratory quinone was menaquinone-7 (MK-7), and the peptidoglycan type of the cell wall was A1γ based on meso-diaminopimelic acid as the diagnostic diamino acid. The genomic DNA G+C content was 42.3 mol% (HPLC) or 41.4 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ18T is proposed to represent a novel species, Bacillusurumqiensis within the genus Bacillus. The type strain is BZ-SZ-XJ18T (=DSM 29145T=JCM 30195T).

  14. Halobacillus sediminis 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

    2015-12-01

    A Gram-staining-positive, moderately halophilic bacterium, designated strain NGS-2T, was isolated from sediment of a solar saltern pond located in Shinan, Korea. Strain NGS-2T was a strictly aerobic, non-motile rod that grew at pH 5.0-10.0 (optimum, pH 8.0), at 10-30 °C (optimum, 28 °C) and in the presence of 1-20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain NGS-2T belonged to the genus Halobacillus, with sequence similarity of 98.4-95.8 % to existing type strains, showing the highest sequence similarity to Halobacillus dabanensis D-8T (98.4 %), H. litoralis SL-4T (98.4 %), H. trueperi SL-5T (98.2 %), H. faecis IGA7-4T (98.2 %), H. profundi IS-Hb4T (98.1 %) and H. mangrovi MS10T (98.0 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methylethanolamine and an unknown glycolipid. The cell-wall peptidoglycan was based on l-Orn-d-Asp, the predominant isoprenoid quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C15: 0 and anteiso-C17: 0. The DNA G+C content of the novel isolate was 45.0 mol%. Levels of DNA-DNA relatedness between strain NGS-2T and the type strains of 12 other species of the genus ranged from 32 to 3 %. On the basis of the polyphasic analysis conducted in this study, strain NGS-2T represents a novel species of the genus Halobacillus, for which the name Halobacillus sediminis sp. nov. is proposed. The type strain is NGS-2T ( = KACC 18263T = NBRC 110639T).

  15. (Per)chlorate reduction by the thermophilic bacterium Moorella perchloratireducens sp. nov., isolated from underground gas storage.

    PubMed

    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 mum in diameter and 2 to 8 mum 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 degrees C, with an optimum at 55 to 60 degrees 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.

  16. Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil.

    PubMed

    Liu, Xu-Yun; Li, Chun-Xiu; Luo, Xiao-Jing; Lai, Qi-Liang; Xu, Jian-He

    2014-09-01

    A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel

  17. Klebsiella sp. FIRD 2, a TBT-resistant bacterium isolated from contaminated surface sediment along Strait of Johor Malaysia.

    PubMed

    Abubakar, Abdussamad; Mustafa, Muskhazli B; Johari, Wan Lutfi Wan; Zulkifli, Syaizwan Zahmir; Ismail, Ahmad; Mohamat-Yusuff, Ferdaus Binti

    2015-12-15

    A possible tributyltin (TBT)-degrading bacterium isolated from contaminated surface sediment was successfully identified as Klebsiella sp. FIRD 2. It was found to be the best isolate capable of resisting TBT at a concentration of 1000 μg L(-1). This was a concentration above the reported contaminated level at the sampling station, 790 μg L(-1). Further studies revealed that the isolate was Gram negative and resisted TBT concentrations of up to 1500 μg L(-1) in a Minimal Salt Broth without the addition of any carbon source within the first 48 h of incubation. It is expected that additional work could be conducted to check the degradation activity of this new isolate and possibly improve the degradation capacity in order to contribute to finding a safe and sustainable remediation solution of TBT contamination.

  18. A bacterium capable of using phytol as its sole carbon source, isolated from algal sediment of Mud Lake, Florida.

    PubMed

    Hoag, K B; Bradley, W H; Tousimis, A J; Price, D L

    1969-07-01

    A species of Flavobacterium that consistently attacks pure phytol and can use it as a sole source of carbon has been isolated from the blue-green algal sediment of Mud Lake, Florida. Biochemical tests demonstrate that this bacterium also readily uses various other organic compounds. This bacterium may account for the degradation products of chlorophyll and its side chain phytol, which have been found in the Mud Lake algal sediment. Phytol and its degradation products play a role in Refsum's disease, but phytol is also the most promising precursor of the isoprenoid hydrocarbons found in oil shale of the Green River Formation (Eocene) of Colorado, Utah, and Wyoming. The discovery of this species of Flavobacterium is a significant product of a protracted study of the bacteriology, phycology, zoology, and geochemistry of the algal sediment forming in Mud Lake, which is believed to be a modern analogue of the kind of algal sediment that, through geologic time, became oil shale.

  19. Larsenimonas suaedae sp. nov., a moderately halophilic, endophytic bacterium isolated from the euhalophyte Suaeda salsa.

    PubMed

    Xia, Zhi-Jie; Wu, Hong-Zhen; Cui, Chun-Xiao; Chen, Qi; Zhao, Guo-Yan; Wang, Hai-Xia; Dai, Mei-Xue

    2016-08-01

    A moderately halophilic, Gram-stain-negative, non-endospore-forming endophytic bacterium designated strain ST307T was isolated from the euhalophyte Suaeda salsa in Dongying, China. Strain ST307T was aerobic, rod-shaped, motile and orange-yellow-pigmented. The organism grew at NaCl concentrations of 0.6-20 % (w/v) (optimum 5-6 %, w/v), at temperatures of 5-45 °C (optimum 35 °C) and at pH 5-9 (optimum pH 7-8). It accumulated poly-β-hydroxybutyric acid and produced exopolysaccharides. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The predominant lipoquinone was ubiquinone Q-9. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a glycoaminolipid and a phosphoglycoaminolipid. The DNA G+C content was 60.5 mol%. Phylogenetic analyses of 16S rRNA gene sequences and concatenated atpA, rpoD and secA gene sequences revealed that the strain represents a member of the genus Larsenimonas. The closest related type strain was Larsenimonas salina M1-18T. Mean DNA-DNA relatedness values between strain ST307T and the related species L. salina M1-18T, Chromohalobacter beijerinckii DSM 7218T, C. canadensis DSM 6769T, C. israelensis DSM 6768T, C. marismortui CGMCC 1.2321T, C. nigrandesensis DSM 14323T, C. salexigens DSM 3043T and C. sarecensis DSM 15547T were 15±2-45±1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain ST307T clearly represents a novel species of the genus Larsenimonas. The name Larsenimonassuaedae sp. nov. is proposed, with ST307T (=CGMCC 1.8902T=DSM 22428T) as the type strain.

  20. Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica.

    PubMed

    Rozahon, Manziram; Ismayil, Nurimangul; Hamood, Buayshem; Erkin, Raziya; Abdurahman, Mehfuzem; Mamtimin, Hormathan; Abdukerim, Muhtar; Lal, Rup; Rahman, Erkin

    2014-09-01

    An endophytic bacterium, designated K-38(T), was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38(T) was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38(T) grew at temperatures of 25-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0-3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38(T) was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3(T), followed by Rhizobium nepotum 39/7(T) (96.5 %) and Rhizobium borbori DN316(T) (96.2 %). Phylogenetic analysis of strain K-38(T) based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium. The DNA G+C content was determined to be 63.5 mol%. DNA-DNA relatedness between K-38(T) and R. rosettiformans W3(T) was 48.4 %, indicating genetic separation of strain K-38(T) from the latter strain. The major components of the cellular fatty acids in strain K-38(T) were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38(T) include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38(T). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38(T) represents a novel species of the genus Rhizobium, for which the name Rhizobium populi sp. nov. is proposed

  1. Marinococcus salis sp., nov., a moderately halophilic bacterium isolated from a salt marsh.

    PubMed

    Vishnuvardhan Reddy, Sultanpuram; Thirumala, Mothe; Farooq, Mohammed; Sasikala, Chintalapati; Venkata Ramana, Chintalapati

    2016-12-01

    A novel Gram-stain-positive, coccoid-shaped, facultative anaerobic, motile and halophilic bacterium strain 5M(T) was isolated from Surajbari in India. Based on the 16S rRNA gene sequence analysis, it was identified as belonging to the genus Marinococcus and was most closely related to Marinococcus luteus KCTC 13214(T) (99.3 %, sequence similarity), Marinococcus halotolerans KCTC 19045(T) (99.0 %), Marinococcus halophilus LMG 17439(T) (98.8 %) and Marinococcus tarijensis LMG 26930(T) (98.7 %). However, the DNA-DNA relatedness of strain 5M(T) with M. luteus KCTC 13214(T), M. halotolerans KCTC 19045(T), M. halophilus LMG 17439(T) and M. tarijensis LMG 26930(T) was 42.6 ± 0.8, 48.6 ± 0.8, 40.9 ± 0.8 and 39.8 ± 0.9 %, respectively. Strain 5M(T) grows optimally at 5 % (w/v) NaCl, pH 7.5-8.5 and 37 °C. The cell-wall peptidoglycan of strain 5M(T) contains meso-diaminopimelic acid. Polar lipids of the strain 5M(T) include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and two unknown lipids. The predominant isoprenoid quinone was MK-7. DNA G+C content was 48.9 mol%, and anteiso-C15:0 (40.9 %) was the predominant fatty acid. The results of phylogenetic, biochemical tests and chemotaxonomic allowed a clear differentiation of strain 5M(T) from all of its nearest phylogenetic neighbours, which represents a novel member of the genus Marinococcus, for which the name Marinococcus salis sp., nov., is proposed. The type strain is 5M(T) (=KCTC 33743(T) = LMG 29101(T) = CGMCC 1.15385(T)).

  2. Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment.

    PubMed

    Shivaji, S; Reddy, P Vishnu Vardhan; Rao, S S S Nageshwara; Begum, Zareena; Manasa, Poorna; Srinivas, T N R

    2012-09-01

    A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11B(T), was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C(15 : 0) (14.9 %), anteiso-C(15 : 0) (11.4 %), iso-C(15 : 1) G (13.1 %), C(15 : 1)ω6c (5.4 %), C(17 : 1)ω6c (6.7 %), summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c; 9.3 %) and summed feature 9 (10-methyl C(16 : 0) and/or iso-C(17 : 1)ω9c; 5.9 %). Strain M12-11B(T) contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of Cyclobacterium amurskyense, Cyclobacterium marinum and Cyclobacterium lianum were most closely related to M12-11B(T) with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family Cyclobacteriaceae had sequence similarities of <92.0 %. However, DNA-DNA hybridization with Cyclobacterium amurskyense KCTC 12363(T) and Cyclobacterium marinum DSM 745(T) showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11B(T). Based on the results of DNA-DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11B(T) represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11B(T) (= KCTC 23011(T) = NBRC 106168(T)) and it has a DNA G+C content of 40.5 mol%.

  3. 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

  4. Salimesophilobacter vulgaris gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater.

    PubMed

    Zhang, Yan-Zhou; Fang, Ming-Xu; Zhang, Wen-Wu; Li, Tian-Tian; Wu, Min; Zhu, Xu-Fen

    2013-04-01

    A novel anaerobic, heterotrophic bacterium, designated strain Zn2(T), was isolated from the wastewater of a paper mill in Zhejiang, China. Cells were gram-type-positive rods, 0.5-0.8 µm wide and 2-4 µm long, and were motile by a lateral flagellum. The ranges of temperature and pH for growth were 10-50 °C and pH 6.0-9.5. Optimal growth occurred at 35 °C and pH 7.3-7.5. The strain did not require NaCl for growth, but its inclusion in the medium improved growth (optimum concentration 6 %). Substrates utilized as sole carbon sources were peptone, tryptone, Casamino acids, D-xylose, salicin, glycerol, formate, acetate and propionate. The main products of carbohydrate fermentation were acetate, formate, propionate and lactate. Elemental sulfur, thiosulfate and Fe(III) were used as electron acceptors, but sulfate, sulfite, nitrate, nitrite and Mn(IV) were not. Growth was inhibited by the addition of 10 µg ampicillin, penicillin, tetracycline or chloramphenicol ml(-1). iso-C15 : 0, C14 : 0, C16 : 0, C16 : 1 cis9 and C18 : 1 cis9 were the major fatty acids. Strain Zn2(T) did not contain any detectable menaquinones or ubiquinones. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, two unknown phospholipids and four unknown glycolipids. The genomic DNA G+C content was 37 mol%, as determined by HPLC. 16S rRNA gene sequence analysis revealed that strain Zn2(T) was a member of family Clostridiaceae, and was most closely related to the type strains of Geosporobacter subterraneus, Thermotalea metallivorans and Caminicella sporogenes, showing 91.2, 90.3 and 91.1 % sequence similarity, respectively. On the basis of its phenotypic and genotypic properties, strain Zn2(T) is suggested to represent a novel species of a new genus, for which the name Salimesophilobacter vulgaris gen. nov., sp. nov. is proposed. The type strain of Salimesophilobacter vulgaris is Zn2(T) ( = DSM 24770(T)

  5. Oceanirhabdus sediminicola gen. nov., sp. nov., an anaerobic bacterium isolated from sea sediment.

    PubMed

    Pi, Ruo-Xi; Zhang, Wen-Wu; Fang, Ming-Xu; Zhang, Yan-Zhou; Li, Tian-Tian; Wu, Min; Zhu, Xu-Fen

    2013-11-01

    A novel anaerobic bacterium, designated NH-JN4(T) was isolated from a sediment sample collected in the South China Sea. Cells were Gram-stain-positive, spore-forming, peritrichous and rod-shaped (0.5-1.2×2.2-7 µm). The temperature and pH ranges for growth were 22-42 °C and pH 6.0-8.5. Optimal growth occurred at 34-38 °C and pH 6.5-7.0. The NaCl concentration range for growth was 0.5-6 % (w/v) with an optimum of 2.5 %. Catalase and oxidase were not produced. Substrates which could be utilized were peptone, tryptone, yeast extract, beef extract and glycine. Main fermentation products from PYG medium were formate, acetate, butyrate and ethanol. Strain NH-JN4(T) could utilize sodium sulfite as an electron acceptor. No respiratory quinone was detected. The predominant fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0 DMA. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The DNA G+C content was 35.8 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain NH-JN4(T) was a member of family Clostridiaceae, and was most closely related to Clostridium limosum ATCC 25620(T), Clostridium proteolyticum DSM 3090(T), Clostridium histolyticum ATCC 19401(T) and Clostridium tepidiprofundi SG 508(T), showing 94.0, 93.0, 92.9 and 92.3 % sequence similarity, respectively. On the basis of phenotypic, genotypic and chemotaxonomic properties, strain NH-JN4(T) represents a novel species of a new genus in the family Clostridiaceae, for which the name Oceanirhabdus sediminicola gen. nov., sp. nov. is proposed. The type strain of the type species is NH-JN4(T) ( = JCM 18501(T) = CCTCC AB 2013103(T) = KCTC 15322(T)).

  6. 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

  7. Production of bioplastics and hydrogen gas by photosynthetic microorganisms

    NASA Astrophysics Data System (ADS)

    Yasuo, Asada; Masato, Miyake; Jun, Miyake

    1998-03-01

    Our efforts have been aimed at the technological basis of photosynthetic-microbial production of materials and an energy carrier. We report here accumulation of poly-(3-hydroxybutyrate) (PHB), a raw material of biodegradable plastics and for production of hydrogen gas, and a renewable energy carrier by photosynthetic microorganisms (tentatively defined as cyanobacteria plus photosynthetic bateria, in this report). A thermophilic cyanobacterium, Synechococcus sp. MA19 that accumulates PHB at more than 20% of cell dry wt under nitrogen-starved conditions was isolated and microbiologically identified. The mechanism of PHB accumulation was studied. A mesophilic Synechococcus PCC7942 was transformed with the genes encoding PHB-synthesizing enzymes from Alcaligenes eutrophus. The transformant accumulated PHB under nitrogen-starved conditions. The optimal conditions for PHB accumulation by a photosynthetic bacterium grown on acetate were studied. Hydrogen production by photosynthetic microorganisms was studied. Cyanobacteria can produce hydrogen gas by nitrogenase or hydrogenase. Hydrogen production mediated by native hydrogenase in cyanobacteria was revealed to be in the dark anaerobic degradation of intracellular glycogen. A new system for light-dependent hydrogen production was targeted. In vitro and in vivo coupling of cyanobacterial ferredoxin with a heterologous hydrogenase was shown to produce hydrogen under light conditions. A trial for genetic trasformation of Synechococcus PCC7942 with the hydrogenase gene from Clostridium pasteurianum is going on. The strong hydrogen producers among photosynthetic bacteria were isolated and characterized. Co-culture of Rhodobacter and Clostriumdium was applied to produce hydrogen from glucose. Conversely in the case of cyanobacteria, genetic regulation of photosynthetic proteins was intended to improve conversion efficiency in hydrogen production by the photosynthetic bacterium, Rhodobacter sphaeroides RV. A mutant acquired by

  8. 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.

  9. 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

  10. Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake.

    PubMed

    Gorlenko, Vladimir; Tsapin, Alexandre; Namsaraev, Zorigto; Teal, Tracy; Tourova, Tatyana; Engler, Diane; Mielke, Randy; Nealson, Kenneth

    2004-05-01

    A novel, obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from the sediment of an alkaline hot spring located on Paoha Island in Mono Lake, California, USA. This rod-shaped bacterium was motile via peritrichous flagella. Isolated strains grew optimally in 5-25 g NaCl l(-1), at pH 9.0-9.5 and at a temperature of 58 degrees C and were fermentative and mainly proteolytic, utilizing peptone, Casamino acids and yeast extract. Optimal growth was seen in the presence of elemental sulfur, polysulfide or thiosulfate with concomitant reduction to hydrogen sulfide. Sulfite was also formed in an equal ratio to sulfide during reduction of thiosulfate. The novel isolate could also reduce Fe(III) and Se(IV) in the presence of organic matter. On the basis of physiological properties, 16S rRNA gene sequence and DNA-DNA hybridization data, strain PAOHA-1(T) (=DSM 14826(T)=UNIQEM 227(T)) belongs to the genus Anaerobranca and represents a novel species, Anaerobranca californiensis sp. nov.

  11. 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).

  12. Excited-state absorption in bacteriochlorophyll a-protein from the green photosynthetic bacterium Prosthecochloris aestuarii: Reinterpretation of the absorption difference spectrum

    SciTech Connect

    Amerongen, H. van; Struve, W.S. )

    1991-10-31

    Excited-state absorption arising from transitions between singly and doubly excited exciton components in strongly coupled photosynthetic antennae profoundly influences the absorption difference spectra observed in pump-probe spectroscopy. Model calculations of the absorption difference spectrum in the BChl a-protein complex from P. aestuarii are compared with the experimental spectrum.

  13. 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.

  14. Trapping kinetics in mutants of the photosynthetic purple bacterium Rhodobacter sphaeroides: influence of the charge separation rate and consequences for the rate-limiting step in the light-harvesting process.

    PubMed

    Beekman, L M; van Mourik, F; Jones, M R; Visser, H M; Hunter, C N; van Grondelle, R

    1994-03-22

    The primary light-harvesting processes, energy transfer in the light-harvesting antenna, and trapping of the excited states by reaction centers were studied in several mutant strains of the photosynthetic purple bacterium Rhodobacter sphaeroides. The mutants had reaction centers in which the rates of electron transfer were modified by site-directed mutations at the M210 position. Low-intensity pump-probe laser spectroscopy was used to monitor the absorbance transients in the Qy region of the antenna pigments, and it was found that despite a wide variation in charge separation rates within the RC, produced by the alterations at Tyr M210, there was relatively little corresponding variation in the overall trapping rate. These effects of the mutations on the trapping kinetics demonstrate that the rate-limiting step of the overall light-harvesting process is the transfer of the excitations from the antenna to the reaction center.

  15. 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

  16. 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

  17. 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

  18. 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

    2016-07-21

    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.

  19. 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

  20. Equilibration kinetics in isolated and membrane-bound photosynthetic reaction centers upon illumination: a method to determine the photoexcitation rate.

    PubMed

    Manzo, Anthony J; Goushcha, Alexander O; Barabash, Yuri M; Kharkyanen, Valery N; Scott, Gary W

    2009-07-01

    Kinetics of electron transfer, following variation of actinic light intensity, for photosynthetic reaction centers (RCs) of purple bacteria (isolated and membrane-bound) were analyzed by measuring absorbance changes in the primary photoelectron donor absorption band at 865 nm. The bleaching of the primary photoelectron donor absorption band in RCs, following a sudden increase of illumination from the dark to an actinic light intensity of I(exp), obeys a simple exponential law with the rate constant alphaI(exp) + k(rec), in which alpha is a parameter relating the light intensity, measured in mW/cm(2), to a corresponding theoretical rate in units of reciprocal seconds, and k(rec) is the effective rate constant of the charge recombination in the photosynthetic RCs. In this work, a method for determining the alpha parameter value is developed and experimentally verified for isolated and membrane-bound RCs, allowing for rigorous modeling of RC macromolecule dynamics under varied photoexcitation conditions. Such modeling is necessary for RCs due to alterations of the forward photoexcitation rates and relaxation rates caused by illumination history and intramolecular structural dynamics effects. It is demonstrated that the classical Bouguer-Lambert-Beer formalism can be applied for the samples with relatively low scattering, which is not necessarily the case with strongly scattering media or high light intensity excitation.

  1. Isolation, Colonization, and Chlorpyrifos Degradation Mediation of the Endophytic Bacterium Sphingomonas Strain HJY in Chinese Chives (Allium tuberosum).

    PubMed

    Feng, Fayun; Ge, Jing; Li, Yisong; Cheng, Jinjin; Zhong, Jianfeng; Yu, Xiangyang

    2017-02-15

    The endophyte-plant interaction can benefit the host in many different ways. An endophytic bacterium strain (HJY) capable of degrading chlorpyrifos (CP) was isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng). The isolated bacterium HJY classified as Sphingomonas sp. strain HJY could use CP as the sole carbon source. After being marked with the gfp gene, the colonization and distribution of strain HJY-gfp were directly observed in different tissues of Chinese chives with a confocal laser scanning microscope. The inoculation of strain HJY-gfp in Chinese chives resulted in a higher degradation of CP inside the plants than in uninoculated plants. With drench application, up to 70 and 66% of CP were removed from shoots and roots of inoculated Chinese chives, respectively. Moreover, up to 75% of CP was removed from the soil containing plants inoculated with HJY-gfp. With foliage application, the applied concentration of chlorpyrifos affected the degradation performance of strain HJY in Chinese chives. Significant differences were observed only between inoculated and uninoculated Chinese chives with the low applied concentration of CP. Together, other than natural endophyte-assisted plant protection for food safety, the interaction of HJY and plant may be also a promising strategy for in situ bioremediation of soil contaminated with CP.

  2. 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.

  3. Biodegradation of geosmin by a novel Gram-negative bacterium; isolation, phylogenetic characterisation and degradation rate determination.

    PubMed

    Hoefel, Daniel; Ho, Lionel; Monis, Paul T; Newcombe, Gayle; Saint, Christopher P

    2009-06-01

    Biologically active sand filters within water treatment plants (WTPs) are now recognised as an effective barrier for the removal of geosmin. However, little is known regarding the actual microbiological processes occurring or the bacteria capable of degrading geosmin. This study reports the enrichment and isolation of a Gram-negative bacterium, Geo48, from the biofilm of a WTP sand filter where the isolate was shown to effectively degrade geosmin individually. Experiments revealed that Geo48 degraded geosmin in a planktonic state by a pseudo-first-order mechanism. Initial geosmin concentrations ranging from 100 to 1000ng/l were shown to directly influence geosmin degradation in reservoir water by Geo48, with rate constants increasing from 0.010h(-1) (R(2)=0.93) to 0.029h(-1) (R(2)=0.97) respectively. Water temperature also influenced degradation of geosmin by Geo48 where temperatures of 11, 22 and 30 degrees C resulted in rate constants of 0.017h(-1) (R(2)=0.98), 0.023h(-1) (R(2)=0.91) and 0.019h(-1) (R(2)=0.85) respectively. Phylogenetic analysis using the 16S rRNA gene of Geo48 revealed it was a member of the Alphaproteobacteria and clustered with 99% bootstrap support with an isolate designated Geo24, a Sphingopyxis sp. previously described as degrading geosmin but only as a member of a bacterial consortium. Of the previously described bacteria, Geo48 was most similar to Sphingopyxis alaskensis (97.2% sequence similarity to a 1454bp fragment of the 16S rRNA gene). To date, this is the only study to report the isolation and characterisation of a Gram-negative bacterium from a biologically active sand filter capable of the sole degradation of geosmin.

  4. Thiocapsa marina sp. nov., a novel, okenone-containing, purple sulfur bacterium isolated from brackish coastal and marine environments.

    PubMed

    Caumette, Pierre; Guyoneaud, Remy; Imhoff, Johannes F; Süling, Jörg; Gorlenko, Vladimir

    2004-07-01

    Four marine, phototrophic, purple sulfur bacteria (strains 5811T, 5812, BM-3 and BS-1) were isolated in pure culture from different brackish to marine sediments in the Mediterranean Sea, the White Sea and the Black Sea. Single cells of these strains were coccus-shaped, non-motile and did not contain gas vesicles. The colour of cell suspensions that were grown in the light was purple-red. Bacteriochlorophyll a and carotenoids of the okenone series were present as photosynthetic pigments. Photosynthetic membrane systems were of the vesicular type. Hydrogen sulfide, thiosulfate, elemental sulfur and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions; carbon dioxide was utilized as the carbon source. During growth on sulfide, elemental sulfur globules were stored inside the cells. In the presence of hydrogen sulfide, several organic substances could be photoassimilated. Comparative 16S rDNA sequence analysis revealed an affiliation of these four strains to the genus Thiocapsa. Both phylogenetic analysis and the results of DNA-DNA hybridization studies revealed that these strains formed a separate cluster within the genus Thiocapsa. Thus, according to phenotypic characteristics and mainly the carotenoid composition, 16S rDNA sequence analysis and DNA-DNA hybridization data, it is proposed that these strains should be classified as a novel species, Thiocapsa marina sp. nov., with strain 5811T (=DSM 5653T=ATCC 43172T) as the type strain.

  5. 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.

  6. Isolation and characterization of an anaerobic, cellulolytic bacterium, Clostridium cellulovorans sp. nov

    SciTech Connect

    Sleat, R.; Mah, R.A.; Robinson, R.

    1984-07-01

    A new anaerobic, mesophilic, spore-forming cellulolytic bacterium is described. Cellulose is cleared within 24 to 48 h around colonies formed in cellulose agar roll tubes. Cells stain gram negative and are nonmotile rods which form oblong spores either centrally or subterminally in a clostridial swelling. Colonies are irregular with an opaque edge and a center devoid of both vegetative cells and spores. Cellulose, xylan, pectin, cellubiose, glucose, maltose, galactose, sucrose, lactose, and mannose serve as substrates for growth. H/sub 2/, CO/sub 2/, acetate, butyrate, formate, and lactate are produced during fermentation of cellulose or cellobiose. The temperature and pH for optimum growth are 37/sup 0/C and 7.0, respectively. The DNA composition is 26 to 27 mol% guanine plus cytosine. This bacterium resembles Clostridium lochhheadii in morphological and some biochemical characteristics but is not identical to it. The name Clostridium cellulovorans sp. nov. is proposed. The type strain is 743B (ATCC 35296).

  7. Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine

    SciTech Connect

    Takai, Ken; Moser, Duane P.; Onstott, Tullis C.; Spoelstra, N; Pfiffner, Susan M.; Dohnalkova, Alice; Fredrickson, Jim K.

    2001-07-01

    A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores, Growth was observed over the temperature range 20-50 degreesC (optimum 40 degreesC; 45 min doubling time) and ph range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone. tryptone and casein, Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol%, Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C Cram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1(T)= JCM 10712(T)= ATCC 700919(T)). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.

  8. 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.

  9. Desulfovibrio marrakechensis sp. nov., a 1,4-tyrosol-oxidizing, sulfate-reducing bacterium isolated from olive mill wastewater.

    PubMed

    Chamkh, Fatima; Spröer, Cathrin; Lemos, Paulo Costa; Besson, Stephane; El Asli, Abdel-Ghani; Bennisse, Rhizlane; Labat, Marc; Reis, Maria; Qatibi, Abdel-Illah

    2009-05-01

    A novel mesophilic sulfate-reducing bacterium, EMSSDQ(4)(T), was isolated from olive mill wastewater in the semi-arid region of Morocco (Marrakech). Cells were Gram-negative, catalase-positive, straight rods that were non-motile and non-spore-forming and contained cytochrome c(3) and desulfoviridin. The DNA G+C content was 65.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the genus Desulfovibrio with Desulfovibrio carbinoliphilus D41(T), Desulfovibrio alcoholivorans SPSN(T), Desulfovibrio fructosivorans JJ(T) and Desulfovibrio carbinolicus EDK82(T) as the most closely related strains with validly published names. In addition to the classical substrates used by Desulfovibrio species, the isolate oxidized 1,4-tyrosol, one of the most abundant phenolic compounds occurring in olive mill wastewater, to 4-hydroxyphenylacetate without ring cleavage. D. alcoholivorans SPSN(T) was also found to carry out this reaction. Under air, strain EMSSDQ(4)(T) exhibited limited growth on lactate and yeast extract in the absence of sulfate. On the basis of genotypic and phenotypic characteristics, it is proposed that the isolate represents a novel species, Desulfovibrio marrakechensis sp. nov. The type strain is EMSSDQ(4)(T) (=DSM 19337(T) =ATCC BAA-1562(T)).

  10. Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine.

    PubMed

    Takai, K; Moser, D P; Onstott, T C; Spoelstra, N; Pfiffner, S M; Dohnalkova, A; Fredrickson, J K

    2001-07-01

    A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km below land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores. Growth was observed over the temperature range 20-50 degrees C (optimum 40 degrees C; 45 min doubling time) and pH range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein. Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol %. Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C gram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.

  11. Isolation and characterization of an active mannanase-producing anaerobic bacterium, Clostridium tertium KT-5A, from lotus soil.

    PubMed

    Kataoka, N; Tokiwa, Y

    1998-03-01

    Of 10 strains of mannanase-producing anaerobic bacteria isolated from soils and methanogenic sludges, Clostridium tertium KT-5A, which was isolated from lotus soil, produced high amounts of extracellular beta-1,4-mannanase. The isolate was an aerotolerant anaerobe without quinon systems; the cell growth cultivated with no addition of reducing agents was also stable. High yields of mannanase were obtained by inducing enzyme production with galactomannan guar gum and beef extract/peptone as carbon and nitrogen sources, respectively. Fermentation end products on galactomannan fermentation were formate, acetate, lactate, butyrate, carbon dioxide and hydrogen. The extracellular mannanase displayed high activity on galactomannans of locust bean gum galactose/mannose (G/M) ratio 1:4 and spino gum (G/M 1:3), but weak activity on guar gum galactomannan (G/M 1:2) and konjac glucomannan. As far as is known, this is the first report on the isolation of an active mannanase-producing anaerobic bacterium from natural environments.

  12. Bacillus coreaensis sp. nov.: a xylan-hydrolyzing bacterium isolated from the soil of Jeju Island, Republic of Korea.

    PubMed

    Chi, Won-Jae; Youn, Young Sang; Park, Jae-Seon; Hong, Soon-Kwang

    2015-07-01

    A xylan-degrading bacterium, designated as MS5(T) strain, was isolated from soil collected from the Jeju Island, Republic of Korea. Strain MS5(T) was Gram-stain-positive, aerobic, and motile by polar flagellum. The major fatty acids identified in this bacterium were iso-C15:0 (32.3%), C16:0 (27.3%), and anteiso-C15:0 (10.2%). A similarity search based on the 16S rRNA gene sequence revealed that the strain belongs to the class Bacilli and shared the highest similarity with the type strains Bacillus beringensis BR035(T) (98.7%) and Bacillus korlensis ZLC-26(T) (98.6%) which form a coherent cluster in a neighbor-joining phylogenetic tree. The DNA G+C content of strain MS5(T) was 43.0 mol%. The major menaquinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNADNA relatedness values between strain MS5(T) and two closely related species, B. beringensis BR035(T) and B. korlensis ZLC-26(T), were less than 70%. DNA-DNA relatedness analysis and 16S rRNA sequence similarity, as well as phenotypic and chemotaxonomic characteristics suggest that the strain MS5(T) constitutes a novel Bacillus species, for which the name Bacillus coreaensis sp. nov. is proposed. The type strain is MS5(T) (=DSM25506(T) =KCTC13895(T)).

  13. Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans

    PubMed Central

    Parro, Víctor; Moreno-Paz, Mercedes

    2003-01-01

    A random genomic library from an environmental isolate of the Gram-negative bacterium Leptospirillum ferrooxidans has been printed on a microarray. Gene expression analysis was carried out with total RNA extracted from L. ferrooxidans cultures in the presence or absence of ammonium as nitrogen source under aerobic conditions. Although practically nothing is known about the genome sequence of this bacterium, this approach allowed us the selection and sequencing of only those clones bearing genes that showed an altered expression pattern. By sequence comparison, we have identified most of the genes of nitrogen fixation regulon in L. ferrooxidans, like the nifHDKENX operon, encoding the structural components of Mo-Fe nitrogenase; nifSU-hesB-hscBA-fdx operon, for Fe-S cluster assembly; the amtB gene (ammonium transporter); modA (molybdenum ABC type transporter); some regulatory genes like ntrC, nifA (the specific activator of nif genes); or two glnB-like genes (encoding the PII regulatory protein). Our results show that shotgun DNA microarrays are very powerful tools to accomplish gene expression studies with environmental bacteria whose genome sequence is still unknown, avoiding the time and effort necessary for whole genome sequencing projects. PMID:12808145

  14. Isolation and characterization of a thermotolerant ammonia-oxidizing bacterium Nitrosomonas sp. JPCCT2 from a thermal power station.

    PubMed

    Itoh, Yoshikane; Sakagami, Keiko; Uchino, Yoshihito; Boonmak, Chanita; Oriyama, Tetsuro; Tojo, Fuyumi; Matsumoto, Mitsufumi; Morikawa, Masaaki

    2013-01-01

    A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly different from N. nitrosa Nm90, 47.9%. JPCCT2 was capable of growing at temperatures up to 48 °C, while N. nitrosa Nm90 and N. communis Nm2 could not grow at 42°C. Moreover, JPCCT2 grew similarly at concentrations of carbonate 0 and 5 gL(-1). This is the first report that Nitrosomonas bacterium is capable of growing at temperatures higher than 37°C.

  15. Petrotoga halophila sp. nov., a thermophilic, moderately halophilic, fermentative bacterium isolated from an offshore oil well in Congo.

    PubMed

    Miranda-Tello, Elizabeth; Fardeau, Marie-Laure; Joulian, Catherine; Magot, Michel; Thomas, Pierre; Tholozan, Jean-Luc; Ollivier, Bernard

    2007-01-01

    A novel thermophilic, moderately halophilic, rod-shaped bacterium, strain MET-B(T), with a sheath-like outer structure (toga) was isolated from an offshore oil-producing well in Congo, West Africa. Strain MET-B(T) was a Gram-negative bacterium with the ability to reduce elemental sulfur, but not sulfate, thiosulfate or sulfite into sulfide. The optimum growth conditions were 60 degrees C, pH 6.7-7.2 and 4-6 % NaCl. The DNA G+C content was 34.6 mol%. Strain MET-B(T) was phylogenetically related to members of the genus Petrotoga; Petrotoga miotherma, Petrotoga olearia and Petrotoga mexicana were the closest relatives, with type strains exhibiting more than 99 % identity in an analysis of small-subunit rRNA gene sequences. The values for DNA-DNA relatedness between the type strains of these three species and strain MET-B(T) were less than 42 %. As MET-B(T) was found to be genetically and physiologically different from other species of the genus Petrotoga, this strain is proposed as representing a novel species, for which the name Petrotoga halophila sp. nov. is proposed. The type strain is MET-B(T) (=DSM 16923(T)=CCUG 50214(T)).

  16. Clostridium tunisiense sp. nov., a new proteolytic, sulfur-reducing bacterium isolated from an olive mill wastewater contaminated by phosphogypse.

    PubMed

    Thabet, Olfa Ben Dhia; Fardeau, Marie-Laure; Joulian, Catherine; Thomas, Pierre; Hamdi, Moktar; Garcia, Jean-Louis; Ollivier, Bernard

    2004-06-01

    A new sporulated fermentative bacterium designated strain E1(T) (T=type strain), was isolated from an anaerobic mud of an olive mill wastewater basin contaminated by phosphogypse produced by a Tunisian factory. Strain E1(T) was a motile Gram-positive slightly curved rod with spherical terminal spore swelling the cell. It grew between 18 degrees C and 43 degrees C with an optimum at 37 degrees C and pH 7.8 (range 5.5-8.7), without NaCl (range 0-3%). Strain E1(T) was a chemoorganotrophic anaerobic bacterium fermenting only proteins and amino acids. Yeast extract was required for growth. Elemental sulfur was used as terminal electron acceptor. The G+C content of the DNA was 32.6 mol%. The closest phylogenetical relatives of strain E1(T) were Clostridium thiosulfatireducens and C. subterminale (97.3% similarity for partial rRNA gene sequences). DNA-DNA hybridization values between strain E1(T) and both species were 17% and 20.8%, respectively. On the basis of differences in genotypic and phenotypic characteristics, strain E1(T) (DSM 15206(T), CIP 107666(T)) is proposed as the type strain of a new species, C. tunisiense sp. nov. GenBank accession number for the 16S rRNA gene sequence of strain E1(T) is AY187622.

  17. Isolation and Characterization of a Thermotolerant Ammonia-Oxidizing Bacterium Nitrosomonas sp. JPCCT2 from a Thermal Power Station

    PubMed Central

    Itoh, Yoshikane; Sakagami, Keiko; Uchino, Yoshihito; Boonmak, Chanita; Oriyama, Tetsuro; Tojo, Fuyumi; Matsumoto, Mitsufumi; Morikawa, Masaaki

    2013-01-01

    A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly different from N. nitrosa Nm90, 47.9%. JPCCT2 was capable of growing at temperatures up to 48°C, while N. nitrosa Nm90 and N. communis Nm2 could not grow at 42°C. Moreover, JPCCT2 grew similarly at concentrations of carbonate 0 and 5 gL−1. This is the first report that Nitrosomonas bacterium is capable of growing at temperatures higher than 37°C. PMID:24256971

  18. First report of a lipopeptide biosurfactant from thermophilic bacterium Aneurinibacillus thermoaerophilus MK01 newly isolated from municipal landfill site.

    PubMed

    Sharafi, Hakimeh; Abdoli, Mahya; Hajfarajollah, Hamidreza; Samie, Nima; Alidoust, Leila; Abbasi, Habib; Fooladi, Jamshid; Zahiri, Hossein Shahbani; Noghabi, Kambiz Akbari

    2014-07-01

    A biosurfactant-producing thermophile was isolated from the Kahrizak landfill of Tehran and identified as a bacterium belonging to the genus Aneurinibacillus. A thermostable lipopeptide-type biosurfactant was purified from the culture medium of this bacterium and showed stability in the temperature range of 20-90 °C and pH range of 5-10. The produced biosurfactant could reduce the surface tension of water from 72 to 43 mN/m with a CMC of 1.21 mg/mL. The strain growing at a temperature of 45 °C produces a substantial amount of 5 g/L of biosurfactant in the medium supplemented with sunflower oil as the sole carbon source. Response surface methodology was employed to optimize the biosurfactant production using sunflower oil, sodium nitrate, and yeast extract as variables. The optimization resulted in 6.75 g/L biosurfactant production, i.e., 35% improved as compared to the unoptimized condition. Thin-layer chromatography, FTIR spectroscopy, 1H-NMR spectroscopy, and biochemical composition analysis confirmed the lipopeptide structure of the biosurfactant.

  19. Isolation of a Butyrate-Utilizing Bacterium in Coculture with Methanobacterium thermoautotrophicum from a Thermophilic Digester †

    PubMed Central

    Henson, J. Michael; Smith, P. H.

    1985-01-01

    Sludge from a thermophilic, 55°C digester produced methane without a lag period when enriched with butyrate. The sludge was found by most-probable-number enumeration to have ca. 5 × 106 butyrate-utilizing bacteria per ml. A thermophilic butyrate-utilizing bacterium was isolated in coculture with Methanobacterium thermoautotrophicum. This bacterium was a gram-negative, slightly curved rod, occurred singly, was nonmotile, and did not appear to produce spores. When this coculture was incubated with Methanospirillum hungatei at 37°C, the quantity of methane produced was less than 5% of the methane produced when the coculture was incubated at 55°C, the routine incubation temperature. The coculture required clarified digester fluid. The addition of yeast extract to medium containing 5% clarified digester fluid stimulated methane production when a Methanosarcina sp. was present. Hydrogen in the gas phase prevented butyrate utilization. However, when the hydrogen was removed, butyrate utilization began. Penicillin G and d-cycloserine caused the complete inhibition of butyrate utilization by the coculture. The ability of various ecosystems to convert butyrate to methane was studied. Marine sediments enriched with butyrate required a 2-week incubation period before methanogenesis began. Hypersaline sediments did not produce methane after 3 months when enriched with butyrate. Images PMID:16346813

  20. Isolation and characterization of a bacterium capable of removing taste- and odor-causing 2-methylisoborneol from water.

    PubMed

    Lauderdale, Chance V; Aldrich, Henry C; Lindner, Angela S

    2004-11-01

    2-Methylisoborneol (MIB), a metabolite of blue-green algae, has been implicated in causing unpalatable drinking water throughout the world. Current non-biological water treatment technologies are ineffective in removing MIB from potable water or are cost-prohibitive, and biological applications may address these problems. We have isolated and characterized a bacterium derived from lake water and capable of aerobically degrading MIB. Light microscopy and transmission electron microscopy revealed that this strain is a spore-forming, flagellated bacterium that is bacilloid in shape, and 16S rRNA phylogenetic analysis determined that it is most closely related to Bacillus fusiformis and Bacillus sphaericus, both members of the Bacillus sphaericus senso lato taxon. While the growth and oxidation potential of this strain was shown to be affected beyond certain MIB concentrations in the mg/l range, it was capable of depleting MIB at mg/l and ng/l concentrations and of removing MIB to concentrations yielding no observed odor.

  1. Proton efflux coupled to dark H/sub 2/ oxidation in whole cells of a marine sulfur photosynthetic bacterium (Chromatium sp. strain Miami PBS1071)

    SciTech Connect

    Kumazawa, S.; Izawa, S.; Mitsui, A.

    1983-04-01

    Whole cells of photoanaerobically grown Chromatium sp. strain Miami PBS1071, a marine sulfur purple bacterium, oxidized H/sub 2/ in the dark through the oxyhydrogen reaction at rates of up to 59 nmol of H/sub 2/ per mg (dry weight) per min. H/sub 2/ oxidation was routinely measured in H/sub 2/ pulse experiments with air-equilibrated cells. The reaction was accompanied by a reversible H/sup +/ efflux from the cells, suggesting an outward H/sup +/ translocation reaction coupled to H/sub 2/ oxidation. Anaerobic H/sub 2/ uptake with 2,5-dimethyl-p-benzoguinone as an oxidant also showed a weak H/sup +/-translocating activity. Carbonylcyanide 3-chlorophenylhydrazone (1 ..mu..M) stimulated H/sub 2/ oxidation and abolished the associated H/sup +/ changes when H/sub 2/ oxidation was observed in O/sub 2/ pulse experiments with H/sub 2/-Ar-equilibrated cells. However, the uncoupler inhibited both H/sub 2/ oxidation and H/sup +/ changes when measurements were made in H/sub 2/ pulse experiments with air-equilibrated cells. It is suggested that in this bacterium the susceptibility of hydrogenase to reversible O/sub 2/ inactivation in situ is enhanced by the presence of uncoupling agents.

  2. The `heavy' subunit of the photosynthetic reaction centre from Rhodopseudomonas viridis: isolation of the gene, nucleotide and amino acid sequence

    PubMed Central

    Michel, H.; Weyer, K. A.; Gruenberg, H.; Lottspeich, F.

    1985-01-01

    The gene coding for the `heavy' subunit of the photosynthetic reaction centre from Rhodopseudomonas viridis was isolated in an expression vector. Expression of the heavy subunit in Escherichia coli was detected with antibodies raised against crystalline reaction centres. The entire subunit, and not a fusion protein, was expressed in E. coli. The protein coding region of the gene was sequenced and the amino acid sequence derived. Part of the amino acid sequence was confirmed by chemical sequence analysis of the protein. The heavy subunit consists of 258 amino acids and its mol. wt. is 28 345. It possesses one membrane-spanning α-helical segment, as was revealed by the concomitant X-ray structure analysis. ImagesFig. 1.Fig. 2. PMID:16453623

  3. Degradation of [Dha(7)]MC-LR by a Microcystin Degrading Bacterium Isolated from Lake Rotoiti, New Zealand.

    PubMed

    Somdee, Theerasak; Thunders, Michelle; Ruck, John; Lys, Isabelle; Allison, Margaret; Page, Rachel

    2013-01-01

    For the first time a microcystin-degrading bacterium (NV-3 isolate) has been isolated and characterized from a NZ lake. Cyanobacterial blooms in New Zealand (NZ) waters contain microcystin (MC) hepatotoxins at concentrations which are a risk to animal and human health. Degradation of MCs by naturally occurring bacteria is an attractive bioremediation option for removing MCs from drinking and recreational water sources. The NV-3 isolate was identified by 16S rRNA sequence analysis and found to have 100% nucleotide sequence homology with the Sphingomonas MC-degrading bacterial strain MD-1 from Japan. The NV-3 isolate (concentration of 1.0 × 10(8) CFU/mL) at 30°C degraded a mixture of [Dha(7)]MC-LR and MC-LR (concentration 25  μ g/mL) at a maximum rate of 8.33  μ g/mL/day. The intermediate by-products of [Dha(7)]MC-LR degradation were detected and similar to MC-LR degradation by-products. The presence of three genes (mlrA, mlrB, and mlrC), that encode three enzymes involved in the degradation of MC-LR, were identified in the NV-3 isolate. This study confirmed that degradation of [Dha(7)]MC-LR by the Sphingomonas isolate NV-3 occurred by a similar mechanism previously described for MC-LR by Sphingomonas strain MJ-PV (ACM-3962). This has important implications for potential bioremediation of toxic blooms containing a variety of MCs in NZ waters.

  4. 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.

  5. Isolation, purification and spectrometric analysis of PSP toxins from moraxella sp., a bacterium associated with a toxic dinoflagellate

    SciTech Connect

    Boyce, S.D.; Doucette, G.J.

    1994-12-31

    Paralytic shellfish poisoning (PSP) is a seafood intoxication syndrome caused by the injestion of shellfish contaminated with toxins produced by algae known as dinoflagellates. The PSP toxins, saxitoxin and its derivatives, act to block voltage-dependent sodium channels and can cause paralysis and even death at higher doses. It is well documented that bacteria coexist with many harmful or toxic algal species, though the exact nature of the association in relation to toxin production is unknown. Recently, the bacterium Moraxella sp. was isolated from the PSP toxin producing dinoflagellate Alexandrium tamarense. Through HPLC analysis and saxitoxin receptor binding assays performed on crude bacterial extracts, it appears that Moraxella sp. is capable of producing saxitoxin and several of its derivatives. However, physical confirmation (e.g. mass spectrometry) of these results is still needed.

  6. A toxaphene-degrading bacterium related to Enterobacter cloacae, strain D1 isolated from aged contaminated soil in Nicaragua.

    PubMed

    Lacayo-Romero, Martha; Quillaguamán, Jorge; van Bavel, Bert; Mattiasson, Bo

    2005-09-01

    Enterobacter sp. strain D1 is a facultative anaerobic, Gram-negative heterotrophic bacterium isolated from toxaphene-contaminated soil. This organism was identified and characterized through phylogenetic and taxonomic studies. Based on 16S rDNA analysis, the strain D1 was clustered closely with the species Enterobacter cloacae subsp. dissolvens (LMG 2683) and E. cloacae (ATCC 13047T). Strain D1 resembled these E. cloacae strains with respect to various biochemical and nutritional characteristics, but also exhibited differences. Moreover, strain D1 is able to grow and survive with toxaphene supplied in the medium in the range 3-96 mg/L. Amongst the chemical components of toxaphene, octachlorocamphenes, nonachlorobornanes and decachlorobornanes were seen to be rapidly metabolized, although levels of hexachlorocamphenes and heptachlorobornanes were found to be slowly degraded, and subsequently accumulated during the last stage of the cultivation.

  7. Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut

    PubMed Central

    Khelaifia, S.; Croce, O.; Lagier, J.-C.; Robert, C.; Couderc, C.; Di Pinto, F.; Davoust, B.; Djossou, F.; Raoult, D.; Fournier, P.-E.

    2015-01-01

    Strain Vm-5T was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5T (CSUR P971 = DSM 28587). PMID:26649181

  8. Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga.

    PubMed

    Nedashkovskaya, Olga I; Balabanova, Larissa A; Zhukova, Natalia V; Kim, So-Jeong; Bakunina, Irina Y; Rhee, Sung-Keun

    2014-10-01

    A Gram-negative, aerobic, rod-shaped, motile by gliding and yellow-pigmented bacterium, designated strain 10Alg 130(T), that displayed the ability to destroy polysaccharides of red and brown algae, was isolated from the red alga Ahnfeltia tobuchiensis. The phylogenetic analysis based on 16S rRNA gene sequence placed the novel strain within the genus Flavobacterium, the type genus of the family Flavobacteriaceae, the phylum Bacteroidetes, with sequence similarities of 96.2 and 95.7 % to Flavobacterium jumunjiense KCTC 23618(T) and Flavobacterium ponti CCUG 58402(T), and 95.3-92.5 % to other recognized Flavobacterium species. The prevalent fatty acids of strain 10Alg 130(T) were iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C15:0 and iso-C17:1ω9c. The polar lipid profile consisted of phosphatidylethanolamine, two unknown aminolipids and three unknown lipids. The DNA G+C content of the type strain was 34.3 mol%. The new isolate and the type strains of recognized species of the genus Flavobacterium could strongly be distinguished by a number of phenotypic characteristics. A combination of the genotypic and phenotypic data showed that the algal isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ahnfeltiae sp. nov. is proposed. The type strain is 10Alg 130(T) (=KCTC 32467(T) = KMM 6686(T)).

  9. Desulfonatronum paiuteum sp. nov.: A New Alkaliphilic, Sulfate-Reducing Bacterium, Isolated from Soda Mono Lake, California

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena; Hoover, Richard B.; Marsic, Damien; Whitman, William; Cleland, David; Krader, Paul; Six, N. Frank (Technical Monitor)

    2002-01-01

    A novel alkaliphilic, sulfate reducing bacterium strain MLF1(sup T) was isolated from sediments of soda Mono Lake, California. Gram-negative vibrion cells, motile by singular polar flagellum, with sizes 0.5 - 0.6x 1.2 - 2.0 micron occurred singly, in pairs or short spirilla. Growth was observed over the temperature range of +15 C to +48 C (optimum +37 C), NaCl concentration range is greater than 1 - 7 %, wt/vol (optimum 3 %, wt/vol) and pH range 7.8 - 10.5 (optimum pH 9.0 - 9.4). The novel isolate is strictly alkaliphilic, requires high carbonate concentration in medium, obligately anaerobic and catalase negative. As electron donors strain MLF1(sup T) uses hydrogen, formate, ethanol. Sulfate, sulfite, and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The sole end product of growth on formate was H2S. Strain MLF1(sup T) is resistant to kanamycin and gentamycin, but sensitive to chloramphenicol and tetracycline. Na2MoO4 inhibits growth of strain MLF1(sup T). The sum of G+C in DNA is 63.1 mol% (by HPLC method). On the basis of physiological and molecular properties, the isolate was considered as novel species of genus Desulfonatronum; and the name Desulfonatronum paiuteum sp. nov., is proposed (type strain MLF1(sup T) = ATCC BAA-395(sup T) = DSMZ 14708(sup T).

  10. Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse.

    PubMed

    Pfeiffer, Nora; Desmarchelier, Charles; Blaut, Michael; Daniel, Hannelore; Haller, Dirk; Clavel, Thomas

    2012-11-01

    We used selective agar media for culturing bacteria from the caecum of mice fed a high calorie diet. In addition to the isolation of Enterobacteriaceae growing on a medium containing cholesterol and bile salts, we focused on the characterization of strain CT-m2(T), which, based on 16S rDNA analysis, did not appear to correspond to any currently described organisms. The isolate belongs to the Clostridium cluster XIV and is most closely related to members of the Lachnospiraceae, including the genera Anaerostipes, Blautia, Butyrivibrio, Clostridium, Coprococcus, Eubacterium, Robinsoniella, Roseburia, Ruminococcus and Syntrophococcus (≤90 % similarity). Strain CT-m2(T) is a non-motile Gram-positive rod that does not form spores and has a G + C content of DNA of 48.5 %. Cells grow under strictly anoxic conditions (100 % N₂) and produce acetate and butyrate after growth in reduced WCA broth. In contrast to related species, the new bacterium does not metabolize glucose and is positive for phenylalanine arylamidase, and its major cellular fatty acid is C₁₄:₀. Based on phylogenetic and phenotypic studies, the isolate merits recognition as a member of a novel genus and species, for which the name Acetatifactor muris is proposed. The type strain is CT-m2(T) (= DSM 23669(T) = ATCC BAA-2170(T)).

  11. Nitrosomonas stercoris sp. nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure

    PubMed Central

    Nakagawa, Tatsunori; Takahashi, Reiji

    2015-01-01

    Among ammonia-oxidizing bacteria, Nitrosomonas eutropha-like microbes are distributed in strongly eutrophic environments such as wastewater treatment plants and animal manure. In the present study, we isolated an ammonia-oxidizing bacterium tolerant of high ammonium levels, designated strain KYUHI-ST, from composted cattle manure. Unlike the other known Nitrosomonas species, this isolate grew at 1,000 mM ammonium. Phylogenetic analyses based on 16S rRNA and amoA genes indicated that the isolate belonged to the genus Nitrosomonas and formed a unique cluster with the uncultured ammonia oxidizers found in wastewater systems and animal manure composts, suggesting that these ammonia oxidizers contributed to removing higher concentrations of ammonia in strongly eutrophic environments. Based on the physiological and phylogenetic data presented here, we propose and call for the validation of the provisional taxonomic assignment Nitrosomonas stercoris, with strain KYUHI-S as the type strain (type strain KYUHI-ST = NBRC 110753T = ATCC BAA-2718T). PMID:26156554

  12. Aerobic and anoxic growth and nitrate removal capacity of a marine denitrifying bacterium isolated from a recirculation aquaculture system.

    PubMed

    Borges, Maria-Teresa; Sousa, André; De Marco, Paolo; Matos, Ana; Hönigová, Petra; Castro, Paula M L

    2008-01-01

    Bacterial biofilters used in marine recirculation aquaculture systems need improvements to enhance nitrogen removal efficiency. Relatively little is known about biofilter autochthonous population structure and function. The present study was aimed at isolating and characterizing an autochthonous denitrifying bacterium from a marine biofilter installed at a recirculation aquaculture system. Colonization of four different media in a marine fish farm was followed by isolation of various denitrifying strains and molecular classification of the most promising one, strain T2, as a novel member of the Pseudomonas fluorescens cluster. This strain exhibits high metabolic versatility regarding N and C source utilization and environmental conditions for growth. It removed nitrate through aerobic assimilatory metabolism at a specific rate of 116.2 mg NO(3)-N g dw(-1) h(-1). Dissimilatory NO(3)-N removal was observed under oxic conditions at a limited rate, where transient NO(2)-N formed represented 22% (0.17 mg L(-1)) of the maximum transient NO(2)-N observed under anoxic conditions. Dissimilatory NO(3)-N removal under anoxic conditions occurred at a specific rate of 53.5 mg NO(3)-N g dw(-1) h(-1). The isolated denitrifying strain was able to colonize different materials, such as granular activated carbon (GAC), Filtralite and Bioflow plastic rings, which allow the development of a prototype bioreactor for strain characterization under dynamic conditions and mimicking fish-farm operating conditions.

  13. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park.

    PubMed

    Hamilton-Brehm, Scott D; Mosher, Jennifer J; Vishnivetskaya, Tatiana; Podar, Mircea; Carroll, Sue; Allman, Steve; Phelps, Tommy J; Keller, Martin; Elkins, James G

    2010-02-01

    A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47(T), was isolated from Obsidian Pool, Yellowstone National Park, WY. The isolate was a nonmotile, non-spore-forming, Gram-positive rod approximately 2 microm long by 0.2 microm wide and grew at temperatures between 55 and 85 degrees C, with the optimum at 78 degrees C. The pH range for growth was 6.0 to 8.0, with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rate at 0.75 h(-1). The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass, and Populus. OB47(T) was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbitol, carboxymethylcellulose, and casein. Yeast extract stimulated growth, and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation end products were mainly acetate, H2, and CO2, although lactate and ethanol were produced in 5-liter batch fermentations. The G+C content of the DNA was 35 mol%, and sequence analysis of the small subunit rRNA gene placed OB47(T) within the genus Caldicellulosiruptor. Based on its phylogenetic and phenotypic properties, the isolate is proposed to be designated Caldicellulosiruptor obsidiansis sp. nov. and OB47 is the type strain (ATCC BAA-2073).

  14. Methylobacillus rhizosphaerae sp. nov., a novel plant-associated methylotrophic bacterium isolated from rhizosphere of red pepper.

    PubMed

    Madhaiyan, M; Poonguzhali, S; Senthilkumar, M; Pragatheswari, D; Lee, K-C; Lee, J-S

    2013-03-01

    A novel plant-associated obligate methylotrophic bacterium, designated strain Ca-68(T), was isolated from the rhizosphere soil of field-grown red pepper from India. The isolates are strictly aerobic, Gram negative, motile rods multiplying by binary fission and formaldehyde is assimilated via the ribulose monophosphate pathway. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species Methylobacillus flagellatus, Methylobacillus glycogens and Methylobacillus pratensis, with which it showed pairwise similarity of 97.8, 97.4 and 96.2 %, respectively. The major fatty acids are C(16:0), C(10:0) 3OH and C(16:1) ω7c. The G+C content of the genomic DNA is 59.7 mol%. The major ubiquinone is Q-8. Dominant phospholipids are phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on 16S rRNA gene sequence analysis and DNA-DNA relatedness (14-19 %) with type strains of the genus Methylobacillus, the novel isolate was classified as a new species of this genus and named Methylobacillus rhizosphaerae Ca-68(T) (=KCTC 22383(T) = NCIMB 14472(T)).

  15. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park

    SciTech Connect

    Hamilton-Brehm, Scott; Elkins, James G; Phelps, Tommy Joe; Keller, Martin; Carroll, Sue L; Allman, Steve L; Podar, Mircea; Mosher, Jennifer J; Vishnivetskaya, Tatiana A

    2010-01-01

    A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47T, was isolated from Obsidian Pool, Yellowstone National Park, WY, USA. The isolate was a non-motile, non-spore forming, Gram-positive rod approximately 2 m long by 0.2 m wide and grew at temperatures between 55-85oC with the optimum at 78oC. The pH range for growth was 6.0-8.0 with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rates at 0.75 hr-1. The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass and Populus. OB47T was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbital, carboxymethylcellulose and casein. Yeast extract stimulated growth and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation end products were mainly acetate, H2, and CO2 although lactate and ethanol were produced in 5 l batch fermentations. The G+C content of the DNA was 35 mol% and sequence analysis of the small subunit ribosomal RNA gene placed OB47T within the genus Caldicellulosiruptor. Based on its phylogenetic and phenotypic properties, the isolate is proposed to be designated Caldicellulosiruptor obsidiansis sp. nov. and OB47T is the type stain (ATCC = ____, JCM = ____).

  16. Thermosipho affectus sp. nov., a thermophilic, anaerobic, cellulolytic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent.

    PubMed

    Podosokorskaya, O A; Kublanov, I V; Reysenbach, A-L; Kolganova, T V; Bonch-Osmolovskaya, E A

    2011-05-01

    A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain ik275mar(T), was isolated from a Mid-Atlantic Ridge deep-sea hydrothermal vent. Cells were rods surrounded by a sheath-like structure (toga), 0.4-0.9 µm in width and 1.2-6.0 µm in length. Strain ik275mar(T) grew at 37-75 °C, pH 5.6-8.2 and at NaCl concentrations of 10-55 g l(-1). Under optimum conditions (70 °C, pH 6.6, NaCl 20 g l(-1)), doubling time was 32 min. The isolate was able to ferment carbohydrates including starch, cellulose and cellulose derivatives. Acetate, H(2) and CO(2) were the main products of glucose fermentation. G+C content of DNA was 27 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain ik275mar(T) is a member of the genus Thermosipho. 16S rRNA gene sequence identity with the other species of the genus Thermosipho ranged from 93.7 to 94.5 %. Based on the phylogenetic analysis and physiological properties of the novel isolate, we propose a novel species, Thermosipho affectus sp. nov., with type strain ik275mar(T) ( = DSM 23112(T)  = VKM B-2574(T)).

  17. Mycobacterium minnesotense sp. nov., a photochromogenic bacterium isolated from sphagnum peat bogs.

    PubMed

    Hannigan, Geoffrey D; Krivogorsky, Bogdana; Fordice, Daniel; Welch, Jacqueline B; Dahl, John L

    2013-01-01

    Several intermediate-growing, photochromogenic bacteria were isolated from sphagnum peat bogs in northern Minnesota, USA. Acid-fast staining and 16S rRNA gene sequence analysis placed these environmental isolates in the genus Mycobacterium, and colony morphologies and PCR restriction analysis patterns of the isolates were similar. Partial sequences of hsp65 and dnaJ1 from these isolates showed that Mycobacterium arupense ATCC BAA-1242(T) was the closest mycobacterial relative, and common biochemical characteristics and antibiotic susceptibilities existed between the isolates and M. arupense ATCC BAA-1242(T). However, compared to nonchromogenic M. arupense ATCC BAA-1242(T), the environmental isolates were photochromogenic, had a different mycolic acid profile and had reduced cell-surface hydrophobicity in liquid culture. The data reported here support the conclusion that the isolates are representatives of a novel mycobacterial species, for which the name Mycobacterium minnesotense sp. nov. is proposed. The type strain is DL49(T) (=DSM 45633(T) = JCM 17932(T) = NCCB 100399(T)).

  18. Isolation of a potent antibiotic producer bacterium, especially against MRSA, from northern region of the Persian Gulf

    PubMed Central

    Darabpour, Esmaeil; Ardakani, Mohammad Roayaei; Motamedi, Hossein; Ronagh, Mohammad Taghi

    2012-01-01

    Nowadays, emergence and prevalence of MRSA (Methicillin Resistant Staphylococcus aureus) strain have become a great global concern in 21st century, so, it is necessary to discover new antibiotics against this pathogen. The aim of this study was isolation and evaluation marine bacteria from the Persian Gulf in order to finding antibiotic compounds against some pathogenic bacteria. For this purpose, water and sediment samples were collected from the Persian Gulf during March to October 2009. The antibacterial activity of the isolated bacteria was assessed using disc diffusion method. The Growth Curve Interference (GCI) parameter against MRSA was determined for the high potential antibiotic producing strain. The most important factors affecting fermentation conditions in antibiotic production were also optimized. Definite identification of intended isolate was confirmed by 16S rRNA sequencing. Altogether, 51 bacterial colony was isolated and among them only 3 bacterium showed antibacterial activity. Pseudoalteromonaspiscicida PG-01 isolated from a sediment sample was chosen as the best antibiotic producing strain. This strain was effective against all tested Gram-positive bacteria, had good anti-MRSA activity and also GCI value against MRSA was two times lower than MIC value. Among the optimized fermentation parameters, carbon and nitrogen sources play major role in efficacy of optimized antibiotic production. Ultrastructural study on the effect of intended antibiotic compounds on MRSA using TEM revealed that the target site for this compound is cell wall. Considering the antibacterial effect of PG-01 strain especially against MRSA, intended antibiotic compounds can gives hope for treatment of diseases caused by multi-drug resistant bacteria. PMID:22642595

  19. Isolation and identification of hexazinone-degrading bacterium from sugarcane-cultivated soil in Kenya.

    PubMed

    Ngigi, Anastasiah; Getenga, Zachary; Boga, Hamadi; Ndalut, Paul

    2014-03-01

    The s-triazine herbicide hexazinone [3-cyclohexyl-6-dimethylamino-1-methyl-1,3,5-triazine-2,4(1H,3H)-dione], is widely used in agriculture for weed control. Laboratory biodegradation experiments for hexazinone in liquid cultures were carried out using sugarcane-cultivated soils in Kenya. Liquid culture experiments with hexazinone as the only carbon source led to the isolation of a bacterial strain capable of its degradation. Through morphological, biochemical and molecular characterization by 16S rRNA, the isolate was identified as Enterobacter cloacae. The isolate degraded hexazinone up to 27.3% of the initially applied concentration of 40 μg mL(-1) after 37 days of incubation in a liquid culture medium. The study reports the degradation of hexazinone and characterization of the isolated bacterial strain.

  20. Savagea faecisuis gen. nov., sp. nov., a tylosin- and tetracycline-resistant bacterium isolated from a swine-manure storage pit

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular methods was performed on three strains of an unknown Gram-positive staining, nonspore-forming, motile aerobic rod-shaped bacterium resistant to tetracycline and tylosin isolated from a swine-manure storage pi...

  1. Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman Islands, India.

    PubMed

    Jaiswal, Shubham K; Saxena, Rituja; Mittal, Parul; Gupta, Ankit; Sharma, Vineet K

    2017-02-02

    The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric region of mangroves in the Andaman Islands, is comprised of 3,644,788 bp and 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an aerobic bacterium capable of performing assimilatory sulfate reduction, dissimilatory nitrate reduction, and denitrification.

  2. Genome sequence of Desulfovibrio sp. A2, a highly copper resistant, sulfate-reducing bacterium isolated from effluents of a zinc smelter at the Urals.

    PubMed

    Mancini, Stefano; Abicht, Helge K; Karnachuk, Olga V; Solioz, Marc

    2011-12-01

    Desulfovibrio sp. A2 is an anaerobic gram-negative sulfate-reducing bacterium with remarkable tolerance to copper. It was isolated from wastewater effluents of a zinc smelter at the Urals. Here, we report the 4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify potential copper resistance mechanisms.

  3. Draft Genome Sequence of Paenibacillus Strain P1XP2, a Polysaccharide-Degrading, Thermophilic, Facultative Anaerobic Bacterium Isolated from a Commercial Bioreactor Degrading Food Waste

    PubMed Central

    Adelskov, Joseph

    2015-01-01

    The analysis of the ~5.8-Mb draft genome sequence of a moderately thermophilic, heterotrophic, facultative anaerobic bacterium, Paenibacillus strain P1XP2, identified genes for enzymes with the potential for degrading complex food wastes, a property consistent with the ecological habitat of the isolate. PMID:25635015

  4. Draft Genome Sequence of Paenibacillus Strain P1XP2, a Polysaccharide-Degrading, Thermophilic, Facultative Anaerobic Bacterium Isolated from a Commercial Bioreactor Degrading Food Waste.

    PubMed

    Adelskov, Joseph; Patel, Bharat K C

    2015-01-29

    The analysis of the ~5.8-Mb draft genome sequence of a moderately thermophilic, heterotrophic, facultative anaerobic bacterium, Paenibacillus strain P1XP2, identified genes for enzymes with the potential for degrading complex food wastes, a property consistent with the ecological habitat of the isolate.

  5. Draft Genome Sequence of Rhodococcus erythropolis VSD3, a Diesel Fuel-Degrading and Plant Growth-Promoting Bacterium Isolated from Hedera helix Leaves.

    PubMed

    Stevens, Vincent; Thijs, Sofie; McAmmond, Breanne; Langill, Tori; Van Hamme, Jonathan; Weyens, Nele; Vangronsveld, Jaco

    2017-02-23

    We report here the 6.55-Mb draft genome sequence of Rhodococcus erythropolis VSD3, a Gram-positive bacterium of the Nocardiaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. The exploration of its genome will contribute to the assessment of its application as an inoculant in phylloremediation approaches.

  6. Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of São Paulo State, Brazil

    PubMed Central

    Alfonso Vargas, Nadia Catalina; Zimpel, Cristina Kraemer; Pessoa, Adalberto; Rivera, Irma Nelly Gutierrez

    2016-01-01

    We report here the draft genome sequence of Aeromonas caviae CH129, a marine-derived bacterium isolated from the coast of São Paulo state, Brazil. Genomic analysis revealed genes encoding enzymes involved in binding, transport, and chitin metabolism and different virulence-associated factors. PMID:27908996

  7. Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea

    PubMed Central

    Lafi, Feras F.; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.

    2016-01-01

    Pseudomonas argentinensis strain SA190 is a plant endophytic-inhabiting bacterium that was isolated from root nodules of the desert plant Indigofera argentea collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of SA190, highlighting several functional genes related to plant growth–promoting activity, environment adaption, and antifungal activity. PMID:28007863

  8. Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds.

    PubMed

    Hwang, C; Copeland, A; Lucas, S; Lapidus, A; Barry, K; Detter, J C; Glavina Del Rio, T; Hammon, N; Israni, S; Dalin, E; Tice, H; Pitluck, S; Chertkov, O; Brettin, T; Bruce, D; Han, C; Schmutz, J; Larimer, F; Land, M L; Hauser, L; Kyrpides, N; Mikhailova, N; Ye, Q; Zhou, J; Richardson, P; Fields, M W

    2016-11-03

    Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

  9. Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of São Paulo State, Brazil.

    PubMed

    Cardozo, Flávio Augusto; Alfonso Vargas, Nadia Catalina; Zimpel, Cristina Kraemer; Pessoa, Adalberto; Rivera, Irma Nelly Gutierrez

    2016-12-01

    We report here the draft genome sequence of Aeromonas caviae CH129, a marine-derived bacterium isolated from the coast of São Paulo state, Brazil. Genomic analysis revealed genes encoding enzymes involved in binding, transport, and chitin metabolism and different virulence-associated factors.

  10. Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds

    PubMed Central

    Copeland, A.; Lucas, S.; Lapidus, A.; Barry, K.; Detter, J. C.; Glavina del Rio, T.; Hammon, N.; Israni, S.; Dalin, E.; Tice, H.; Pitluck, S.; Chertkov, O.; Brettin, T.; Bruce, D.; Han, C.; Schmutz, J.; Larimer, F.; Land, M. L.; Hauser, L.; Kyrpides, N.; Mikhailova, N.; Ye, Q.; Zhou, J.; Richardson, P.; Fields, M. W.

    2016-01-01

    Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes. QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms. PMID:27811105

  11. Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina

    PubMed Central

    Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M. Sofía; Ee, Robson; Tan-Guan-Sheng, Adrian; Donati, Edgardo R.

    2016-01-01

    Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment. PMID:27540078

  12. Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman Islands, India

    PubMed Central

    Jaiswal, Shubham K.; Saxena, Rituja; Mittal, Parul; Gupta, Ankit

    2017-01-01

    ABSTRACT The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric region of mangroves in the Andaman Islands, is comprised of 3,644,788 bp and 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an aerobic bacterium capable of performing assimilatory sulfate reduction, dissimilatory nitrate reduction, and denitrification. PMID:28153890

  13. Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea.

    PubMed

    Barbato, Marta; Mapelli, Francesca; Chouaia, Bessem; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

    2015-12-10

    We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

  14. Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

    PubMed Central

    Barbato, Marta; Mapelli, Francesca; Chouaia, Bessem; Crotti, Elena; Daffonchio, Daniele

    2015-01-01

    We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5. PMID:26659675

  15. Complete Genome Sequence of Alkaliphilus metalliredigens QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-contaminated Leachate Ponds

    DOE PAGES

    Hwang, C.; Copeland, A.; Lucas, Susan; ...

    2016-11-03

    Alkaliphilus metalliredigens QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes. QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

  16. Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China)

    PubMed Central

    Poltaraus, Andrey B.; Sokolova, Diyana S.; Grouzdev, Denis S.; Ivanov, Timophey M.; Malakho, Sophia G.; Korshunova, Alena V.; Rozanov, Aleksey S.; Tourova, Tatiyana P.

    2016-01-01

    The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus. PMID:27284131

  17. Genome Sequence of Megasphaera cerevisiae NSB1, a Bacterium Isolated from a Canning Line and Able To Grow in Beer with High Alcohol Content

    PubMed Central

    Bergsveinson, Jordyn; Thomson, Euan; Jacoby, Derek; Coady, Yvonne

    2017-01-01

    ABSTRACT The genome sequence of the brewery isolate Megasphaera cerevisiae NSB1 was determined. Strain NSB1 tolerates 5% (vol/vol) alcohol, which is higher than previously reported for M. cerevisiae. The NSB1 genome will help elucidate genetics required for alcohol tolerance and niche adaptation of this Gram-negative beer-spoilage bacterium. PMID:28232423

  18. Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China

    PubMed Central

    Hao, Kun; Li, Hongna; Li, Feng

    2016-01-01

    Bacillus pumilus strain PDSLzg-1, an efficient hydrocarbon-degrading bacterium, was isolated from oil-contaminated soil. Here, we present the complete sequence of its circular chromosome and circular plasmid. The genomic information is essential for the study of degradation of oil by B. pumilus PDSLzg-1. PMID:27795249

  19. Newly isolated but uncultivated magnetotactic bacterium of the phylum Nitrospirae from Beijing, China.

    PubMed

    Lin, Wei; Li, Jinhua; Pan, Yongxin

    2012-02-01

    Magnetotactic bacteria (MTB) in the phylum Nitrospirae synthesize up to hundreds of intracellular bullet-shaped magnetite magnetosomes. In the present study, a watermelon-shaped magnetotactic bacterium (designated MWB-1) from Lake Beihai in Beijing, China, was characterized. This uncultivated microbe was identified as a member of the phylum Nitrospirae and represents a novel phylogenetic lineage with ≥6% 16S rRNA gene sequence divergence from all currently described MTB. MWB-1 contained 200 to 300 intracellular bullet-shaped magnetite magnetosomes and showed a helical swimming trajectory under homogeneous magnetic fields; its magnetotactic velocity decreased with increasing field strength, and vice versa. A robust phylogenetic framework for MWB-1 and all currently known MTB in the phylum Nitrospirae was constructed utilizing maximum-likelihood and Bayesian algorithms, which yielded strong evidence that the Nitrospirae MTB could be divided into four well-supported groups. Considering its population densities in sediment and its high numbers of magnetosomes, MWB-1 was estimated to account for more than 10% of the natural remanent magnetization of the surface sediment. Taken together, the results of this study suggest that MTB in the phylum Nitrospirae are more diverse than previously realized and can make important contributions to the sedimentary magnetization in particular environments.

  20. Physiological traits of the symbiotic bacterium Teredinibacter turnerae isolated from the mangrove shipworm Neoteredo reynei.

    PubMed

    Trindade-Silva, Amaro E; Machado-Ferreira, Erik; Senra, Marcus V X; Vizzoni, Vinicius F; Yparraguirre, Luciana A; Leoncini, Orilio; Soares, Carlos A G

    2009-07-01

    Nutrition in the Teredinidae family of wood-boring mollusks is sustained by cellulolytic/nitrogen fixing symbiotic bacteria of the Teredinibacter clade. The mangrove Teredinidae Neoteredo reynei is popularly used in the treatment of infectious diseases in the north of Brazil. In the present work, the symbionts of N. reynei, which are strictly confined to the host's gills, were conclusively identified as Teredinibacter turnerae. Symbiont variants obtained in vitro were able to grow using casein as the sole carbon/nitrogen source and under reduced concentrations of NaCl. Furthermore, cellulose consumption in T. turnerae was clearly reduced under low salt concentrations. As a point of interest, we hereby report first hand that T. turnerae in fact exerts antibiotic activity. Furthermore, this activity was also affected by NaCl concentration. Finally, T. turnerae was able to inhibit the growth of Gram-negative and Gram-positive bacteria, this including strains of Sphingomonas sp., Stenotrophomonas maltophilia, Bacillus cereus and Staphylococcus sciuri. Our findings introduce new points of view on the ecology of T. turnerae, and suggest new biotechnological applications for this marine bacterium.

  1. The structures of glycolipids isolated from the highly thermophilic bacterium Thermus thermophilus Samu-SA1.

    PubMed

    Leone, Serena; Molinaro, Antonio; Lindner, Buko; Romano, Ida; Nicolaus, Barbara; Parrilli, Michelangelo; Lanzetta, Rosa; Holst, Otto

    2006-08-01

    Thermophiles constitute a class of microorganisms able to grow at extremely elevated temperatures. Some of these species are classified as Gram-negative bacteria, because of the presence of an outer membrane in the cell envelope, which is located on the top of a thick murein layer. Unlike typical Gram-negative bacteria, the outer membranes of Thermus species are not composed of lipopolysaccharides but of peculiar glycolipids (GL), whose structures seem to be strictly involved in the adaptation to high temperatures. In this work, the complete structures of the major GL components from the cell envelope of the thermophilic bacterium Thermus thermophilus Samu-SA1 are presented. Protocols conventionally adopted for Gram-negative bacteria were used, and, for the first time, GL from Thermus were analyzed in their native form. Two GL and one phosphoglycolipid (PGL) were detected and characterized. The two GL, analyzed by nuclear magnetic resonance (NMR) spectroscopy and electrospray ionization Fourier transform ion cyclotron resonance (ESI FT-ICR) mass spectrometry, possessed the same tetrasaccharide structure linked to a glycerol unit or, alternatively, to a long-chain diol. Moreover, a PGL from Thermus was characterized for the first time, in which N-glyceroyl-heptadecaneamine was present. These molecules are chemically related to other GL from thermophile bacteria, in which they play a crucial role in the adaptation of cell membranes to heat.

  2. Newly Isolated but Uncultivated Magnetotactic Bacterium of the Phylum Nitrospirae from Beijing, China

    PubMed Central

    Li, Jinhua; Pan, Yongxin

    2012-01-01

    Magnetotactic bacteria (MTB) in the phylum Nitrospirae synthesize up to hundreds of intracellular bullet-shaped magnetite magnetosomes. In the present study, a watermelon-shaped magnetotactic bacterium (designated MWB-1) from Lake Beihai in Beijing, China, was characterized. This uncultivated microbe was identified as a member of the phylum Nitrospirae and represents a novel phylogenetic lineage with ≥6% 16S rRNA gene sequence divergence from all currently described MTB. MWB-1 contained 200 to 300 intracellular bullet-shaped magnetite magnetosomes and showed a helical swimming trajectory under homogeneous magnetic fields; its magnetotactic velocity decreased with increasing field strength, and vice versa. A robust phylogenetic framework for MWB-1 and all currently known MTB in the phylum Nitrospirae was constructed utilizing maximum-likelihood and Bayesian algorithms, which yielded strong evidence that the Nitrospirae MTB could be divided into four well-supported groups. Considering its population densities in sediment and its high numbers of magnetosomes, MWB-1 was estimated to account for more than 10% of the natural remanent magnetization of the surface sediment. Taken together, the results of this study suggest that MTB in the phylum Nitrospirae are more diverse than previously realized and can make important contributions to the sedimentary magnetization in particular environments. PMID:22113917

  3. Isolation and Characterization of Intracellular Protein Inclusions Produced by the Entomopathogenic Bacterium Photorhabdus luminescens

    PubMed Central

    Bowen, David J.; Ensign, Jerald C.

    2001-01-01

    Cells of the entomopathogenic bacterium Photorhabdus luminescens contain two types of morphologically distinct crystalline inclusion proteins. The larger rectangular inclusion (type 1) and a smaller bipyramid-shaped inclusion (type 2) were purified from cell lysates by differential centrifugation and isopycnic density gradient centrifugation. Both structures are composed of protein and are readily soluble at pH 11 and 4 in 1% sodium dodecyl sulfate (SDS) and in 8 M urea. Electrophoretic analysis reveals that each inclusion is composed of a single protein subunit with a molecular mass of 11,000 Da. The proteins differ in amino acid composition, protease digestion pattern, and immunological cross-reactivity. The protein inclusions are first visible in the cells at the time of late exponential growth. Western blot analyses showed that the proteins appeared in cells during mid- to late exponential growth. When at maximum size in stationary-phase cells, the proteins constitute 40% of the total cellular protein. The protein inclusions are not used during long-term starvation of the cells and were not toxic when injected into or fed to Galleria mellonella larvae. PMID:11571191

  4. Virulent to avirulent conversion of Legionnaires' disease bacterium (Legionella pneumophila)--its effect on isolation techniques.

    PubMed

    McDade, J E; Shepard, C C

    1979-06-01

    Suspensions of the Legionnaries' disease bacterium (Legionella pneumophila; LDB) were prepared from the yolk sacs of infected egg embryos, the spleens of infected guinea pigs, and cultures of the organism propagated on enriched Mueller-Hinton agar. Each suspension was titrated to determine the number of bacterial colonies (cfu), yolk sac 50% lethal doses (YSLD50), guinea pig 50% infectious doses (GPID50), and guinea pig 50% lethal doses (GPLD50) produced by 1 ml of inoculum. The numbers of cfu/YSLD50, GPID50, and GPLD50 were then calculated for each suspension. The suspension from yolk sacs had 1 cfu/YSLD50 and 10 cfu/GPID50. The suspension from spleens of guinea pigs also had 1 cfu/YSLD50. Organisms propagated on Mueller-Hinton agar, however, had greater than 10(7) cfu/YSLD50 and 10(5) cfu/GPID50. Thus, the LDB lost virulence when it was cultivated on agar. Guinea pigs vaccinated either subcutaneously or intraperitoneally with LDB grown on Mueller-Hinton agar resisted challenge with virulent LDB.

  5. Isolation and Bioaugmentation of an Estradiol-Degrading Bacterium and Its Integration into a Mature Biofilm▿

    PubMed Central

    Iasur-Kruh, Lilach; Hadar, Yitzhak; Minz, Dror

    2011-01-01

    Bioaugmentation can alter the potential activity as well as the composition of the naturally occurring microbial biota during bioremediation of a contaminated site. The focus of the current study is the pollutant 17β-estradiol (E2), which can cause endocrine effects and is potentially harmful to aquatic biota and to public health. The community composition and function of biofilms, originating from a wetland system, as affected by augmentation of an estradiol-degrading bacterium (EDB-LI1) under different conditions, were investigated. EDB-LI1 inoculation into biofilm from two wetland ponds representing early and advanced water treatment stages, respectively, yielded three significant observations, as follows: (i) EDB-LI1, enriched from a biofilm of a constructed wetland wastewater treatment system, was detected (by quantitative PCR [qPCR] analysis) in this environment in the augmented biofilm only; (ii) the augmented biofilm acquired the ability to remove estradiol; and (iii) the bacterial community composition (analyzed by PCR-denaturing gradient gel electrophoresis [DGGE]) of the augmented biofilm differed from that of the control biofilm. Furthermore, EDB-LI1 bioaugmentation showed a higher level of removal of estradiol with biofilms that originated from the advanced-treatment-stage wetland pond than those from the early-treatment-stage pond. Hence, the bioaugmentation efficiency of EDB-LI1 depends on both the quality of the feed water and the microbial community composition in the pond. PMID:21478310

  6. Klebsiella michiganensis sp. nov., a new bacterium isolated from a tooth brush holder.

    PubMed

    Saha, Ratul; Farrance, Christine E; Verghese, Bindhu; Hong, Sunhee; Donofrio, Robert S

    2013-01-01

    Isolate W14(T) recovered from a household tooth brush holder was found to be gram-negative, a facultative anaerobic, non-motile, capsulated, and a non-endospore-forming straight rod. Based on phylogenetic analysis with 16S rRNA gene sequence, isolate W14(T) was affiliated to the genus Klebsiella. The closest phylogenetic relative was K. oxytoca with 99 % similarity in the 16S rRNA gene sequence. The major whole-cell fatty acids were C(16:0) (31.23 %), C(18:1ω6c)/C(18:1ω7c) (21.10 %), and C(16:1ω7c)/C(16:1ω6c) (19.05 %). The sequence similarities of isolate W14(T) based on rpoB, gyrA, and gyrB were 97, 98, and 98 % with K. oxytoca, and 97, 93, and 90 % with K. mobilis (=Enterobacter aerogenes), respectively. The ribotyping pattern showed a 0.46 similarity with K. oxytoca ATCC 13182(T) and 0.24 with K. mobilis ATCC 13048(T). The DNA G+C content of isolate W14(T) was 54.6 mol%. The DNA-DNA relatedness was 55.7 % with K. oxytoca ATCC 13182(T). Using the identification technology of MALDI-TOF mass spectrometry, the top matches for this isolate were K. oxytoca ATCC 13182(T) (Match Factor Score 1.998) and K. mobilis (Score 1.797). On the basis of phenotypic, biochemical, chemotaxonomic, and molecular studies, isolate W14(T) could be differentiated from other members of the genus Klebsiella including K. mobilis. Therefore, it is proposed that isolate W14(T) (=ATCC BAA-2403(T)=DSM 25444(T)) should be classified as the type strain of a novel species of the genus Klebsiella, K. michiganensis sp. nov.

  7. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species.

  8. Thalassobius abyssi sp. nov., a marine bacterium isolated from the cold-seep sediment.

    PubMed

    Nogi, Yuichi; Mori, Kozue; Makita, Hiroko; Hatada, Yuji

    2015-11-09

    A novel marine bacterial strain designated JAMH 043T was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-negative, rod-shaped, non-motile and aerobic chemo-organotrophs. The cells of the isolate grew optimally at 25 °C, pH 7.0-7.5, and with 3% (w/v) NaCl. The major respiratory quinone was Q-10. The predominant fatty acid was C18:1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Thalassobius in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of closest related species, Thalassobius aestuarii JC2049T, was 98.4 %. The DNA G+C content of the novel strain was 58.0 mol%. The hybridization values for DNA-DNA relatedness between strain JAMH043T and reference strains belonging to the genus Thalassobius were less than 14.1±2.2 %. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Thalassobius, for which the name Thalassobius abyssi sp. nov. is proposed. Type strain is JAMH 043T (=JCM 30900T =DSMZ 100673T).

  9. An efficient thermotolerant and halophilic biosurfactant-producing bacterium isolated from Dagang oil field for MEOR application

    NASA Astrophysics Data System (ADS)

    Wu, Langping; Richnow, Hans; Yao, Jun; Jain, Anil

    2014-05-01

    Dagang Oil field (Petro China Company Limited) is one of the most productive oil fields in China. In this study, 34 biosurfactant-producing strains were isolated and cultured from petroleum reservoir of Dagang oil field, using haemolytic assay and the qualitative oil-displacement test. On the basis of 16S rDNA analysis, the isolates were closely related to the species in genus Pseudomonas, Staphylococcus and Bacillus. One of the isolates identified as Bacillus subtilis BS2 were selected for further study. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties at 37ºC as well as at higher temperature of 55ºC. The biosurfactant produced by the strain BS2 could reduce the surface tension of the culture broth from 70.87 mN/m to 28.97 mN/m after 8 days of incubation at 37ºC and to 36.15 mN/m after 20 days of incubation at 55ºC, respectively. The biosurfactant showed stability at high temperature (up to 120ºC), a wide range of pH (2 to 12) and salt concentrations (up to 12%) offering potential for biotechnology. Fourier transform infrared (FT-IR) spectrum of extracted biosurfactant tentatively characterized the produced biosurfactant as glycolipid derivative. Elemental analysis of the biosurfactant by energy dispersive X-ray spectroscopy (EDS) reveals that the biosurfactant was anionic in nature. 15 days of biodegradation of crude oil suggested a preferential usage of n-alkane upon microbial metabolism of BS2 as a carbon substrate and consequently also for the synthesis of biosurfactants. Core flood studies for oil release indicated 9.6% of additional oil recovery over water flooding at 37ºC and 7.2% of additional oil recovery at 55 ºC. Strain BS2 was characterized as an efficient biosurfactant-producing, thermotolerant and halophillic bacterium and has the potential for application for microbial enhanced oil recovery (MEOR) through water flooding in China's oil fields even in situ as adapted to reservoir chemistry and

  10. Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.

    PubMed

    Han, Song-Ih; Kim, Ju-Ok; Lee, Ye-Rim; Ekpeghere, Kalu I; Koh, Sung-Cheol; Whang, Kyung-Sook

    2016-06-01

    A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)).

  11. Characterization of a phenol-degrading bacterium isolated from an industrial effluent and its potential application for bioremediation.

    PubMed

    Paisio, Cintia E; Talano, Melina A; González, Paola S; Pajuelo-Domínguez, Eloisa; Agostini, Elizabeth

    2013-01-01

    The use of native microorganisms is a useful strategy for phenol bioremediation. In the present work, a bacterial strain, named RTE1.4, was isolated from effluents of a chemical industry. The strain was able to grow at high concentrations of phenol and its derivatives, such as guaiacol, 2,4-dichlorophenol and pentachlorophenol, as well as in a medium containing industrial effluents. This bacterium was identified as Acinetobacter sp. using morphological, physiological, biochemical and 16S rRNA gene analysis. Acinetobacter sp. RTE1.4 degraded phenol (200 to 600 mg/L) at wide pH range and temperature (5-9 and 25-37 degrees C, respectively) demonstrating high adaptation ability to different conditions. The strain would metabolize phenol by the ortho-pathway since catechol 1,2-dioxygenase activity was detected. When bacteria were grown in medium containing phenol, an altered whole-cell protein pattern was observed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), with the lack of some low-molecular mass polypeptides and an increase in the relative abundance of high-molecular mass proteins after treatment. Considering that the use of native strains in bioremediation studies shows several ecological advantages and that the studied bacterium showed high tolerance and biodegradation capabilities, Acinetobacter sp. RTE1.4 could be an appropriate microorganism for improving bioremediation and biotreatment of areas polluted with phenol and/or some of its derivatives. Moreover, the establishment of the optimal growth conditions (pH, temperature, concentration of the pollutant) would provide baseline data for bulk production of the strain and its use in bioremediation processes.

  12. Alkalibacterium olivoapovliticus gen. nov., sp. nov., a new obligately alkaliphilic bacterium isolated from edible-olive wash-waters.

    PubMed

    Ntougias, S; Russell, N J

    2001-05-01

    A novel Gram-positive, obligately alkaliphilic, non-sporulating, rod-shaped, flagellated bacterium is described. Three different strains of the bacterium were isolated from the wash-waters of edible-olive production. The strains are motile, psychrotolerant, halotolerant, facultatively anaerobic bacteria with a pH optimum of 9.0-9.4 for two strains and 9.8-10.2 for the third. They are catalase- and oxidase-negative. A range of hexoses and some disaccharides composed of hexoses, but not pentoses are metabolized by the bacterial strains: D(+)-glucose, D(+)-glucose 6-phosphate, D(+)-cellobiose, starch or sucrose are the carbohydrates best utilized. No common amino acids are utilized by the three alkaliphilic strains, but yeast extract can serve as sole carbon and energy source. The major membrane phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid, all containing saturated and unsaturated, even-carbon-numbered fatty acyl chains with hexadecanoic and hexadecen(7)oic as the predominant components. The G+C content of the DNA in all three strains is 39.7+/-1.0 mol% and the DNA relatedness by hybridization is >88% for all pairings of the three strains. The results of 16S rRNA sequence comparisons revealed that the strains represent a new alkaliphilic linkage in the order Bacillales, belonging to the Carnobacterium/Aerococcus-like spectrum. It is proposed that the strains should be assigned to a new genus and species, Alkalibacterium olivoapovliticus. The three strains, designated WW2-SN4aT, WW2-SN4c and WW2-SN5, have been deposited with Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as DSM 13175T, DSM 12937 and DSM 12938 respectively, and in the National Collection of Industrial and Marine Bacteria as NCIMB 13710T, NCIMB 13711 and NCIMB 13712, respectively. The type species of this genus is Alkalibacterium olivoapovliticus and the type strain is WW2-SN4aT.

  13. Relaxation dynamics of the LH2 complex from a photosynthetic purple bacterium Thiorhodospira sibirica studied by the near-IR femtosecond pump-probe method

    SciTech Connect

    Razjivin, A P; Pishchal'nikov, R Yu; Kozlovskii, V S; Kompanets, V O; Chekalin, Sergei V; Moskalenko, A A; Makhneva, Z K

    2005-01-31

    Photoinduced changes in the absorption spectrum of the LH2 (B800-830-850) complex from a Thiorhodospira sibirica (Trs. sibirica) bacterium are studied by the pump-probe method. The complex has the anomalous absorption spectrum exhibiting three bands in the near-IR region at 793, 826.5, and 846.5 nm. At room temperature, the excitation energy transfer from the B800, B830, and B859 bands was detected with the time constants {tau}{sub 1{approx}}0.5 ps, {tau}{sub 2{approx}}2.5 ps, and {tau}{sub 3} of the order of a few hundreds of picoseconds, respectively. A rapid energy transfer from the B830 band compared to energy transfer from the B850 band ({tau}{sub 2}||{tau}{sub 3}) suggests that all the three bands belong to the same complex (i.e., that the LH2 complex from Trs. sibirica is homogeneous). A slower energy transfer (by three - five times) from the B830 band of the LH2 complex from Trs. sibirica compared to energy transfer from the B800 band of the LH2 complexes (B800-850 and especially B800-820) from other purple bacteria suggests that the electronic structures of ensembles of bacteriochlorophyll molecules in these complexes are substantially different. (laser applications and other topics in quantum electronics)

  14. Stark absorption spectroscopy on the carotenoids bound to B800-820 and B800-850 type LH2 complexes from a purple photosynthetic bacterium, Phaeospirillum molischianum strain DSM120.

    PubMed

    Horibe, Tomoko; Qian, Pu; Hunter, C Neil; Hashimoto, Hideki

    2015-04-15

    Stark absorption spectroscopy was applied to clarify the structural differences between carotenoids bound to the B800-820 and B800-850 LH2 complexes from a purple photosynthetic bacterium Phaeospirillum (Phs.) molischianum DSM120. The former complex is produced when the bacteria are grown under stressed conditions of low temperature and dim light. These two LH2 complexes bind carotenoids with similar composition, 10% lycopene and 80% rhodopin, each with the same number of conjugated CC double bonds (n=11). Quantitative classical and semi-quantum chemical analyses of Stark absorption spectra recorded in the carotenoid absorption region reveal that the absolute values of the difference dipole moments |Δμ| have substantial differences (2 [D/f]) for carotenoids bound to either B800-820 or B800-850 complexes. The origin of this striking difference in the |Δμ| values was analyzed using the X-ray crystal structure of the B800-850 LH2 complex from Phs. molischianum DSM119. Semi-empirical molecular orbital calculations predict structural deformations of the major carotenoid, rhodopin, bound within the B800-820 complex. We propose that simultaneous rotations around neighboring CC and CC bonds account for the differences in the 2 [D/f] of the |Δμ| value. The plausible position of the rotation is postulated to be located around C21-C24 bonds of rhodopin.

  15. Isolation and polyphasic characterization of a novel hyper catalase producing thermophilic bacterium for the degradation of hydrogen peroxide.

    PubMed

    Sooch, Balwinder Singh; Kauldhar, Baljinder Singh; Puri, Munish

    2016-11-01

    A newly isolated microbial strain of thermophilic genus Geobacillus has been described with emphasis on polyphasic characterization and its application for degradation of hydrogen peroxide. The validation of this thermophilic strain of genus Geobacillus designated as BSS-7 has been demonstrated by polyphasic taxonomy approaches through its morphological, biochemical, fatty acid methyl ester profile and 16S rDNA sequencing. This thermophilic species of Geobacillus exhibited growth at broad pH and temperature ranges coupled with production of extraordinarily high quantities of intracellular catalase, the latter of which as yet not been reported in any member of this genus. The isolated thermophilic bacterial culture BSS-7 exhibited resistance against a variety of organic solvents. The immobilized whole cells of the bacterium successfully demonstrated the degradation of hydrogen peroxide (H2O2) in a packed bed reactor. This strain has potential application in various analytical and diagnostic methods in the form of biosensors and biomarkers in addition to applications in the textile, paper, food and pharmaceutical industries.

  16. Selective inhibition of toxic cyanobacteria by β-carboline-containing bacterium Bacillus flexus isolated from Saudi freshwaters

    PubMed Central

    Alamri, Saad A.; Mohamed, Zakaria A.

    2013-01-01

    A bacterial strain SSZ01 isolated from a eutrophic lake in Saudi Arabia dominated by cyanobacterial blooms, showed an antialgal activity against cyanobacteria species. Based on the analysis of the 16S rDNA gene sequence, the isolated strain (SSZ01) most likely belonged to the genus Bacillus with a 99% similarity to Bacillus flexus strain EMGA5. The thin layer chromatography (TLC) analysis of the ethyl acetate extract of this bacterium revealed that this strain can produce harmine and norharmane compared to different β-carboline analog standards. Harmine and norharmane were also detected in considerable amounts in bacterial growth medium, indicating a potential excretion of these compounds into the aquatic environment. The crude extract of Bacillus flexus as well as pure materials of harmine and norharmane inhibited the growth of tested species of cyanobacteria. However, the bacterial crude extract has a higher toxicity against tested species of cyanobacteria than harmine and norharmane. In addition, harmine was more toxic to cyanobacteria than norharmane. On the other hand, neither pure compounds of harmine and norharmane nor crude bacterial extract showed any antialgal activity against tested species of green algae. The results of the present study suggest that B. flexus SSZ01 or its crude extract containing harmine and norharmane could be a candidate for the selective control of cyanobacterial blooms without affecting other algal species. PMID:24235872

  17. Virgibacillus ainsalahensis sp. nov., a Moderately Halophilic Bacterium Isolated from Sediment of a Saline Lake in South of Algeria.

    PubMed

    Amziane, Meriam; Darenfed-Bouanane, Amel; Abderrahmani, Ahmed; Selama, Okba; Jouadi, Lydia; Cayol, Jean-Luc; Nateche, Farida; Fardeau, Marie-Laure

    2017-02-01

    A Gram-positive, moderately halophilic, endospore-forming bacterium, designated MerV(T), was isolated from a sediment sample of a saline lake located in Ain Salah, south of Algeria. The cells were rod shaped and motile. Isolate MerV(T) grew at salinity interval of 0.5-25% NaCl (optimum, 5-10%), pH 6.0-12.0 (optimum, 8.0), and temperature between 10 and 40 °C (optimum, 30 °C).The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, a phospholipid, and two lipids, and MK-7 is the predominant menaquinone. The predominant cellular fatty acids were anteiso C15:0 and anteiso C17:0. The DNA G+C content was 45.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MerV(T) was most closely related to Virgibacillus halodenitrificans (gene sequence similarity of 97.0%). On the basis of phenotypic, chemotaxonomic properties, and phylogenetic analyses, strain MerV(T) (=DSM = 28944(T)) should be placed in the genus Virgibacillus as a novel species, for which the name Virgibacillus ainsalahensis is proposed.

  18. Chromohalobacter salarius sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain.

    PubMed

    Aguilera, Margarita; Cabrera, Antonio; Incerti, Claudia; Fuentes, Susana; Russell, Nick J; Ramos-Cormenzana, Alberto; Monteoliva-Sánchez, Mercedes

    2007-06-01

    A moderately halophilic, Gram-negative bacterium (strain CG4.1(T)), which was isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile rod that produced colonies with a yellow pigment. Strain CG4.1(T) grew at salinities of 3-25 % (w/v), at 15-45 degrees C and at pH 5-9. The organism reduced nitrate, hydrolysed starch and had phenylalanine deaminase activity. The major fatty acids were C(18 : 1)omega7c, C(16 : 0) and C(19 : 0) cyclo omega8c. The DNA G+C content was 63.6 mol%. On the basis of phenotypic and phylogenetic data, strain CG4.1(T) appears to be a member of the genus Chromohalobacter and clustered closely with Chromohalobacter species, with 95-96 % similarity between their 16S rRNA gene sequences. However, DNA-DNA relatedness between the isolate and the type strains of Chromohalobacter species was low. Therefore, it is proposed that strain CG4.1(T) represents a novel species, Chromohalobacter salarius sp. nov. The type strain is strain CG4.1(T) (=CECT 5903(T)=LMG 23626(T)).

  19. Cloning and characterization of a novel oligoalginate lyase from a newly isolated bacterium Sphingomonas sp. MJ-3.

    PubMed

    Park, Hwan Hee; Kam, Natania; Lee, Eun Yeol; Kim, Hee Sook

    2012-04-01

    A bacterium possessing alginate-degrading activity was isolated from marine brown seaweed soup liquefied by salted and fermented anchovy. The isolated strain was designated as Sphingomonas sp. MJ-3 based on the analyses of 16S ribosomal DNA sequences, 16S-23S internal transcribed spacer region sequences, biochemical characteristics, and cellular fatty acid composition. A novel alginate lyase gene was cloned from genomic DNA library and then expressed in Escherichia coli. When the deduced amino acid sequence was compared with the sequences on the databases, interestingly, the cloned gene product was predicted to consist of AlgL (alginate lyase L)-like and heparinase-like protein domain. The MJ-3 alginate lyase gene shared below 27.0% sequence identity with exolytic alginate lyase of Sphingomonas sp. A1. The optimal pH and temperature for the recombinant MJ-3 alginate lyase were 6.5 and 50°C, respectively. The final degradation products of alginate oligosaccharides were analyzed by electrospray ionization mass spectrometry and proved to be alginate monosaccharides. Based on the results, the recombinant alginate lyase from Sphingomonas sp. MJ-3 is regarded as an oligoalginate lyase that can degrade oligoalginate and alginate into alginate monosaccharides.

  20. Pseudomonas linyingensis sp. nov.: a novel bacterium isolated from wheat soil subjected to long-term herbicides application.

    PubMed

    He, Wei-Hong; Wang, Ya-Nan; Du, Xun; Zhou, Yang; Jia, Bin; Bian, Jiang; Liu, Shuang-Jiang; Chen, Guo-Can

    2012-11-01

    A strain of genus Pseudomonas, LYBRD3-7(T) was isolated from long-term sulfonylurea herbicides applied wheat-field soil in Linying located in Henan province of China. This strain is a strictly aerobic and Gram-negative short rod-shaped bacterium with single flagellum. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate as a member of Pseudomonas, and most closely to Pseudomonas tuomuerensis CGMCC 1.1365(T) (97.1 %) and P. alcaligenes IAM12411(T) (97.1 %). Morphological characters and chemotaxonomic data confirmed the affiliation of strain LYBRD3-7(T) to the genus Pseudomonas. The results of phylogenetic analysis, physiological and biochemical studies, and DNA-DNA hybridization allowed the differentiation of genotype and phenotype between strain LYBRD3-7(T) and the phylogenetic closest species with valid names. The name proposed for the new species is Pseudomonas linyingensis sp. nov. The type strain is LYBRD3-7(T) (=CGMCC 1.10701(T ) =LMG 25967(T)).

  1. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park.

    PubMed

    Hamilton-Brehm, Scott D; Gibson, Robert A; Green, Stefan J; Hopmans, Ellen C; Schouten, Stefan; van der Meer, Marcel T J; Shields, John P; Damsté, Jaap S S; Elkins, James G

    2013-03-01

    A novel sulfate-reducing bacterium designated OPF15(T) was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70-90 °C and an optimum of 83 °C. Optimal pH was around 6.5-7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15(T) was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15(T) representing the type strain.

  2. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park

    SciTech Connect

    Hamilton-Brehm, Scott D.; Gibson, Robert A.; Green, Stefan J.; Hopmans, Ellen C.; Schouten, Stefan; van der Meer, Marcel T. J.; Shields, John P.; Damsté, Jaap S. S.; Elkins, James G.

    2013-01-24

    A novel sulfate-reducing bacterium designated OPF15T was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70 90 C and an optimum of 83 C. Optimal pH was around 6.5 7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15T was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15T representing the type strain.

  3. First case of human infection due to Pseudomonas fulva, an environmental bacterium isolated from cerebrospinal fluid.

    PubMed

    Almuzara, Marisa N; Vazquez, Miryam; Tanaka, Naoto; Turco, Marisa; Ramirez, Maria S; Lopez, Eduardo L; Pasteran, Fernando; Rapoport, Melina; Procopio, Adriana; Vay, Carlos A

    2010-02-01

    We report the first case of human infection due to Pseudomonas fulva. P. fulva caused acute meningitis following the placement of a drainage system in a 2-year-old female. Additionally, the isolate displayed a VIM-2 carbapenemase in a class 1 integron context.

  4. Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus.

    PubMed

    Kenzaka, Takehiko; Yamada, Yasuhiro; Tani, Katsuji

    2014-05-15

    Burkholderia sp. strain A1 was isolated from a decaying log present in the breeding environment of a stag beetle. The draft genome sequence indicates that strain A1 harbors many biosynthesis molecules, which have antimicrobial properties, and thus potentially eliminates the fungi by producing antifungal compounds, such as siderophores.

  5. Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus

    PubMed Central

    Kenzaka, Takehiko; Yamada, Yasuhiro

    2014-01-01

    Burkholderia sp. strain A1 was isolated from a decaying log present in the breeding environment of a stag beetle. The draft genome sequence indicates that strain A1 harbors many biosynthesis molecules, which have antimicrobial properties, and thus potentially eliminates the fungi by producing antifungal compounds, such as siderophores. PMID:24831148

  6. Mineralization and Potential for Fossilization of an Extremotolerant Bacterium Isolated from a Past Mars Analog Environment

    NASA Astrophysics Data System (ADS)

    Gaboyer, F.; Bohmeier, M.; Foucher, F.; Le Milbeau, C.; Gautret, P.; Richard, A.; Sauldubois, A.; Guegan, R.; Westall, F.

    2016-05-01

    To better characterize the preservation of biomarkers during microbial fossilization, we mineralized a bacterial strain isolated from a cold-acidic-oligotrophic lake in SiO2 and CaSO4 and studied it using SEM, TEM, FT-IR, Raman, GC-MS or Rock-Eval.

  7. Pseudomonas mendocina, an environmental bacterium isolated from a patient with human infective endocarditis.

    PubMed Central

    Aragone, M R; Maurizi, D M; Clara, L O; Navarro Estrada, J L; Ascione, A

    1992-01-01

    Pseudomonas mendocina has been isolated from soil and water samples. Although it has been recovered from some human clinical samples, its pathogenic role has not yet been documented. We report the first known case of endocarditis in humans due to P. mendocina. PMID:1624580

  8. Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment.

    PubMed

    Nogi, Yuichi; Mori, Kozue; Uchida, Hiromi; Hatada, Yuji

    2015-09-01

    A novel marine bacterial strain designated JAMH 011(T) was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 31 °C, with the optimum at 25 °C. The major respiratory quinone was Q-10. The predominant fatty acid was C18 : 1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Shimia in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of the closest related species, Shimia haliotis WM35(T), was 98.1%. The DNA G+C content of the novel strain was 57.3 mol%. The hybridization values for DNA-DNA relatedness between strain JAMH 011(T) and reference strains belonging to the genus Shimia were less than 9.4 ± 0.7%. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Shimia, for which the name Shimia sagamensis sp. nov. is proposed. The type strain is JAMH 011(T) ( = JCM 30583(T) = DSM 29734(T)).

  9. Enterococcus bulliens sp. nov., a novel lactic acid bacterium isolated from camel milk.

    PubMed

    Kadri, Zaina; Spitaels, Freek; Cnockaert, Margo; Praet, Jessy; El Farricha, Omar; Swings, Jean; Vandamme, Peter

    2015-11-01

    Four lactic acid bacteria isolates obtained from fresh dromedary camel milk produced in Dakhla, a city in southern Morocco, were characterised in order to determine their taxonomic position. The four isolates had highly similar MALDI-TOF MS and RAPD fingerprints and identical 16S rRNA gene sequences. Comparative sequence analysis revealed that the 16S rRNA gene sequence of the four isolates was most similar to that of Enterococcus sulfureus ATCC 49903(T) and Enterococcus italicus DSM 15952(T) (99.33 and 98.59% similarity, respectively). However, sequence analysis of the phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase (atpA) genes revealed that the taxon represented by strain LMG 28766(T) was well separated from E. sulfureus LMG 13084(T) and E. italicus LMG 22039(T), which was further confirmed by DNA-DNA hybridization values that were clearly below the species demarcation threshold. The novel taxon was easily differentiated from its nearest neighbour species through sequence analysis of protein encoding genes, MALDI-TOF mass spectrometry and multiple biochemical tests, but had a similar percentage G+C content of about 39%. We therefore propose to formally classify these isolates as Enterococcus bulliens sp. nov., with LMG 28766(T) (=CCMM B1177(T)) as the type strain.

  10. Genome Sequence of Delftia acidovorans HK171, a Nematicidal Bacterium Isolated from Tomato Roots

    PubMed Central

    Han, Jae Woo; Oh, Mira; Choi, Gyung Ja

    2017-01-01

    ABSTRACT Delftia acidovorans strain HK171, isolated from tomato roots, exhibited nematicidal activity against Meloidogyne incognita. Here, we present the genome sequence of D. acidovorans strain HK171, which consists of one circular chromosome of 6,430,384 bp, with 66.9% G+C content. PMID:28254991

  11. Draft Genome Sequences of Three Closely Related Isolates of the Purple Nonsulfur Bacterium Rhodovulum sulfidophilum

    PubMed Central

    Guzman, Michael S.; McGinley, Beau; Santiago-Merced, Natalia; Gupta, Dinesh

    2017-01-01

    ABSTRACT We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a single population that will serve as a model system for understanding genomic traits that underlie metabolic variation within closely related marine purple nonsulfur bacteria in natural microbial communities. PMID:28302776

  12. Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum).

    PubMed

    van der Wolf, Jan M; Nijhuis, Els H; Kowalewska, Malgorzata J; Saddler, Gerry S; Parkinson, Neil; Elphinstone, John G; Pritchard, Leighton; Toth, Ian K; Lojkowska, Ewa; Potrykus, Marta; Waleron, Malgorzata; de Vos, Paul; Cleenwerck, Ilse; Pirhonen, Minna; Garlant, Linda; Hélias, Valérie; Pothier, Joël F; Pflüger, Valentin; Duffy, Brion; Tsror, Leah; Manulis, Shula

    2014-03-01

    Pectinolytic bacteria have been recently isolated from diseased potato plants exhibiting blackleg and slow wilt symptoms found in a number of European countries and Israel. These Gram-reaction-negative, motile, rods were identified as belonging to the genus Dickeya, previously the Pectobacterium chrysanthemi complex (Erwinia chrysanthemi), on the basis of production of a PCR product with the pelADE primers, 16S rRNA gene sequence analysis, fatty acid methyl esterase analysis, the production of phosphatases and the ability to produce indole and acids from α-methylglucoside. Differential physiological assays used previously to differentiate between strains of E. chrysanthemi, showed that these isolates belonged to biovar 3. Eight of the isolates, seven from potato and one from hyacinth, were analysed together with 21 reference strains representing all currently recognized taxa within the genus Dickeya. The novel isolates formed a distinct genetic clade in multilocus sequence analysis (MLSA) using concatenated sequences of the intergenic spacer (IGS), as well as dnaX, recA, dnaN, fusA, gapA, purA, rplB, rpoS and gyrA. Characterization by whole-cell MALDI-TOF mass spectrometry, pulsed field gel electrophoresis after digestion of whole-genome DNA with rare-cutting restriction enzymes, average nucleotide identity analysis and DNA-DNA hybridization studies, showed that although related to Dickeya dadantii, these isolates represent a novel species within the genus Dickeya, for which the name Dickeya solani sp. nov. (type strain IPO 2222(T) = LMG25993(T) = NCPPB4479(T)) is proposed.

  13. Carotenoid-to-Bacteriochlorophyll Energy Transfer in the LH1-RC Core Complex of a Bacteriochlorophyll b Containing Purple Photosynthetic Bacterium Blastochloris viridis.

    PubMed

    Magdaong, Nikki Cecil M; Niedzwiedzki, Dariusz M; Goodson, Carrie; Blankenship, Robert E

    2016-06-16

    Carotenoid-to-bacteriochlorophyll energy transfer has been widely investigated in bacteriochlorophyll (BChl) a-containing light harvesting complexes. Blastochloris viridis utilizes BChl b, whose absorption spectrum is more red-shifted than that of BChl a. This has implications on the efficiency and pathways of carotenoid-to-BChl energy transfer in this organism. The carotenoids that comprise the light-harvesting reaction center core complex (LH1-RC) of B. viridis are 1,2-dihydroneurosporene and 1,2-dihydrolycopene, which are derivatives of carotenoids found in the light harvesting complexes of several BChl a-containing purple photosynthetic bacteria. Steady-state and ultrafast time-resolved optical spectroscopic measurements were performed on the LH1-RC complex of B. viridis at room and cryogenic temperatures. The overall efficiency of carotenoid-to-bacteriochlorophyll energy transfer obtained from steady-state absorption and fluorescence measurements were determined to be ∼27% and ∼36% for 1,2-dihydroneurosporene and 1,2-dihydrolycopene, respectively. These results were combined with global fitting and target analyses of the transient absorption data to elucidate the energetic pathways by which the carotenoids decay and transfer excitation energy to BChl b. 1,2-Dihydrolycopene transfers energy to BChl b via the S2 → Qx channel with kET2 = (500 fs)(-1) while 1,2-dihydroneurosporene transfers energy via S1→ Qy (kET1 = (84 ps)(-1)) and S2 → Qx (kET2 = (2.2 ps)(-1)) channels.

  14. A heavy metal tolerant novel bacterium, Bacillus malikii sp. nov., isolated from tannery effluent wastewater.

    PubMed

    Abbas, Saira; Ahmed, Iftikhar; Kudo, Takuji; Iqbal, Muhammad; Lee, Yong-Jae; Fujiwara, Toru; Ohkuma, Moriya

    2015-12-01

    The taxonomic position of a Gram-stain positive and heavy metal tolerant bacterium, designated strain NCCP-662(T), was investigated by polyphasic characterisation. Cells of strain NCCP-662(T) were observed to be rod to filamentous shaped, motile and strictly aerobic, and to grow at 10-50 °C (optimum 30-37 °C) and at pH range of 6-10 (optimum pH 7-8). The strain was found to be able to tolerate 0-12 % NaCl (w/v) and heavy metals (Cr 1200 ppm, Pb 1800 ppm and Cu 1200 ppm) in tryptic soya agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence of strain NCCP-662(T) showed that it belongs to the genus Bacillus and showed high sequence similarity (98.2 and 98.0 %, respectively) with the type strains of Bacillus niabensis 4T19(T) and Bacillus halosaccharovorans E33(T). The chemotaxonomic data showed that the major quinone is MK-7; the predominant cellular fatty acids are anteiso-C15 :0, iso-C14:0, iso-C16:0 and C16:0 and iso-C15:0; the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol along with several unidentified glycolipids, phospholipids and polar lipids. The DNA G+C content was determined to be 36.9 mol%. These data also support the affiliation of strain NCCP-662(T) with the genus Bacillus. The level of DNA-DNA relatedness between strain NCCP-662(T) and B. niabensis JCM 16399(T) was 20.5 ± 0.5 %. On the basis of physiological and biochemical characteristics, phylogenetic analyses and DNA-DNA hybridization data, strain NCCP-662(T) can be clearly differentiated from the validly named Bacillus species and thus represents a new species, for which the name Bacillus malikii sp. nov. is proposed with the type strain NCCP-662(T) (= LMG 28369(T) = DSM 29005(T) = JCM 30192(T)).

  15. The isolation and characterization of a new iron-sulfur protein from photosynthetic membranes.

    PubMed

    Malkin, R; Aparicio, P J; Arnon, D I

    1974-06-01

    A new iron-sulfur protein, distinct from the soluble chloroplast ferredoxin, was isolated from chloroplast membranes. The isolated protein, purified to homogeneity, had a molecular weight of about 8000 and 4 atoms of iron and 4 inorganic sulfides per mole. Its absorption spectrum had a broad absorbance band in the 400 nm region, a shoulder at approximately 310 nm, and a peak around 280 nm. The absorbance ratio A(400) to A(280) was 0.55. The electron paramagnetic resonance spectrum (measured at 12 degrees K) of the reduced protein was similar to that of other reduced iron-sulfur proteins, showing a major resonance line at g = 1.94. The isolated protein, when photoreduced by spinach chloroplasts, can in turn transfer electrons to mammalian cytochrome c. However, the photoreduced protein cannot replace soluble ferredoxin in NADP(+) reduction because of its apparent inability to interact with the chloroplast enzyme, ferredoxin-NADP(+) reductase. The relation of the isolated iron-sulfur protein to the bound ferredoxin that acts as the primary electron acceptor in Photosystem I is discussed.

  16. Tibeticola sediminis gen. nov., sp. nov., a thermophilic bacterium isolated from hot spring.

    PubMed

    Khan, Inam Ullah; Hussain, Firasat; Tian, Ye; Habib, Neeli; Xian, Wen-Dong; Jiang, Zhao; Amin, Arshia; Yuan, Chang-Guo; Zhou, En-Min; Zhi, Xiao-Yang; Li, Wen-Jun

    2017-01-06

    Two closely related thermophilic bacterial strains, designated YIM 73013T and YIM 73008 were isolated from a sediment sample collected from a hot spring in Tibet, western Tibet province, China. Taxonomic positions of the two isolates were investigated using a polyphasic approach. The novel isolates were Gram-staining negative, aerobic, short rod shaped and motile by means of a polar flagellum. They were oxidase and catalase positive and were able to grow at 30-55 °C (optimum, 37-45 °C), pH 6.0-8.0 (optimum, pH 7.0) and with NaCl tolerance up to 1 % (w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 73013T and YIM 73008 formed a distinct lineage with respect to closely related genera in the family Comamonadaceae and shared highest 16S rRNA gene sequences similarities with Acidovorax caeni R-24608T (96.3 % and 96.4 %, respectively). The respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids observed were C17:1ω6c, C16:0 and Summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The genomic DNA G+C contents of strains YIM 73013T and YIM 73008 were 68.7 mol% and 68.3 mol%, respectively. Based on the morphological, phylogenetic and chemotaxonomic results, the two isolates merit representation of a novel species in a new genus, for which the name Tibeticola sediminis gen. nov., sp. nov. is proposed. The type strain is YIM 73013T (=DSM 101684T =KCTC 42873T).

  17. High Metabolomic Microdiversity within Co-Occurring Isolates of the Extremely Halophilic Bacterium Salinibacter ruber

    PubMed Central

    Antón, Josefa; Lucio, Marianna; Peña, Arantxa; Cifuentes, Ana; Brito-Echeverría, Jocelyn; Moritz, Franco; Tziotis, Dimitrios; López, Cristina; Urdiain, Mercedes; Schmitt-Kopplin, Philippe; Rosselló-Móra, Ramon

    2013-01-01

    Salinibacter ruber is an extremely halophilic member of the Bacteroidetes that thrives in crystallizer ponds worldwide. Here, we have analyzed two sets of 22 and 35 co-occurring S. ruber strains, newly isolated respectively, from 100 microliters water samples from crystalizer ponds in Santa Pola and Mallorca, located in coastal and inland Mediterranean Spain and 350 km apart from each other. A set of old strains isolated from the same setting were included in the analysis. Genomic and taxonomy relatedness of the strains were analyzed by means of PFGE and MALDI-TOF, respectively, while their metabolomic potential was explored with high resolution ion cyclotron resonance Fourier transform mass spectrometry (ICR-FT/MS). Overall our results show a phylogenetically very homogeneous species expressing a very diverse metabolomic pool. The combination of MALDI-TOF and PFGE provides, for the newly isolated strains, the same scenario presented by the previous studies of intra-specific diversity of S. ruber using a more restricted number of strains: the species seems to be very homogeneous at the ribosomal level while the genomic diversity encountered was rather high since no identical genome patterns could be retrieved from each of the samples. The high analytical mass resolution of ICR-FT/MS enabled the description of thousands of putative metabolites from which to date only few can be annotated in databases. Some metabolomic differences, mainly related to lipid metabolism and antibiotic-related compounds, provided enough specificity to delineate different clusters within the co-occurring strains. In addition, metabolomic differences were found between old and new strains isolated from the same ponds that could be related to extended exposure to laboratory conditions. PMID:23741374

  18. Isolation of proteorhodopsin-bearing bacterium JL-3 from fresh water and characterization of the proteorhodopsin.

    PubMed

    Zhu, Wenjun; Lan, Yanli; Lou, Xiangdi; Han, Ning; Ran, Tingting; Xu, Langlai; Xu, Dongqing; Wang, Wei-Wu

    2013-07-01

    Proteorhodopsins (PRs), light-driven proton pumps, constitute the largest family of the microbial rhodopsins. PRs are widely distributed in the oceanic environment and freshwater, but no bacteria with PRs have been isolated from freshwater so far. To facilitate isolation of the bacteria with PR genes, we constructed a vector system that can be used to clone potential PR genes and render color changes when overexpressed in Escherichia coli. Using this method, we successfully isolated a strain with PR gene from freshwater and identified it as Exiguobacterium sp. JL-3. The full length PR gene was then cloned using the SEFA PCR method. Protein sequence alignment showed that JL-3_PR shares high sequence identity (84-89%) with the PRs from Exiguobacterium strains, but low sequence identity (< 38%) with other PRs. Surprisingly, we could not detect any proton-pumping activity in the native JL-3 cells and protoplasts, but the recombinant JL-3_PR do pump protons when overexpressed in E. coli. Sequence analysis further revealed that the PRs from Exiguobacterium had an unusual lysine as the proton donor instead of the typical acidic residue. These data suggest that JL-3_PR is a sensory PR rather than a proton pump.

  19. Isolation and characterization of a marine algicidal bacterium against the harmful raphidophyceae Chattonella marina.

    PubMed

    Kim, Yun Sook; Lee, Dae-Sung; Jeong, Seong-Yun; Lee, Woe Jae; Lee, Myung-Suk

    2009-02-01

    A bacterial strain named AB-4 showing algicidal activity against Chattonella marina was isolated from coastal water of ULjin, Republic of Korea. The isolated strain was identified as Bacillus sp. by culture morphology, biochemical reactions, and homology research based on 16S rDNA. The bacterial culture led to the lysis of algal cells, suggesting that the isolated strain produced a latent algal-lytic compound. Amongst changes in algicidal activity by different culture filtrate volumes, the 10% (100 microl/ml) concentration showed the biggest change in algicidal activity; there, estimated algicidal activity was 95%. The swimming movements of Chattonella marina cells were inhibited because of treatment of the bacterial culture; subsequently, Chattonella marina cells became swollen and rounded. With longer exposure time, algal cells were disrupted and cellular components lost their integrity and decomposed. The released algicide(s) were heat-tolerant and stable in pH variations, except pH 3, 4, and 5. Culture filtrate of Bacillus sp. AB-4 was toxic against harmful algae bloom (HAB) species and nontoxic against livefood organisms. Bacillus sp. AB-4 showed comparatively strong activity against Akashiwo sanguinea, Fibriocapsa japonica, Heterosigma akashiwo, and Scrippsiella trochoidea. These results suggest that the algicidal activity of Bacillus sp. AB-4 is potentially useful for controlling outbreaks of Chattonella marina.

  20. Tenacibaculum dicentrarchi sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from European sea bass.

    PubMed

    Piñeiro-Vidal, Maximino; Gijón, Daniel; Zarza, Carles; Santos, Ysabel

    2012-02-01

    A novel Gram-stain-negative rod-shaped gliding bacterial strain, designated 35/09(T), was isolated from diseased European sea bass (Dicentrarchus labrax L.) in Spain. Colonies were pale-yellow-pigmented with uneven edges and did not adhere to the agar. The DNA G+C content of the isolate was 31.3 mol%. 16S rRNA gene sequence analysis indicated affiliation to the genus Tenacibaculum (family Flavobacteriaceae, phylum 'Bacteroidetes'). Sequence similarities between the isolate and type strains of other members of the genus were 93.1-97.3 %. The major fatty acids (>5 % of the total fatty acids) were iso-C(15 : 0) (24.8 %), iso-C(15 : 0) 3-OH (18.0 %), anteiso-C(15 : 0) (8.1 %), C(15 : 1)ω6c (6.9 %) and iso-C(15 : 1) (6.2 %). Genotypic and phenotypic data indicate that strain 35/09(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum dicentrarchi sp. nov. is proposed; the type strain is 35/09(T) ( = CECT 7612(T) = NCIMB 14598(T)).

  1. Gluconacetobacter kakiaceti sp. nov., an acetic acid bacterium isolated from a traditional Japanese fruit vinegar.

    PubMed

    Iino, Takao; Suzuki, Rei; Tanaka, Naoto; Kosako, Yoshimasa; Ohkuma, Moriya; Komagata, Kazuo; Uchimura, Tai

    2012-07-01

    Two novel acetic acid bacteria, strains G5-1(T) and I5-1, were isolated from traditional kaki vinegar (produced from fruits of kaki, Diospyros kaki Thunb.), collected in Kumamoto Prefecture, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains G5-1(T) and I5-1 formed a distinct subline in the genus Gluconacetobacter and were closely related to Gluconacetobacter swingsii DST GL01(T) (99.3% 16S rRNA gene sequence similarity). The isolates showed 96-100% DNA-DNA relatedness with each other, but <53% DNA-DNA relatedness with closely related members of the genus Gluconacetobacter. The isolates could be distinguished from closely related members of the genus Gluconacetobacter by not producing 2- and 5-ketogluconic acids from glucose, producing cellulose, growing without acetic acid and with 30% (w/v) d-glucose, and producing acid from sugars and alcohols. Furthermore, the genomic DNA G+C contents of strains G5-1(T) and I5-1 were a little higher than those of their closest phylogenetic neighbours. On the basis of the phenotypic characteristics and phylogenetic position, strains G5-1(T) and I5-1 are assigned to a novel species, for which the name Gluconacetobacter kakiaceti sp. nov. is proposed; the type strain is G5-1(T) (=JCM 25156(T)=NRIC 0798(T)=LMG 26206(T)).

  2. Isolation and characterization of photosynthetic reaction centers from Rhodopseudomonas capsulata and Rhodopseudomonas sphaeroides

    SciTech Connect

    Worland, S.T.

    1984-09-01

    Reaction centers were isolated by affinity chromatography on equine cytochrome C. Peripheral proteins were removed with 0.05% LDAO. Absorption and EPR spectra and bleaching assays indicate that the reaction centers retained their electron donors and acceptors in the native environment. Three reaction center polypeptides were isolated and submitted for amino-terminal sequence determination. By comparing these sequences to those deduced from DNA, it was established that the M and L subunits are post-translationally modified to remove the aminoterminal Met, whereas the H subunit is not. Inhibition of O/sub 2/ evolution in photosystem II particles from spinach by naphthoquinone derivatives show O/sub 2/ inhibition by bromomethyl and acetoxymethyl derivatives but not with hydroxymethyl derivatives. Inhibition by acetoxymethyl derivatives in irreversible and dependent on illumination suggesting that reduction of the quinone is necessary. Therefore acetoxymethyl derivatives may be useful as suicide reagents for labelling quinone binding sites. Procedures were developed to extract one or both of the quinones present in reaction centers and preserve the integrity of the co-factor binding sites. The H and M subunits were cleaned using furmic acid. Both fragments were isolated from the H subunit, while the larger fragment was isolated from the M subunit. Electrophoretic mobilities of the isolated fragments agrees well with the expected molecular weights. The L subunit was digested with Staphylococcus areus vs protease. The pattern obtained was consistant with the potential sites of cleavage, but it was not possible to assign cleavage sites unambiguously. 112 references, 37 figures, 2 tables.

  3. Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment.

    PubMed

    Könneke, Martin; Kuever, Jan; Galushko, Alexander; Jørgensen, Bo Barker

    2013-03-01

    A sulfate-reducing bacterium, designated JHA1(T), was isolated from a permanently cold marine sediment sampled in an Artic fjord on the north-west coast of Svalbard. The isolate was originally enriched at 4 °C in a highly diluted liquid culture amended with hydrogen and sulfate. Strain JHA1(T) was a psychrophile, growing fastest between 14 and 16 °C and not growing above 20 °C. Fastest growth was found at neutral pH (pH 7.2-7.4) and at marine concentrations of NaCl (20-30 g l(-1)). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain JHA1(T) was a member of the family Desulfobacteraceae in the Deltaproteobacteria. The isolate shared 99 % 16S rRNA gene sequence similarity with an environmental sequence obtained from permanently cold Antarctic sediment. The closest recognized relatives were Desulfobacula phenolica DSM 3384(T) and Desulfobacula toluolica DSM 7467(T) (both <95 % sequence similarity). In contrast to its closest phylogenetic relatives, strain JHA1(T) grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity indicated the operation of the reductive acetyl-CoA pathway for inorganic carbon assimilation. Beside differences in physiology and morphology, strain JHA1(T) could be distinguished chemotaxonomically from the genus Desulfobacula by the absence of the cellular fatty acid C16 : 0 10-methyl. Phylogenetic differentiation from other genera was further supported by DsrAB and AprBA sequence analysis. Based on the described phylogenetic and phenotypic differences between strain JHA1(T) and its closest relatives, the establishment of a novel genus and a novel species, Desulfoconvexum algidum gen. nov., sp. nov. is proposed. The type strain is JHA1(T) ( = DSM 21856(T)  = JCM 16085(T)).

  4. Biodegradation of 17alpha-methyltestosterone and isolation of MT-degrading bacterium from sediment of Nile tilapia masculinization pond.

    PubMed

    Homklin, Supreeda; Wattanodorn, Theerachit; Ong, Say Kee; Limpiyakorn, Tawan

    2009-01-01

    The fast growing and highly tolerant fish Nile tilapia is one of the most commonly raised fish in the aquaculture industry. To produce an all-male population, a common practice is to feed the Nile tilapia fry with 17alpha-methyltestosterone (MT)-impregnated food. Uneaten fish food with MT may accumulate in the masculinization ponds and be released into the receiving waters. Not much is known about the fate of MT in the fish farms and in the receiving streams. The objective of this study is to investigate the biodegradation of MT under aerobic condition and to isolate responsible microorganisms. Aerobic biodegradation tests were conducted with MT concentrations of 0.3, 1.0, 5.0, 7.0, and 10.0 mg/L using sediment from the masculinization pond as microbial seed. The results suggested that MT is biodegradable. Lag phase was not observed in all cases. With initial concentrations of 0.3, 1.0, 5.0, 7.0, and 10.0 mg/l, the first-order degradation rates were 0.52, 0.23, 0.17, 0.13 and 0.10 day(-1), respectively. Degradation rates were found to decrease with an increase in the initial MT concentration. Analysis of 16S rRNA gene sequences of a strain isolated from the sediment indicated that the strain was highly similar to Pimelobacter simplex strain S151 (100%) which is in the genus Nocardioidaceae. Using this strain, MT is degraded with a first-order degradation rate of 0.044 h(-1) excluding the lag phase. This is the first work reporting biodegradation of MT and isolation of MT-degrading bacterium from environment.

  5. Bacillus eiseniae sp. nov., a swarming, moderately halotolerant bacterium isolated from the intestinal tract of an earthworm (Eisenia fetida L.).

    PubMed

    Hong, Sung Wook; Park, Jung Min; Kim, Soo-Jin; Chung, Kun Sub

    2012-09-01

    A swarming and moderately halotolerant bacterium, designated strain A1-2(T), was isolated from the intestinal tract of the earthworm Eisenia fetida L. Cells were endospore-forming rods that were facultatively anaerobic, catalase-positive, oxidase-negative and motile by peritrichous flagella. The isolate grew optimally at 30 °C and pH 7.0, and could grow with up to 9 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain A1-2(T) belonged to the genus Bacillus and exhibited 16S rRNA gene sequence similarities of 96.8, 96.0, 96.0, 96.4 and 96.7 % with Bacillus drentensis LMG 21831(T), B. horneckiae PT-45(T), B. niacini BAC 1015, B. infantis SMC 4352-1(T) and B. shackletonii LMG 18435(T), respectively. DNA-DNA relatedness values between the isolate and the reference strains were ≤ 38.3 %. The DNA G+C content of strain A1-2(T) was 38.5 mol%. The predominant menaquinone was MK-7 and the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C(15 : 0) (51.5 %) and anteiso-C(15 : 0) (29.6 %) and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and phenotypic characteristics, it is concluded that strain A1-2(T) represents a novel species of the genus Bacillus, for which we propose the name Bacillus eiseniae sp. nov. The type strain is A1-2(T) (= KCCM 90092(T) = JCM 16993(T)).

  6. Phenotypic and genotypic properties of Microbacterium yannicii, a recently described multidrug resistant bacterium isolated from a lung transplanted patient with cystic fibrosis in France

    PubMed Central

    2013-01-01

    Background Cystic fibrosis (CF) lung microbiota consists of diverse species which are pathogens or opportunists or have unknown pathogenicity. Here we report the full characterization of a recently described multidrug resistant bacterium, Microbacterium yannicii, isolated from a CF patient who previously underwent lung transplantation. Results Our strain PS01 (CSUR-P191) is an aerobic, rod shaped, non-motile, yellow pigmented, gram positive, oxidase negative and catalase positive bacterial isolate. Full length 16S rRNA gene sequence showed 98.8% similarity with Microbacterium yannicii G72T type strain, which was previously isolated from Arabidopsis thaliana. The genome size is 3.95Mb, with an average G+C content of 69.5%. In silico DNA-DNA hybridization analysis between our Microbacterium yannicii PS01isolate in comparison with Microbacterium testaceum StLB037 and Microbacterium laevaniformans OR221 genomes revealed very weak relationship with only 28% and 25% genome coverage, respectively. Our strain, as compared to the type strain, was resistant to erythromycin because of the presence of a new erm 43 gene encoding a 23S rRNA N-6-methyltransferase in its genome which was not detected in the reference strain. Interestingly, our patient received azithromycin 250 mg daily for bronchiolitis obliterans syndrome for more than one year before the isolation of this bacterium. Conclusions Although significance of isolating this bacterium remains uncertain in terms of clinical evolution, this bacterium could be considered as an opportunistic human pathogen as previously reported for other species in this genus, especially in immunocompromised patients. PMID:23642186

  7. Shewanella vesiculosa sp. nov., a psychrotolerant bacterium isolated from an Antarctic coastal area.

    PubMed

    Bozal, Núria; Montes, Ma Jesus; Miñana-Galbis, David; Manresa, Angeles; Mercadé, Elena

    2009-02-01

    Two strains of psychrotolerant bacteria, designated M7(T) and M5, isolated from Antarctic coastal marine environments were studied to determine their taxonomic position. The organisms comprised Gram-negative, rod-shaped, facultatively anaerobic cells that were motile by means of single polar flagella. Neither of the bacterial isolates had a requirement for Na(+). These two psychrotolerant strains grew at temperatures ranging from -4 to 30 degrees C. Both strains were capable of producing H(2)S from thiosulfate and were able to use sodium nitrate and trimethylamine N-oxide as terminal electron acceptors during anaerobic growth. 16S rRNA gene sequence analysis placed M7(T) and M5 within the genus Shewanella; the strains showed the highest similarity (99.9 and 99.2 % respectively) with respect to the type strains of Shewanella livingstonensis and Shewanella frigidimarina. However the levels of gyrB sequence similarity between strain M7(T) and the type strains of S. livingstonensis and S. frigidimarina were 87.6 and 87.4 %, respectively. DNA-DNA hybridization experiments performed between the Antarctic isolate M7(T) and S. livingstonensis LMG 19866(T) and S. frigidimarina LMG 19475(T) revealed levels of relatedness of 32 and 35 %, respectively. Strain M5 showed 100 % DNA relatedness with respect to strain M7(T). The DNA G+C content of these bacteria was 42 mol%. Several phenotypic characteristics, the cellular fatty acid compositions and the quinone content of strains M7(T) and M5 served to differentiate them from related shewanellae. On the basis of the data from this polyphasic taxonomic study, M7(T) and M5 constitute a single genospecies. They represent a novel species of the genus Shewanella, for which the name Shewanella vesiculosa sp. nov. is proposed. The type strain is M7(T) (=LMG 24424(T) =CECT 7339(T)).

  8. Induction of larval metamorphosis of the coral Acropora millepora by tetrabromopyrrole isolated from a Pseudoalteromonas bacterium.

    PubMed

    Tebben, Jan; Tapiolas, Dianne M; Motti, Cherie A; Abrego, David; Negri, Andrew P; Blackall, Linda L; Steinberg, Peter D; Harder, Tilmann

    2011-04-29

    The induction of larval attachment and metamorphosis of benthic marine invertebrates is widely considered to rely on habitat specific cues. While microbial biofilms on marine hard substrates have received considerable attention as specific signals for a wide and phylogenetically diverse array of marine invertebrates, the presumed chemical settlement signals produced by the bacteria have to date not been characterized. Here we isolated and fully characterized the first chemical signal from bacteria that induced larval metamorphosis of acroporid coral larvae (Acropora millepora). The metamorphic cue was identified as tetrabromopyrrole (TBP) in four bacterial Pseudoalteromonas strains among a culture library of 225 isolates obtained from the crustose coralline algae Neogoniolithon fosliei and Hydrolithon onkodes. Coral planulae transformed into fully developed polyps within 6 h, but only a small proportion of these polyps attached to the substratum. The biofilm cell density of the four bacterial strains had no influence on the ratio of attached vs. non-attached polyps. Larval bioassays with ethanolic extracts of the bacterial isolates, as well as synthetic TBP resulted in consistent responses of coral planulae to various doses of TBP. The lowest bacterial density of one of the Pseudoalteromonas strains which induced metamorphosis was 7,000 cells mm(-2) in laboratory assays, which is on the order of 0.1-1% of the total numbers of bacteria typically found on such surfaces. These results, in which an actual cue from bacteria has been characterized for the first time, contribute significantly towards understanding the complex process of acroporid coral larval settlement mediated through epibiotic microbial biofilms on crustose coralline algae.

  9. Meiothermus roseus sp. nov., a thermophilic bacterium isolated from a geothermal area.

    PubMed

    Ming, Hong; Duan, Yan-Yan; Guo, Qian-Qian; Yin, Yi-Rui; Zhou, En-Min; Liu, Lan; Li, Shuai; Nie, Guo-Xing; Li, Wen-Jun

    2015-10-01

    Two closely related thermophilic bacterial strains, designated YIM 71031(T) and YIM 71039, were isolated from a hot spring in Tengchong county, Yunnan province, south-western China. The novel isolates were observed to be Gram-negative, aerobic, rod-shaped and yellow-pigmented bacteria. The strains were found to be able to grow at 37-65 °C, pH 6.0-9.0 and with a NaCl tolerance up to 1.0 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences placed these two isolates in the genus Meiothermus. They were found to be closely related to Meiothermus timidus DSM 17022(T) (98.6 % similarity), and formed a cluster with this species. The predominant menaquinone was identified as MK-8 and the major fatty acids (>10 %) as anteiso-C15:0, iso-C15:0, anteiso-C17:0, iso-C16:0 and C16:0. The genomic DNA G+C contents of strains YIM 71031(T) and YIM 71039 were determined to be 64.0 and 65.4 mol%, respectively. DNA-DNA hybridizations showed low values between strains YIM 71031(T) and YIM 71039 and their closely related neighbour M. timidus DSM 17022(T). Morphological phylogenetic and chemotaxonomic results suggest that strains YIM 71031(T) and YIM 71039 are representatives of a new species within the genus Meiothermus, for which the name Meiothermus roseus sp. nov. is proposed. The type strain is YIM 71031(T) (=KCTC 42495(T) =NBRC 110900(T)).

  10. Effects of Soil pH on the Biodegradation of Chlorpyrifos and Isolation of a Chlorpyrifos-Degrading Bacterium

    PubMed Central

    Singh, Brajesh K.; Walker, Allan; Morgan, J. Alun W.; Wright, Denis J.

    2003-01-01

    We examined the role of microorganisms in the degradation of the organophosphate insecticide chlorpyrifos in soils from the United Kingdom and Australia. The kinetics of degradation in five United Kingdom soils varying in pH from 4.7 to 8.4 suggested that dissipation of chlorpyrifos was mediated by the cometabolic activities of the soil microorganisms. Repeated application of chlorpyrifos to these soils did not result in the development of a microbial population with an enhanced ability to degrade the pesticide. A robust bacterial population that utilized chlorpyrifos as a source of carbon was detected in an Australian soil. The enhanced ability to degrade chlorpyrifos in the Australian soil was successfully transferred to the five United Kingdom soils. Only soils with a pH of ≥6.7 were able to maintain this degrading ability 90 days after inoculation. Transfer and proliferation of degrading microorganisms from the Australian soil to the United Kingdom soils was monitored by molecular fingerprinting of bacterial 16S rRNA genes by PCR-denaturing gradient gel electrophoresis (DGGE). Two bands were found to be associated with enhanced degradation of chlorpyrifos. Band 1 had sequence similarity to enterics and their relatives, while band 2 had sequence similarity to strains of Pseudomonas. Liquid enrichment culture using the Australian soil as the source of the inoculum led to the isolation of a chlorpyrifos-degrading bacterium. This strain had a 16S rRNA gene with a sequence identical to that of band 1 in the DGGE profile of the Australian soil. DNA probing indicated that genes similar to known organophosphate-degrading (opd) genes were present in the United Kingdom soils. However, no DNA hybridization signal was detected for the Australian soil or the isolated degrader. This indicates that unrelated genes were present in both the Australian soil and the chlorpyrifos-degrading isolate. These results are consistent with our observations that degradation of

  11. Dickeyafangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia).

    PubMed

    Tian, Yanli; Zhao, Yuqiang; Yuan, Xiaoli; Yi, Jianping; Fan, Jiaqin; Xu, Zhigang; Hu, Baishi; De Boer, Solke H; Li, Xiang

    2016-09-01

    Gram-stain-negative, pectinolytic bacteria were repeatedly isolated from pear trees displaying symptoms of bleeding canker in China. Three strains, JS5T, LN1 and QZH3, had identical 16S rRNA gene sequences that shared 99 % similarity to the type strain of Dickeya dadantii. Phylogenetic analysis of strains JS5T, LN1 and QZH3 with isolates representing all species of the genus Dickeya and related Pectobacterium species supported their affiliation to Dickeya. Multi-locus sequence typing employing concatenated sequences encoding recA, fusA, gapA, purA, rplB, dnaX and the intergenic spacer illustrated a phylogeny which placed strains JS5T, LN1 and QZH3 as a distinct clade, separate from all other species of the genus Dickeya. Average nucleotide identity values obtained in comparison with all species of the genus Dickeya supported the distinctiveness of strain JS5T within the genus Dickeya. Additionally, all three strains were phenotypically distinguished from other species of the genus Dickeya by failing to hydrolyse casein, and by producing acids from (-)-d-arabinose, (+)melibiose, (+)raffinose, mannitol and myo-inositol, but not from 5-keto-d-gluconate or β-gentiobiose. The name Dickeya fangzhongdai sp. nov. is proposed to accommodate these strains; the type strain is JS5T (=CGMCC 1.15464T=DSM 101947T).

  12. Bacillus radicibacter sp. nov., a new bacterium isolated from root nodule of Oxytropis ochrocephala Bunge.

    PubMed

    Wei, Xiu Li; Lin, Yan Bing; Xu, Lin; Han, Meng Sha; Dong, Dan Hong; Chen, Wei Min; Wang, Li; Wei, Ge Hong

    2015-10-01

    A Gram-positive, facultative anaerobic, rod-shaped, and endospore-forming strain, designated 53-2(T) was isolated from the root nodule of Oxytropis ochrocephala Bunge growing on Qilian mountain, China. The strain can grow at pH 7.0-8.0, 10-50 °C and tolerate up to 11% NaCl. Optimal growth occurred at pH 7.2 and 37 °C. The result of BLASTn search based on 16S rRNA gene sequence revealed that strain 53-2(T) , being closest related to Bacillus acidicola 105-2(T) , possessed remote similarity (less than 95.64%) to the species within genus Bacillus. The DNA G + C content was 37.8%. Chemotaxonomic data (major quinone is MK-7; major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipid, and aminoglycophospholipid; fatty acids are anteiso-C15: 0 , iso-C15:0 and anteiso-C17: 0 ) supported the affiliation of the isolate to the genus Bacillus. On the basis of physiological, phylogenetic, and biochemical properties, strain 53-2(T) represents a novel species within genus Bacillus, for which the name Bacillus radicibacter is proposed. The type strain is 53-2(T) (=DSM27302(T) =ACCC06115(T) =CCNWQLS5(T) ).

  13. Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules

    PubMed Central

    Lu, Jun Kun; Dou, Ya Jing; Zhu, Ya Jie; Wang, Sheng Kun; Sui, Xin Hua

    2014-01-01

    Three slow-growing rhizobial strains, designated RITF806T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus Bradyrhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus Bradyrhizobium, which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus Bradyrhizobium, indicating that these three strains constituted a novel group distinct from any recognized species of the genus Bradyrhizobium. Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806T ( = CCBAU 101088T = JCM 19881T) as the type strain. The DNA G+C content of strain RITF806T is 64.6 mol% (Tm). PMID:24585376

  14. Isolation and identification of chemical constituents from the bacterium Bacillus sp. and their nematicidal activities.

    PubMed

    Zeng, Liming; Jin, Hui; Lu, Dengxue; Yang, Xiaoyan; Pan, Le; Cui, Haiyan; He, Xiaofeng; Qiu, Hongdeng; Qin, Bo

    2015-10-01

    A strain SMrs28 was isolated from the rhizosphere soil of a toxic plant Stellera chamaejasme and identified as Bacillus sp. on the basis of morphological and partial 16S rRNA gene sequence analysis. The crude extract of SMrs28 fermentation broth showed strong nematocidal activities in preliminary test. To define the active nematocidal metabolites of SMrs28, a novel compound (1), 4-oxabicyclo[3.2.2]nona-1(7), 5,8-triene, along with five known compounds (2-6), were isolated from the strain by various column chromatographic techniques and characterized on the basis of spectroscopic analysis. Results of the in vitro nematicidal tests showed that the metabolites presented different levels of activity at certain exposure conditions. Compounds (1-3) displayed LC50 values of 904.12, 451.26, 232.98 µg/ml and 1594.0, 366.62, 206.38 µg/ml against Bursaphelenchus xylophilus and Ditylenchus destructor at 72 h, respectively. This is the first report of the nematicidal activity of the compounds as constituents of Bacillus sp.. Our findings help to find potential chemical structures to develop nematicides from microbial source for the management of nematode-infected plant diseases.

  15. Biosurfactant-producing bacterium, Pseudomonas aeruginosa MA01 isolated from spoiled apples: physicochemical and structural characteristics of isolated biosurfactant.

    PubMed

    Abbasi, Habib; Hamedi, Mir Manochehr; Lotfabad, Tayebe Bagheri; Zahiri, Hossein Shahbani; Sharafi, Hakimeh; Masoomi, Fatemeh; Moosavi-Movahedi, Ali Akbar; Ortiz, Antonio; Amanlou, Massoud; Noghabi, Kambiz Akbari

    2012-02-01

    An extensive investigation was conducted to isolate indigenous bacterial strains with outstanding performance for biosurfactant production from different types of spoiled fruits, food-related products and food processing industries. An isolate was selected from 800 by the highest biosurfactant yield in soybean oil medium and it was identified by 16S rRNA and the two most relevant hypervariable regions of this gene; V3 and V6 as Pseudomonas aeruginosa MA01. The isolate was able to produce 12 g/l of a glycolipid-type biosurfactant and generally less efficient to emulsify vegetable oils compared to hydrocarbons and could emulsify corn and coconut oils more than 50%. However, emulsification index (E(24)) of different hydrocarbons including hexane, toluene, xylene, brake oil, kerosene and hexadecane was between 55.8% and 100%. The surface tension of pure water decreased gradually with increasing biosurfactant concentration to 32.5 mNm(-1) with critical micelle concentration (CMC) value of 10.1mg/l. Among all carbon substrates examined, vegetable oils were the most effective on biosurfactant production. Two glycolipid fractions were purified from the biosurfactant crude extracts, and FTIR and ES-MS were used to determine the structure of these compounds. The analysis indicated the presence of three major monorhamnolipid species: R(1)C(10)C(10), R(1)C(10)C(12:1), and R(1)C(10)C(12); as well as another three major dirhamnolipid species: R(2)C(10)C(10), R(2)C(10)C(12:1), and R(2)C(10)C(12). The strain sweep experiment for measuring the linear viscoelastic of biosurfactant showed that typical behavior characteristics of a weak viscoelastic gel, with storage modulus greater than loss modulus at all frequencies examined, both showing some frequency dependence.

  16. Blastomonas aquatica sp. nov., a bacteriochlorophyll-containing bacterium isolated from lake water.

    PubMed

    Xiao, Na; Liu, Yongqin; Liu, Xiaobo; Gu, Zhengquan; Jiao, Nianzhi; Liu, Hongcan; Zhou, Yuguang; Shen, Liang

    2015-05-01

    Yellow or orange-to-brown pigmented, ovoid or rod-shaped, Gram-negative staining, aerobic strains PE 4-5(T) and N5-10 m-1 were isolated from brackish water in Lake Peng Co and fresh to brackish water in Lake Namtso on the Tibetan Plateau, China. Bacteriochlorophyll a was produced by the isolates. The predominant cellular fatty acids were C16 : 1, C17 : 1 and C18 : 1 unsaturated fatty acids, C17 : 1ω6c (55.3%), C17 : 1ω8c (13.0%) and C18 : 1ω7c (10.4%) for PE 4-5(T) and C18 : 1ω7c (54.7%) and C16 : 1ω7c (18.0%) for N5-10 m-1. The polar lipid profiles of strains PE 4-5(T) and N5-10 m-1 were composed of diphosphatidylglycerol, phosphatidylcholine (not detected in N5-10 m-1), phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unknown phospholipid. The predominant respiratory quinone was ubiquinone Q10 and the DNA G+C content was 66.0 mol% for both strains. The16S rRNA gene sequence of strain PE 4-5(T) shared 99.0% similarity with that of N5-10 m-1, and 97.56% similarity with those of Blastomonas natatoria LMG 17322(T) and Blastomonas ursincola DSM 9006(T), respectively. The DNA-DNA hybridization relatedness between strains PE 4-5(T) and N5-10 m-1 was 79.0 ± 1.0%, but below 70% with the type strains in the genus Blastomonas . Based on the variability of phylogenetic and phenotypic characteristics, the isolates should be classified as representatives of a novel species of the genus Blastomonas; the name Blastomonas aquatica sp. nov. is proposed. The type strain is PE 4-5(T) ( =JCM 30179(T) =CGMCC 1.12851(T)).

  17. Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment.

    PubMed

    Arnau, Víctor Gonzalo; Sánchez, Leandro Arturo; Delgado, Osvaldo Daniel

    2015-02-01

    A psychrotolerant strain, 8H1(T), was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4-35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1(T) to the 'Pseudomonas fluorescens group', displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1(T) could be discriminated from closely related species of the genus Pseudomonas and placed in the 'Pseudomonas gessardii subgroup', including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA-DNA hybridization analysis between 8H1(T) and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1(T) ( = DSM 26522(T) = CCUG 63249(T) = LMG 27247(T)).

  18. Polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine, gas vacuolate bacterium from Antarctica.

    PubMed

    Irgens, R L; Gosink, J J; Staley, J T

    1996-07-01

    Several strains of a novel heterotrophic gas vacuolate bacterium were isolated from antarctic marine waters. The results of phylogenetic analyses in which 16S ribosomal DAN sequencing was used, coupled with phenotypic tests, indicated that strain 34-P(T) (T = type strain) belongs to a new genus and species of the beta subgroup of the Proteobacteria, for which the name Polaromonas vacuolata is proposed. Although the other four strains studied probably belong to this new species, DNA-DNA hybridization tests were not conducted. The closest phylogenetic relatives of P. vacuolata are the photosynthetic nonsulfur purple bacterium Rhodoferax fermentans and the hydrogen autotroph Variovorax paradoxus.

  19. Procedure for rapid isolation of photosynthetic reaction centers using cytochrome c affinity chromatography

    SciTech Connect

    Brudvig, G.W.; Worland, S.T.; Sauer, K.

    1983-02-01

    Horse heart cytochrome c linked to Sepharose 4B is used to purify reaction centers from Rhodopseudomonas sphaeroides R-26. This procedure allows for an initial recovery of 80-90% of the bacterial reaction centers present in chromatophore membranes. High purity reaction centers (A/sub 280//A/sub 802/ < 1.30) can be obtained with a 30% recovery. Reaction centers from wild-type Rps. sphaeroides and Rps. capsulata also bind to a cytochrome c column. Cytochrome c affinity chromatography can also be used to isolate photosystem I complexes from spinach chloroplasts.

  20. Isolation and characterization of a fucoidan-degrading bacterium from Laminaria japonica

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Li, Bafang; Zhao, Xue; Piao, Meizi

    2013-11-01

    Fucoidan, a polysaccharide containing abundant fucose and sulfate ester group, was prepared from Laminaria japonica. In order to obtain fucoidan-degrading enzyme, bacteria capable of degrading fucoidan were screened from kelp. A bacterial strain named RC2-3 was obtained, which degraded fucoidan by the maximum extent of 54% ± 1.3%, the highest among all bacterial isolates. High-performance size exclusion chromatography (HPSEC) showed that the molecular weight of fucoidan was gradually reduced by RC2-3 with culturing time, suggesting the production of fucoidan-degrading enzyme by RC2-3. Phylogenetic analysis of partial 16S ribosomal RNA gene (16S rDNA) sequence showed that RC2-3 belonged to the family Flavobacteriaceae. However, it showed different physiological and biochemical characteristics from the known Flavobacteriaceae members producing fucoidan-degrading enzyme, thus RC2-3 was proposed to be a new member of this family.

  1. Isolation and characterization of a bacterium that degrades various polyester-based biodegradable plastics.

    PubMed

    Teeraphatpornchai, T; Nakajima-Kambe, T; Shigeno-Akutsu, Y; Nakayama, M; Nomura, N; Nakahara, T; Uchiyama, H

    2003-01-01

    Microorganisms isolated from soil samples were screened for their ability to degrade various biodegradable polyester-based plastics. The most active strain, designated as strain TB-13, was selected as the best strain for degrading these plastics. From its phenotypic and genetic characteristics, strain TB-13 was closely related to Paenibacillus amyloyticus. It could degrade poly(lactic acid), poly(butylene succinate), poly(butylene succinate-co-adipate), poly(caprolactone) and poly(ethylene succinate) but not poly(hydroxybutylate-co-valerate). However, it could not utilize these plastics as sole carbon sources. Both protease and esterase activities, which may be involved in the degradation of plastic, were constitutively detected in the culture broth.

  2. Paenibacillus tibetensis sp. nov., a psychrophilic bacterium isolated from alpine swamp meadow soil.

    PubMed

    Han, Li-Li; He, Ji-Zheng; Zheng, Yuan-Ming; Zeng, Jun; Zhang, Li-Mei

    2015-05-01

    A novel psychrophilic strain, SSB001(T), was isolated from an alpine swamp meadow soil in Tibet, China, and identified as a representative of a novel phylogenetic subclade in the genus Paenibacillus , with Paenibacillus antarcticus (96.2%), Paenibacillus macquariensis (96.53%) and Paenibacillus glacialis (96.2%) as the most closely related species on the basis of 16S rRNA gene sequence analyses. The strain was distinguished from defined species of the genus Paenibacillus by further study of rpoB gene sequences, phenotypic characterization, cellular fatty acid composition, quinones, polar lipids and meso-diaminopimelic acid in the peptidoglycan. Based upon these results, we propose the strain as a representative of a novel species named Paenibacillus tibetensis sp. nov., with SSB001(T) ( =ACCC 19728(T) =DSM 29321(T)) as the type strain. The DNA G+C content (mol%) of strain SSB001(T) was 40.18 mol% (HPLC).

  3. Spongiimicrobium salis gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae isolated from a marine sponge.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2016-09-01

    A Gram-stain-negative, strictly aerobic, pale-yellow pigmented, rod-shaped, chemoheterotrophic bacterium, designated A6F-11(T), was isolated from a marine sponge collected in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (92.9 %) sequence similarity with Arenibacter palladensis LMG 21972(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. The major fatty acids of strain A6F-11(T) were iso-C15:1 G, iso-C15:0, C16:1 ω6c and/or C16:1 ω7c and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 34.7 mol%, and the major respiratory quinone was menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel taxon in the family Flavobacteriaceae, for which the name Spongiimicrobium salis gen. nov., sp. nov. is proposed. The type strain of S. salis gen. nov., sp. nov. is A6F-11(T) (= KCTC 42753(T) = NBRC 111401(T)).

  4. Pseudovibrio denitrificans strain Z143-1, a heptylprodigiosin-producing bacterium isolated from a Philippine tunicate.

    PubMed

    Sertan-de Guzman, Alice A; Predicala, Rey Z; Bernardo, Evelyn B; Neilan, Brett A; Elardo, Sheila P; Mangalindan, Gina C; Tasdemir, Deniz; Ireland, Chris M; Barraquio, Wilfredo L; Concepcion, Gisela P

    2007-12-01

    Microbial isolate Z143-1 found to be associated with an unidentified tunicate was characterized due to its significant antimicrobial activity. Z143-1 is similar to Pseudovibrio ascidiaceicola and Pseudovibrio denitrificans in morphological, physiological and biochemical characteristics, except for its ability to ferment glucose and produce a characteristic red pigment. Fatty acid methyl ester analysis revealed a predominance of the fatty acid 18:1 omega7c at 80.55%, at levels slightly lower than the Pseudovibrio denitrificans type strain DN34(T) (87.7%). The mol% G+C of Z143-1 is 54.02, relatively higher than the Pseudovibrio denitrificans type strain DN34(T) and Pseudovibrio ascidiaceicola with mol% G+C of 51.7 and 51.4, respectively. However, phylogenetic analysis of the 16S rRNA gene sequence of Z143-1 showed 100% similarity with the Pseudovibrio denitrificans type strain DN34(T). In this study, the bacterium Z143-1 is reported as a new strain of Pseudovibrio denitrificans. While there is no report of a secondary metabolite for Pseudovibrio denitrificans, Z143-1 produces the red pigment heptylprodigiosin, also known as 16-methyl-15-heptyl-prodiginine, which shows anti-Staphylococcus aureus activity.

  5. Parvibacter caecicola gen. nov., sp. nov., a bacterium of the family Coriobacteriaceae isolated from the caecum of a mouse.

    PubMed

    Clavel, Thomas; Charrier, Cédric; Wenning, Mareike; Haller, Dirk

    2013-07-01

    A single strain, NR06(T), was isolated from the intestine of a TNF(deltaARE) mouse. Based on phylogenetic analysis of partial 16S rRNA gene sequences, strain NR06(T) belongs in the family Coriobacteriaceae within the Actinobacteria. The most closely related species with validly published names are members of the genera Adlercreutzia, Asaccharobacter and Enterorhabdus (<96 % sequence similarity). Strain NR06(T) was characterized by a high prevalence of monomethylmenaquinone-6 (MMK-6; 76 %) and the presence of meso-diaminopimelic acid in the cell wall. One of the major cellular fatty acids of strain NR06(T) was C15 : 0 ISO. Glucose was detected as a whole cell sugar. Strain NR06(T) was resistant to the antibiotic colistin and was positive for arginine and leucine arylamidase activity. Based on these characteristics, strain NR06(T) differed from related described bacteria. Therefore, the name Parvibacter caecicola gen. nov., sp. nov. is proposed to accommodate the novel bacterium. The type strain of the type species is NR06(T) ( = DSM 22242(T) = CCUG 57646(T)).

  6. Rhizobium phenanthrenilyticum sp. nov., a novel phenanthrene-degrading bacterium isolated from a petroleum residue treatment system.

    PubMed

    Wen, Ya; Zhang, Juan; Yan, Qiuxiang; Li, Shunpeng; Hong, Qing

    2011-01-01

    Strain F11(T), a phenanthrene-degrading bacterium, was isolated from a petroleum residue treatment system, and classified under the genus Rhizobium based on the similarity analysis of its 16S rRNA and recA gene sequences. Strain F11(T) falls into the same phylogenetic clade with Rhizobium oryzae Alt 505(T) (96.8% 16S rRNA gene sequence similarity) and Rhizobium pseudoryzae J34A-127(T) (96.2%). Major cellular fatty acids of strain F11(T) are C(16:0) (6.24%) and summed feature 8 (C(18:1ω7c) and/or C(18:1ω6c), 76.59%), which are also the major fatty acids of R. oryzae Alt 505(T) and R. pseudoryzae J34A-127(T). The DNA G+C content of strain F11(T) was 59.3±0.4 mol%. Based on the phylogenetic analysis as well as biochemical and physiological characteristics, strain F11(T) could be separated from all recognized Rhizobium species. Strain F11(T) (=DSM 21882(T) =CCTCC AB 209029(T)) was considered to be representative of a novel species of Rhizobium, for which the name Rhizobium phenanthrenilyticum sp. nov. is proposed.

  7. Isolation and characterization of a plasmid DNA from periodontopathogenic bacterium, Eikenella corrodens 1073, which affects pilus formation and colony morphology.

    PubMed

    Azakami, Hiroyuki; Akimichi, Hiromi; Usui, Masakatsu; Yumoto, Hiromichi; Ebisu, Shigeyuki; Kato, Akio

    2005-05-23

    Eikenella corrodens (Ec) is one of a group of periodontopathogenic bacteria. A plasmid DNA (8.7 kb) isolated from Ec 1073 was designated pMU1. Agarose gel electrophoresis and Southern analysis suggested that pMU1-like plasmids were carried in 2 Ec strains, including 1073, with higher hemagglutination (HA) activity than other strains. We determined the nucleotide sequence of this plasmid and identified 7 ORFs. A homology search revealed that 4 ORFs of pMU1 were homologous to ORFs in pJTPS1, found in a spontaneous avirulent mutant of the phytopathogenic bacterium, Ralstonia solanacearum. pJTPS1 is a putative hypovirulent plasmid, which is thought to control the virulence of R. solanacearum. We also found the ORF to be homologous to the recombinase specific to the type IV pilin gene. We introduced a part of pMU1 into the Ec 23834 strain, which has a pilus structure on its cell surface and forms corroding colonies on solid medium. No pilus structure was observed on the surface of transformants, most of which formed non-corroding colonies. When such transformants (or Ec 1073) were cured of pMU1 with acridine orange, they remained non-foliated and non-corroding. The results suggest that pMU1 might irreversibly affect pilus formation and colony morphology, and might be involved in the pathogenicity and virulence of Ec.

  8. Mitigation of Membrane Biofouling in MBR Using a Cellulolytic Bacterium, Undibacterium sp. DM-1, Isolated from Activated Sludge.

    PubMed

    Nahm, Chang Hyun; Lee, Seonki; Lee, Sang Hyun; Lee, Kibaek; Lee, Jaewoo; Kwon, Hyeokpil; Choo, Kwang-Ho; Lee, Jung-Kee; Jang, Jae Young; Lee, Chung-Hak; Park, Pyung-Kyu

    2017-03-28

    Biofilm formation on the membrane surface results in the loss of permeability in membrane bioreactors (MBRs) for wastewater treatment. Studies have revealed that cellulose is not only produced by a number of bacterial species but also plays a key role during formation of their biofilm. Hence, in this study, cellulase was introduced to a MBR as a cellulose-induced biofilm control strategy. For practical application of cellulase to MBR, a cellulolytic (i.e., cellulase-producing) bacterium, Undibacterium sp. DM-1, was isolated from a lab-scale MBR for wastewater treatment. Prior to its application to MBR, it was confirmed that the cell-free supernatant of DM-1 was capable of inhibiting biofilm formation and of detaching the mature biofilm of activated sludge and cellulose-producing bacteria. This suggested that cellulase could be an effective anti-biofouling agent for MBRs used in wastewater treatment. Undibacterium sp. DM-1-entrapping beads (i.e., cellulolytic-beads) were applied to a continuous MBR to mitigate membrane biofouling 2.2-fold, compared with an MBR with vacant-beads as a control. Subsequent analysis of the cellulose content in the biofilm formed on the membrane surface revealed that this mitigation was associated with an approximately 30% reduction in cellulose by cellulolytic-beads in MBR.

  9. Marinimicrobium haloxylanilyticum sp. nov., a new moderately halophilic, polysaccharide-degrading bacterium isolated from Great Salt Lake, Utah.

    PubMed

    Møller, Mette Fogh; Kjeldsen, Kasper Urup; Ingvorsen, Kjeld

    2010-11-01

    A new moderately halophilic, strictly aerobic, Gram-negative bacterium, strain SX15(T), was isolated from hypersaline surface sediment of the southern arm of Great Salt Lake (Utah, USA). The strain grew on a number of carbohydrates and carbohydrate polymers such as xylan, starch, carboxymethyl cellulose and galactomannan. The strain grew at salinities ranging from 2 to 22% NaCl (w/v). Optimal growth occurred in the presence of 7-11% NaCl (w/v) at a temperature of 35°C and a pH of 6.7-8.2. Major whole-cell fatty acids were C16:0 (30.5%), C18:0 (14.8%), C18:1ω7c (13.1%) and C12:0 (7.8%). The G+C content of the DNA was 60 ± 0.5 mol%. By 16S rRNA gene sequence analysis, strain SX15(T) was shown to be affiliated to members of the gammaproteobacterial genus Marinimicrobium with pair wise identity values of 92.9-94.6%. The pheno- and genotypic properties suggest that strain SX15(T) represents a novel species of the genus Marinimicrobium for which the name Marinimicrobium haloxylanilyticum is proposed. The type strain is SX15(T) (= DSM 23100(T) = CCUG 59572(T)).

  10. Isolation, plant colonization potential, and phenanthrene degradation performance of the endophytic bacterium Pseudomonas sp. Ph6-gfp.

    PubMed

    Sun, Kai; Liu, Juan; Gao, Yanzheng; Jin, Li; Gu, Yujun; Wang, Wanqing

    2014-06-26

    This investigation provides a novel method of endophyte-aided removal of polycyclic aromatic hydrocarbons (PAHs) from plant bodies. A phenanthrene-degrading endophytic bacterium Pseudomonas sp. Ph6 was isolated from clover (Trifolium pratense L.) grown in a PAH-contaminated site. After being marked with the GFP gene, the colonization and distribution of strain Ph6-gfp was directly visualized in plant roots, stems, and leaves for the first time. After ryegrass (Lolium multiflorum Lam.) roots inoculation, strain Ph6-gfp actively and internally colonized plant roots and transferred vertically to the shoots. Ph6-gfp had a natural capacity to cope with phenanthrene in vitro and in planta. Ph6-gfp degraded 81.1% of phenanthrene (50 mg · L(-1)) in a culture solution within 15 days. The inoculation of plants with Ph6-gfp reduced the risks associated with plant phenanthrene contamination based on observations of decreased concentration, accumulation, and translocation factors of phenanthrene in ryegrass. Our results will have important ramifications in the assessment of the environmental risks of PAHs and in finding ways to circumvent plant PAH contamination.

  11. Isolation, plant colonization potential, and phenanthrene degradation performance of the endophytic bacterium Pseudomonas sp. Ph6-gfp

    NASA Astrophysics Data System (ADS)

    Sun, Kai; Liu, Juan; Gao, Yanzheng; Jin, Li; Gu, Yujun; Wang, Wanqing

    2014-06-01

    This investigation provides a novel method of endophyte-aided removal of polycyclic aromatic hydrocarbons (PAHs) from plant bodies. A phenanthrene-degrading endophytic bacterium Pseudomonas sp. Ph6 was isolated from clover (Trifolium pratense L.) grown in a PAH-contaminated site. After being marked with the GFP gene, the colonization and distribution of strain Ph6-gfp was directly visualized in plant roots, stems, and leaves for the first time. After ryegrass (Lolium multiflorum Lam.) roots inoculation, strain Ph6-gfp actively and internally colonized plant roots and transferred vertically to the shoots. Ph6-gfp had a natural capacity to cope with phenanthrene in vitro and in planta. Ph6-gfp degraded 81.1% of phenanthrene (50 mg.L-1) in a culture solution within 15 days. The inoculation of plants with Ph6-gfp reduced the risks associated with plant phenanthrene contamination based on observations of decreased concentration, accumulation, and translocation factors of phenanthrene in ryegrass. Our results will have important ramifications in the assessment of the environmental risks of PAHs and in finding ways to circumvent plant PAH contamination.

  12. Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.

    PubMed

    Reddy, Gundlapally S N; Prakash, Jogadhenu S S; Prabahar, Vadivel; Matsumoto, Genki I; Stackebrandt, Erko; Shivaji, Sisinthy

    2003-01-01

    Strain CMS 76orT, an orange-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. On the basis of chemotaxonomic and phylogenetic properties, strain CMS 76orT was identified as a member of the genus Kocuria. It exhibited a 16S rDNA similarity of 99.8% and DNA-DNA similarity of 71% with Kocuria rosea (ATCC 186T). Phenotypic traits confirmed that strain CMS 78orT and K. rosea were well differentiated. Furthermore, strain CMS 76orT could be differentiated from the other reported species of Kocuria, namely Kocuria kristinae (ATCC 27570T), Kocuria varians (ATCC 15306T), Kocuria rhizophila (DSM 11926T) and Kocuria palustris (DSM 11025T), on the basis of a number of phenotypic features. Therefore, it is proposed that strain CMS 76orT (= MTCC 3702T = DSM 14382T) be assigned to a novel species of the genus Kocuria, as Kocuria polaris.

  13. Characterization of the plant growth promoting bacterium, Enterobacter cloacae MSR1, isolated from roots of non-nodulating Medicago sativa.

    PubMed

    Khalifa, Ashraf Y Z; Alsyeeh, Abdel-Moneium; Almalki, Mohammed A; Saleh, Farag A

    2016-01-01

    The aim of the present study was to characterize the endophytic bacterial strain designated MSR1 that was isolated from inside the non-nodulating roots of Medicago sativa after surface-sterilization. MSR1 was identified as Enterobacter cloacae using both 16S rDNA gene sequence analysis and API20E biochemical identification system (Biomerieux, France). Furthermore, this bacterium was characterized using API50CH kit (Biomerieux, France) and tested for antibacterial activities against some food borne pathogens. The results showed that E. cloacae consumed certain carbohydrates such as glycerol, d-xylose, d-maltose and esculin melibiose as a sole carbon source and certain amino acids such as arginine, tryptophan ornithine as nitrogen source. Furthermore, MSR1 possessed multiple plant-growth promoting characteristics; phosphate solubility, production of phytohormones acetoin and bioactive compounds. Inoculation of Pisum sativum with MSR1 significantly improved the growth parameters (the length and dry weight) of this economically important grain legume compared to the non-treated plants. To our knowledge, this is the first report addressing E. cloacae which exist in roots of alfalfa growing in Al-Ahsaa region. The results confirmed that E. cloacae exhibited traits for plant growth promoting and could be developed as an eco-friendly biofertilizer for P. sativum and probably for other important plant species in future.

  14. Dyella thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soil of sunflower (Helianthus annuus L.).

    PubMed

    Anandham, Rangasamy; Kwon, Soon-Wo; Indira Gandhi, Pandiyan; Kim, Soo-Jin; Weon, Hang-Yeon; Kim, Yi-Seul; Sa, Tong-Min; Kim, Yong-Ki; Jee, Hyeong-Jin

    2011-02-01

    A Gram-negative, aerobic, motile, rod-shaped, thiosulfate-oxidizing bacterium, designated ATSB10(T), was isolated from rhizosphere soil of sunflower (Helianthus annuus L.). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ATSB10(T) was closely related to members of the genera Dyella (96.4-98.1 % 16S rRNA gene sequence similarity) and Luteibacter (96.4-97.0 %) and Fulvimonas soli LMG 19981(T) (96.7 %) and Frateuria aurantia IFO 3245(T) (97.8 %). The predominant fatty acids were iso-C(16 : 0), iso-C(17 : 1)ω9c and iso-C(15 : 0). The major quinone was Q-8. The G+C content of the genomic DNA was 66.0 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, an unknown phospholipid, unknown aminophospholipids and an unknown aminolipid. On the basis of phenotypic properties, phylogenetic distinctiveness and DNA-DNA relatedness, strain ATSB10(T) represents a novel species in the genus Dyella, for which the name Dyella thiooxydans sp. nov. is proposed. The type strain is ATSB10(T) (=KACC 12756(T) =LMG 24673(T)).

  15. Identification and biological activity of potential probiotic bacterium isolated from the stomach mucus of breast-fed lamb

    PubMed Central

    Sepová, H. Kiňová; Dubnicková, M.; Bilková, A.; Bukovský, M.; Bezáková, L.

    2011-01-01

    The lactic acid bacterium E isolated from the stomach mucus of breast-fed lamb was identified by sequencing of 16S rDNA fragment and species-specific PCR as Lactobacillus reuteri. Its potential antimicrobial activity and ability to modulate immune system in vitro and in vivo was determined. The growth inhibition of potential pathogens decreased from Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enterica ser. Minnesota to Escherichia coli. The lowest inhibition activity was observed in the case of Candida albicans. The ability of L. reuteri E to modulate biological activities of human and mouse mononuclear cells was estimated in vitro and in vivo, respectively. The production of IL-1β by monocytes in vitro was significantly induced by L. reuteri E (relative activity 2.47). The ability to modulate biological activities of mononuclear cells by living L. reuteri E cells in vitro in comparison to disintegrated L. reuteri E cells in vivo differed. For example lysozyme activity in vitro was inhibited while in vivo was stimulated (relative activities 0.30 and 1.83, respectively). The peroxidase activity in vitro was stimulated while in vivo was inhibited (relative activities 1.53 and 0.17, respectively). Obtained results indicate that L. reuteri E is potential candidate to be used in probiotic preparations for animals and/or human. PMID:24031741

  16. Purification and characterization of a novel alginate lyase from the marine bacterium Cobetia sp. NAP1 isolated from brown algae.

    PubMed

    Yagi, Hisashi; Fujise, Asako; Itabashi, Narumi; Ohshiro, Takashi

    2016-12-01

    The application of marine resources, instead of fossil fuels, for biomass production is important for building a sustainable society. Seaweed is valuable as a source of marine biomass for producing biofuels such as ethanol, and can be used in various fields. Alginate is an anionic polysaccharide that forms the main component of brown algae. Various alginate lyases (e.g. exo- and endo-types and oligoalginate lyase) are generally used to degrade alginate. We herein describe a novel alginate lyase, AlgC-PL7, which belongs to the polysaccharide lyase 7 family. AlgC-PL7 was isolated from the halophilic Gram-negative bacterium Cobetia sp. NAP1 collected from the brown algae Padina arborescens Holmes. The optimal temperature and pH for AlgC-PL7 activity were 45 °C and 8, respectively. Additionally, AlgC-PL7 was thermostable and salt-tolerant, exhibited broad substrate specificity, and degraded alginate into monosaccharides. Therefore, AlgC-PL7 is a promising enzyme for the production of biofuels.

  17. Keratinase production and biodegradation of whole chicken feather keratin by a newly isolated bacterium under submerged fermentation.

    PubMed

    Sahoo, Dipak K; Das, Arpan; Thatoi, Hrudayanath; Mondal, Keshab C; Mohapatra, Pradeep K Das

    2012-07-01

    A new feather-degrading bacterium PKD 5 was isolated from feather dumping soil and identified as Bacillus weihenstephanensis based on morphological and physiochemical characteristics as well as 16S rRNA gene analysis. Extracellular keratinase was produced during submerged aerobic cultivation in a medium containing chicken feather as sole carbon and energy source and supplemented with salt solutions (NaCl 5.0, MgSO₄ 1.0, K₂HPO₄ 1.0, (NH₄)₂SO₄, 2.0 g/l). The optimal conditions for keratinase production include initial pH of 7.0, inoculum size of 2% (v/v), and cultivation at 40 °C. The maximum keratinase production and keratinolytic activity of PKD 5 was achieved after 7 days of fermentation under shaking condition (120 rpm). The enzyme has found application in developing cost-effective feather by-products for feeds and fertilizers. The manuscript first time describes B. weihenstephanensis PKD 5-mediated keratinase production under submerged fermentation and whole chicken feather biodegradation.

  18. Caenibacillus caldisaponilyticus gen. nov., sp. nov., a thermophilic, spore-forming and phospholipid-degrading bacterium isolated from acidulocompost.

    PubMed

    Tsujimoto, Yoshiyuki; Saito, Ryo; Furuya, Hiroto; Ishihara, Daisuke; Sahara, Takehiko; Kimura, Nobutada; Nishino, Tokuzo; Tsuruoka, Naoki; Shigeri, Yasushi; Watanabe, Kunihiko

    2016-07-01

    A thermophilic and phospholipid-degrading bacterium, designated strain B157T, was isolated from acidulocompost, a garbage compost processed under acidic conditions at moderately high temperature. The organism was Gram-stain-positive, aerobic, spore-forming and rod-shaped. Growth was observed to occur at 40-65 °C and pH 4.8-8.1 (optimum growth: 50-60 °C, pH 6.2). The strain was catalase- and oxidase-positive. The cell wall contained meso-diaminopimelic acid, alanine, glutamic acid and galactose. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major fatty acids were anteiso-C17 : 0 and iso-C17 : 0. Comparative 16S rRNA gene sequence analysis showed that strain B157T was related most closely to Tuberibacillus calidus 607T (94.8 % identity), and the phylogenetic analysis revealed that it belonged to the family Sporolactobacillaceae. The DNA G+C content was determined as 51.8 mol%. In spite of many similarities with the type strains of members of the family Sporolactobacillaceae, genotypic analyses suggest that strain B157T represents a novel species of a new genus, Caenibacilluscaldisaponilyticus gen. nov., sp. nov. The type strain of Caenibacilluscaldisaponilyticus is B157T (=NBRC 111400T=DSM 101100T).

  19. Alicyclobacillus cellulosilyticus sp. nov., a thermophilic, cellulolytic bacterium isolated from steamed Japanese cedar chips from a lumbermill

    PubMed Central

    Sugihara, Asami; Moriwaki, Yoshito; Ueoka, Takahiro; Shimane, Yasuhiro; Minegishi, Hiroaki

    2014-01-01

    A thermophilic bacterium, strain SueokaT, was isolated from steamed Japanese cedar chips from a lumber mill in Gobo, Japan. The strain was able to grow on carboxymethyl cellulose at 60 °C, was Gram-stain-negative, and grew between 40.0 and 67.5 °C (optimum at 55 °C) and between pH 3.5 and 6.5 (optimum at pH 4.8). Comparative analysis of 16S rRNA gene sequences revealed 91.9 , 90.9 , and 90.8 % similarity to Alicyclobacillus macrosporangiidusT, Alicyclobacillus pomorumT, and Alicyclobacillus acidocaldariusT, respectively. The major quinone was MK-7 and the predominant cellular fatty acids were ω-cyclohexane C19 : 0 and ω-cyclohexane C17 : 0. The DNA G+C content was 60.8 mol%. Based on the results of this study, strain SueokaT is a novel species of the genus Alicyclobacillus, and the namehttp://dx.doi.org/10.1601/nm.5071Alicyclobacillus cellulosilyticus sp. nov. (type strain SueokaT = JCM 18487T = KCTC 33007T) is proposed. PMID:24711593

  20. Genetic characterization, nickel tolerance, biosorption, kinetics, and uptake mechanism of a bacterium isolated from electroplating industrial effluent.

    PubMed

    Nagarajan, N; Gunasekaran, P; Rajendran, P

    2015-04-01

    Electroplating industries in Madurai city produce approximately 49,000 L of wastewater and 1200 L of sludge every day revealing 687-5569 ppm of nickel (Ni) with other contaminants. Seventeen Ni-tolerant bacterial strains were isolated from nutrient-enriched effluents. Among them one hyper Ni accumulating strain was scored and identified as Bacillus cereus VP17 on the basis of morphology, biochemical tests, 16S rDNA gene sequencing, and phylogenetic analysis. Equilibrium data of Ni(II) ions using the bacterium as sorbent at isothermal conditions (37 °C) and pH 6 were best adjusted by Langmuir (R(2) = 0.6268) and Freundlich models (R(2) = 0.9505). Experimental validation reveals Ni sorption takes place on a heterogeneous surface of the biosorbent, and predicted metal sorption capacity is 434 ppm. The pseudo-second-order kinetic model fitted the biosorption kinetic data better than the pseudo-first-order kinetic model (R(2) = 0.9963 and 0.3625). Scanning electron microscopy, energy dispersive X-ray, and Fourier transform infrared spectroscopy studies of the bacterial strain with and without Ni(II) ion reveals the biosorption mechanism. The results conclude possibilities of using B. cereus VP17 for Ni bioremediation.

  1. Desulfosporosinus burensis sp. nov., a spore-forming, mesophilic, sulfate-reducing bacterium isolated from a deep clay environment.

    PubMed

    Mayeux, Bruno; Fardeau, Marie-Laure; Bartoli-Joseph, Manon; Casalot, Laurie; Vinsot, Agnès; Labat, Marc

    2013-02-01

    A novel anaerobic, gram-positive, spore-forming, curved rod-shaped, mesophilic and sulfate-reducing bacterium was isolated from pore water collected in a borehole at -490 m in Bure (France). This strain, designated BSREI1(T), grew at temperatures between 5 °C and 30 °C (optimum 25 °C) and at a pH between 6 and 8 (optimum 7). It did not require NaCl for growth, but tolerated it up to 1.5 % NaCl. Sulfate, thiosulfate and elemental sulfur were used as terminal electron acceptors. Strain BSREI1(T) used crotonate, formate, lactate, pyruvate, fructose, glycerol and yeast extract as electron donors in the presence of sulfate. The sole quinone was MK-7. The G+C content of the genomic DNA was 43.3 mol%. Strain BSREI1(T) had the type strains of Desulfosporosinus lacus (16S rRNA gene sequence similarity of 96.83 %), Desulfosporosinus meridiei (96.31 %) and Desulfosporosinus hippei (96.16 %) as its closest phylogenetic relatives. On the basis of phylogenetic and physiological properties, strain BSREI1(T) is proposed as a representative of a novel species of the genus Desulfosporosinus, Desulfosporosinus burensis sp. nov.; the type strain is BSREI1(T) ( = DSM 24089(T) = JCM 17380(T)).

  2. Characterization of the plant growth promoting bacterium, Enterobacter cloacae MSR1, isolated from roots of non-nodulating Medicago sativa

    PubMed Central

    Khalifa, Ashraf Y.Z.; Alsyeeh, Abdel-Moneium; Almalki, Mohammed A.; Saleh, Farag A.

    2015-01-01

    The aim of the present study was to characterize the endophytic bacterial strain designated MSR1 that was isolated from inside the non-nodulating roots of Medicago sativa after surface-sterilization. MSR1 was identified as Enterobacter cloacae using both 16S rDNA gene sequence analysis and API20E biochemical identification system (Biomerieux, France). Furthermore, this bacterium was characterized using API50CH kit (Biomerieux, France) and tested for antibacterial activities against some food borne pathogens. The results showed that E. cloacae consumed certain carbohydrates such as glycerol, d-xylose, d-maltose and esculin melibiose as a sole carbon source and certain amino acids such as arginine, tryptophan ornithine as nitrogen source. Furthermore, MSR1 possessed multiple plant-growth promoting characteristics; phosphate solubility, production of phytohormones acetoin and bioactive compounds. Inoculation of Pisum sativum with MSR1 significantly improved the growth parameters (the length and dry weight) of this economically important grain legume compared to the non-treated plants. To our knowledge, this is the first report addressing E. cloacae which exist in roots of alfalfa growing in Al-Ahsaa region. The results confirmed that E. cloacae exhibited traits for plant growth promoting and could be developed as an eco-friendly biofertilizer for P. sativum and probably for other important plant species in future. PMID:26858542

  3. Isolation, Characterization, and Degradation Performance of the 17β-Estradiol-Degrading Bacterium Novosphingobium sp. E2S

    PubMed Central

    Li, Shunyao; Liu, Juan; Sun, Minxia; Ling, Wanting; Zhu, Xuezhu

    2017-01-01

    A 17β-estradiol (E2)-degrading bacterium E2S was isolated from the activated sludge in a sewage treatment plant (STP). The morphology, biological characteristics, and 16S ribosomal RNA (rRNA) gene sequence of strain E2S indicated that it belonged to the genus Novosphingobium. The optimal degrading conditions were 30 °C and pH 7.0. The ideal inoculum volume was 5% (v/v), and a 20-mL degradation system was sufficient to support the removal ability of strain E2S. The addition of extra NaCl to the system did not benefit the E2 degradation in batch culture by this strain. Strain E2S exhibited high degradation efficiency with initial substrate concentrations of 10–50 mg·L−1. For example, in mineral salt medium containing 50 mg·L−1 of E2, the degradation efficiency was 63.29% after seven days. In cow manure samples supplemented with 50 mg·L−1 of E2, strain E2S exhibited 66.40% degradation efficiency after seven days. The finding of the E2-degrading strain E2S provided a promising method for removing E2 from livestock manure in order to reduce the potential environmental risks of E2. PMID:28125060

  4. Sulfurospirillum cavolei sp. nov., a facultatively anaerobic sulfur-reducing bacterium isolated from an underground crude oil storage cavity.

    PubMed

    Kodama, Yumiko; Ha, Le Thu; Watanabe, Kazuya

    2007-04-01

    A novel facultatively anaerobic sulfur-reducing bacterium, designated strain Phe91(T), was isolated from petroleum-contaminated groundwater in an underground crude oil storage cavity at Kuji in Iwate, Japan. Cells of strain Phe91(T) were slightly curved rods with single polar flagella. Optimum growth was observed at pH 7.0 and 30 degrees C. The novel strain utilized elemental sulfur, thiosulfate, sulfite, dithionite, arsenate, nitrate and DMSO as electron acceptors with lactate as an energy and carbon source, but nitrite was not utilized. Microaerophilic growth was also observed. Fumarate, pyruvate, lactate, malate, succinate, hydrogen (with acetate as a carbon source) and formate (with acetate) could serve as electron donors. Fumarate, pyruvate and malate were fermented. The DNA G+C content was 42.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Phe91(T) was affiliated with the genus Sulfurospirillum in the class Epsilonproteobacteria and was most closely related to Sulfurospirillum deleyianum (sequence similarity 97 %). However, the DNA-DNA hybridization value between strain Phe91(T) and S. deleyianum was only 14 %. Based on the physiological and phylogenetic data, Phe91(T) should be classified as a representative of a novel species in the genus Sulfurospirillum; the name Sulfurospirillum cavolei sp. nov. is proposed, with Phe91(T) (=JCM 13918(T)=DSM 18149(T)) as the type strain.

  5. Isolation and characterization of an NAD+-degrading bacterium PTX1 and its role in chromium biogeochemical cycle

    SciTech Connect

    Puzon, Geoffrey J.; Huang, Yan C.; Dohnalkova, Alice; Xun, Luying

    2008-06-01

    Microorganisms can reduce toxic chromate to less toxic trivalent chromium [Cr(III)]. Besides Cr(OH)3 precipitates, some soluble organo-Cr(III) complexes are readily formed upon microbial, enzymatic, and chemical reduction of chromate. However, the biotransformation of the organo-Cr(III) complexes has not been characterized. We have previously reported the formation of a nicotinamide adenine dinucleotide (NAD+)-Cr(III) complex after enzymatic reduction of chromate. Although the NAD+-Cr(III) complex was stable under sterile conditions, microbial cells were identified as precipitates in a non-sterile NAD+-Cr(III) solution after extended incubation. The most dominant bacterium PTX1 was isolated and assigned to Leifsonia genus by phylogenetic analysis of 16S rRNA gene sequence. PTX1 grew slowly on NAD+ with a doubling time of 17 h, and even more slowly on the NAD+-Cr(III) complex with an estimated doubling time of 35 days. The slow growth suggests that PTX1 passively grew on trace NAD+ dissociated from the NAD+-Cr(III) complex, facilitating further dissociation of the complex and formation of Cr(III) precipitates. Thus, organo-Cr(III) complexes might be an intrinsic link of the chromium biogeochemical cycle; they can be produced during chromate reduction and then further mineralized by microorganisms.

  6. Bacillus dabaoshanensis sp. nov., a Cr(VI)-tolerant bacterium isolated from heavy-metal-contaminated soil.

    PubMed

    Cui, Xiaowen; Wang, Yueqiang; Liu, Jing; Chang, Ming; Zhao, Yong; Zhou, Shungui; Zhuang, Li

    2015-05-01

    A Cr(VI)-tolerant, Gram-staining-positive, rod-shaped, endospore-forming and facultative anaerobic bacterium, designated as GSS04(T), was isolated from a heavy-metal-contaminated soil. Strain GSS04(T) was Cr(VI)-tolerant with a minimum inhibitory concentration of 600 mg l(-1) and was capable of reducing Cr(VI) under both aerobic and anaerobic conditions. Growth occurred with presence of 0-3 % (w/v) NaCl (optimum 1 %), at pH 5.5-10.0 (optimum pH 7.0) and 15-50 °C (optimum 30-37 °C). The main respiratory quinone was MK-7 and the major fatty acids were anteiso-C15:0 and iso-C15:0. The DNA G+C content was 41.1 mol%. The predominant polar lipid was diphosphatidylglycerol. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relative was Bacillus shackletonii DSM 18868(T) (97.6 %). The DNA-DNA hybridization between GSS04(T) and its closest relatives revealed low relatedness (<70 %). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS04(T) represents a novel species of the genus Bacillus, for which the name Bacillus dabaoshanensis sp. nov. is proposed. The type strain is GSS04(T) (=CCTCC AB 2013260(T) = KCTC 33191(T)).

  7. Rhizomicrobium electricum sp. nov., a facultatively anaerobic, fermentative, prosthecate bacterium isolated from a cellulose-fed microbial fuel cell.

    PubMed

    Kodama, Yumiko; Watanabe, Kazuya

    2011-08-01

    A facultatively anaerobic, prosthecate bacterium, strain Mfc52(T), was isolated from a microbial fuel cell inoculated with soil and fed with cellulose as the sole fuel. Cells were Gram-negative, non-spore-forming, straight or slightly curved rods, and some of them had one or two polar prosthecae (stalks). Cells reproduced by binary fission or by budding from mother cells having prosthecae. Strain Mfc52(T) fermented various sugars and produced lactate, acetate and fumarate. Ferric iron, nitrate, oxygen and fumarate served as electron acceptors, while sulfate and malate did not. Nitrate was reduced to nitrite. The DNA G+C content was 64.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Mfc52(T) was affiliated with the genus Rhizomicrobium in the class Alphaproteobacteria and most closely related to Rhizomicrobium palustre with a sequence similarity of 97 %. Based on these physiological and phylogenetic characteristics, the name Rhizomicrobium electricum sp. nov. is proposed; the type strain is Mfc52(T) ( = JCM 15089(T)  = KCTC 5806(T)).

  8. Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity.

    PubMed

    Huang, Yan; Sun, Yingjie; Ma, Shichun; Chen, Lu; Zhang, Hui; Deng, Yu

    2013-08-01

    A novel thermophilic, anaerobic, keratinolytic bacterium designated KD-1 was isolated from grassy marshland. Strain KD-1 was a spore-forming rod with a Gram-positive type cell wall, but stained Gram-negative. The temperature, pH, and NaCl concentration range necessary for growth was 30-65 °C (optimum 55 °C), 6.0-10.5 (optimum 8.0-8.5), and 0-6% (optimum 0.2%) (w/v), respectively. Strain KD-1 possessed extracellular keratinase, and the optimum activity of the crude enzyme was pH 8.5 and 70 °C. The enzyme was identified as a thermostable serine-type protease. The strain was sensitive to rifampin, chloramphenicol, kanamycin, and tetracycline and was resistant to erythromycin, neomycin, penicillin, and streptomycin. The main cellular fatty acid was predominantly C15:0 iso (64%), and the G+C content was 28 mol%. Morphological and physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequencing identified KD-1 as a new species of a novel genus of Clostridiaceae with 95.3%, 93.8% 16S rRNA gene sequence similarity to Clostridium ultunense BS(T) (DSM 10521(T)) and Tepidimicrobium xylanilyticum PML14(T) (= JCM 15035(T)), respectively. We propose the name Keratinibaculum paraultunense gen. nov., sp. nov., with KD-1 (=JCM 18769(T) =DSM 26752(T)) as the type strain.

  9. Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable.

    PubMed

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

    2016-06-01

    A Gram-positive, aerobic, non-motile and extremely halophilic bacterial strain, designated K9(T), was isolated from kimchi, a Korean fermented food. The strain was observed as endospore-forming rod-shaped cells showing oxidase and catalase activity. It was found to grow at 10.0-30.0 % (w/v) NaCl (optimum, 15.0-20.0 %), pH 7.0-8.0 (optimum, pH 7.5) and 15-40 °C (optimum, 30 °C). The polar lipids of strain K9(T) were identified as phosphatidylglycerol, three unidentified phospholipids and an unidentified glycolipid. The isoprenoid quinone was identified as menaquinone-7. The major cellular fatty acids (>20 % of the total) were found to be anteisio-C15:0 and anteisio-C17:0. The cell wall peptidoglycan composition was determined to contain meso-diaminopimelic acid. The G + C content of genomic DNA was determined to be 48.2 mol %. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolated strain is closely related to Lentibacillus salinarum AHS-1(T) (96.7 % sequence similarity). Based on its phenotypic, chemotaxonomic and phylogenetic data, strain K9(T) is considered to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus kimchii sp. nov., is proposed. The type strain is K9(T) (=KACC 18490(T) = JCM 30234(T)).

  10. Isolation, growth, and metabolism of an obligately anaerobic, selenate- respiring bacterium, strain SES-3

    USGS Publications Warehouse

    Oremland, R.S.; Blum, J.S.; Culbertson, C.W.; Visscher, P.T.; Miller, L.G.; Dowdle, P.; Strohmaier, F.E.

    1994-01-01

    A gram-negative, strictly anaerobic, motile vibrio was isolated from a selenate-respiring enrichment culture. The isolate, designated strain SES-3, grew by coupling the oxidation of lactate to acetate plus CO2 with the concomitant reduction of selenate to selenite or of nitrate to ammonium. No growth was observed on sulfate or selenite, but cell suspensions readily reduced selenite to elemental selenium (Se0). Hence, SES-3 can carry out a complete reduction of selenate to Se0. Washed cell suspensions of selenate- grown cells did not reduce nitrate, and nitrate-grown cells did not reduce selenate, indicating that these reductions are achieved by separate inducible enzyme systems. However, both nitrate-grown and selenate-grown cells have a constitutive ability to reduce selenite or nitrite. The oxidation of [14C]lactate to 14CO2 coupled to the reduction of selenate or nitrate by cell suspensions was inhibited by CCCP (carbonyl cyanide m- chlorophenylhydrazone), cyanide, and azide. High concentrations of selenite (5 mM) were readily reduced to Se0 by selenate-grown cells, but selenite appeared to block the synthesis of pyruvate dehydrogenase. Tracer experiments with [75Se]selenite indicated that cell suspensions could achieve a rapid and quantitative reduction of selenite to Se0. This reduction was totally inhibited by sulfite, partially inhibited by selenate or nitrite, but unaffected by sulfate or nitrate. Cell suspensions could reduce thiosulfate, but not sulfite, to sulfide. These results suggest that reduction of selenite to Se0 may proceed, in part, by some of the components of a dissimilatory system for sulfur oxyanions.

  11. Thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent.

    PubMed

    Alain, Karine; Postec, Anne; Grinsard, Elodie; Lesongeur, Françoise; Prieur, Daniel; Godfroy, Anne

    2010-01-01

    A novel, strictly anaerobic, thermophilic, sulfate-reducing bacterium, designated strain AT1325(T), was isolated from a deep-sea hydrothermal vent at the Rainbow site on the Mid-Atlantic Ridge. This strain was subjected to a polyphasic taxonomic analysis. Cells were Gram-negative motile rods (approximately 2.4 x 0.6 microm) with a single polar flagellum. Strain AT1325(T) grew at 55-75 degrees C (optimum, 65-70 degrees C), at pH 5.5-8.0 (optimum, 6.5-7.5) and in the presence of 1.5-4.5 % (w/v) NaCl (optimum, 2.5 %). Cells grew chemolithoautotrophically with H2 as an energy source and SO4(2-) as an electron acceptor. Alternatively, the novel isolate was able to use methylamine, peptone or yeast extract as carbon sources. The dominant fatty acids (>5 % of the total) were C(16 : 0), C(18 : 1)omega7c, C(18 : 0) and C(19 : 0) cyclo omega8c. The G+C content of the genomic DNA of strain AT1325(T) was 45.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain AT1325(T) within the family Thermodesulfobacteriaceae, in the bacterial domain. Comparative 16S rRNA gene sequence analysis indicated that strain AT1325(T) belonged to the genus Thermodesulfatator, sharing 97.8 % similarity with the type strain of Thermodesulfatator indicus, the unique representative species of this genus. On the basis of the data presented, it is suggested that strain AT1325(T) represents a novel species of the genus Thermodesulfatator, for which the name Thermodesulfatator atlanticus sp. nov. is proposed. The type strain is AT1325(T) (=DSM 21156(T)=JCM 15391(T)).

  12. Bacillus piscis sp. nov., a novel bacterium isolated from the muscle of the antarctic fish Dissostichus mawsoni.

    PubMed

    Lee, Jae-Bong; Jeon, Seon Hwa; Choi, Seok-Gwan; Jung, Hee-Young; Kim, Myung Kyum; Srinivasan, Sathiyaraj

    2016-12-01

    In this paper, a new bacterial strain designated as 16MFT21(T) is isolated from the muscle of a fish caught in the Antarctic Ocean. Strain 16MFT21(T) is a Gram-staining-positive, catalase-oxidase-positive, rod-shaped facultative-aerobic bacterium. The phylogenetic analysis that is based on the 16S-rRNA gene sequence of strain 16MFT21(T) revealed that it belongs to the genus Bacillus in the family Bacillaceae in the class Bacilli. The highest degrees of the sequence similarity of the strain 16MFT21(T) is with Bacillus licheniformis ATCC 14580(T) (96.6%) and Bacillus sonorensis NBRC 101234(T) (96.6%). The isolate formed a pale-yellow pigment, and it grew in the presence of 0% to 10% (w/v) NaCl (optimum at 2% NaCl), a pH of 6.0 to 10.0 (optimum pH from 7.0 to 8.0), and from 4°C to 30°C (optimum at 30°C). The major polar lipids consist of diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The predominant fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The main respiratory quinone is menaquinone-7 (MK-7), and based on the use of the meso-diaminopimelic acid as the diagnostic diamino acid, the peptidoglycan cell-wall type is A1γ. Based on the phylogenetic, phenotypic, and chemotaxonomic data, strain 16MFT21(T) (=KCTC 18866(T) =JCM 31664(T)) for which the name Bacillus piscis sp. nov. is proposed should be classified as a new species.

  13. Brevibacillus nitrificans sp. nov., a nitrifying bacterium isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks.

    PubMed

    Takebe, Fumihiko; Hirota, Kikue; Nodasaka, Yoshinobu; Yumoto, Isao

    2012-09-01

    A heterotrophic nitrifying bacterium, designated strain DA2(T), was isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks. Cells of strain DA2(T) were Gram-positive, facultatively anaerobic, sporulating rods that were motile by means of peritrichous flagella; they were able to grow at pH 5-8. The major isoprenoid quinone of strain DA2(T) was menaquinone-7 (MK-7) and its cellular fatty acid profile consisted mainly of iso-C(15 : 0) (18.6 %) and anteiso-C(15 : 0) (69.1 %). The DNA G+C content was 54.1 mol%. 16S rRNA gene sequence phylogeny suggested that strain DA2(T) is a member of the genus Brevibacillus, with highest sequence similarities (in parentheses) to the type strains of Brevibacillus choshinensis (99.7 %), B. formosus (99.4 %), B. brevis (99.4 %), B. agri (99.0 %), B. reuszeri (98.8 %), B. parabrevis (98.7 %), B. centrosporus (98.6 %), B. limnophilus (97.4 %), B. panacihumi (97.3 %) and B. invocatus (97.3 %). DNA-DNA hybridization showed less than 60 % relatedness between strain DA2(T) and type strains of the most closely related species given above. Given the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analysis based on the 16S rRNA sequence and DNA-DNA relatedness data, the isolate merits classification as a novel species, for which the name Brevibacillus nitrificans is proposed; the type strain of this species is DA2(T) (= JCM 15774(T) = NCIMB 14531(T)).

  14. Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations.

    PubMed

    Grange, Zoe L; Gartrell, Brett D; Biggs, Patrick J; Nelson, Nicola J; Marshall, Jonathan C; Howe, Laryssa; Balm, Matthew G M; French, Nigel P

    2015-10-01

    Predicting and preventing outbreaks of infectious disease in endangered wildlife is problematic without an understanding of the biotic and abiotic factors that influence pathogen transmission and the genetic variation of microorganisms within and between these highly modified host communities. We used a common commensal bacterium, Campylobacter spp., in endangered Takahe (Porphyrio hochstetteri) populations to develop a model with which to study pathogen dynamics in isolated wildlife populations connected through ongoing translocations. Takahe are endemic to New Zealand, where their total population is approximately 230 individuals. Takahe were translocated from a single remnant wild population to multiple offshore and mainland reserves. Several fragmented subpopulations are maintained and connected through regular translocations. We tested 118 Takahe from 8 locations for fecal Campylobacter spp. via culture and DNA extraction and used PCR for species assignment. Factors relating to population connectivity and host life history were explored using multivariate analytical methods to determine associations between host variables and bacterial prevalence. The apparent prevalence of Campylobacter spp. in Takahe was 99%, one of the highest reported in avian populations. Variation in prevalence was evident among Campylobacter species identified. C. sp. nova 1 (90%) colonized the majority of Takahe tested. Prevalence of C. jejuni (38%) and C. coli (24%) was different between Takahe subpopulations, and this difference was associated with factors related to population management, captivity, rearing environment, and the presence of agricultural practices in the location in which birds were sampled. Modeling results of Campylobacter spp. in Takahe metapopulations suggest that anthropogenic management of endangered species within altered environments may have unforeseen effects on microbial exposure, carriage, and disease risk. Translocation of wildlife between locations could

  15. Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust.

    PubMed

    Sylvan, Jason B; Hoffman, Colleen L; Momper, Lily M; Toner, Brandy M; Amend, Jan P; Edwards, Katrina J

    2015-06-01

    A facultatively anaerobic bacterium, designated strain 1MBB1T, was isolated from basaltic breccia collected from 341 m below the seafloor by seafloor drilling of Rigil Guyot during Integrated Ocean Drilling Program Expedition 330. The cells were straight rods, 0.5 μm wide and 1-3 μm long, that occurred singly and in chains. Strain 1MBB1T stained Gram-positive. Catalase and oxidase were produced. The isolate grew optimally at 30 °C and pH 7.5, and could grow with up to 12 % (w/v) NaCl. The DNA G+C content was 40.5 mol%. The major cellular fatty acids were C16:1ω11c (26.5 %), anteiso-C15:0 (19.5 %), C16:0 (18.7 %) and iso-C15:0 (10.4 %), and the cell-wall diamino acid was meso-diaminopimelic acid. Endospores of strain 1MBB1T oxidized Mn(II) to Mn(IV), and siderophore production by vegetative cells was positive. Phylogenetic analysis of the 16S rRNA gene indicated that strain 1MBB1T was a member of the family Bacillaceae, with Bacillus foraminis CV53T and Bacillus novalis LMG 21837T being the closest phylogenetic neighbours (96.5 and 96.2 % similarity, respectively). This is the first novel species described from deep subseafloor basaltic crust. On the basis of our polyphasic analysis, we conclude that strain 1MBB1T represents a novel species of the genus Bacillus, for which we propose the name Bacillus rigiliprofundi sp. nov. The type strain is 1MBB1T ( = NCMA B78T = LMG 28275T).

  16. Chimaereicella boritolerans sp. nov., a boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae isolated from soil.

    PubMed

    Ahmed, Iftikhar; Yokota, Akira; Fujiwara, Toru

    2007-05-01

    A non-motile, Gram-negative, boron-tolerant and alkaliphilic bacterium was isolated from soil of the Hisarcik area in the Kutahya Province of Turkey that was naturally high in boron minerals. The novel isolate, designated T-22(T), formed rod-shaped cells, was catalase- and oxidase-positive and tolerated up to 300 mM boron. The strain also survived on agar medium containing up to 3 % (w/v) NaCl. The pH range for growth of this strain was 6.5-10.0 (optimum pH 8.0-9.0) and the temperature range was 16-37 degrees C (optimum 28-30 degrees C). Phylogenetic analysis based on 16S rRNA gene sequences revealed a clear affiliation with the genus Chimaereicella, with 97.4 % sequence similarity to Chimaereicella alkaliphila AC-74(T), which was the highest similarity among cultivated bacteria. The DNA-DNA relatedness with C. alkaliphila AC-74(T) was 28.3 %. The major respiratory quinone system was MK-7 and the predominant cellular fatty acids were iso-C(15 : 0), iso-C(17 : 1)omega9c, iso-C(17 : 0) 3-OH and summed feature 3 (iso-C(15 : 0) 2-OH and/or iso-C(16 : 1)omega7c). The DNA G+C content was 42.5 mol%. Based on the phylogenetic analysis and physiological, chemotaxonomic and genetic data, we concluded that strain T-22(T) should be classified in the genus Chimaereicella, and we propose the name Chimaereicella boritolerans sp. nov. for this novel species. The type strain is strain T-22(T) (=DSM 17298(T)=NBRC 101277(T)=ATCC BAA-1189(T)).

  17. Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain.

    PubMed

    Cabrera, Antonio; Aguilera, Margarita; Fuentes, Susana; Incerti, Claudia; Russell, Nick J; Ramos-Cormenzana, Alberto; Monteoliva-Sánchez, Mercedes

    2007-02-01

    A moderately halophilic bacterium, strain CG2.1T, isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile, Gram-negative rod that produced orange-pigmented colonies. Strain CG2.1T was able to grow at salinities of 3-25 % (w/v) and at temperatures of 15-40 degrees C. The pH range for growth was 5-9. Strain CG2.1T was a heterotroph capable of utilizing various carbohydrates as carbon sources. The organism reduced nitrate and showed phenylalanine deaminase activity. The major fatty acids were C(18 : 1)omega7c, C(16 : 0) and C(19 : 0) cyclo omega8c. The DNA G+C content was 60.9 mol%. On the basis of the phenotypic and phylogenetic data, strain CG2.1T appeared to be a member of the genus Halomonas and clustered closely with Halomonas marisflavi (97.1 % 16S rRNA gene sequence similarity). However, the level of DNA-DNA relatedness between the novel isolate and the most closely related Halomonas species was low. On the basis of these data, strain CG2.1T represents a novel member of the genus Halomonas, for which the name Halomonas indalinina is proposed. The type strain is CG2.1T (=CECT 5902T=LMG 23625T).

  18. Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field.

    PubMed

    Yang, Jung-Eun; Kim, Se-Young; Im, Wan-Taek; Yi, Tae-Hoo

    2011-06-01

    A Gram-negative, aerobic, non-motile, non-spore-forming, yellow-pigmented, rod-shaped bacterium, designated strain THG 01(T), was isolated from the soil of a ginseng field in Pocheon province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain THG 01(T) grew well at 25-37 °C and pH 6.0-7.5 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity data, strain THG 01(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium anhuiense D3(T) (97.5 % similarity), Flavobacterium johnsoniae UW101(T) (96.8 %) and Flavobacterium denitrificans ED5(T) (96.7 %). 16S rRNA gene sequence similarities between the novel strain and members of other recognized species within the family Flavobacteriaceae were less than 96.7 %. The G+C content of the genomic DNA of strain THG 01(T) was 32.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone was MK-6 and major fatty acids were iso-C(15 : 0), iso-C(15 : 0) 3-OH and C(16 : 1)ω7c and/or C(16 : 1)ω6c ) supported the affiliation of strain THG 01(T) to the genus Flavobacterium. DNA-DNA hybridization experiments showed that DNA-DNA relatedness values between strain THG 01(T) and its closest phylogenetic neighbours were below 11 %. The results of physiological and biochemical tests enabled strain THG 01(T) to be differentiated genotypically and phenotypically from recognized species of the genus Flavobacterium. The isolate therefore represents a novel species, for which the name Flavobacterium ginsenosidimutans sp. nov. is proposed, with THG 01(T) ( = KACC 14525(T) = JCM 16720(T)) as the type strain.

  19. Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings.

    PubMed

    Min, Ui-Gi; Kim, So-Jeong; Hong, Heeji; Kim, Song-Gun; Gwak, Joo-Han; Jung, Man-Young; Kim, Jong-Geol; Na, Jeong-Geol; Rhee, Sung-Keun

    2016-06-01

    A strictly anaerobic bacterium, strain B5(T), was isolated from sediment of an abandoned coal mine in Taebaek, Republic of Korea. Cells of strain B5(T) were non-spore-forming, straight, Gram-positive rods. The optimum pH and temperature for growth were pH 7.0 and 30°C, respectively, while the strain was able to grow within pH and temperature ranges of 5.5-7.5 and 25-45°C, respectively. Growth of strain B5(T) was observed at NaCl concentrations of 0 to 6.0% (w/v) with an optimum at 3.0-4.0% (w/v). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and three unknown polar lipids. Strain B5(T) grew anaerobically by reducing nitrate, nitrite, ferric-citrate, ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone-2-sulfonate in the presence of proteinaceous compounds, organic acids, and carbohydrates as electron donors. The isolate was not able to grow by fermentation. Strain B5(T) did not grow under aerobic or microaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B5(T) is most closely related to the genus Tepidibacillus (T. fermentans STGH(T); 96.3%) and Vulcanibacillus (V. modesticaldus BR(T); 94.6%). The genomic DNA G+C content (36.9 mol%) of strain B5(T) was higher than those of T. fermentans STGH(T) (34.8 mol%) and V. modesticaldus BR(T) (34.5 mol%). Based on its phenotypic, chemotaxonomic, and phylogenetic properties, we describe a new species of a novel genus Calculibacillus, represented by strain B5(T) (=KCTC 15397(T) =JCM 19989(T)), for which we propose the name Calculibacillus koreensis gen. nov., sp. nov.

  20. Characterization of Sporohalobacter salinus sp. nov., an anaerobic, halophilic, fermentative bacterium isolated from a hypersaline lake.

    PubMed

    Ben Abdallah, Manel; Karray, Fatma; Mhiri, Najla; Cayol, Jean-Luc; Tholozan, Jean-Luc; Alazard, Didier; Sayadi, Sami

    2015-02-01

    Halophilic, obligately anaerobic, Gram-stain-negative bacterial strains were isolated from a sediment sample taken from under the salt crust of El-Jerid hypersaline lake in southern Tunisia by using tryptone or glucose as the substrate. One strain, CEJFT1B(T), was characterized phenotypically and phylogenetically. Cells were non-motile, non-spore-forming, short rods. Strain CEJFT1B(T) was able to grow in the presence of 5-30 % (w/v) NaCl (optimum 20 %) and at 30-60 °C (optimum 45 °C). It grew at pH 5.5-7.8 and the optimum pH for growth was 6.8. The isolate required yeast extract for growth. Substrates utilized by strain CEJFT1B(T) as the sole carbon source included glucose, fructose, sucrose, pyruvate, Casamino acids and starch. Individual amino acids such as glutamate, lysine, methionine, serine, tyrosine, and amino acid mixtures formed by the Stickland reaction such as alanine-glycine, valine-proline, leucine-proline, isoleucine-proline were also utilized. Products of glucose fermentation were acetate (major product), butyrate, H2 and CO2. The genomic DNA G+C content of strain CEJFT1B(T) was 32.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CEJFT1B(T) should be assigned to the genus Sporohalobacter. The sequence similarity between strain CEJFT1B(T) and Sporohalobacter lortetii was 98.5 %, but DNA-DNA hybridization between the two strains revealed a relatedness value of 56.4 %, indicating that they are not related at the species level. The combination of phylogenetic analysis, DNA-DNA hybridization data, and differences in substrate utilization support the view that strain CEJFT1B(T) represents a novel species of the genus Sporohalobacter, for which the name Sporohalobacter salinus sp. nov. is proposed. The type strain is CEJFT1B(T) ( = DSM 26781(T) = JCM 19279(T)).

  1. Furoquinoline alkaloids isolated from Balfourodendron riedelianum as photosynthetic inhibitors in spinach chloroplasts.

    PubMed

    Veiga, Thiago André Moura; King-Díaz, Beatriz; Marques, Anna Sylvia Ferrari; Sampaio, Olivia Moreira; Vieira, Paulo Cezar; da Silva, Maria Fátima das Graças Fernandes; Lotina-Hennsen, Blas

    2013-03-05

    In the search for natural inhibitors of plant growth, we investigate the mechanism of action of the natural furoquinoline alkaloids isolated from Balfourodendron riedelianum (Rutaceae): evolitrine (1), kokusaginine (2), γ-fagarine (3), skimmianine (4) and maculosidine (5) on the photosynthesis light reactions. Their effect on the electron transport chain on thylakoids was analyzed. Alkaloids 1, 2, 4 and 5 inhibited ATP synthesis, basal, phosphorylating and uncoupled electron transport acting as Hill reaction inhibitors on spinach chloroplasts. Alkaloid 3 was not active. The inhibition and interaction site of alkaloids 1, 2, 4 and 5 on the non-cyclic electron transport chain was studied by polarography and fluorescence of the chlorophyll a (Chl a). The results indicate that the target for 1 was localized on the donor and acceptor side of PS II. In addition alkaloids 2 and 5 affect the PS I electron acceptors on leaf discs.

  2. Studies on Hydrogen Production by Photosynthetic Bacteria after Anaerobic Fermentation of Starch by a Hyperthermophile, Pyrococcus furiosus

    NASA Astrophysics Data System (ADS)

    Sugitate, Toshihiro; Fukatsu, Makoto; Ishimi, Katsuhiro; Kohno, Hideki; Wakayama, Tatsuki; Nakamura, Yoshihiro; Miyake, Jun; Asada, Yasuo

    In order to establish the sequential hydrogen production from waste starch using a hyperthermophile, Pyrococcus furiosus, and a photosynthetic bacterium, basic studies were done. P. furiosus produced hydrogen and acetate by anaerobic fermentation at 90°C. A photosynthetic bacterium, Rhodobacter sphaeroides RV, was able to produce hydrogen from acetate under anaerobic and light conditions at 30°C. However, Rb. sphaeroides RV was not able to produce hydrogen from acetate in the presence of sodium chloride that was essential for the growth and hydrogen production of P. furiosus although it produced hydrogen from lactate at a reduced rate with 1% sodium chloride. A newly isolated strain, CST-8, from natural environment was, however, able to produce hydrogen from acetate, especially with 3 mM L-alanine and in the presence of 1% sodium chloride. The sequential hydrogen production with P. furiosus and salt-tolerant photosynthetic bacteria could be probable at least in the laboratory experiment scale.

  3. An Extremely Oligotrophic Bacterium, Rhodococcus erythropolis N9T-4, Isolated from Crude Oil▿

    PubMed Central

    Ohhata, Naoko; Yoshida, Nobuyuki; Egami, Hiroshi; Katsuragi, Tohoru; Tani, Yoshiki; Takagi, Hiroshi

    2007-01-01

    Rhodococcus erythropolis N9T-4, which was isolated from crude oil, showed extremely oligotrophic growth and formed its colonies on a minimal salt medium solidified using agar or silica gel without any additional carbon source. N9T-4 did not grow under CO2-limiting conditions but could grow on a medium containing NaHCO3 under the same conditions, suggesting that the oligotrophic growth of N9T-4 depends on CO2. Proteomic analysis of N9T-4 revealed that two proteins, with molecular masses of 45 and 55 kDa, were highly induced under the oligotrophic conditions. The primary structures of these proteins exhibited striking similarities to those of methanol: N,N′-dimethyl-4-nitrosoaniline oxidoreductase and an aldehyde dehydrogenase from Rhodococcus sp. These enzyme activities were three times higher under oligotrophic conditions than under n-tetradecane-containing heterotrophic conditions, and gene disruption for the aldehyde dehydrogenase caused a lack of growth on the minimal salt medium. Furthermore, 3-hexulose 6-phosphate synthase and phospho-3-hexuloisomerase activities, which are key enzymes in the ribulose monophosphate pathway in methylotrophic bacteria, were detected specifically in the cell extract of oligotrophically grown N9T-4. These results suggest that CO2 fixation involves methanol (formaldehyde) metabolism in the oligotrophic growth of R. erythropolis N9T-4. PMID:17675378

  4. [Isolation, charcaterization of an anthracene degrading bacterium Martelella sp. AD-3 and cloning of dioxygenase gene].

    PubMed

    Cui, Chang-Zheng; Feng, Tian-Cai; Yu, Ya-Qi; Dong, Fei; Yang, Xin-Mei; Feng, Yao-Yu; Liu, Yong-Di; Lin, Han-Ping

    2012-11-01

    Anthracene, among the 16 US EPA polycyclic aromatic hydrocarbons (PAHs), is a typical low molecular weight environmental contaminant, which gains concern on its biodegradation under hypersaline condition. In this study, an anthracene-degrading bacterial strain was isolated from highly saline petroleum-contaminated soil. Based on its physiological, biochemical characteristics and 16S rDNA sequence analysis, the bacteria was preliminary identified and named as Martelella sp. AD-3. The strain was able to utilize anthracene as sole carbon source for growth and the degradation occurred under broad salinities (0.1% to 10%) and varying pHs (6.0 to 10.0). The optimized degradation conditions were initial concentration 25 mg x L(-1), culture temperature 30 degrees C, pH 9.0 and salinity 3%. And 94.6% of anthracene was degraded by strain AD-3 under the optimal conditions within 6 days. Degenerate primers design was performed with a reported dioxygenase alpha subunit homologous gene. A length of 307 bp fragment of the partial dioxygenase gene sequences (GenBank accession: JF823991.1) was amplified by nested PCR. The clones amino acid sequence from strain AD-3 showed 95% identity to that of the partial naphthalene dioxygenase large-subunit from Marinobacter sp. NCE312 (AF295033). The results lay a foundation for the further study of molecular mechanism involved in the PAHs biodegradation by strain AD-3.

  5. Marinobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from the Arctic.

    PubMed

    Zhang, De-Chao; Li, Hui-Rong; Xin, Yu-Hua; Chi, Zhen-Ming; Zhou, Pei-Jin; Yu, Yong

    2008-06-01

    Strain 20041(T) was isolated from sea-ice of the Canadian Basin (7 degrees 23' 14'' N 14 degrees 06' 55'' W). Phylogenetic analysis based on 16S rRNA gene homology showed that strain 20041(T) was related to members of the genus Marinobacter and had highest 16S rRNA gene sequence similarity with the type strain of Marinobacter maritimus. Cells were Gram-negative, rod-shaped, psychrophilic and motile. The temperature range for growth was 0-22 degrees C, with optimum growth occurring at 16-18 degrees C and at approximately pH 6.0-9.0. Strain 20041(T) had ubiquinone-9 as the major respiratory quinone and iso-C(15 : 0) 2OH and/or C(16 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c and C(12 : 0) 3OH as major fatty acids. The genomic DNA G+C content was 55.4 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain 20041(T) is considered to represent a novel species, for which the name Marinobacter psychrophilus sp. nov. is proposed. The type strain is 20041(T) (=CGMCC 1.6499(T)=JCM 14643(T)).

  6. Moritella dasanensis sp. nov., a psychrophilic bacterium isolated from the Arctic ocean.

    PubMed

    Kim, Hak Jun; Park, Soyoung; Lee, Jung Min; Park, Seungil; Jung, Woongsic; Kang, Jae-Shin; Joo, Hyung Min; Seo, Ki-Won; Kang, Sung-Ho

    2008-04-01

    An aerobic, motile, Gram-negative, ice-active substance-producing, rod-shaped psychrophile, designated strain ArB 0140T, was isolated from seawater collected from near a glacier in Kongsfjorden, Svalbard Archipelago, Norway. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain ArB 0140T showed a distinct phyletic line within the genus Moritella. Characteristic chemotaxonomic data [predominant isoprenoid quinone, Q8; major fatty acids, C14 : 0, C14 : 1, C16 : 0, C16 : 1 and C22 : 6 (docosahexaenoic acid; DHA)] also corroborated the affiliation of strain ArB 0140T to the genus Moritella. The maximal growth rate of the novel strain was observed at 9 degrees C, with a maximum temperature for growth of 18 degrees C. The genomic DNA G+C content was 46.9 mol%. Based on the data obtained from this polyphasic study, including DNA-DNA relatedness, physiological and biochemical tests and ice-controlling activity, strain ArB 0140T was found to be genetically and phenotypically different from other recognized species of the genus Moritella. Therefore strain ArB 0140T represents a novel species, for which the name Moritella dasanensis sp. nov. is proposed. The type strain is ArB 0140T (=KCTC 10814T=KCCM 42845T=JCM 14759T).

  7. Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.

    PubMed

    Liu, Qing; Liu, Hongcan; Zhang, Jianli; Zhou, Yuguang; Xin, Yuhua

    2013-08-01

    In this study, two psychrophilic bacterial strains were isolated from the China No. 1 glacier in Xinjiang, north-west China. Cells were Gram-positive rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belonged to the genus Cryobacterium. Phylogenetic analysis showed that they clustered together and are most closely related to Cryobacterium luteum CGMCC 1.11210(T), Cryobacterium flavum CGMCC 1.11215(T), Cryobacterium psychrophilum CGMCC 1.4292(T), Cryobacterium psychrotolerans CGMCC 1.5382(T) and Cryobacterium roopkundense CGMCC 1.10672(T). The major cellular fatty acids of the novel strains were anteiso-C15 : 0, anteiso-C15 : 1 A, iso-C16 : 0 and iso-C15 : 0. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid in the cell membrane. The results of DNA-DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strains Hh34(T) and Hh28 from related species. However, their high DNA-DNA relatedness showed that they belong to the same novel species. Strain Hh34(T) (= NBRC 107883(T) = CGMCC 1.11211(T)) was selected as the type strain to represent this novel species, for which the name Cryobacterium levicorallinum sp. nov. is proposed.

  8. Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species.

    PubMed

    Ren, Da Wei; Chen, Wen Feng; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin

    2011-03-01

    A group of rhizobial strains isolated from nodules of multiple legume species grown in different geographical regions of China had identical 16S rRNA genes. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the novel strains formed a subclade in the genus Rhizobium together with Rhizobium galegae, Rhizobium huautlense and Rhizobium alkalisoli, with 99.8  % gene sequence similarity between the strains. The DNA-DNA relatedness values between the representative strain CCBAU 05176(T) and R. galegae ATCC 43677(T), R. huautlense S02(T) and R. alkalisoli CCBAU 01393(T) were 22.6  %, 8.9  % and 15.9  %, respectively. The novel strains were distinguished from recognized species of the genus Rhizobium by using a polyphasic approach, including PCR-based restriction fragment length polymorphism analysis (RFLP) of the 16S-23S intergenic spacer (IGS), phenotypic and physiological tests, sequence comparisons of housekeeping genes and cellular fatty acid profiles. Therefore, it is suggested that this group of strains represents a novel species for which the name Rhizobium vignae sp. nov. is proposed. The type strain is CCBAU 05176(T) (=HAMBI 3039(T)=LMG 25447(T)).

  9. Tepidimonas taiwanensis sp. nov., a novel alkaline-protease-producing bacterium isolated from a hot spring.

    PubMed

    Chen, Tien-Lai; Chou, Yi-Ju; Chen, Wen-Ming; Arun, Bhagwath; Young, Chiu-Chung

    2006-02-01

    The bacterial strain designated I1-1(T) was isolated from a hot spring located in the Pingtung area, southern Taiwan. Cells of this organism were Gram reaction negative rods, motile by a single polar flagellum. Optimum conditions for growth were 55 degrees C and pH 7. Strain I1-1(T) grew well in lower nutrient media such as 5-10% Luria-Bertani broth, and its extracellular products expressed alkaline protease activity. The 16S rRNA gene sequence analysis indicates that strain I1-1(T) is a member of beta-Proteobacteria. On the basis of a phylogenetic analysis of 16S rDNA sequences, DNA-DNA similarity data, whole-cell protein analysis, physiological and biochemical characteristics, as well as fatty acid compositions, the organism belonged to the genus Tepidimonas and represented a novel species within this genus. The predominant cellular fatty acids of strain I1-1(T) were 16:0 (about 41%), 18:1 omega7c (about 13%), and summed feature 3 [16:1 omega7c or 15:0 iso 2OH or both (about 26%)]. Its DNA base ratio was 68.1 mol%. We propose to classify strain I1-1(T) (=BCRC 17406(T)=LMG 22826(T)) as Tepidimonas taiwanensis sp. nov.

  10. Biodegradation of Picolinic Acid by a Newly Isolated Bacterium Alcaligenes faecalis Strain JQ135.

    PubMed

    Qiu, Jiguo; Zhang, Junjie; Zhang, Yanting; Wang, Yuhong; Tong, Lu; Hong, Qing; He, Jian

    2017-04-01

    We isolated a bacterial strain JQ135 from municipal wastewater, which was capable of efficiently degrading picolinic acid (PA). Based on the physico-biochemical characteristics and 16S rDNA analysis, strain JQ135 was identified as Alcaligenes faecalis. In addition, strain JQ135 produced an orange pigment when cultured in the Luria-Bertani medium, which is different from the previously reported strains of A. faecalis. During the degradation of PA by the resting strain JQ135 cells, only one intermediate, 6-hydroxypicolinic acid (6HPA), was detected by ultraviolet spectrophotometry, high-pressure liquid chromatography, and liquid chromatography-mass spectrometry. A random transposon mutagenesis library of strain JQ135 was constructed. One mutant, Mut-G31, could convert PA into 6HPA without further degradation. The disrupted gene (orf2) was amplified from Mut-G31, and its product showed 32% identity to the 3-deoxy-D-manno-octulosonic acid kinase (KdkA) from Haemophilus influenzae. Results from complementation analysis confirmed that GTG was the initiation codon of the kdkA-like orf2, and that it was essential for PA biodegradation by strain JQ135. This study provides the first genetic evidence for the bacterial degradation of PA.

  11. Hardy Bacterium Isolated From Two Geographically Distinct Spacecraft Assembly Cleanroom Facilities

    NASA Technical Reports Server (NTRS)

    Vaisham-payan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra; Moissl-Eichinger, Christine

    2012-01-01

    Earlier studies have confirmed that a tenacious hardy bacterial population manages to persist and survive throughout a spacecraft assembly process. The widespread detection of these organisms underscores the challenges in eliminating them completely. Only comprehensive and repetitive microbial diversity studies of geographically distinct cleanroom facilities will bolster the understanding of planetary protection relevant microbes. Extensive characterizations of the physiological traits demonstrated by cleanroom microbes will aid NASA in gauging the forward contamination risk that hardy bacteria (such as Tersicoccus phoenicis) pose to spacecraft. This study reports on the isolation and identification of two gram-positive, non-motile, non-spore-forming bacterial strains from the spacecraft assembly facilities at Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana. DNA-DNA relatedness values between the novel strains indicates that these novel strains were indeed members of a same species. Phylogenetic evidence derived from a 16S ribosomal DNA analysis indicated that both the novel strains are less closely related to all other Arthrobacter species.

  12. Bacillus sp. strain DJ-1, potent arsenic hypertolerant bacterium isolated from the industrial effluent of India.

    PubMed

    Joshi, Dhaval N; Flora, S J S; Kalia, Kiran

    2009-07-30

    Arsenic hypertolerant bacterial cells were isolated from the common industrial effluent treatment plant, Vapi, India. Strain DJ-1 sustaining 400 mM, As (V) out of 16 bacterial strains was identified as Bacillus sp. strain DJ-1 through 16S rRNA ribotyping. The maximum arsenic accumulation of 9.8+/-0.5 mg g(-1) (dry weight) was observed during stationary phase of growth. Intracellular compartmentalization has shown 80% of arsenic accumulation in cytoplasm. The lack of arsC gene and arsenate reductase activity indicated that Bacillus sp. strain DJ-1 may lack classical ars operon and detoxification may be mediated through some novel mechanism. The arsenite binding protein was purified by affinity chromatography and characterized as DNA protection during starvation (DPS) protein by electrospray ionization mass spectrometry. The induction of DPS showed the adaptation of bacteria in arsenic stress condition and/or in detoxification mechanism, relies on its ability to bind with arsenic. These results indicate the hypertolerance with higher intracellular accumulation of arsenic by Bacillus sp. strain DJ-1, which could be mediated by DPS protein thus signifying this organism is a potential candidate for the removal of arsenic from industrial wastewater, which needs further study.

  13. [Isolation of a methane-utilizing bacterium and its application in measuring methane gas].

    PubMed

    Zhao, Gengui; Zheng, Jun; Wen, Guangming; Yang, Suping; Dong, Chuan

    2008-03-01

    A bacterial strain ME16 was isolated from Jinyang Lake in Taiyuan of Shanxi Province, China. Gas chromatography analysis showed that the strain could use methane as the sole carbon and energy source. Based on 16S rDNA sequence analysis, the strain was identified as Pseudomonas aeruginosa. Effects of inoculum size, temperature, methane content and initial pH of media on cell growth were studied. In addition, we examined the response time of methane gas to dissolved oxygen and the relationship between consumption of dissolved oxygen and different methane gas content with PVA-H3BO3 immobilized cell of ME16 using electrochemical method. The optimal conditions for cell growth were 2% inoculum size, 25% methane content, 30 degrees C and pH 6.0. Response time was within 100 s after adding of immobilized cells to reaction system. The linear range of measured methane content was from 0 to 16%, with the correlation coefficient 0.9954. Hence, this strain has potential application in developing of methane biosensor.

  14. Anoxybacillus kamchatkensis subsp. asaccharedens subsp. nov., a thermophilic bacterium isolated from a hot spring in Batman.

    PubMed

    Gul-Guven, Reyhan; Guven, Kemal; Poli, Annarita; Nicolaus, Barbara

    2008-12-01

    A new thermophilic spore-forming strain KG8(T) was isolated from the mud of Taslidere hot spring in Batman. Strain KG8(T) was aerobe, Gram-positive, rod-shaped, motile, occurring in pairs or filamentous. Growth was observed from 35-65 degrees C (optimum 55 degrees C) and at pH 5.5-9.5 (optimum pH 7.5). It was capable of utilizing starch, growth was observed until 3% NaCl (w/v) and it was positive for nitrate reduction. On the basis of 16S rRNA gene sequence similarity, strain KG8(T) was shown to be related most closely to Anoxybacillus species. Chemotaxonomic data (major isoprenoid quinone-menaquinone-7; major fatty acid-iso-C15:0 and iso-C17:0) supported the affiliation of strain KG8(T) to the genus Anoxybacillus. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain KG8(T). Based on these results we propose assigning a novel subspecies of Anoxybacillus kamchatkensis, to be named Anoxybacillus kamchatkensis subsp. asaccharedens subsp. nov. with the type strain KG8(T) (DSM 18475(T)=CIP 109280(T)).

  15. Bacillus rhizosphaerae sp. nov., an novel diazotrophic bacterium isolated from sugarcane rhizosphere soil.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Lee, Jung-Sook; Lee, Keun-Chul; Hari, Kuppusamy

    2011-10-01

    A Gram-positive, non-pigmented, rod-shaped, diazotrophic bacterial strain, designated SC-N012(T), was isolated from rhizosphere soil of sugarcane 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. Sequence analysis of the 16S rRNA gene of SC-N012(T) revealed the closest match (98.9% pair wise similarity) with Bacillus clausii DSM 8716(T). However, DNA-DNA hybridization experiments indicated low levels of genomic relatedness (32%) with this strain. The major components of the fatty acid profile are iso-C(15:0), anteiso-C(15:0), iso-C(17:0) and anteiso-C(17:0). The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The G+C content of the genomic DNA is 43.0 mol%. The lipids present in strain SC-N012(T) are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and two unknown phospholipids. Their predominant respiratory quinone was MK-7. Studies of DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing allowed strain SC-N012(T) to be described as members of novel species of the genus Bacillus, for which the name Bacillus rhizosphaerae sp. nov. is proposed. The type strain is SC-N012(T) (=DSM 21911(T) = NCCB 100267(T)).

  16. Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica.

    PubMed

    Zhang, Lei; Shi, Xu; Si, Meiru; Li, Changfu; Zhu, Lingfang; Zhao, Liang; Shen, Xihui; Wang, Yao

    2014-10-01

    During a study of endophytic bacteria from traditional Chinese medicinal plants, a bacterial strain, designated PTYR-5(T), was isolated from the leaf of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTYR-5(T) is a member of the genus Rhizobium, exhibiting the highest sequence similarities to R. cellulosilyticum LMG 23642(T) (97.2%), R. huautlense LMG 18254(T) (97.2%) and R. alkalisoli CCBAU 01393(T) (97.1%). The levels of 16S rRNA gene sequence similarity with respect to other Rhizobium species with validly published names were less than 97.0%. Phylogenies of the housekeeping genes atpD, recA and glnII confirmed its distinct position, showing low similarity with respect to those of recognized Rhizobium species (no more than 94.1, 90.0 and 88.0% similarity, respectively). The DNA-DNA relatedness values of strain PTYR-5(T) with R. cellulosilyticum LMG 23642(T), R. huautlense LMG 18254(T) and R. alkalisoli CCBAU 01393(T) were 33.6, 21.4 and 29.5 %, respectively. Based on phenotypic, phylogenetic and genotypic data, strain PTYR-5(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium smilacinae sp. nov. is proposed. The type strain is PTYR-5(T) (=CCTCC AB 2013016(T)=KCTC 32300(T)=LMG 27604(T)).

  17. Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris.

    PubMed

    Mnasri, Bacem; Liu, Tian Yan; Saidi, Sabrine; Chen, Wen Feng; Chen, Wen Xin; Zhang, Xiao Xia; Mhamdi, Ridha

    2014-05-01

    Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum, are further studied here. Their 16S rRNA genes showed 98.5-99% similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA-DNA relatedness between strain 23C2T and the type strains of R. loessense, R. mongolense, R. gallicum and R. yanglingense ranged from 58.1 to 61.5%. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52%. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T (=CCBAU 101087T=HAMBI3541T) was designated as the type strain.

  18. Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand.

    PubMed

    Ramana, Ch V; Parag, B; Girija, K R; Ram, B Raghu; Ramana, V Venkata; Sasikala, Ch

    2013-02-01

    Two strains (JC85(T) and JC108) of Gram-stain-negative, motile bacteria were isolated from endolithic beach sand samples on an oligotrophic medium. Based on the 16S rRNA gene sequence analysis, both strains were identified as belonging to the genus Rhizobium. Strain JC108 had 16S rRNA gene sequence similarity of 100 % with Rhizobium pusense NRCPB10(T) and formed a cluster with this strain. Strain JC85(T) had 96.9 % 16S rRNA gene sequence similarity and was 18 % related (based on DNA-DNA hybridization) to Rhizobium borbori DN316(T). With other strains of the genus Rhizobium, the 16S rRNA gene sequence similarity was less than 96.3 %. Strain JC85(T) could tolerate up to 3 % salinity, fix N(2), was resistant to ampicillin (10 µg) and was positive for catalase and oxidase. The major fatty acid was C(18 : 1)ω7c (69 %) with minor amounts of C(19 : 0) cyclo ω8c (8.9 %), C(16 : 0) (6.9 %), C(12 : 0) (5.7 %) and C(19 : 1)ω7c/C(19 : 1)ω6c (2.2 %). Polar lipids of strain JC85(T) include two unidentified aminophospholipids (APL1,2), two unidentified phospholipids (PL1,2), phosphatidylcholine and four unidentified lipids (L1-4). Q-10 is the major quinone of strain JC85(T). Based on polyphasic taxonomic analysis, strain JC85(T) represents a novel species for which, the name Rhizobium subbaraonis JC85(T) is proposed. The type strain is JC85(T) ( = DSM 24765(T) = KCTC 23614(T)).

  19. Winogradskyella eckloniae sp. nov., a marine bacterium isolated from the brown alga Ecklonia cava.

    PubMed

    Kim, Ji-Young; Park, So-Hyun; Seo, Ga-Young; Kim, Young-Ju; Oh, Duck-Chul

    2015-09-01

    A novel bacterial strain, designated EC29(T), was isolated from the brown alga Ecklonia cava collected on Jeju Island, Republic of Korea. Cells of strain EC29(T) were Gram-stain-negative, aerobic, rod-shaped and motile by gliding. Growth was observed at 10-30 °C (optimum, 20-25 °C), at pH 6.0-9.5 (optimum, pH 7.5) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain belonged to the genus Winogradskyella. Strain EC29(T) exhibited the highest 16S rRNA gene sequence similarities, of 96.5-97.8%, to the type strains of Winogradskyella pulchriflava EM106(T), Winogradskyella echinorum KMM 6211(T) and Winogradskyella ulvae KMM 6390(T). Strain EC29(T) exhibited < 27% DNA-DNA relatedness with Winogradskyella pulchriflava EM106(T) and Winogradskyella echinorum KMM 6211(T). The predominant fatty acids of strain EC29(T) were iso-C15 : 0, iso-C15 : 1 G, C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and anteiso-C15 : 0. The DNA G+C content was 31.1 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Based on a polyphasic study, strain EC29(T) is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella eckloniae sp. nov. is proposed. The type strain is EC29(T) ( = KCTC 32172(T) = JCM 18703(T)).

  20. Celeribacter persicus sp. nov., a polycyclic-aromatic-hydrocarbon-degrading bacterium isolated from mangrove soil.

    PubMed

    Jami, Mansooreh; Lai, Qiliang; Ghanbari, Mahdi; Moghadam, Mohsen Shahriari; Kneifel, Wolfgang; Domig, Konrad J

    2016-04-01

    A Gram-stain-negative, mesophilic bacterial strain, designated SBU1T, which degrades polycyclic aromatic hydrocarbons was isolated from the sediments of the mangrove forests of Nayband Bay in the Iranian Persian Gulf during a bioremediation experiment. The 16S rRNA gene sequence of strain SBU1T exhibited highest similarities with Celeribacter indicus P73T (98.52%) and Celeribacter neptunius H 14T (97.05%). Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain SBU1T fell within a cluster consisting of the type strains of species of the genus Celeribacter and formed a stable clade with C. indicus P73T in trees generated with three algorithms. The fatty acid profile of strain SBU1T consisted of the major fatty acids C18:1ω7c/ω6c and C18:1ω7c 11-methyl. The major compounds in the polar lipid profile were one phosphatidylglycerol and four unidentified phospholipids. The quinone system exclusively comprised ubiquinone (Q-10). The DNA G+C content was 60.4 mol%. A combination of phylogenetic analysis, DNA-DNA hybridization estimation, average nucleotide identity results and differential phenotypic and chemotaxonomic characteristics demonstrated that strain SBU1T could be distinguished from its close relatives. Therefore, strain SBU1T is considered to represent a novel species of the genus Celeribacter for which the name Celeribacter persicus sp. nov. is proposed. The type strain is SBU1T (=MCCC 1A00672T=DSM 100434T).

  1. Salinimonas lutimaris sp. nov., a polysaccharide-degrading bacterium isolated from a tidal flat.

    PubMed

    Yoon, Jung-Hoon; Kang, So-Jung; Lee, Soo-Young

    2012-05-01

    A Gram-negative, non-motile, non-endospore-forming bacterial strain, designated DPSR-4(T), was isolated from a tidal flat sediment on the southern coast of Korea. Strain DPSR-4(T) grew optimally at 25-30°C, at pH 7.0-7.5 and in the presence of 2% (w/v) NaCl. A Neighbour-Joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DPSR-4(T) clustered with Salinimonas chungwhensis BH030046(T) by a high bootstrap resampling value of 99.7%. Strain DPSR-4(T) exhibited 96.2% 16S rRNA gene sequence similarity to that of S. chungwhensis BH030046(T) and 93.7-96.6% sequence similarity to the sequences of type strains of Alteromonas species. Strain DPSR-4(T) contained Q-8 as the predominant ubiquinone and iso-C(15:0) 2-OH and/or C(16:1) ω7c, C(16:0) and C(18:1) ω7c as the major fatty acids. The major polar lipids detected in strain DPSR-4(T) and S. chungwhensis KCTC 12239(T) were phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content was 53.4 mol%. Differential phenotypic properties and phylogenetic distinctiveness of strain DPSR-4(T) demonstrated that this strain is distinguishable from the sole recognized species of the genus Salinimonas, S. chungwhensis. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DPSR-4(T) is considered to represent a novel species of the genus Salinimonas, for which the name Salinimonas lutimaris sp. nov. is proposed. The type strain is DPSR-4(T) (KCTC 23464(T), CCUG 60743(T)).

  2. Winogradskyella multivorans sp. nov., a polysaccharide-degrading bacterium isolated from seawater of an oyster farm.

    PubMed

    Yoon, Jung-Hoon; Lee, Soo-Young

    2012-08-01

    A novel bacterial strain, designated T-Y1(T), capable of degrading a variety of polysaccharides was isolated from seawater of an oyster farm in the South Sea, Korea. It was found to be aerobic, Gram-negative, non-flagellated, non-gliding and rod-shaped. Strain T-Y1(T) grew optimally at 25 °C, at pH 7.0-7.5 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain T-Y1(T) belonged to the genus Winogradskyella. Strain T-Y1(T) exhibited 16S rRNA gene sequence similarity values of 95.0-96.8 % to the type strains of recognized Winogradskyella species and less than 94.5 % to other validly named species. The chemotaxonomic data concurred with the phylogenetic inference. Strain T-Y1(T) contained MK-6 as the predominant menaquinone and anteiso-C(15:0), iso-C(15:0), iso-C(15:1) G and iso-C(16:0) 3-OH as the major fatty acids. The major polar lipids of strain T-Y1(T) were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 36.2 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, enabled strain T-Y1(T) to be differentiated from the recognized Winogradskyella species. On the basis of the data presented here, strain T-Y1(T) is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella multivorans sp. nov. is proposed. The type strain is T-Y1(T) (=KCTC 23891(T) = CCUG 62216(T)).

  3. Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen.

    PubMed

    Zhang, Kegui; Song, Lei; Dong, Xiuzhu

    2010-09-01

    Two strictly anaerobic, proteolytic bacterial strains, designated strain D3RC-2(T) and D3RC-3r, were isolated from a cellulose-degrading mixed culture enriched from yak rumen content. The strains were Gram-stain negative and non-spore-forming with cell sizes of 0.5-0.8 x 0.6-2.0 mum. The temperature range for growth was 24-46 degrees C (optimum 38-39 degrees C) and the pH range was between 5.6 and 8.7 (optimum 7.0-7.3). Both strains used soya peptone, tryptone, l-phenylalanine, l-leucine, l-methionine, l-serine, l-valine, l-threonine and l-histidine as carbon and nitrogen sources, but did not use any of the saccharides tested. The major fermentation products from PY medium were acetate, propionate and iso-butyrate. The DNA G+C contents of strains D3RC-2(T) and D3RC-3r were 41.0+/-0.1 mol% and 41.3+/-0.1 mol% (HPLC), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains represented a new phyletic sublineage within the family Clostridiaceae, with <93.8 % 16S rRNA gene sequence similarity to recognized species. On the basis of the phenotypic, genotypic and physiological evidence, strains D3RC-2(T) and D3RC-3r are proposed as representing a novel species of a new genus, for which the name Proteiniclasticum ruminis gen. nov., sp. nov. is proposed. The type strain of the type species is D3RC-2(T) (=AS 1.5057(T)=JCM 14817(T)).

  4. Isolation and identification of a novel, lipase-producing bacterium, Pseudomnas aeruginosa KM110

    PubMed Central

    Mobarak-Qamsari, E; Kasra-Kermanshahi, R; Moosavi-nejad, Z

    2011-01-01

    Background and Objectives Lipases are particularly important due to the fact that they specifically hydrolyze acyl glycerol, oils and greases, which is of great interest for different industrial applications. Materialst and Methods In this study, several lipase-producing bacteria were isolated from wastewater of an oil processing plant. The strain possessing the highest lipase activity was identified both biochemically and sequencing of 16S rRNA gene. Then we increase lipase activity by improving conditions of production medium. Also, lipase from this strain was preliminarily characterized for use in industrial application. Results The 16S rRNA sequensing revealed it as a new strain of Pseudomonas aeruginosa and the type strain was KM110. An overall 3-fold enhanced lipase production (0.76 U mL−1) was achieved after improving conditions of production medium. The olive oil and peptone was found to be the most suitable substrate for maximum enzyme production. Also the enzyme exhibited maximum lipolytic activity at 45°C where it was also stably maintained. At pH 8.0, the lipase had the highest stability but no activity. It was active over a pH range of 7.0–10.0. The lipase activity was inhibited by Zn2+ & Cu2+ (32 and 27%, respectively) at 1mM. The enzyme lost 29% of its initial activity in 1.0% SDS concentration, whereas, Triton X-100, Tween-80 & DMSO did not significantly inhibit lipase activity. Conclusions Based on the findings of present study, lipase of P. aeruginosa KM110 is a potential alkaline lipase and a candidate for industrial applications such as detergent, leather and fine chemical industries. PMID:22347589

  5. Pseudomonas coleopterorum sp. nov., a cellulase-producing bacterium isolated from the bark beetle Hylesinus fraxini.

    PubMed

    Menéndez, Esther; Ramírez-Bahena, Martha H; Fabryová, Anna; Igual, José M; Benada, Oldrich; Mateos, Pedro F; Peix, Alvaro; Kolařík, Miroslav; García-Fraile, Paula

    2015-09-01

    We isolated a strain coded Esc2Am(T) during a study focused on the microbial diversity of adult specimens of the bark beetle Hylesinus fraxini. Its 16S rRNA gene sequence had 99.4% similarity with respect to its closest relative, Pseudomonas rhizosphaerae IH5(T). The analysis of partial sequences of the housekeeping genes rpoB, rpoD and gyrB confirmed that strain Esc2Am(T) formed a cluster with P. rhizosphaerae IH5(T) clearly separated from the remaining species of the genus Pseudomonas. Strain Esc2Am(T) had polar flagella and could grow at temperatures from 4 °C to 30 °C. The respiratory quinone was Q9 and the main fatty acids were C16 : 0, C18 : 1ω7c and/or C18 : 1ω6c in summed feature 8 and C16 : 1ω7c and/or C16 : 1ω6c in summed feature 3. DNA-DNA hybridization results showed 51% relatedness with respect to P. rhizosphaerae IH5(T). Oxidase, catalase and urease-positive, the arginine dihydrolase system was present but nitrate reduction and β-galactosidase production were negative. Aesculin hydrolysis was positive. Based on the results from the genotypic, phenotypic and chemotaxonomic analyses, we propose the classification of strain Esc2Am(T) as representing a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas coleopterorum sp. nov. The type strain is Esc2Am(T) ( = LMG 28558(T)= CECT 8695(T)).

  6. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil.

    PubMed

    Lee, Jae-Jin; Kang, Myung-Suk; Joo, Eun Sun; Kim, Myung Kyum; Im, Wan-Taek; Jung, Hee-Young; Srinivasan, Sathiyaraj

    2015-07-01

    A Gram-negative, yellow-pigmented, long-rod shaped bacterial strain designated DY10(T) was isolated from a soil sample collected at Mt. Deogyusan, Jeonbuk province, South Korea. Optimum growth observed at 30°C and pH 7. No growth was observed above 1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain DY10(T) belonged to the genus Spirosoma and was distantly related to Spirosoma arcticum R2-35(T) (91.0%), Spirosoma lingual DSM 74(T) (90.8%), Spirosoma endophyticum EX36(T) (90.7%), Spirosoma panaciterrae DSM 21099(T) (90.5%), Spirosoma rigui WPCB118(T) (90.2%), Spirosoma spitsbergense DSM 19989(T) (89.8%), Spirosoma luteum DSM 19990(T) (89.6%), Spirosoma oryzae RHs22(T) (89.6%), and Spirosoma radiotolerans DG5A(T) (89.1%). Strain DY10(T) showed resistance to gamma and ultraviolet radiation. The chemotaxonomic characteristics of strain DY10(T) were consistent with those of the genus Spirosoma, with the quinone system with MK-7 as the predominant menaquinone, iso-C15:0, C16:1 ω5c, and summed feature3 (C16:1 ω7c/C16:1 ω6c), and phosphatidylethanolamine as the major polar lipid. The G+C content of the genomic DNA was 53.0 mol%. Differential phenotypic properties with the closely related type strains clearly distinguished strain DY10(T) from previously described members of the genus Spirosoma and represents a novel species in this genus, for which the name Spirosoma montaniterrae sp. nov. is proposed. The type strain is DY10(T) (=KCTC 23999(T) =KEMB 9004-162(T) =JCM 18492(T)).

  7. Chitinophaga longshanensis sp. nov., a mineral-weathering bacterium isolated from weathered rock.

    PubMed

    Gao, Shan; Zhang, Wen-Bin; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi

    2015-02-01

    A Gram-stain-negative, aerobic, yellow-pigmented, non-motile, non-spore-forming, rod-shaped bacterial strain, Z29(T), was isolated from the surface of weathered rock (potassic trachyte) from Nanjing, Jiangsu Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain Z29(T) belongs to the genus Chitinophaga in the family Chitinophagaceae. Levels of 16S rRNA gene sequence similarity between strain Z29(T) and the type strains of recognized species of the genus Chitinophaga ranged from 92.7 to 98.2 %. The main fatty acids of strain Z29(T) were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. It also contained menaquinone 7 (MK-7) as the respiratory quinone and homospermidine as the main polyamine. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids, unknown phospholipids and unknown lipids. The total DNA G+C content of strain Z29(T) was 51.3 mol%. Phenotypic properties and chemotaxonomic data supported the affiliation of strain Z29(T) with the genus Chitinophaga. The low level of DNA-DNA relatedness (ranging from 14.6 to 29.8 %) to the type strains of other species of the genus Chitinophaga and differential phenotypic properties demonstrated that strain Z29(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga longshanensis sp. nov. is proposed. The type strain is Z29(T) ( = CCTCC AB 2014066(T) = LMG 28237(T)).

  8. Tenacibaculum xiamenense sp. nov., an algicidal bacterium isolated from coastal seawater.

    PubMed

    Li, Yi; Wei, Jun; Yang, Caiyun; Lai, Qiliang; Chen, Zhangran; Li, Dong; Zhang, Huajun; Tian, Yun; Zheng, Wei; Zheng, Tianling

    2013-09-01

    A Gram-stain-negative, elongated rod-shaped, yellow-pigmented, aerobic bacterial strain, designated WJ-1(T), was isolated from coastal seawater in Xiamen, Fujian province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WJ-1(T) fell within the genus Tenacibaculum and was most closely associated with Tenacibaculum aestuarii SMK-4(T) (96.7% 16S rRNA gene sequence similarity); lower similarities were shown to other members of the genus Tenacibaculum (<96.2%). The strain formed a distinct lineage with Tenacibaculum litopenaei B-I(T) (96.0%), Tenacibaculum geojense YCS-6(T) (94.5%) and Tenacibaculum jejuense CNURIC 013(T) (95.4%). Growth was observed at temperatures from 16 to 38 °C, at salinities from 2 to 4% and at pH 6-9. The major fatty acids were summed feature 3 (C(16:1)ω6c and/or C(16 1)ω7c), iso-C(17:0) 3-OH, iso-C(15:0) and iso-C(15:0) 3-OH. The DNA G+C content of strain WJ-1(T) was 33.2 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Differential phenotypic properties and phylogenetic distinctiveness in this study distinguished strain WJ-1(T) from all other members of the genus Tenacibaculum. According to the morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain WJ-1(T) represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculum xiamenense sp. nov. is proposed. The type strain is WJ-1(T) ( =CGMCC 1.12378(T) =LMG 27422(T)).

  9. Cloning, expression, and isolation of the mannitol transport protein from the thermophilic bacterium Bacillus stearothermophilus.

    PubMed Central

    Henstra, S A; Tolner, B; ten Hoeve Duurkens, R H; Konings, W N; Robillard, G T

    1996-01-01

    A mannitol phosphotransferase system (PTS) was identified in Bacillus stearothermophilus by in vitro complementation with Escherichia coli EI, HPr, and IIA(Mtl). Degenerate primers based on regions of high amino acid similarity in the E. coli and Staphylococcus carnosus EII(Mt1) were used to develop a digoxigenin-labeled probe by PCR. Using this probe, we isolated three overlapping DNA fragments totaling 7.2 kb which contain the genes mtlA, mtlR, mtlF, and mtlD, encoding the mannitol IICB,a regulator, IIA, and a mannitol-1-phosphate dehydrogenase, respectively. The mtl4 gene consists of 1,413 bp coding for a 471-amino-acid protein with a calculated mass of 50.1 kDa. The amino acid sequence shows high similarity with the sequence of IICB(Mtl) of S. carnosus and the IICB part of the IICBA(Mtl)s of E. coli and B. subtilis. The enzyme could be functionally expressed in E. coli by placing it behind the strong tac promoter. The rate of thermal inactivation at 60 degrees C of B. stearothermophilus HCB(Mt1) expressed in E. coli was two times lower than that of E. coli IICB(Mtl). IICB(Mtl) in B. stearothermophilus is maximally active at 85 degrees C and thus very thermostable. The enzyme was purified on Ni-nitrilotriacetic acid resin to greater than 95% purity after six histidines were fused to the C-terminal part of the transporter. PMID:8824601

  10. Caloramator boliviensis sp. nov., a thermophilic, ethanol-producing bacterium isolated from a hot spring.

    PubMed

    Crespo, Carla; Pozzo, Tania; Karlsson, Eva Nordberg; Alvarez, Maria Teresa; Mattiasson, Bo

    2012-07-01

    A novel moderately thermophilic, anaerobic, ethanol-producing bacterial strain, 45B(T), was isolated from a mixed sediment water sample collected from a hot spring at Potosi, Bolivia. The cells were straight to slightly curved rods approximately 2.5 µm long and 0.5 µm wide. The strain was Gram-stain-variable, spore-forming and monotrichously flagellated. Growth of the strain was observed at 45-65 °C and pH 5.5-8.0, with optima of 60 °C and pH 6.5. The substrates utilized by strain 45B(T) were xylose, cellobiose, glucose, arabinose, sucrose, lactose, maltose, fructose, galactose, mannose, glycerol, xylan, carboxymethylcellulose and yeast extract. The main fermentation product from xylose and cellobiose was ethanol (0.70 and 0.45 g ethanol per gram of consumed sugar, respectively). Acetate, lactate, propionate, carbon dioxide and hydrogen were also produced in minor quantities. 1,3-Propanediol was produced when glycerol-containing medium was supplemented with yeast extract. The major cellular fatty acids were anteiso-C(15:0), C(16:0), iso-C(16:0), C(15:1), iso-C(14:0), C(13:0) and C(14:0). The polar lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminoglycolipid and 15 other unidentified lipids were predominant. The DNA G+C content of strain 45B(T) was 32.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain 45B(T) is located within the Gram-type positive Bacillus-Clostridium branch of the phylogenetic tree. On the basis of morphological and physiological properties and phylogenetic analysis, strain 45B(T) represents a novel species, for which the name Caloramator boliviensis sp. nov. is proposed; the type strain is 45B(T) (=DSM 22065(T)=CCUG 57396(T)).

  11. Bacillus lonarensis sp. nov., an alkalitolerant bacterium isolated from a soda lake.

    PubMed

    Reddy, Sultanpuram Vishnuvardhan; Thirumala, Mothe; Farooq, Mohammed; Sasikala, Chintalapati; Ramana, Chintalapati Venkata

    2015-01-01

    A novel Gram-stain-positive, rod-shaped, motile and endospore-forming novel bacterial strain 25nlg(T) was isolated from Lonar soda lake, in India. Based on the 16S rRNA gene sequence analysis, it was identified as a member of Firmicutes, being most closely related to Bacillus patagoniensis PAT 05(T) (96.6 %) and other members in the genus Bacillus (<96.0 %). Strain 25nlg(T) was catalase and oxidase-positive. The strain grows optimally at a pH of 9.5 with 4-6 % (w/v) NaCl and temperature of 35-37 °C. The cell wall of the strain 25nlg(T) contains meso-diaminopimelic acid as the diagnostic amino acid. Polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid (PL2), an aminophospholipid (APL2) and three unknown lipids (L2-4). The predominant isoprenoid quinone was MK-7. iso-C15:0 (41.7 %) was the predominant fatty acid, and significant proportions of anteiso-C15:0 (20.8 %), C12:0 (5.5 %), anteiso-C17:0 (4.9 %), iso-C17:0 (4.5 %) were also detected in the strain 25nlg(T). The DNA G+C content of the strain 25nlg(T) was 40.5 mol%. The results of molecular, physiological and biochemical tests allowed a clear phenotypic differentiation of strain 25nlg(T) from all other members of the genus Bacillus. Strain 25nlg(T) represents a novel member of the genus Bacillus, for which the name Bacillus lonarensis sp. nov. is proposed. The type strain is 25nlg(T) (=KCTC 33413(T) = LMG 27974(T) = CGMCC = 1.12817(T)).

  12. Bacillus caseinilyticus sp. nov., an alkali- and thermotolerant bacterium isolated from a soda lake.

    PubMed

    Vishnuvardhan Reddy, Sultanpuram; Thirumala, Mothe; Farooq, Mohammed

    2015-08-01

    A novel Gram-stain-positive, rod-shaped, motile, endospore-forming and proteolytic bacterial strain, SPT, was isolated from Lonar soda lake, in India. On the basis of 16S rRNA gene sequence analysis it was identified as belonging to the class Firmibacteria and was most closely related to Bacillus cellulosilyticus DSM 2522T (96.7%) and other members of the genus Bacillus ( < 95.9%). Strain SPT was catalase- and oxidase-positive. The cell-wall peptidoglycan of strain SPT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three phospholipids, two aminolipids and two unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15 : 0 (26.8%) was the predominant fatty acid and significant proportions (>5%) of iso-C15 : 0 (20.9%), C16 : 1ω7c alcohol (6.3%), iso-C16 : 0 (6.3%) and anteiso-C17 : 0 (5.3  %) were also detected in strain SPT. The DNA G+C content of strain SPT was 38.9 mol%. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain SPT from all other members of the genus Bacillus. Strain SPT represents a novel member of the genus Bacillus, for which the name Bacilluscaseinilyticus sp. nov. is proposed. The type strain is SPT ( = MCC 2612T = JCM 30246T).

  13. Draft Genome Sequence of Rhodococcus erythropolis VSD3, a Diesel Fuel-Degrading and Plant Growth-Promoting Bacterium Isolated from Hedera helix Leaves

    PubMed Central

    Stevens, Vincent; Thijs, Sofie; McAmmond, Breanne; Langill, Tori; Van Hamme, Jonathan; Weyens, Nele

    2017-01-01

    ABSTRACT We report here the 6.55-Mb draft genome sequence of Rhodococcus erythropolis VSD3, a Gram-positive bacterium of the Nocardiaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. The exploration of its genome will contribute to the assessment of its application as an inoculant in phylloremediation approaches. PMID:28232452

  14. Kordia ulvae sp. nov., a bacterium isolated from the surface of green marine algae Ulva sp.

    PubMed

    Qi, Feng; Huang, Zhaobin; Lai, Qiliang; Li, Dengfeng; Shao, Zongze

    2016-04-20

    A novel bacterial strain SC2T was isolated from Ulva sp. a green marine algae. Strain SC2T was Gram-negative, aerobic, rod-shaped and had no flagellum. Oxidase and catalase were positive. Strain SC2T can degrade skim milk, agar, soluble starch, Tween 20 and Tween 80. The optimal salinity and temperature of strain SC2T were 2% and 30 °C, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that strain SC2T was affiliated to the genus Kordia, with highest sequence similarity to Kordia algicida OT-1T (97.23%), Kordia antarctica IMCC3317T (97.23%) and Kordia jejudonensis SSK3-3T (97.02%); other species of the genus Kordia shared 93.98%-95.78% sequence similarity. The ANI value and the DNA-DNA hybridization estimated value between strain SC2T and three type strains (K. algicida OT-1T, K. antarctica IMCC3317T and K. jejudonensis SSK3-3T) were found to be 79.4%-82.4% and 24.2%-27.0%, respectively. The predominant fatty acids (>5.0%) were C16:0, iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, summed feature 3 (comprised C16:1 ω7c/C16:1 ω6c), summed feature 8 (comprised C18:1 ω7c/C18:1 ω6c) and summed feature 9 (comprised iso-C17:1 ω9c/C16:0 10-methyl). The respiratory quinone was Menaquinone-6 (MK-6). The polar lipid profile consisted of four unknown lipids, three unidentified phospholipids, one unidentified aminolipid and one phosphatidylethanolamine. The G+C content of the genomic DNA was 34.5 mol%. The combined genotypic and phenotypic data showed that strain SC2T represents a novel species within the genus Kordia, for which the name Kordia ulvae sp. nov. is proposed, with the type strain SC2T (= KCTC 42872T = MCCC 1A01772T = LMG 29123T).

  15. Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater.

    PubMed

    Liu, Yang; Wang, Run-Ping; Ren, Chong; Lai, Qi-Liang; Zeng, Run-Ying

    2015-12-01

    A motile, Gram-stain-negative, non-pigmented bacterial strain, designated MGL06T, was isolated from seawater of the South China Sea on selection medium containing 0.1 % (w/v) malachite green. Strain MGL06T showed highest 16S rRNA gene sequence similarity to Rhizobium vignae CCBAU 05176T (97.2 %), and shared 93.2-96.9 % with the type strains of other recognized Rhizobium species. Phylogenetic analyses based on 16S rRNA and housekeeping gene sequences showed that strain MGL06T belonged to the genus Rhizobium. Mean levels of DNA-DNA relatedness between strain MGL06T and R. vignae CCBAU 05176T, Rhizobium huautlense S02T and Rhizobium alkalisoli CCBAU 01393T were 20 ± 3, 18 ± 2 and 14 ± 3 %, respectively, indicating that strain MGL06T was distinct from them genetically. Strain MGL06T did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR or based on the draft genome sequence. Strain MGL06T contained Q-10 as the predominant ubiquinone. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c with minor amounts of C19 : 0 cyclo ω8c, C16 : 0 and C18 : 1ω7c 11-methyl. Polar lipids of strain MGL06T included unknown glycolipids, phosphatidylcholine, aminolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown polar lipid and aminophospholipid. Based on its phenotypic and genotypic data, strain MGL06T represents a novel species of the genus Rhizobium, for which the name Rhizobium marinum sp. nov. is proposed. The type strain is MGL06T ( = MCCC 1A00836T = JCM 30155T).

  16. Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic.

    PubMed

    Sánchez-Porro, Cristina; Kaur, Bhavleen; Mann, Henrietta; Ventosa, Antonio

    2010-12-01

    A Gram-negative, heterotrophic, aerobic, non-endospore-forming, peritrichously flagellated and motile bacterial strain, designated BH1(T), was isolated from samples of rusticles, which are formed in part by a consortium of micro-organisms, collected from the RMS Titanic wreck site. The strain grew optimally at 30-37°C, pH 7.0-7.5 and in the presence of 2-8 % (w/v) NaCl. We carried out a polyphasic taxonomic study in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparison indicated that strain BH1(T) clustered within the branch consisting of species of Halomonas. The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %). Other closely related species were Halomonas alkaliphila (96.5 % sequence similarity), Halomonas hydrothermalis (96.3 %), Halomonas gomseomensis (96.3 %), Halomonas venusta (96.3 %) and Halomonas meridiana (96.2 %). The major fatty acids of strain BH1(T) were C(18 : 1)ω7c (36.3 %), C(16 : 0) (18.4 %) and C(19 : 0) cyclo ω8c (17.9 %). The DNA G+C content was 60.0 mol% (T(m)). Ubiquinone 9 (Q-9) was the major lipoquinone. The phenotypic features, fatty acid profile and DNA G+C content further supported the placement of strain BH1(T) in the genus Halomonas. DNA-DNA hybridization values between strain BH1(T) and H. neptunia CECT 5815(T), H. variabilis DSM 3051(T), H. boliviensis DSM 15516(T) and H. sulfidaeris CECT 5817(T) were 19, 17, 30 and 29 %, respectively, supporting the differential taxonomic status of BH1(T). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain BH1(T) is considered to represent a novel species, for which the name Halomonas titanicae sp. nov. is proposed. The type strain is BH1(T) (=ATCC BAA-1257(T) =CECT 7585(T) =JCM 16411(T) =LMG 25388(T)).

  17. Winogradskyella psychrotolerans sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from Arctic sediment.

    PubMed

    Begum, Z; Srinivas, T N R; Manasa, P; Sailaja, B; Sunil, B; Prasad, S; Shivaji, S

    2013-05-01

    A novel Gram-negative, rod-coccus shaped, non-motile, strain, RS-3(T), was isolated from a sediment sample collected from the marine transect of Kongsfjorden, Ny-Ålesund, Svalbard, Arctic. Colonies and broth cultures were yellowish in colour due to the presence of carotenoids. Strain RS-3(T) was positive for oxidase, aesculinase, caseinase, gelatinase and urease activities and negative for amylase, catalase, lipase, lysine decarboxylase, ornithine decarboxylase, DNase and β-galactosidase activities. The predominant fatty acids were iso-C15 : 0 (18.0), anteiso-C15 : 0 (16.8), iso-C15 : 1 G (14.2), anteiso-C15 : 1 A (6.0) and iso-C15 : 0 3-OH (6.8). Strain RS-3(T) contained MK-6 (72.42 %) and MK-7 (27.58 %) as the major respiratory quinones and phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids make up the polar lipid composition. The DNA G+C content of strain RS-3(T) was 34.7±1.2 mol%. The 16S rRNA gene sequence analysis indicated that Winogradskyella pacifica and Winogradskyella thalassocola are the most closely related species with sequence similarities to the type strains of these species of 98.5 and 97.7 %, respectively. However, DNA-DNA hybridization with Winogradskyella pacifica KCTC 22997(T) and Winogradskyella thalassocola DSM 15363(T) showed a relatedness of 22 and 42.5 % with respect to strain RS-3(T). Based on the DNA-DNA hybridization values, phenotypic and chemotaxonomic characteristics and phylogenetic inference, strain RS-3(T) is proposed as a novel species of the genus Winogradskyella, for which the name Winogradskyella psychrotolerans sp. nov. is proposed. The type strain of Winogradskyella psychrotolerans sp. nov. is RS-3(T) ( = CIP 110154(T) = NBRC 106169(T)). An emended description of the genus Winogradskyella is provided.

  18. Shewanella arctica sp. nov., an iron-reducing bacterium isolated from Arctic marine sediment.

    PubMed

    Kim, So-Jeong; Park, Soo-Je; Oh, Yong-Sik; Lee, Sang-Ah; Shin, Kee-Sun; Roh, Dong-Hyun; Rhee, Sung-Keun

    2012-05-01

    Two strains of dissimilatory iron-reducing bacteria, which could couple lactate oxidation to iron reduction for energy conservation, were isolated from Arctic marine sediment. The strains, IR12(T) and IR26, were both Gram-staining-negative, catalase- and oxidase-positive and facultative anaerobes. Their cells were rod-shaped and motile by means of a polar flagellum. Both strains grew in the presence of 0.5-3.5 % (w/v) NaCl, with an absolute requirement for Na(+). Both were psychrotolerant since they could grow at 4-28 °C but had an optimum growth temperature of 20 °C. Both grew at pH 4.5-9.0 (optimum, pH 7.5). The major fatty acids of strains IR12(T) and IR26 were summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c) and C(16 : 0). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains IR12(T) and IR26 belonged to the class Gammaproteobacteria and were most closely related to Shewanella vesiculosa M7(T), Shewanella livingstonensis NF22(T) and Shewanella frigidimarina ACAM 591(T) (with 98.5 and 98.8 %, 98.5 and 98.8 %, and 98.5 and 98.8 % sequence similarities, respectively). The genomic DNA G+C contents of strains IR12(T) and IR26 were 40.0 and 40.3 mol%, respectively. DNA-DNA relatedness data indicated that the two novel strains represented a single species that was distinct from S. vesiculosa M7(T), S. livingstonensis NF22(T) and S. frigidimarina ACAM 591(T). Based on the phylogenetic, phenotypic and DNA-DNA relatedness data, the two new strains represent a single novel species of the genus Shewanella, for which the name Shewanella arctica sp. nov. is proposed. The type strain is IR12(T) ( = KCTC 23109(T) = JCM 16723(T)).

  19. Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing.

    PubMed

    Feng, Guang-Da; Yang, Song-Zhen; Li, Hua-Ping; Zhu, Hong-Hui

    2016-01-01

    A heavy metal-resistant and dimethyl disulfide-producing bacterial strain, designated 6NM-7T, was isolated from wolfram mine tailing, Dayu County, Jiangxi Province, PR China. Strain 6NM-7T was aerobic, Gram-stain-negative and motile by means of a single polar flagellum. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain 6NM-7T was affiliated with the genus Massilia and was closely related to Massilia norwichensis LMG 28164T (98.8 % 16S rRNA gene sequence similarity), Massilia kyonggiensis KACC 17471T (98.4 %), Massilia niastensis KACC 12599T (97.8 %), Massilia tieshanensis KACC 14940T (97.3 %), Massilia haematophila KACC 13771T (97.2 %), Massilia namucuonensis CGMCC 1.11014T (97.1 %) and Massilia aerilata KACC 12505T (97.1 %). The DNA-DNA relatedness values between strain 6NM-7T and its closely related type strains were all below 70 %. The major respiratory quinone was unbiquinone 8 (Q-8) and the major cellular fatty acids consisted of C16 : 0 (33.2 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 21.8 %), C17 : 0 cyclo (20.8 %), C18 : 1ω7c (7.4 %) and C10 : 0 3-OH (5.8 %). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain 6NM-7T was 66.8 ± 0.6 mol%. On the basis of the results of this polyphasic taxonomic study, strain 6NM-7T should be assigned to a novel species of the genus Massilia, for which the name Massilia putida sp. nov. is proposed. The type strain is 6NM-7T ( = DSM 27523T = KCTC 42761T).

  20. Luteibacter jiangsuensis sp. nov.: a methamidophos-degrading bacterium isolated from a methamidophos-manufacturing factory.

    PubMed

    Wang, Li; Wang, Guang-li; Li, Shun-peng; Jiang, Jian-dong

    2011-01-01

    A Gram-stain-negative, non-motile, rod-shaped bacterial strain, JW-64-1(T), capable of degrading methamidophos was isolated from a methamidophos-manufacturing factory in China, and was subjected to a polyphasic taxonomic investigation. Strain JW-64-1(T) produced circular, smooth, transparent, yellow-colored colonies (1.0-2.0 mm) on LB agar after 2 days incubation. It grew optimally at 25-30°C and pH 7.0 without the presence of NaCl. The G+C content of the total DNA was 63.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW-64-1(T) fell within the cluster comprising Luteibacter species. The 16S rRNA gene sequence of strain JW-64-1(T) was most closely related to Luteibacter rhizovicinus DSM 16549(T) (98.6%), followed by Luteibacter yeojuensis DSM 17673(T) (98.4%) and L. anthropi CCUG 25036(T) (98.2%). The major cellular fatty acids of strain JW-64-1(T) were iso-C(15:0) (24.1%), iso-C(17:0) (20.2%) and summed feature 9 comprising iso-C(17:1) ω9c and/or C(16:0) 10-methyl (20.3%). The major isoprenoid quinine was Q-8 (98%), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphoaminolipid, aminolipids-1, aminolipids-2, and phospholipids. The values for DNA-DNA relatedness between strain JW-64-1(T) and the closest phylogenetic relatives of L. rhizovicinus and Luteibacter yeojuensis were 34.8 ± 2.6 and 25.6 ± 3.1%, respectively. On the basis of the phenotypic, chemotaxonomic, DNA-DNA relatedness and phylogenetic analysis based on the 16S rRNA gene sequences, strain JW-64-1(T) represents a novel species of the genus Luteibacter, for which the name Luteibacter jiangsuensis sp. nov. is proposed. The type strain is JW-64-1(T) (=CGMCC 1.10133(T) = DSM 22396(T)).

  1. Anoxybacillus suryakundensis sp. nov, a Moderately Thermophilic, Alkalitolerant Bacterium Isolated from Hot Spring at Jharkhand, India

    PubMed Central

    Deep, Kamal; Poddar, Abhijit; Das, Subrata K.

    2013-01-01

    Four closely related facultative anaerobe, moderately thermophilic, Gram positive rods (JS1T, JS5, JS11, and JS15) were isolated from sediment samples from a hot spring at Suryakund, Jharkhand, India. Colonies were pale yellow, rough surface with uneven edges on TSA after 72 h incubation. Heterotrophic growth was observed at 40-60°C and pH 5.5-11.5; optimum growth occurred at 55°C and pH 7.5. 16S rRNA gene sequence analysis revealed the strains belong to genus Anoxybacillus. DNA-DNA homology values among strains were above 70% and showed distinct ERIC and REP PCR profile. On the basis of morphology and biochemical characteristics, strain JS1T was studied further. Strain JS1T showed 99.30% sequence similarity with A. flavithermus subsp. yunnanensis, 99.23% with A. mongoliensis, 99.16% with A. eryuanensis, 98.74% with A. flavithermus subsp. flavithermus, 98.54% with A. tengchongensis, 98.51% with A. pushchinoensis, 97.91% with A. thermarum, 97.82% with A. kaynarcensis, 97.77% with A. ayderensis and A. kamchatkensis, 97.63% with A. salavatliensis, 97.55% with A. kestanbolensis, 97.48% with A. contaminans, 97.27% with A. gonensis and 97.17% with A. voinovskiensis. In 16S rRNA secondary structure based phylogenetic comparison, strain JS1T was clustered with Anoxybacillus eryuanensis, A. mongoliensis, and A. flavithermus subsp. yunnanensis and showed 15 species specific base substitutions with maximum variability in helix 6. Moreover, DNA-DNA relatedness between JS1T and the closely related type strains were well below 70%. The DNA G+C content was 42.1 mol%. The major fatty acids were C15:0 iso, C16:0 iso and C17:0iso. The polar lipids were a phosphatidylgylycerol, a diphosphatidylglycerol, a phosphatidylethnolamine, a phosphatidylcholine, a phosphatidyl monomethylethanolamine and four unknown lipids. Based on polyphasic approach, strain JS1T represent a novel species of the genus Anoxybacillus for which Anoxybacillus suryakundensis sp. nov. is proposed. The type

  2. Caloranaerobacter ferrireducens sp. nov., an anaerobic, thermophilic, iron (III)-reducing bacterium isolated from deep-sea hydrothermal sulfide deposits.

    PubMed

    Zeng, Xiang; Zhang, Zhao; Li, Xi; Jebbar, Mohamed; Alain, Karine; Shao, Zongze

    2015-06-01

    A thermophilic, anaerobic, iron-reducing bacterium (strain DY22619T) was isolated from a sulfide sample collected from an East Pacific Ocean hydrothermal field at a depth of 2901 m. Cells were Gram-stain-negative, motile rods (2-10 µm in length, 0.5 µm in width) with multiple peritrichous flagella. The strain grew at 40-70 °C inclusive (optimum 60 °C), at pH 4.5-8.5 inclusive (optimum pH 7.0) and with sea salts concentrations of 1-10 % (w/v) (optimum 3 % sea salts) and NaCl concentrations of 1.5-5.0 % (w/v) (optimum 2.5 % NaCl). Under optimal growth conditions, the generation time was around 55 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, amino acids, carbohydrates and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamate, methionine, threonine, fructose, mannose, galactose, glucose, palatinose, rhamnose, turanose, gentiobiose, xylose, sorbose, pyruvate, tartaric acid, α-ketobutyric acid, α-ketovaleric acid, galacturonic acid and glucosaminic acid. Strain DY22619T was strictly anaerobic and facultatively dependent on various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulfate, thiosulfate or nitrate. The genomic DNA G+C content was 29.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that the closest relative of strain DY22619T was Caloranaerobacter azorensis MV1087T, sharing 97.41 % 16S rRNA gene sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Caloranaerobacter, for which the name Caloranaerobacterhttp://dx.doi.org/10.1601/nm.4081ferrireducens sp. nov. is proposed. The type strain is DY22619T ( = JCM 19467T = DSM 27799T = MCCC1A06455T).

  3. Sphingobium barthaii sp. nov., a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterium isolated from cattle pasture soil.

    PubMed

    Maeda, Allyn H; Kunihiro, Marie; Ozeki, Yasuhiro; Nogi, Yuichi; Kanaly, Robert A

    2015-09-01

    A Gram-stain-negative, yellow, rod-shaped bacterium, designated strain KK22(T), was isolated from a microbial consortium that grew on diesel fuel originally recovered from cattle pasture soil. Strain KK22(T) has been studied for its ability to biotransform high molecular weight polycyclic aromatic hydrocarbons. On the basis of 16S rRNA gene sequence phylogeny, strain KK22(T) was affiliated with the genus Sphingobium in the phylum Proteobacteria and was most closely related to Sphingobium fuliginis TKP(T) (99.8%) and less closely related to Sphingobium quisquiliarum P25(T) (97.5%). Results of DNA-DNA hybridization (DDH) revealed relatedness values between strain KK22(T) and strain TKP(T) and between strain KK22(T) and strain P25(T) of 21 ± 4% (reciprocal hybridization, 27 ± 2%) and 15 ± 2% (reciprocal hybridization, 17 ± 1%), respectively. Chemotaxonomic analyses of strain KK22(T) showed that the major respiratory quinone was ubiquinone Q-10, that the polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidyl-N-methylethylethanolamine and sphingoglycolipid, and that C18 : 1ω7c and C14 : 0 2-OH were the main fatty acid and hydroxylated fatty acids, respectively. This strain was unable to reduce nitrate and the genomic DNA G+C content was 64.7 mol%. Based upon the results of the DDH analyses, the fact that strain KK22(T) was motile, and its biochemical and physiological characteristics, strain KK22(T) could be separated from recognized species of the genus Sphingobium. We conclude that strain KK22(T) represents a novel species of this genus for which the name Sphingobium barthaii sp. nov. is proposed; the type strain is KK22(T) ( = DSM 29313(T) = JCM 30309(T)).

  4. Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor.

    PubMed

    Balk, Melike; Weijma, Jan; Stams, Alfons J M

    2002-07-01

    A novel, anaerobic, non-spore-forming, mobile, Gram-negative, thermophilic bacterium, strain TMOT, was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 C with methanol as the sole substrate. The G+C content of the DNA of strain TMOT was 39.2 mol%. The optimum pH, NaCl concentration, and temperature for growth were 7.0, 1.0%, and 65 degrees C, respectively. Strain TMOT was able to degrade methanol to CO2 and H2 in syntrophic culture with Methanothermobacter thermautotrophicus AH or Thermodesulfovibrio yellowstonii. Thiosulfate, elemental sulfur, Fe(III) and anthraquinone-2,6-disulfonate were able to serve as electron acceptors during methanol degradation. In the presence of thiosulfate or elemental sulfur, methanol was converted to CO2 and partly to alanine. In pure culture, strain TMOT was also able to ferment methanol to acetate, CO2 and H2. However, this degradation occurred slower than in syntrophic cultures or in the presence of electron acceptors. Yeast extract was required for growth. Besides growing on methanol, strain TMOT grew by fermentation on a variety of carbohydrates including monomeric and oligomeric sugars, starch and xylan. Acetate, alanine, CO2, H2, and traces of ethanol, lactate and alpha-aminobutyrate were produced during glucose fermentation. Comparison of 16S rDNA genes revealed that strain TMOT is related to Thermotoga subterranea (98%) and Thermotoga elfii (98%). The type strain is TMOT (= DSM 14385T = ATCC BAA-301T). On the basis of the fact that these organisms differ physiologically from strain TMOT, it is proposed that strain TMOT be classified as a new species, within the genus Thermotoga, as Thermotoga lettingae.

  5. Desulfomicrobium thermophilum sp. nov., a novel thermophilic sulphate-reducing bacterium isolated from a terrestrial hot spring in Colombia.

    PubMed

    Thevenieau, France; Fardeau, Marie-Laure; Ollivier, Bernard; Joulian, Catherine; Baena, Sandra

    2007-03-01

    A moderately thermophilic, sulphate-reducing bacterium, designated strain P6-2(T), was isolated from a terrestrial hot spring located at a height of 2,500 m in the Andean region, Colombia (5 degrees 43'69''N, 73 degrees 6'10''W). Cells of strain P6-2(T) were rod-shaped, stained Gram-negative and were motile by means of a single polar flagellum. The strain grew lithotrophically with H(2) as the electron donor and organotrophically on lactate, pyruvate, ethanol, malate, fumarate, n-propanol and succinate in the presence of sulphate as the terminal electron acceptor. Fumarate and pyruvate was fermented. Strain P6-2(T) grew optimally at 55 degrees C (range 37-60 degrees C), pH 6.6 (range 5.8-8.8) in the presence of 0.5% NaCl (range 0-4.5%) with lactate and sulphate and produced acetate, CO(2) and H(2)S as the major end-products. Sulphate, sulphite and thiosulphate could be used as electron acceptors but not elemental sulphur or nitrate. The G + C content of the genomic DNA was 58.7 mol%. The 16S rRNA sequence analysis indicated that strain P6-2(T) was a member of the class Deltaproteobacteria, domain Bacteria with Desulfomicrobium baculatum being the closest relative (similarity value of 94%). Phylogeny of genes encoding alpha- and beta-subunits of the dissimilatory sulphite reductase (dsrAB genes) supported its affiliation to members of the genus Desulfomicrobium. On the basis of this evidence, we propose to assign strain P6-2(T) as new species of the genus Desulfomicrobium, D. thermophilum sp. nov., with strain P6-2(T) as the type strain (= DSM 16697(T) = CCUG 49732(T)).

  6. Geosporobacter subterraneus gen. nov., sp. nov., a spore-forming bacterium isolated from a deep subsurface aquifer.

    PubMed

    Klouche, Nihel; Fardeau, Marie-Laure; Lascourrèges, Jean-François; Cayol, Jean-Luc; Hacene, Hocine; Thomas, Pierre; Magot, Michel

    2007-08-01

    A novel, strictly anaerobic, chemo-organotrophic bacterium, designated strain VNs68(T), was isolated from a well that collected water from a deep aquifer at a depth of 800 m in the Paris Basin, France. Cells were thin, non-motile, Gram-positive rods forming terminal endospores (3.0-5.0 x 0.5 microm). Strain VNs68(T) grew at temperatures between 30 and 55 degrees C (optimum 42 degrees C) and at pH 5.6-8.4 (optimum pH 7.3). It did not require salt for growth but tolerated up to 40 g NaCl l(-1). Strain VNs68(T) was an obligate heterotroph fermenting carbohydrates such as glucose, xylose, fructose, ribose and cellobiose. Casamino acids and amino acids (arginine, serine, lysine, alanine, aspartate, asparagine, isoleucine, histidine) were also fermented. The main fermentation products from glucose were acetate with H(2) and CO(2). Sulfate, sulfite, thiosulfate, elemental sulfur, nitrate and nitrite were not used as electron acceptors. The G+C content of the genomic DNA was 42.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs68(T) was affiliated to cluster XI, order Clostridiales, domain Bacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain VNs68(T) is considered to represent a novel species of a new genus, for which the name Geosporobacter subterraneus gen. nov., sp. nov. is proposed. The type strain of Geosporobacter subterraneus is VNs68(T) (=DSM 17957(T) =JCM 14037(T)).

  7. Structural characterization of the core oligosaccharide isolated from the lipopolysaccharide of the haloalkaliphilic bacterium Salinivibrio sharmensis strain BAG(T).

    PubMed

    Carillo, Sara; Pieretti, Giuseppina; Lindner, Buko; Romano, Ida; Nicolaus, Barbara; Lanzetta, Rosa; Parrilli, Michelangelo; Corsaro, Maria Michela

    2013-03-07

    Salinivibrio genus is included in the family Vibrionaceae and up to now is constituted by only five members. All the species are moderately halophilic bacteria found in salted meats, brines, and several hypersaline environments. Halophilic microorganisms are good sources of biomolecules, such as proteases, that have a great industrial interest as demonstrated by recent studies. All these bacteria possess on their outer membrane amphiphilic molecules named lipopolysaccharides, which are of great interest because of their involvement in the mechanisms of interaction between the microbial life and environmental factors. A novel haloalkaliphilic, facultative anaerobic and Gram-negative Salinivibrio-like microorganism, named S. sharmensis strain BAG(T), was recovered from a saline lake in Ras Mohammed Park (Egypt). The aim of this work is the isolation and structural characterization of the core oligosaccharidic fraction of the lipopolysaccharide from this bacterium. By means of HPAEC-PAD we were able to purify two glycoforms, fully depicted by ESI FT-ICR mass spectrometry, chemical analysis, and NMR spectroscopy. Like other haloalkaliphilic bacteria, the core region was found to be characterized by the presence of several negatively charged residues, such as uronic acids. All the data contributed to give the following structure α-D-Glc-(1-->4)-β-D-GalNAc-(1--4)-β-D-Glc1-->4α-D-GlcA-(1-->2)-α-L,D-Hep-(1-->3)-α-D,D-Hep-(1-->5)-α-D-Kdo4P-(2-->6)-LipidA2<--1β-D-GlcA.

  8. Characterization and Antibacterial Potential of Lactic Acid Bacterium Pediococcus pentosaceus 4I1 Isolated from Freshwater Fish Zacco koreanus

    PubMed Central

    Bajpai, Vivek K.; Han, Jeong-Ho; Rather, Irfan A.; Park, Chanseo; Lim, Jeongheui; Paek, Woon Kee; Lee, Jong Sung; Yoon, Jung-In; Park, Yong-Ha

    2016-01-01

    This study was undertaken to characterize a lactic acid bacterium 4I1, isolated from the freshwater fish, Zacco koreanus. Morphological, biochemical, and molecular characterization of 4I1 revealed it to be Pediococcus pentosaceus 4I1. The cell free supernatant (CFS) of P. pentosaceus 4I1 exhibited significant (p < 0.05) antibacterial effects (inhibition zone diameters: 16.5–20.4 mm) against tested foodborne pathogenic bacteria with MIC and MBC values of 250–500 and 500–1,000 μg/mL, respectively. Further, antibacterial action of CFS of P. pentosaceus 4I1 against two selected bacteria Staphylococcus aureus KCTC-1621 and Escherichia coli O157:H7 was determined in subsequent assays. The CFS of P. pentosaceus 4I1 revealed its antibacterial action against S. aureus KCTC-1621 and E. coli O157:H7 on membrane integrity as confirmed by a reduction in cell viability, increased potassium ion release (900 and 800 mmol/L), reduced absorption at 260-nm (3.99 and 3.77 OD), and increased relative electrical conductivity (9.9 and 9.7%), respectively. Gas chromatography–mass spectrometry (GC–MS) analysis of the CFS of P. pentosaceus 4I1 resulted in the identification of seven major compounds, which included amino acids, fatty acids and organic acids. Scanning electron microscopic-based morphological analysis further confirmed the antibacterial effect of CFS of P. pentosaceus 4I1 against S. aureus KCTC-1621 and E. coli O157:H7. In addition, the CFS of P. Pentosaceus 4I1 displayed potent inhibitory effects on biofilms formation by S. aureus KCTC-1621 and E. coli O157:H7. The study indicates the CFS of P. pentosaceus 4I1 offers an alternative means of controlling foodborne pathogens. PMID:28066360

  9. Degradation of 2,6-di-tert-butylphenol by an isolated high-efficiency bacterium strain.

    PubMed

    Zhang, Ya-lei; Fang, Zhen-wei; Xu, De-qiang; Xiao, Yi-ping; Zhao, Jian-fu; Qiang, Zhi-min

    2005-01-01

    An aerobic bacterium strain, F-3-4, capable of effectively degrading 2, 6-ditert-butylphenol (2, 6-DTBP), was isolated and screened out from an acrylic fiber wastewater and the biofilm in the wastewater treatment facilities. This strain was identified as Alcaligenes sp. through morphological, physiological and biochemical examinations. After cultivation, the strain was enhanced by 26.3% in its degradation capacity for 2,6-DTBP. Results indicated that the strain was able to utilize 2,6-DTBP, lysine, lactamine, citrate, n-utenedioic acid and malic acid as the sole carbon and energy source, alkalinize acetamide, asparagine, L-histidine, acetate, citrate and propionate, but failed to utilize glucose, D-fructose, D-seminose, D-xylose, serine and phenylalanine as the sole carbon and energy source. The optimal growth conditions were determined to be: temperature 37 degrees C, pH 7.0, inoculum size 0.1% and shaker rotary speed 250 r/min. Under the optimal conditions, the degradation kinetics of 2,6-DTBP with an initial concentration of 100 mg/L was studied. Results indicated that 62.4% of 2,6-DTBP was removed after 11 d. The degradation kinetics could be expressed by Eckenfelder equation with a half life of 9.38 d. In addition, the initial concentration of 2,6-DTBP played an important role on the degradation ability of the strain. The maximum initial concentration of 2,6-DTBP was determined to be 200 mg/L. Above this level, the strain was overloaded and exhibited significant inhibition.

  10. Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost.

    PubMed

    Steven, Blaire; Chen, Min Qun; Greer, Charles W; Whyte, Lyle G; Niederberger, Thomas D

    2008-06-01

    A Gram-positive, aerobic, rod-shaped bacterium (strain Eur1 9.5(T)) was isolated from a 9-m-deep permafrost sample from the Canadian high Arctic. Strain Eur1 9.5(T) could not be cultivated in liquid medium and grew over the temperature range 5-37 degrees C; no growth was observed at 42 degrees C and only slow growth was observed at 5 degrees C following 1 month of incubation. Eur1 9.5(T) grew over the pH range 5.5-8.9 and tolerated NaCl concentrations of 0-0.5 % (w/v). Eur1 9.5(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. Eur1 9.5(T) contained iso-C(15 : 0) as the major cellular fatty acid and menaquinone 7 (MK-7) as the major respiratory quinone. The cell-wall peptidoglycan was of type A1gamma. The DNA G+C content was 53.1 mol%. The 16S rRNA gene sequence of strain Eur1 9.5(T) was only distantly related (

  11. NMR structural study of fructans produced by Bacillus sp. 3B6, bacterium isolated in cloud water.

    PubMed

    Matulová, Mária; Husárová, Slavomíra; Capek, Peter; Sancelme, Martine; Delort, Anne-Marie

    2011-03-01

    Bacillus sp. 3B6, bacterium isolated from cloud water, was incubated on sucrose for exopolysaccharide production. Dialysis of the obtained mixture (MWCO 500) afforded dialyzate (DIM) and retentate (RIM). Both were separated by size exclusion chromatography. RIM afforded eight fractions: levan exopolysaccharide (EPS), fructooligosaccharides (FOSs) of levan and inulin types with different degrees of polymerization (dp 2-7) and monosaccharides fructose:glucose=9:1. Levan was composed of two components with molecular mass ~3500 and ~100kDa in the ratio 2.3:1. Disaccharide fraction contained difructose anhydride DFA IV. 1-Kestose, 6-kestose, and neokestose were identified as trisaccharides in the ratio 2:1:3. Fractions with dp 4-7 were mixtures of FOSs of levan (2,6-βFruf) and inulin (1,2-βFruf) type. DIM separation afforded two dominant fractions: monosaccharides with fructose: glucose ratio 1:3; disaccharide fraction contained sucrose only. DIM trisaccharide fraction contained 1-kestose, 6-kestose, and neokestose in the ratio1.5:1:2, penta and hexasaccharide fractions contained FOSs of levan type (2,6-βFruf) containing α-glucose. In the pentasaccharide fraction also the presence of a homopentasaccharide composed of 2,6-linked βFruf units only was identified. Nystose, inulin (1,2-βFruf) type, was identified as DIM tetrasaccharide. Identification of levan 2,6-βFruf and inulin 1,2-βFruf type oligosaccharides in the incubation medium suggests both levansucrase and inulosucrase enzymes activity in Bacillus sp. 3B6.

  12. Huanghella arctica gen. nov., sp. nov., a bacterium of the family Cytophagaceae isolated from Arctic tundra soil.

    PubMed

    Jiang, Fan; Xiao, Mengchen; Chen, Lu; Kan, Wenjing; Peng, Fang; Dai, Jun; Chang, Xulu; Li, Wenxin; Fang, Chengxiang

    2013-02-01

    A novel, strictly aerobic, red-pigmented, gram-reaction-negative bacterium, designated strain R9-9(T), was isolated from tundra soil collected near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). The novel strain was subjected to a taxonomic study using a polyphasic approach. It grew optimally at 20-22 °C and at pH 7.0. Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain R9-9(T) represents a distinct phyletic line that reflects a novel generic status within the family Cytophagaceae. The novel strain showed relatively low 16S rRNA gene sequence similarities (<88.0 %) to members of established genera. Strain R9-9(T) contained summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c), iso-C(17 : 0) 3-OH, iso-C(15 : 0) and C(16 : 1)ω5c as its major cellular fatty acids, phosphatidylethanolamine as its main polar lipid, and MK-7 as its major respiratory quinone. The genomic DNA G+C content was 56.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain R9-9(T) is considered to represent a novel species in a new genus in the family Cytophagaceae, for which the name Huanghella arctica gen. nov., sp. nov. is proposed. The type strain is R9-9(T) ( = CCTCC AB 2010418(T) = NRRL B-59750(T)).

  13. Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.

    PubMed

    Choi, Dong H; Cho, Byung C

    2006-04-01

    A rod-shaped marine bacterium, designated strain CL-TF09T, isolated from a tidal flat in Ganghwa, Korea, was characterized based on its physiological and biochemical features, fatty acid profile and phylogenetic position. 16S rRNA gene sequence analysis revealed a clear affiliation with the family Flavobacteriaceae. Strain CL-TF09T showed the closest phylogenetic relationship with the genera Tenacibaculum and Polaribacter; sequence similarities between CL-TF09T and the type strains of Tenacibaculum and Polaribacter species ranged from 90.7 to 91.8 %. Cells of strain CL-TF09T were non-motile and grew on solid media as yellow colonies. The strain grew in the presence of 1-5 % sea salts, within a temperature range of 5-30 degrees C and at pH 7-8. The strain had iso-C(15 : 0) 3-OH (17.4 %), iso-C(15 : 0) (16.7 %), anteiso-C(15 : 0) (15.1 %) and iso-C(16 : 0) 3-OH (13.4 %) as predominant fatty acids. The DNA G+C content was 33.9 mol%. Based on the physiological, fatty acid composition and phylogenetic data presented, strain CL-TF09T is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Lutibacter litoralis gen. nov., sp. nov. is proposed. The type strain is CL-TF09T (=KCCM 42118T = JCM 13034T).

  14. A novel isolated Terrabacter-like bacterium can mineralize 2-aminopyrimidine, the principal metabolite of microbial sulfadiazine degradation.

    PubMed

    Tappe, Wolfgang; Hofmann, Diana; Disko, Ulrich; Koeppchen, Stephan; Kummer, Sirgit; Vereecken, Harry

    2015-04-01

    Recently we showed that during the degradation of sulfadiazine (SDZ) by Microbacterium lacus strain SDZm4 the principal metabolite 2-aminopyrimidine (2-AP) accumulated to the same molar amount in the culture as SDZ disappeared (Tappe et al. Appl Environ Microbiol 79:2572-2577, 2013). Although 2-AP is considered a recalcitrant agent, long-term lysimeter experiments with (14)C-pyrimidine labeled SDZ ([(14)C]pyrSDZ) provided indications for substantial degradation of the pyrimidine moiety of the SDZ molecule. Therefore, we aimed to enrich 2-AP degrading bacteria and isolated a pure culture of a Terrabacter-like bacterium, denoted strain 2APm3. When provided with (14)C-labeled SDZ, M. lacus strain SDZm4 degraded [(14)C]pyrSDZ to [(14)C]2-AP. Resting cells of 2APm3 at a concentration of 5 × 10(6) cells ml(-1) degraded 62 µM [(14)C]2-AP to below the detection limit (0.6 µM) within 5 days. Disappearance of 2-AP resulted in the production of at least two transformation products (M1 and M2) with M2 being identified as 2-amino-4-hydroxypyrimidine. After 36 days, the transformation products disappeared and 83 % of the applied [(14)C]2-AP radioactivity was trapped as (14)CO2. From this we conclude that a consortium of two species should be able to almost completely degrade SDZ in soils.

  15. Selective production of 2,3-butanediol and acetoin by a newly isolated bacterium Klebsiella oxytoca M1.

    PubMed

    Cho, Sukhyeong; Kim, Kyung Duk; Ahn, Jae-Hyung; Lee, Jinwon; Kim, Seon-Won; Um, Youngsoon

    2013-08-01

    A newly isolated bacterium, designated as Klebsiella oxytoca M1, produced 2,3-butanediol (2,3-BDO) or acetoin selectively as a major product depending on temperature in a defined medium. K. oxytoca M1 produced 2,3-BDO mainly (0.32~0.34 g/g glucose) at 30 °C while acetoin was a major product (0.32~0.38 g/g glucose) at 37 °C. To investigate factors affecting product profiles according to temperature, the expression level of acetoin reductase (AR) that catalyzes the conversion of acetoin to 2,3-BDO was analyzed using crude protein extracted from K. oxytoca M1 grown at 30 and 37 °C. The AR expression at 37 °C was 12.8-fold lower than that at 30 °C at the stationary phase and reverse transcription PCR (RT-PCR) analysis of the budC (encoding AR) was also in agreement with the AR expression results. When AR was overexpressed using K. oxytoca M1 harboring pUC18CM-budC, 2,3-BDO became a major product at 37 °C, indicating that the AR expression level was a key factor determining the major product of K. oxytoca M1 at 37 °C. The results in this study demonstrate the feasibility of using K. oxytoca M1 for the production of not only 2,3-BDO but also acetoin as a major product.

  16. Aneurinibacillus tyrosinisolvens sp. nov., a tyrosine-dissolving bacterium isolated from organics- and methane-rich seafloor sediment.

    PubMed

    Tsubouchi, Taishi; Mori, Kozue; Miyamoto, Norio; Fujiwara, Yoshihiro; Kawato, Masaru; Shimane, Yasuhiro; Usui, Keiko; Tokuda, Maki; Uemura, Moeka; Tame, Akihiro; Uematsu, Katsuyuki; Maruyama, Tadashi; Hatada, Yuji

    2015-06-01

    A novel Gram-positive-staining, strictly aerobic and heterotrophic bacterium, designated strain LL-002T, was isolated from organics- and methane-rich seafloor sediment at a depth of 100 m in Kagoshima Bay, Kagoshima, Japan. Colonies were lustreless and translucent white in colour. The temperature, pH and salt concentration ranges for growth were 10-30 °C, pH 6.0-6.5 and 0-1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain LL-002T belongs to the genus Aneurinibacillus of the family Paenibacillaceae. 16S rRNA gene sequence similarities between strain LL-002T and the type strains of species of the genus Aneurinibacillus were 92.8-95.7 %; the highest sequence identity was with the type strain of Aneurinibacillus migulanus. The DNA G+C content of strain LL-002T was 46.2 mol%. MK-7 was the predominant menaquinone. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and the cell-wall peptidoglycan contained meso-diaminopimelic acid and glutamic acid, glycine and alanine in addition to muramic acid and glucosamine. The peptidoglycan type was A1γ. In DNA-DNA hybridization assays between strain LL-002T and the type strains of the other species of the genus Aneurinibacillus, the level of hybridization was 6.3-30.1 %. On the basis of its biological features and the 16S rRNA gene sequence comparison presented here, strain LL-002T is considered to represent a novel species of the genus Aneurinibacillus, for which the name Aneurinibacillus tyrosinisolvens sp. nov. is proposed; the type strain is LL-002T ( = NBRC 110097T = CECT 8536T).

  17. Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent.

    PubMed

    Alain, Karine; Callac, Nolwenn; Guégan, Marianne; Lesongeur, Françoise; Crassous, Philippe; Cambon-Bonavita, Marie-Anne; Querellou, Joël; Prieur, Daniel

    2009-06-01

    A novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (1 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60 x 0.40 microm) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H(2) as an energy source, S(0) as an electron acceptor and CO(2) as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209(T) fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209(T) belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209(T) (=DSM 21157(T)=JCM 15390(T)).

  18. Lacinutrix gracilariae sp. nov., a bacterium isolated from the surface of a marine red alga Gracilaria sp.

    PubMed

    Huang, Zhaobin; Li, Guizhen; Lai, Qiliang; Gu, Li; Shao, Zongze

    2015-11-09

    A Gram-negative, aerobic, non-flagellated, rod-shaped bacterium, designated as strain Lxc1T, was isolated from the surface of a marine red alga, Gracilaria sp., which was collected from the coastal regions in Jinjiang, Fujian Province, China. The colony of the strain was orange-yellow, circular and smooth. The 16S rRNA gene of Lxc1T had maximum sequence similarity with Lacinutrix himadriensis E4-9aT (97.1%), followed by L. jangbogonensis PAMC 27137T, L. copepodicola DJ3T, L. algicola AKS293T, and L. mariniflava AKS 432T (similarities <96.4%). Phylogenetic analysis showed strain Lxc1T formed a tight cluster with L. himadriensis E4-9aT and L. copepodicola DJ3T, but represented a novel lineage belonging to the genus Lacinutrix. The predominant fatty acids were iso-C15:1 G (18.3%), iso-C15:0 (16.7%), iso-C17:0-3OH (10.6%), and iso-C15:0-3OH (8.6%). Menaquinone-6 (MK-6) was the only respiratory quinone present. The DNA G+C content of Lxc1T was 31.7 mol%. Combining the results above, it was ascertained that the strain Lxc1T represented a novel species of the genus Lacinutrix, for which the name Lacinutrix gracilariae sp. nov. is proposed. The type strain is Lxc1T (=MCCC 1A01567T=KCTC 42808T).

  19. Microbacter margulisiae gen. nov., sp. nov., a propionigenic bacterium isolated from sediments of an acid rock drainage pond.

    PubMed

    Sánchez-Andrea, Irene; Sanz, Jose Luis; Stams, Alfons J M

    2014-12-01

    A novel anaerobic propionigenic bacterium, strain ADRI(T), was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6×1-1.7 µm), non-motile and non-spore-forming rods. Cells possessed a Gram-negative cell-wall structure and were vancomycin-resistant. Strain ADRI(T) utilized yeast extract and various sugars as substrates and formed propionate, lactate and acetate as major fermentation products. The optimum growth temperature was 30 °C and the optimum pH for growth was pH 6.5, but strain ADRI(T) was able to grow at a pH as low as 3.0. Oxidase, indole formation, and urease and catalase activities were negative. Aesculin and gelatin were hydrolysed. The predominant cellular fatty acids of strain ADRI(T) were anteiso-C15 : 0 (30.3 %), iso-C15 : 0 (29.2 %) and iso-C17 : 0 3-OH (14.9 %). Major menaquinones were MK-8 (52 %) and MK-9 (48 %). The genomic DNA G+C content was 39.9 mol%. Phylogenetically, strain ADRI(T) was affiliated to the family Porphyromonadaceae of the phylum Bacteroidetes. The most closely related cultured species were Paludibacter propionicigenes with 16S rRNA gene sequence similarity of 87.5 % and several species of the genus Dysgonomonas (similarities of 83.5-85.4 % to the type strains). Based on the distinctive ecological, phenotypic and phylogenetic characteristics of strain ADRI(T), a novel genus and species, Microbacter margulisiae gen. nov., sp. nov., is proposed. The type strain is ADRI(T) ( = JCM 19374(T) = DSM 27471(T)).

  20. Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine.

    PubMed

    Guo, Xu; You, Xiao-Yan; Liu, Li-Jun; Zhang, Jia-Yue; Liu, Shuang-Jiang; Jiang, Cheng-Ying

    2009-10-01

    A novel mesophilic, acidophilic, endospore-forming bacterium, designated strain ZJ-6(T), was isolated from Zi-Jin copper mine in Inner Mongolia, China. Cells of strain ZJ-6(T) were rod-shaped, stained Gram-positive or were Gram-variable, and grew aerobically at 25-35 degrees C (optimum, 30 degrees C) and pH 2.0-6.0 (optimum, pH 3.5). 16S rRNA gene sequence analysis showed that strain ZJ-6(T) was related phylogenetically to members of the genus Alicyclobacillus, with 16S rRNA gene sequence similarities of 89.5-94.2 %. Cells contained MK-7 as the major quinone and the DNA G+C content was 51.2 mol%. Strain ZJ-6(T) possessed a number of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including its growth temperature, assimilation of various carbon sources, production of acids from a range of compounds, and the ability to grow chemoautotrophically using ferrous iron, elemental sulfur and tetrathionate as electron donors. The predominant cellular fatty acids of strain ZJ-6(T) were anteiso-C(15 : 0) (67.1 %), iso-C(16 : 0) (7.7 %) and anteiso-C(17 : 0) (7.4 %); omega-alicyclic fatty acids were not found. On the basis of these results, it is concluded that strain ZJ-6(T) represents a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus aeris sp. nov. is proposed; the type strain is ZJ-6(T) (=CGMCC 1.7072(T)=NBRC 104953(T)).

  1. Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Kwon, Soon-Wo; Sa, Tong-Min

    2010-10-01

    A Gram-positive bacterium, designated strain CBMB205(T), was isolated from the rhizosphere soil of traditionally cultivated, field-grown rice. Cells were strictly aerobic, motile, rod-shaped and formed endospores. The best growth was achieved at 30°C and pH 7.0 in ammonium mineral salts (AMS) medium containing 600 mM methanol. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed strain CBMB205(T) in a clade with the species Bacillus amyloliquefaciens, Bacillus vallismortis, Bacillus subtilis, Bacillus atrophaeus, Bacillus mojavensis and Bacillus licheniformis and revealed pairwise similarities ranging from 98.2 to 99.2 %. DNA-DNA hybridization experiments revealed a low level (<36 %) of DNA-DNA relatedness between strain CBMB205(T) and its closest relatives. The major components of the fatty acid profile were C₁₅:₀ anteiso, C₁₅:₀ iso, C₁₆:₀ iso and C₁₇:₀ anteiso. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 45.0 mol%. The lipids present in strain CBMB205(T) were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. The predominant respiratory quinone was MK-7. Studies of DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing enabled strain CBMB205(T) to be described as representing a novel species of the genus Bacillus, for which the name Bacillus methylotrophicus sp. nov. is proposed. The type strain is CBMB205(T) (=KACC 13105(T)=NCCB 100236(T)).

  2. Cellulosibacter alkalithermophilus gen. nov., sp. nov., an anaerobic alkalithermophilic, cellulolytic-xylanolytic bacterium isolated from soil of a coconut garden.

    PubMed

    Watthanalamloet, Amornrat; Tachaapaikoon, Chakrit; Lee, Yun Sik; Kosugi, Akihiko; Mori, Yutaka; Tanasupawat, Somboon; Kyu, Khin Lay; Ratanakhanokchai, Khanok

    2012-10-01

    An obligately anaerobic, cellulolytic-xylanolytic bacterium, designated strain A6(T), was isolated from soil of a coconut garden in the Bangkuntien district of Bangkok, Thailand. The strain was Gram-stain positive, catalase-negative, endospore-forming, motile and rod-shaped with a cell size of 0.2-0.3×2.0-3.0 µm. Optimal growth of strain A6(T) occurred at pH(55 °C) 9.5, 55 °C. Strain A6(T) fermented various carbohydrates, and the end products from the fermentation of cellobiose were acetate, ethanol, propionate and a small amount of butyrate. The major cellular fatty acids were iso-C(14:0) 3-OH, iso-C(15:0), iso-C(16:0) and C(16:0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. No respiratory quinones were detected. The DNA G+C content was 30.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain represented a new phyletic sublineage within the family Clostridiaceae, with <93.0% 16S rRNA gene sequence similarity to recognized species of this family. On the basis of phenotypic, genotypic and physiological evidence, strain A6(T) represents a novel species of a new genus, for which the name Cellulosibacter alkalithermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is A6(T) ( = TISTR 1915(T) = KCTC 5874(T)).

  3. Mutational alteration of a nitrogen-fixing bacterium to sensitivity to infection by bacteriophage Mu: isolation of nif mutations of Klebsiella pneumoniae M5al induced by Mu.

    PubMed Central

    Rao, R N

    1976-01-01

    The nitrogen-fixing bacterium Klebsiella pneumoniae M5al is not sensitive to infection by bacteriophage Mu. A mutant of K. pneumoniae that is sensitive to Mu infection was isolated. Several Mu-induced auxotrophic mutations of K. pneumoniae including nif, trp, and rtl were isolated and genetically characterized. Evidence is presented that the Mu-induced mutations of nif arise as the result of insertion of Mu within (or near) the nif operon(s). The rtl locus, which determines the ability to utilize ribitol as a carbon source, was found to be linked to nif loci. PMID:789339

  4. Anoxybacillusgeothermalis sp. nov., a facultatively anaerobic, endospore-forming bacterium isolated from mineral deposits in a geothermal station.

    PubMed

    Filippidou, Sevasti; Jaussi, Marion; Junier, Thomas; Wunderlin, Tina; Jeanneret, Nicole; Palmieri, Fabio; Palmieri, Ilona; Roussel-Delif, Ludovic; Vieth-Hillebrand, Andrea; Vetter, Alexandra; Chain, Patrick S; Regenspurg, Simona; Junier, Pilar

    2016-08-01

    A novel endospore-forming bacterium designated strain GSsed3T was isolated from deposits clogging aboveground filters from the geothermal power platform of Groß Schönebeck in northern Germany. The novel isolate was Gram-staining-positive, facultatively anaerobic, catalase-positive and oxidase-positive. Optimum growth occurred at 60 °C, 0.5 % (w/v) NaCl and pH 7-8. Analysis of the 16S rRNA gene sequence similarity indicated that strain GSsed3T belonged to the genus Anoxybacillus, and showed 99.8 % sequence similarity to Anoxybacillus rupiensis R270T, 98.2 % similarity to Anoxybacillus tepidamans GS5-97T, 97.9 % similarity to Anoxybacillus voinovskiensis TH13T, 97.7 % similarity to Anoxybacillus caldiproteolyticus DSM 15730T and 97.6 % similarity to Anoxybacillus amylolyticus MR3CT. DNA-DNA hybridization (DDH) indicated only 16 % relatedness to Anoxybacillus rupiensis DSM 17127T. Furthermore, DDH estimation based on genomes analysis indicated only 19.9 % overall nucleotide similarity to Anoxybacillus amylolyticus DSM 15939T. The major respiratory menaquinone was MK-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unknown phosphoglycolipid and one unknown phospholipid. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. The peptidoglycan type was A1γ meso-Dpm-direct. The genomic DNA G+C content of the strain was 46.9 mol%. The phenotypic, genotypic and chemotaxonomic characterization indicated that strain GSsed3T differs from related species of the genus. Therefore, strain GSsed3T is considered to be a representative of a novel species of the genus Anoxybacillus, for which the name Anoxybacillus geothermalis sp. nov. is proposed. The type strain of Anoxybacillus geothermalis is GSsed3T (=CCOS808T =ATCC BAA2555T).

  5. Probing the effect of the binding site on the electrostatic behavior of a series of carotenoids reconstituted into the light-harvesting 1 complex from purple photosynthetic bacterium Rhodospirillum rubrum detected by stark spectroscopy.

    PubMed

    Nakagawa, Katsunori; Suzuki, Satoru; Fujii, Ritsuko; Gardiner, Alastair T; Cogdell, Richard J; Nango, Mamoru; Hashimoto, Hideki

    2008-08-07

    Reconstitutions of the LH1 complexes from the purple photosynthetic bacterium Rhodospirillum rubrum S1 were performed with a range of carotenoid molecules having different numbers of C=C conjugated double bonds. Since, as we showed previously, some of the added carotenoids tended to aggregate and then to remain with the reconstituted LH1 complexes (Nakagawa, K.; Suzuki, S.; Fujii, R.; Gardiner, A.T.; Cogdell, R.J.; Nango, M.; Hashimoto, H. Photosynth. Res. 2008, 95, 339-344), a further purification step using a sucrose density gradient centrifugation was introduced to improve purity of the final reconstituted sample. The measured absorption, fluorescence-excitation, and Stark spectra of the LH1 complex reconstituted with spirilloxanthin were identical with those obtained with the native, spirilloxanthin-containing, LH1 complex of Rs. rubrum S1. This shows that the electrostatic environments surrounding the carotenoid and bacteriochlorophyll a (BChl a) molecules in both of these LH1 complexes were essentially the same. In the LH1 complexes reconstituted with either rhodopin or spheroidene, however, the wavelength maximum at the BChl a Qy absorption band was slightly different to that of the native LH1 complexes. These differences in the transition energy of the BChl a Qy absorption band can be explained using the values of the nonlinear optical parameters of this absorption band, i.e., the polarizability change Tr(Deltaalpha) and the static dipole-moment change |Deltamu| upon photoexcitation, as determined using Stark spectroscopy. The local electric field around the BChl a in the native LH1 complex (ES) was determined to be approximately 3.0x10(6) V/cm. Furthermore, on the basis of the values of the nonlinear optical parameters of the carotenoids in the reconstituted LH1 complexes, it is possible to suggest that the conformations of carotenoids, anhydrorhodovibrin and spheroidene, in the LH1 complex were similar to that of rhodopin glucoside in crystal structure of

  6. Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator.

    PubMed

    Grison, Claire M; Jackson, Stephen; Merlot, Sylvain; Dobson, Alan; Grison, Claude

    2015-05-01

    A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512(T)) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512(T) was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052(T) (98.4%), Rhizobium tibeticum CCBAU 85039(T) (98.1%), Rhizobium grahamii CCGE 502(T) (98.0%) and Rhizobium mesoamericanum CCGE 501(T) (98.0%). The phylogenetic relationships of ChimEc512(T) were confirmed by sequencing and analyses of recA and atpD genes. DNA-DNA relatedness values of strain ChimEc512(T) with R. endophyticum CCGE 2052(T), R. tibeticum CCBAU 85039(T), R. mesoamericanum CCGE 52(T), Rhizobium grahamii CCGE 502(T), Rhizobium etli CCBAU 85039(T) and Rhizobium radiobacter KL09-16-8-2(T) were 27, 22, 16, 18, 19 and 11%, respectively. The DNA G+C content of strain ChimEc512(T) was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512(T) was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA-DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512(T) from species of the genus Rhizobium with validly published names. Strain ChimEc512(T), therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain

  7. Anaerobium acetethylicum gen. nov., sp. nov., a strictly anaerobic, gluconate-fermenting bacterium isolated from a methanogenic bioreactor.

    PubMed

    Patil, Yogita; Junghare, Madan; Pester, Michael; Müller, Nicolai; Schink, Bernhard

    2015-10-01

    A novel strictly anaerobic, mesophilic bacterium was enriched and isolated with gluconate as sole substrate from a methanogenic sludge collected from a biogas reactor. Cells of strain GluBS11T stained Gram-positive and were non-motile, straight rods, measuring 3.0-4.5 × 0.8-1.2 μm. The temperature range for growth was 15-37 °C, with optimal growth at 30 °C, the pH range was 6.5-8.5, with optimal growth at pH 7, and the generation time under optimal conditions was 60 min. API Rapid 32A reactions were positive for α-galactosidase, α-glucosidase and β-glucosidase and negative for catalase and oxidase. A broad variety of substrates was utilized, including gluconate, glucose, fructose, maltose, sucrose, lactose, galactose, melezitose, melibiose, mannitol, erythritol, glycerol and aesculin. Products of gluconate fermentation were ethanol, acetate, formate, H2 and CO2. Neither sulfate nor nitrate served as an electron acceptor. Predominant cellular fatty acids (>10 %) were C14 : 0, C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH and C18 : 1ω7c. The DNA G+C content of strain GluBS11T was 44.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data revealed that strain GluBS11T is a member of subcluster XIVa within the order Clostridiales. The closest cultured relatives are Clostridium herbivorans (93.1 % similarity to the type strain), Clostridium populeti (93.3 %), Eubacterium uniforme (92.4 %) and Clostridium polysaccharolyticum (91.5 %). Based on this 16S rRNA gene sequence divergence (>6.5 %) as well as on chemotaxonomic and phenotypic differences from these taxa, strain GluBS11T is considered to represent a novel genus and species, for which the name Anaerobium acetethylicum gen. nov., sp. nov. is proposed. The type strain of Anaerobium acetethylicum is GluBS11T ( = LMG 28619T = KCTC 15450T = DSM 29698T).

  8. Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment, and emended description of the genus Lacinutrix.

    PubMed

    Srinivas, T N R; Prasad, S; Manasa, P; Sailaja, B; Begum, Z; Shivaji, S

    2013-02-01

    A novel gram-negative, rod-shaped, non-motile, psychrophilic bacterium, designated strain E4-9a(T), was isolated from a marine sediment sample collected at a depth of 276 m from Kongsfjorden, Svalbard, in the Arctic Ocean. The colony colour was golden yellow. Strain E4-9a(T) was positive for amylase activity at 5 °C. The predominant fatty acids were iso-C(15 : 1) G (21.8 %), anteiso-C(15 : 0) (19.1 %), anteiso-C(15 : 1) A (18.6 %), iso-C(15 : 0) (13.8 %) and iso-C(16 : 1) H (6.4 %). Strain E4-9a(T) contained MK-6 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids (AL1, AL4 and AL5), an unidentified phospholipid and four unidentified lipids (L1, L4 to L6). Based on 16S rRNA gene sequence similarity, it was ascertained that the closest related species to E4-9a(T) were Lacinutrix copepodicola, L. algicola and L. mariniflava, with sequence similarity to the respective type strains of 98.5, 96.5 and 95.8 %. Phylogenetic analysis showed that strain E4-9a(T) clustered with the type strain of L. copepodicola and with those of L. algicola and L. mariniflava at distances of 1.5 and 4.8 % (98.5 and 95.2 % similarity), respectively. However, DNA-DNA hybridization with L. copepodicola DJ3(T) showed 59 % relatedness with respect to strain E4-9a(T). The DNA G+C content of strain E4-9a(T) was 29 mol%. Based on the results of DNA-DNA hybridization and phenotypic data, it appears that strain E4-9a(T) represents a novel species of the genus Lacinutrix, for which the name Lacinutrix himadriensis sp. nov. is proposed. The type strain is E4-9a(T) ( = CIP 110310(T)  = KCTC 23612(T)).

  9. Purification and stability characteristics of an alkaline serine protease from a newly isolated Haloalkaliphilic bacterium sp. AH-6.

    PubMed

    Dodia, M S; Rawal, C M; Bhimani, H G; Joshi, R H; Khare, S K; Singh, S P

    2008-02-01

    An alkaline protease secreting Haloalkaliphilic bacterium (Gene bank accession number EU118361) was isolated from the Saurashtra Coast in Western India. The alkaline protease was purified by a single step chromatography on phenyl sepharose 6 FF with 28% yield. The molecular mass was 40 kDa as judged by SDS-PAGE. The enzyme displayed catalysis and stability over pH 8-13, optimally at 9-11. It was stable with 0-4 M NaCl and required 150 mM NaCl for optimum catalysis at 37 degrees C; however, the salt requirement for optimal catalysis increased with temperature. While crude enzyme was active at 25-80 degrees C (optimum at 50 degrees C), the purified enzyme had temperature optimum at 37 degrees C, which shifted to 80 degrees C in the presence of 2 M NaCl. The NaCl not only shifted the temperature profile but also enhanced the substrate affinity of the enzyme as reflected by the increase in the catalytic constant (K(cat)). The enzyme was also calcium dependent and with 2 mM Ca(+2), the activity reached to maximum at 50 degrees C. The crude enzyme was highly thermostable (37-90 degrees C); however, the purified enzyme lost its stability above 50 degrees C and its half life was enhanced by 30 and sevenfold at 60 degrees C with 1 M NaCl and 50 mM Ca(+2), respectively. The activity of the enzyme was inhibited by PMSF, indicating its serine type. While the activity was slightly enhanced by Tween-80 (0.2%) and Triton X-100 (0.05%), it marginally decreased with SDS. In addition, the enzyme was highly stable with oxidizing-reducing agents and commercial detergents and was affected by metal ions to varying extent. The study assumes significance due to the enzyme stability under the dual extremities of pH and salt coupled with moderate thermal tolerance. Besides, the facts emerged on the enzyme stability would add to the limited information on this enzyme from Haloalkaliphilic bacteria.

  10. Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.

    PubMed

    Gao, Jun-lian; Yuan, Mei; Wang, Xu-ming; Qiu, Tian-lei; Li, Ji-wei; Liu, Hong-can; Li, Xiu-ai; Chen, Jian; Sun, Jian-guang

    2015-01-01

    A 1-aminocyclopropane-1-carboxylate deaminase producing bacterium, designated GXGD002(T), was isolated from the rhizosphere of banana plants cultivated in Guangxi province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GXGD002(T) is a member of the genus Variovorax. High levels of 16S rRNA gene sequence similarity are found between strain GXGD002(T) and Variovorax paradoxus DSM 30034(T) (99.4 %), Variovorax ginsengisoli KCTC 12583(T) (99.1 %), Variovorax boronicumulans KCTC 22010(T) (99.0 %), Variovorax soli DSM18216(T) (98.7 %), Variovorax defluvii DSM 27259(T) (98.1 %) and Variovorax dokdonensis KCTC 12544(T) (97.4 %) respectively. However, the DNA-DNA hybridization values between strain GXGD002(T) and its closely related species V. paradoxus DSM 30034(T), V. ginsengisoli KCTC 12583(T) and V. boronicumulans KCTC 22010(T) were found to be 40.7, 30.9 and 23.7 %, respectively. The DNA G + C content of strain GXGD002(T) was found to be 67.8 mol%. The major fatty acids of strain GXGD002(T) are C16:0 (20.3 %), C10:0 3OH (18.4 %), C17:0 cyclo (18.9 %), C18:1w7c (12.3 %) and summed feature 3 (13.9 %). The predominant respiratory quinone was identified as ubiquinone-8 (Q-8) and the major polar lipids as phosphatidylethanolamine and phosphatidylglycerol. The results of polyphasic taxonomic study including physiological and biochemical tests, whole-cell SDS-PAGE profiles and chemotaxonomic analysis allowed a clear differentiation of strain GXGD002(T) from the other species in the genus Variovorax. Based on these results, a new species, Variovorax guangxiensis, is proposed. The type strain is GXGD002(T) (=DSM 27352(T) = ACCC 05911(T)).

  11. Isolation and characterization of Desulfocurvus thunnarius sp. nov., a sulfate-reducing bacterium isolated from an anaerobic sequencing batch reactor treating cooking wastewater.

    PubMed

    Hamdi, Olfa; Ben Hania, Wajdi; Postec, Anne; Bartoli, Manon; Hamdi, Moktar; Bouallagui, Hassib; Fauque, Guy; Ollivier, Bernard; Fardeau, Marie-Laure

    2013-11-01

    A novel anaerobic, chemo-organotrophic, sulfate-reducing bacterium, designated strain Olac 40(T), was isolated from a Tunisian wastewater digestor. Cells were curved, motile rods or vibrios (5.0-7.0×0.5 µm). Strain Olac 40(T) grew at temperatures between 15 and 50 °C (optimum 40 °C), and between pH 5.0 and 9.0 (optimum pH 7.1). It did not require NaCl for growth but tolerated it up to 50 g l(-1) (optimum 2 g l(-1)). In the presence of sulfate or thiosulfate, strain Olac 40(T) used lactate, pyruvate and formate as energy sources. Growth was observed on H2 only in the presence of acetate as carbon source. In the presence of sulfate or thiosulfate, the end products of lactate oxidation were acetate, sulfide and CO2. Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate or nitrite. The genomic DNA G+C content of strain Olac 40(T) was 70 mol%. The profile of polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four phospholipids. The main fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Olac 40(T) was affiliated with the family Desulfovibrionaceae within the class Deltaproteobacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain Olac 40(T) is proposed to be assigned to a novel species of the genus Desulfocurvus, for which the name Desulfocurvus thunnarius is proposed. The type strain is Olac 40(T) ( = DSM 26129(T) = JCM 18546(T)).

  12. Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica

    PubMed Central

    Parmeciano Di Noto, Gisela; Vázquez, Susana C.; MacCormack, Walter P.; Iriarte, Andrés

    2016-01-01

    We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution. PMID:27151790

  13. Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.

    PubMed

    Parmeciano Di Noto, Gisela; Vázquez, Susana C; MacCormack, Walter P; Iriarte, Andrés; Quiroga, Cecilia

    2016-05-05

    We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution.

  14. Metal Reduction and Mineral formation by a Psychrotolerant Fe(III)-Reducing Bacterium Isolated from an Iron-Rich Waters near a Hydrothermal Vent

    NASA Astrophysics Data System (ADS)

    Roh, Y.; Vali, H.; Stapleton, R. D.; Fields, M. M.; Phelps, T. J.; Zhou, J.

    2002-12-01

    Although dissimilatory metal reduction and mineral formation under mesophilic and thermophilic conditions are extensively examined, they are poorly understood under low temperature. The objective of this study was to examine metal reduction and mineral formation using a psychrotolerant iron-reducing bacterium (Shewanella alga, PV-4) isolated from iron-rich waters associated with the Naha vents off the Hawaiian coast. The psychrotolerant iron-reducing bacterium was able to use lactate, formate, and hydrogen as an electron donor while reducing Fe(III)-citrate, Fe(III)-EDTA, Co(III)-EDTA, Cr(VI), Mn(IV), and iron oxyhydroxide (FeOOH) at temperatures between 0 and 37°C. The psychrotolerant bacterium exhibited diverse mineral precipitation capabilities including the formation of magnetite (Fe3O4), siderite (FeCO3), and rhodochrosite (MnCO3). Transmission electron microscopic data showed that PV-4 formed mainly superparamagnetic magnetite at temperatures ranging from 0 to 14°C and formed mainly single-domain magnetite at temperatures ranging from 18 to 37°C. This study indicats that iron-reducing bacteria may contribute to the biogeochemical cycling of metals and carbon at low temperatures and may contribute to the natural remnant magnetism of marine sediments.

  15. Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake

    DOE PAGES

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; ...

    2015-11-19

    Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. Moreover, this organism was sequenced as part of the community science program at the DOE Joint Genome Institute.

  16. Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water.

    PubMed

    Li, Ai-Hua; Liu, Hong-Can; Xin, Yu-Hua; Kim, Song-Gun; Zhou, Yu-Guang

    2014-02-01

    A Gram-stain-positive, aerobic, non-spore-forming, short-rod-shaped bacterium, designated strain MP203(T), was isolated from ice water of Midui Glacier in Tibet Autonomous Region, China. The strain was psychrotolerant, growing at 0-25 °C. 16S rRNA gene sequence analysis showed that strain MP203(T) was most similar to Frigoribacterium faeni NBRC 103066(T), Compostimonas suwonensis KACC 13354(T), Frigoribacterium mesophilum KCTC 19311(T), Marisediminicola antarctica CCTCC AB 209077(T) and Alpinimonas psychrophila JCM 18951(T), with similarities of 97.4, 97.2, 97.2, 97.1 and 97.1%, respectively. The maximum-likelihood phylogenetic tree indicated that strain MP203(T) clustered with nine genera of the family Microbacteriaceae, namely Frigoribacterium, Compostimonas, Marisediminicola, Alpinimonas, Frondihabitans, Clavibacter, Subtercola, Klugiella and Agreia. However, bootstrap analysis showed that there was no significance in the branching pattern of the linage comprising strain MP203(T) and any existing generic lineage of the family Microbacteriaceae. DNA-DNA hybridization results indicated levels of relatedness between strain MP203(T) and Marisediminicola antarctica CCTCC AB 209077(T), Frigoribacterium faeni NBRC 103066(T), Frigoribacterium mesophilum KCTC 19311(T), Compostimonas suwonensis KACC 13354(T) and Alpinimonas psychrophila JCM 18951(T) were 25.8 ± 7.3, 29.6 ± 7.6, 19.7 ± 6.7, 16.0 ± 4.2 and 12.4 ± 5.1 % (mean ± SD), respectively. The G+C content of the genomic DNA was 64.1 mol%. Analysis of the cell-wall peptidoglycan revealed that the peptidoglycan structure of strain MP203(T) was B10 type with Gly[l-Hse]-D-Glu-D-DAB, containing 2, 4-diaminobutyric acid (DAB) as a diagnostic amino acid. The cell-wall sugars were rhamnose, ribose, mannose and glucose. The major fatty acids were anteiso-C(15 : 0), iso-C(16 : 0) and anteiso A-C(15 : 1). An unusual compound identified as anteiso-C(15 : 0)-DMA (1,1-dimethoxy-anteiso-pentadecane) was also present in strain

  17. Caldanaerovirga acetigignens gen. nov., sp. nov., an anaerobic xylanolytic, alkalithermophilic bacterium isolated from Trego Hot Spring, Nevada, USA.

    PubMed

    Wagner, Isaac D; Ahmed, Sibtain; Zhao, Weidong; Zhang, Chuanlun L; Romanek, Christopher S; Rohde, Manfred; Wiegel, Juergen

    2009-11-01

    An anaerobic thermophilic bacterium, designated strain JW/SA-NV4(T), was isolated from a xylan-supplemented enrichment culture from Trego hot spring located within the Black Rock Desert (NV, USA). Cells were generally straight or slightly bent rod-shaped, 0.4-0.8 microm in width and 3-6 microm in length during exponential growth. Cells from stationary phase were variable in size and shape, showing curved or bent morphology. Motility was not seen and flagella were not observed in electron micrographs. Sporulation was not observed. Strain JW/SA-NV4(T) stained Gram-negative but is phylogenetically Gram-type positive. Growth occurred at pH(25 degrees C) 6.8-8.8, with optimum growth at pH 8.4; no growth occurred at pH 9.0 or above or at 6.5 or below. With glucose or xylose as the carbon source, strain JW/SA-NV4(T) grew at 44-74 degrees C; no growth occurred at 76 degrees C or above or at 42 degrees C or below. However, the optimum temperature was 62 and 66 degrees C when grown on glucose and xylose, respectively. The shortest doubling time observed with glucose was approximately 4 h, and with xylose approximately 3.4 h. Strain JW/SA-NV4(T) tolerated an atmosphere containing up to 0.1 % O(2); no growth occurred at a gas atmosphere of 0.2 % O(2). Chemo-organotrophic growth occurred with xylose, glucose, mannose, xylan, pyruvate, fructose, ribose, Casamino acids, mannitol, tryptone, peptone, cellobiose and yeast extract. When grown in mineral media containing 1 g yeast extract l(-1) as an electron donor, thiosulfate and sulfur were reduced to sulfide. The G+C content of the DNA was 38.6 mol% (HPLC). 16S rRNA gene sequence analysis placed strain JW/SA-NV4(T) within the order Thermoanaerobacterales and within the Thermoanaerobacterales Incertae Sedis Family III, specifically between taxa classified within the genera Thermosediminibacter and Thermovenabulum. The closest phylogenetic neighbours were Thermosediminibacter oceani JW/IW-1228P(T) (94.2 % 16S rRNA gene sequence

  18. Draft Genome Sequence of Nocardioides luteus Strain BAFB, an Alkane-Degrading Bacterium Isolated from JP-7-Polluted Soil

    PubMed Central

    Brown, Lisa M.; Gunasekera, Thusitha S.

    2017-01-01

    ABSTRACT Nocardioides luteus strain BAFB is a Gram-positive bacterium that efficiently degrades C8 to C11 alkanes aerobically. The draft genome of N. luteus BAFB is 5.76 Mb in size, with 5,358 coding sequences and 69.9% G+C content. The genes responsible for alkane degradation are present in this strain. PMID:28126947

  19. Characterization of Halanaerobaculum tunisiense gen. nov., sp. nov., a new halophilic fermentative, strictly anaerobic bacterium isolated from a hypersaline lake in Tunisia.

    PubMed

    Hedi, Abdeljabbar; Fardeau, Marie-Laure; Sadfi, Najla; Boudabous, Abdellatif; Ollivier, Bernard; Cayol, Jean-Luc

    2009-03-01

    A new halophilic anaerobe was isolated from the hypersaline surface sediments of El-Djerid Chott, Tunisia. The isolate, designated as strain 6SANG, grew at NaCl concentrations ranging from 14 to 30%, with an optimum at 20-22%. Strain 6SANG was a non-spore-forming, non-motile, rod-shaped bacterium, appearing singly, in pairs, or occasionally as long chains (0.7-1 x 4-13 microm) and showed a Gram-negative-like cell wall pattern. It grew optimally at pH values between 7.2 and 7.4, but had a very broad pH range for growth (5.9-8.4). Optimum temperature for growth was 42 degrees C (range 30-50 degrees C). Strain 6SANG required yeast extract for growth on sugars. Glucose, sucrose, galactose, mannose, maltose, cellobiose, pyruvate, and starch were fermented. The end products from glucose fermentation were acetate, butyrate, lactate, H(2), and CO(2). The G + C ratio of the DNA was 34.3 mol%. Strain 6SANG exhibited 16S rRNA gene sequence similarity values of 91-92% with members of the genus Halobacteroides, H. halobius being its closest phylogenetic relative. Based on phenotypic and phylogenetic characteristics, we propose that this bacterium be classified as a novel species of a novel genus, Halanaerobaculum tunisiense gen. nov., sp. nov. The type strain is 6SANG(T) (=DSM 19997(T)=JCM 15060(T)).

  20. Isolation of a selenite-reducing and cadmium-resistant bacterium Pseudomonas sp. strain RB for microbial synthesis of CdSe nanoparticles.

    PubMed

    Ayano, Hiroyuki; Miyake, Masaki; Terasawa, Kanako; Kuroda, Masashi; Soda, Satoshi; Sakaguchi, Toshifumi; Ike, Michihiko

    2014-05-01

    Bacteria capable of synthesizing CdSe from selenite and cadmium ion were enriched from a soil sample. After repeated transfer of the soil-derived bacterial cultures to a new medium containing selenite and cadmium ion 42 times (during 360 days), an enrichment culture that can simultaneously remove selenite and cadmium ion (1 mM each) from the liquid phase was obtained. The culture's color became reddish-brown, indicating CdSe nanoparticle production, as confirmed by energy-dispersive x-ray spectra (EDS). As a result of isolation operations, the bacterium that was the most responsible for synthesizing CdSe, named Pseudomonas sp. RB, was obtained. Transmission electron microscopy and EDS revealed that this strain accumulated nanoparticles (10-20 nm) consisting of selenium and cadmium inside and on the cells when cultivated in the same medium for the enrichment culture. This report is the first describing isolation of a selenite-reducing and cadmium-resistant bacterium. It is useful for CdSe nanoparticle synthesis in the simple one-vessel operation.

  1. Albidovulum inexpectatum gen. nov., sp. nov., a nonphotosynthetic and slightly thermophilic bacterium from a marine hot spring that is very closely related to members of the photosynthetic genus Rhodovulum.

    PubMed

    Albuquerque, Luciana; Santos, João; Travassos, Pedro; Nobre, M Fernanda; Rainey, Fred A; Wait, Robin; Empadinhas, Nuno; Silva, Manuel T; da Costa, Milton S

    2002-09-01

    Several bacterial isolates, with an optimum growth temperature of about 50 degrees C, were recovered from the marine hot spring at Ferraria on the island of São Miguel in the Azores. The geothermal water emerged from a porous lava flow and rapidly cooled in contact with seawater except at low tide. The bacterial species represented by strains FRR-10(T) and FRR-11 was nonpigmented, strictly aerobic, and organotrophic. Several genes, bchZ, pufB, pufA, pufL, or pufM, encoding the photosynthetic reaction center proteins and the core light-harvesting complexes were not detected in these strains. The organism oxidized thiosulfate to sulfate with enhancement of growth. The organism did not require additional NaCl in the culture medium for growth, but NaCl at 1.0% enhanced growth. Phylogenetic analyses using the 16S rRNA gene sequence of strain FRR-10(T) indicated that the new organism represented a new species of the alpha-3 subclass of the Proteobacteria and that it branches within the species of the genus Rhodovulum. The contradiction of classifying an organism which branches within the radiation of the genus Rhodovulum but does not possess the hallmark characteristics of this genus is discussed. However, the absence of several of these characteristics, namely, the lack of photosynthesis and pigmentation, which could be related to colonization of dark environments, and growth at high temperatures, leads to our proposal that strains FRR-10(T) and FRR-11 should be classified as a new species of a novel genus, Albidovulum inexpectatum, representing, at present, the most thermophilic organism within the alpha-3 subclass of the Proteobacteria.

  2. Electrochemical Characterization of a Novel Exoelectrogenic Bacterium Strain SCS5, Isolated from a Mediator-Less Microbial Fuel Cell and Phylogenetically Related to Aeromonas jandaei

    PubMed Central

    Sharma, Subed Chandra Dev; Feng, Cuijie; Li, Jiangwei; Hu, Anyi; Wang, Han; Qin, Dan; Yu, Chang-Ping

    2016-01-01

    A facultative anaerobic bacterium, designated as strain SCS5, was isolated from the anodic biofilm of a mediator-less microbial fuel cell using acetate as the electron donor and α-FeOOH as the electron acceptor. The isolate was Gram-negative, motile, and shaped as short rods (0.9–1.3 μm in length and 0.4–0.5 μm in width). A phylogenetic analysis of the 16S rRNA, gyrB, and rpoD genes suggested that strain SCS5 belonged to the Aeromonas genus in the Aeromonadaceae family and exhibited the highest 16S rRNA gene sequence similarity (99.45%) with Aeromonas jandaei ATCC 49568. However, phenotypic, cellular fatty acid profile, and DNA G+C content analyses revealed that there were some distinctions between strain SCS5 and the type strain A. jandaei ATCC 49568. The optimum growth temperature, pH, and NaCl (%) for strain SCS5 were 35°C, 7.0, and 0.5% respectively. The DNA G+C content of strain SCS5 was 59.18%. The isolate SCS5 was capable of reducing insoluble iron oxide (α-FeOOH) and transferring electrons to extracellular material (the carbon electrode). The electrochemical activity of strain SCS5 was corroborated by cyclic voltammetry and a Raman spectroscopic analysis. The cyclic voltammogram of strain SCS5 revealed two pairs of oxidation-reduction peaks under anaerobic and aerobic conditions. In contrast, no redox pair was observed for A. jandaei ATCC 49568. Thus, isolated strain SCS5 is a novel exoelectrogenic bacterium phylogenetically related to A. jandaei, but shows distinct electrochemical activity from its close relative A. jandaei ATCC 49568. PMID:27396922

  3. Desulfuromonas carbonis sp. nov., an Fe(III)-, S0- and Mn(IV)-reducing bacterium isolated from an active coalbed methane gas well.

    PubMed

    An, Thuy T; Picardal, Flynn W

    2015-05-01

    A novel, mesophilic, obligately anaerobic, acetate-oxidizing, dissimilatory iron-, sulfur-, and manganese-reducing bacterium, designated strain ICBM(T), was obtained from an active, coalbed methane gas well in Indiana, USA. Strain ICBM(T) was a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium that was rich in c-type cytochromes and formed red colonies in solid medium. Strain ICBM(T) conserved energy to support growth from the oxidation of acetate, propionate, pyruvate, malate, fumarate, succinate and dl-lactate, concomitant with dissimilatory iron reduction. Strain ICBM(T) fermented fumarate yielding succinate and acetate. Strain ICBM(T) was able to grow in the temperature range of 10 °C to 37 °C, NaCl concentration range of 0 to 1.2 M, and pH range of 6.5 to 8.0. The physiological characteristics of strain ICBM(T) indicated that it belongs to the Desulfuromonas cluster. The G+C content of its genomic DNA was 61.2 mol%. The predominant cellular fatty acids were C16 : 0 (39.3%), C16 : 1ω7c and/or iso-C15 : 0 2-OH (36.6%). The closest cultured phylogenetic relative of strain ICBM(T) was Desulfuromonas michiganensis BB1(T) with only 95% 16S rRNA gene sequence similarity. This confirmed that strain ICBM(T) is affiliated with the genus Desulfuromonas . On the basis of phenotypic and genotypic differences between strain ICBM(T) and other taxa of the genus Desulfuromonas , strain ICBM(T) represents a novel species for which the name Desulfuromonas carbonis sp. nov. is proposed (type strain ICBM(T) = DSM 29759(T) = JCM 30471(T)). Strain ICBM(T) is the first Fe(III)-, S(0)-, and Mn(IV)-reducing bacterium that was isolated from a coal bed.

  4. Keratinase production and biodegradation of polluted secondary chicken feather wastes by a newly isolated multi heavy metal tolerant bacterium-Alcaligenes sp. AQ05-001.

    PubMed

    Yusuf, Ibrahim; Ahmad, Siti Aqlima; Phang, Lai Yee; Syed, Mohd Arif; Shamaan, Nor Aripin; Abdul Khalil, Khalilah; Dahalan, Farrah Aini; Shukor, Mohd Yunus

    2016-12-01

    Biodegradation of agricultural wastes, generated annually from poultry farms and slaughterhouses, can solve the pollution problem and at the same time yield valuable degradation products. But these wastes also constitute environmental nuisance, especially in Malaysia where their illegal disposal on heavy metal contaminated soils poses a serious biodegradation issue as feather tends to accumulate heavy metals from the surrounding environment. Further, continuous use of feather wastes as cheap biosorbent material for the removal of heavy metals from effluents has contributed to the rising amount of polluted feathers, which has necessitated the search for heavy metal-tolerant feather degrading strains. Isolation, characterization and application of a novel heavy metal-tolerant feather-degrading bacterium, identified by 16S RNA sequencing as Alcaligenes sp. AQ05-001 in degradation of heavy metal polluted recalcitrant agricultural wastes, have been reported. Physico-cultural conditions influencing its activities were studied using one-factor-at-a-time and a statistical optimisation approach. Complete degradation of 5 g/L feather was achieved with pH 8, 2% inoculum at 27 °C and incubation period of 36 h. The medium optimisation after the response surface methodology (RSM) resulted in a 10-fold increase in keratinase production (88.4 U/mL) over the initial 8.85 U/mL when supplemented with 0.5% (w/v) sucrose, 0.15% (w/v) ammonium bicarbonate, 0.3% (w/v) skim milk, and 0.01% (w/v) urea. Under optimum conditions, the bacterium was able to degrade heavy metal polluted feathers completely and produced valuable keratinase and protein-rich hydrolysates. About 83% of the feathers polluted with a mixture of highly toxic metals were degraded with high keratinase activities. The heavy metal tolerance ability of this bacterium can be harnessed not only in keratinase production but also in the bioremediation of heavy metal-polluted feather wastes.

  5. Isolation of an arsenate-respiring bacterium from a redox front in an arsenic-polluted aquifer in West Bengal, Bengal Basin.

    PubMed

    Osborne, Thomas H; McArthur, John M; Sikdar, Pradip K; Santini, Joanne M

    2015-04-07

    Natural pollution of groundwater by arsenic adversely affects the health of tens of millions of people worldwide, with the deltaic aquifers of SE Asia being particularly polluted. The pollution is caused primarily by, or as a side reaction of, the microbial reduction of sedimentary Fe(III)-oxyhydroxides, but the organism(s) responsible for As release have not been isolated. Here we report the first isolation of a dissimilatory arsenate reducer from sediments of the Bengal Basin in West Bengal. The bacterium, here designated WB3, respires soluble arsenate and couples its reduction to the oxidation of acetate; WB3 is therefore implicated in the process of arsenic pollution of groundwater, which is largely by arsenite. The bacterium WB3 is also capable of reducing dissolved Fe(III) citrate, solid Fe(III)-oxyhydroxide, and elemental sulfur, using acetate as the electron donor. It is a member of the Desulfuromonas genus and possesses a dissimilatory arsenate reductase that was identified using degenerate polymerase chain reaction primers. The sediment from which WB3 was isolated was brown, Pleistocene sand at a depth of 35.2 m below ground level (mbgl). This level was some 3 cm below the boundary between the brown sands and overlying reduced, gray, Holocene aquifer sands. The color boundary is interpreted to be a reduction front that releases As for resorption downflow, yielding a high load of labile As sorbed to the sediment at a depth of 35.8 mbgl and concentrations of As in groundwater that reach >1000 μg/L.

  6. Isolation and purification of the major photosynthetic antenna, fucoxanthin-Chl a/c protein, from cultured discoid germilings of the brown Alga, Cladosiphon okamuranus TOKIDA (Okinawa Mozuku).

    PubMed

    Fujii, Ritsuko; Kita, Mamiko; Iinuma, Yoshiro; Oka, Naohiro; Takaesu, Yuki; Taira, Tomonori; Iha, Masahiko; Cogdell, Richard J; Hashimoto, Hideki

    2012-03-01

    A chlorophyll c binding membrane intrinsic light-harvesting complex, the fucoxanthin-chlorophyll a/c protein (FCP), was isolated from cultured discoid germilings of an edible Japanese brown alga, Cladosiphon (C.) okamuranus TOKIDA (Okinawa Mozuku in Japanese). The discoid germiling is an ideal source of brown algal photosynthetic pigment-protein complexes in terms of its size and easiness of cultivation on a large scale. Ion-exchange chromatography was crucial for the purification of FCP from solubilized thylakoid proteins. The molecular weight of the purified FCP assembly was estimated to be ~56 kDa using blue native-PAGE. Further subunit analyses using 2D-PAGE revealed that the FCP assembled as a trimer consisting of two distinguishable subunits having molecular weights of 18.2 (H) and 17.5 (L) kDa. Fluorescence and fluorescence-excitation spectra confirmed that the purified FCP assembly was functionally intact.

  7. Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin.

    PubMed

    Meyer, T E; Yakali, E; Cusanovich, M A; Tollin, G

    1987-01-27

    A water-soluble yellow protein, previously discovered in the purple photosynthetic bacterium Ectothiorhodospira halophila, contains a chromophore which has an absorbance maximum at 446 nm. The protein is now shown to be photoactive. A pulse of 445-nm laser light caused the 446-nm peak to be partially bleached and red-shifted in a time less than 1 microsecond. The intermediate thus formed was subsequently further bleached in the dark in a biphasic process occurring in approximately 20 ms. Finally, the absorbance of native protein was restored in a first-order process occurring over several seconds. These kinetic processes are remarkably similar to those of sensory rhodopsin from Halobacterium, and to a lesser extent bacteriorhodopsin and halorhodopsin; although these proteins are membrane-bound, they have absorbance maxima at about 570 nm, and they cycle more rapidly. In attempts to remove the chromophore for identification, it was found that a variety of methods of denaturation of the protein caused transient or permanent conversion to a form which has an absorbance maximum near 340 nm. Thus, by analogy to the rhodopsins, the absorption at 446 nm in the native protein appears to result from a 106-nm red shift of the chromophore induced by the protein. Acid denaturation followed by extraction with organic solvents established that the chromophore could be removed from the protein. It is not identical with all-trans-retinal and remains to be identified, although it could still be a related pigment. The E. halophila yellow protein has a circular dichroism spectrum which indicates little alpha-helical secondary structure (19%).(ABSTRACT TRUNCATED AT 250 WORDS)

  8. Halomonas sp. OKOH--a marine bacterium isolated from the bottom sediment of Algoa Bay--produces a polysaccharide bioflocculant: partial characterization and biochemical analysis of its properties.

    PubMed

    Mabinya, Leonard V; Cosa, Sekelwa; Mkwetshana, Noxolo; Okoh, Anthony I

    2011-05-25

    A bioflocculant-producing bacterium isolated from seawater was identified based on 16S rRNA gene nucleotide sequence to have 99% similarity to that of Halomonas sp. Au160H and the nucleotide sequence was deposited as Halomonas sp. OKOH (Genbank accession number is HQ875722). Influences of carbon source, nitrogen source, salt ions and pH on flocculating activity were investigated. The bioflocculant was optimally produced when glucose (87% flocculating activity) and urea (88% flocculating activity) were used as sources of carbon and nitrogen, respectively. Also, initial pH of 7.0 and Ca²⁺ supported optimal production of the bioflocculant with flocculating activities of 87% respectively. Chemical analyses revealed the bioflocculant to be a polysaccharide.

  9. Complete genome sequence of Thermovibrio ammonificans HB-1T, a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent

    SciTech Connect

    Giovannelli, Donato; Ricci, Jessica; Perez-Rodriguez, Ileana; Hugler, Michael; O'Brien, Charles; Keddis, Ramaydalis; Grosche, Ashley; Goodwin, Lynne A.; Bruce, David; Davenport, Karen W.; Detter, J. Chris; Han, James; Han, Cliff; Ivanova, N; Land, Miriam L; Mikhailova, Natalia; Nolan, Matt; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Vetriani, Costantino

    2012-01-01

    Thermovibrio ammonificans type strain HB-1T is a thermophilic (Topt: 75 C), strictly anaero- bic, chemolithoautotrophic bacterium that was isolated from an active, high temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism grows on mineral salts medium in the presence of CO2/H2, using NO3- or S0 as electron acceptors, which are re- duced to ammonium or hydrogen sulfide, respectively. T. ammonificans is one of only three species within the genus Thermovibrio, a member of the family Desulfurobacteriaceae, and it forms a deep branch within the phylum Aquificae. Here we report the main features of the genome of T. ammonificans strain HB-1T (DSM 15698T).

  10. Isolation and characterization of a human intestinal bacterium, Eubacterium sp. ARC-2, capable of demethylating arctigenin, in the essential metabolic process to enterolactone.

    PubMed

    Jin, Jong-Sik; Zhao, Yu-Feng; Nakamura, Norio; Akao, Teruaki; Kakiuchi, Nobuko; Hattori, Masao

    2007-05-01

    Plant lignans, such as pinoresinol diglucoside, secoisolariciresinol diglucoside and arctiin, are metabolized to mammalian lignans, enterolactone or enterodiol, by human intestinal bacteria. Their metabolic processes include deglucosylation, ring cleavage, demethylation, dehydroxylation and oxidation. Here we isolated an intestinal bacterium capable of demethylating arctigenin, an aglycone of arctiin, to 2,3-bis(3,4-dihydroxybenzyl)butyrolactone (1) from human feces, and identified as an Eubacterium species (E. sp. ARC-2), which is similar to Eubacterium limosum on the basis of morphological and biochemical properties and 16S rRNA gene sequencing. By incubating with E. sp. ARC-2, arctigenin was converted to 1 through stepwise demethylation. Demethylation of arctigenin by E. sp. ARC-2 was tetrahydrofolate- and ATP-dependent, indicating that the reaction was catalyzed by methyltransferase. Moreover, E. sp. ARC-2 transformed secoisolariciresinol to 2,3-bis(3,4-dihydroxybenzyl)-1,4-butanediol by demethylation.

  11. Preparative isolation and purification of macrolactin antibiotics from marine bacterium Bacillus amyloliquefaciens using high-speed counter-current chromatography in stepwise elution mode.

    PubMed

    He, Shan; Wang, Hongqiang; Yan, Xiaojun; Zhu, Peng; Chen, Juanjuan; Yang, Rui

    2013-01-11

    Preparative high-speed counter-current chromatography (HSCCC) was successfully applied to the isolation and purification of two macrolactin antibiotics from marine bacterium Bacillus amyloliquefaciens for the first time using stepwise elution with a pair of two-phase solvent systems composed of n-hexane-ethyl acetate-methanol-water at (1:4:1:4, v/v) and (3:4:3:4, v/v). The preparative HSCCC separation was performed on 300 mg of crude sample yielding macrolactin B (22.7 mg) and macrolactin A (40.4 mg) in a one-step separation, with purities over 95% as determined by HPLC. The structures of these compounds were identified by MS, (1)H NMR and (13)C NMR. Our results demonstrated that HSCCC was an efficient technique to separate marine antibiotics, which provide an approach to solve the problem of their sample availability for drug development.

  12. Draft Genome Sequence of Strain Q-1, an Iodide-Oxidizing Alphaproteobacterium Isolated from Natural Gas Brine Water

    PubMed Central

    Ehara, Ayaka; Suzuki, Haruo; Kanesaki, Yu; Yoshikawa, Hirofumi

    2014-01-01

    Here we report the draft genome sequence of strain Q-1, an iodide (I−)-oxidizing heterotrophic bacterium in the class Alphaproteobacteria isolated from natural gas brine water. The genome sequence contained a multicopper oxidase gene probably responsible for iodide oxidation. A photosynthetic gene cluster was found but genes for carbon-fixation were absent. PMID:24994802

  13. Inhibitory effect of organic carbon on CO₂ fixing by non-photosynthetic microbial community isolated from the ocean.

    PubMed

    Hu, Jia-jun; Wang, Lei; Zhang, Shi-ping; Wang, Yuan-qing; Xi, Xue-fei

    2011-07-01

    The inhibitory effect of organic carbon on CO(2) fixation (CF) by the non-photosynthetic microbial community (NPMC) and its mechanism were studied. The results showed that different concentrations of glucose inhibited CF to some extent. However, when these microorganisms pre-cultured with glucose were re-cultured without organic carbon, their CF efficiency differed significantly from the control based on the glucose concentration in the pre-culture. ATP as bioenergy and NADH as reductant had no obvious inhibitory effect on CF; conversely, they improved CF efficiency to some extent, especially when both were present simultaneously. These results implied that not all organic materials inhibited CF by NPMC, and only those that acted as good carbon sources, such as glucose, inhibited CF. Moreover, some metabolites generated during the catabolism of glucose by heterotrophic metabolism of NPMC might inhibit CF, while other cumulated materials present in the cell interior, such as ATP and NADH, might improve CF.

  14. Effects of fertilizer-urea on growth, photosynthetic activity and microcystins production of Microcystis aeruginosa isolated from Dianchi Lake.

    PubMed

    Huang, Wenmin; Bi, Yonghong; Hu, Zhengyu

    2014-05-01

    Urea is the most frequently applied nitrogen (N) fertilizer in agriculture, while its loss is assumed triggering algal blooms in adjacent water bodies. In this context the present study assessed the growth, photosynthetic activity as well as toxin production of Microcystis aeruginosa at different urea concentrations (0.125, 1.25, 12.5, 250 and 2,500 mg/L) using BG11 (containing 250 mg/L NO3(-)-N) as control. The results showed for all endpoints that M. aeruginosa is capable of using urea as N source: the two highest urea treatments delivered comparable values like the control. Low urea concentrations (0.125 and 1.25 mg/L), which were comparable to environmental urea levels, did not sustainably promote the growth, photosynthesis and toxin production of the test species. While, in certain microenvironments urea might potentially reach the concentrations that may affect M. aeruginosa.

  15. The Growth of Steroidobacter agariperforans sp. nov., a Novel Agar-Degrading Bacterium Isolated from Soil, is Enhanced by the Diffusible Metabolites Produced by Bacteria Belonging to Rhizobiales

    PubMed Central

    Sakai, Masao; Hosoda, Akifumi; Ogura, Kenjiro; Ikenaga, Makoto

    2014-01-01

    An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5–BT, belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FST, at the species level with 96.5% similarity. Strain KA5–BT was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15–37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0–8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso–C15:0, C16:1ω7c, and iso–C17:1ω9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FST was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1ω8c. Based on its phylogenetic and phenotypic properties, strain KA5–BT (JCM 18477T = KCTC 32107T) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed. PMID:24621511

  16. Draft Genome Sequence of Geobacillus sp. Isolate T6, a Thermophilic Bacterium Collected from a Thermal Spring in Argentina

    PubMed Central

    Ortiz, Elio M.; Berretta, Marcelo F.; Benintende, Graciela B.; Zandomeni, Rubén O.

    2015-01-01

    Geobacillus sp. isolate T6 was collected from a thermal spring in Salta, Argentina. The draft genome sequence (3,767,773 bp) of this isolate is represented by one major scaffold of 3,46 Mbp, a second one of 207 kbp, and 20 scaffolds of <13 kbp. The assembled sequences revealed 3,919 protein-coding genes. PMID:26184933

  17. Longimicrobium terrae gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers.

    PubMed

    Pascual, Javier; García-López, Marina; Bills, Gerald F; Genilloud, Olga

    2016-05-01

    A novel chemo-organoheterotroph bacterium, strain CB-286315T, was isolated from a Mediterranean forest soil sampled at the Sierra de Tejeda, Almijara and Alhama Natural Park, Spain, by using the diffusion sandwich system, a device with 384 miniature diffusion chambers. 16S rRNA gene sequence analyses identified the isolate as a member of the under-represented phylum Gemmatimonadetes, where 'Gemmatirosa kalamazoonensis' KBS708, Gemmatimonas aurantiaca T-27T and Gemmatimonas phototrophica AP64T were the closest relatives, with respective similarities of 84.4, 83.6 and 83.3 %. Strain CB-286315T was characterized as a Gram-negative, non-motile, short to long rod-shaped bacterium. Occasionally, some cells attained an unusual length, up to 35-40 μm. The strain showed positive responses for catalase and cytochrome-c oxidase and division by binary fission, and exhibited an aerobic metabolism, showing optimal growth under normal atmospheric conditions. Strain CB-286315T was also able to grow under micro-oxic atmospheres, but not under anoxic conditions. The strain is a slowly growing bacterium able to grow under low nutrient concentrations. Major fatty acids included iso-C17 : 1ω9c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and iso-C17 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and three phospholipids. The major isoprenoid quinone was MK-8 and the diagnostic diamino acid was meso-diaminopimelic acid. The DNA G+C content was 67.0 mol%. Based on a polyphasic taxonomic characterization, strain CB-286315T represents a novel genus and species, Longimicrobium terrae gen. nov., sp. nov., within the phylum Gemmatimonadetes. The type strain of Longimicrobium terrae is strain CB-286315T ( = DSM 29007T = CECT 8660T). In order to classify the novel taxon within the existing taxonomic framework, the family Longimicrobiaceae fam. nov., order

  18. Isolation, Free-Living Capacities, and Genome Structure of “Candidatus Glomeribacter gigasporarum,” the Endocellular Bacterium of the Mycorrhizal Fungus Gigaspora margarita

    PubMed Central

    Jargeat, P.; Cosseau, C.; Ola'h, B.; Jauneau, A.; Bonfante, P.; Batut, J.; Bécard, G.

    2004-01-01

    “Candidatus Glomeribacter gigasporarum” is an endocellular β-proteobacterium present in the arbuscular mycorrhizal (AM) fungus Gigaspora margarita. We established a protocol to isolate “Ca. Glomeribacter gigasporarum” from its host which allowed us to carry out morphological, physiological, and genomic investigations on purified bacteria. They are rod shaped, with a cell wall typical of gram-negative bacteria and a cytoplasm rich in ribosomes, and they present no flagella or pili. Isolated bacteria could not be grown in any of the 19 culture media tested, but they could be kept alive for up to 4 weeks. PCR-based investigations of purified DNA from isolated bacteria did not confirm the presence of all genes previously assigned to “Ca. Glomeribacter gigasporarum.” In particular, the presence of nif genes could not be detected. Pulsed-field gel electrophoresis analyses allowed us to estimate the genome size of “Ca. Glomeribacter gigasporarum” to approximately 1.4 Mb with a ca. 750-kb chromosome and a 600- to 650-kb plasmid. This is the smallest genome known for a β-proteobacterium. Such small genome sizes are typically found in endocellular bacteria living permanently in their host. Altogether, our data suggest that “Ca. Glomeribacter gigasporarum” is an ancient obligate endocellular bacterium of the AM fungus G. margarita. PMID:15466041

  19. Candidatus "Thiodictyon syntrophicum", sp. nov., a new purple sulfur bacterium isolated from the chemocline of Lake Cadagno forming aggregates and specific associations with Desulfocapsa sp.

    PubMed

    Peduzzi, Sandro; Storelli, Nicola; Welsh, Allana; Peduzzi, Raffaele; Hahn, Dittmar; Perret, Xavier; Tonolla, Mauro

    2012-05-01

    Strain Cad16(T) is a small-celled purple sulfur bacterium (PSB) isolated from the chemocline of crenogenic meromictic Lake Cadagno, Switzerland. Long term in situ observations showed that Cad16(T) regularly grows in very compact clumps of cells in association with bacteria belonging to the genus Desulfocapsa in a cell-to-cell three dimensional structure. Previously assigned to the genus Lamprocystis, Cad16(T), was here reclassified and assigned to the genus Thiodictyon. Based on comparative 16S rRNA gene sequences analysis, isolate Cad16(T) was closely related to Thiodictyon bacillosum DSM234(T) and Thiodictyon elegans DSM232(T) with sequence similarities of 99.2% and 98.9%, respectively. Moreover, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis separated Cad16(T) from other PSB genera, Lamprocystis and Thiocystis. Major differences in cell morphology (oval-sphere compared to rod-shaped) and arrangement (no netlike cell aggregates), carotenoid group (presence of okenone instead of rhodopinal), chemolithotrophic growth as well as the ability to form syntrophic associations with a sulfate-reducing bacteria of the genus Desulfocapsa suggested a different species within the genus Thiodictyon. This isolate is therefore proposed and described as Candidatus "Thiodictyon syntrophicum" sp. nov., a provisionally novel species within the genus Thiodictyon.

  20. Reuse of red seaweed waste by a novel bacterium, Bacillus sp. SYR4 isolated from a sandbar.

    PubMed

    Kang, Soyeon; Kim, Joong Kyun

    2015-01-01

    A potent bacterial strain was isolated from a sandbar and identified as Bacillus sp. SYR4 for the reuse of red seaweed waste. The isolate possessed both agarase and carrageenase activities. The optimal pH and temperature for the degradation of both agar and carrageenan by the isolate were found to be pH 7.5 and 30 °C, respectively. The effects of cations on cell growth and degradation ability of the isolate were significant in comparison with controls. The isolate produced 0.27 and 0.29 g l(-1) of reducing sugars from 1 g l(-1) of agar and carrageenan, respectively. When the isolate was cultivated in red seaweed powder medium for 10 days, the yield of reducing sugars was 24 %. As a result, the eco-friendly reuse of red seaweed waste by this isolate appears to be feasible for the production of reducing sugars and could be a valuable resource. To the best of our knowledge, this is the first study to directly demonstrate the ability of Bacillus sp. SYR4 to degrade both agar and carrageenan.

  1. Rapid isolation of a facultative anaerobic electrochemically active bacterium capable of oxidizing acetate for electrogenesis and azo dyes reduction.

    PubMed

    Shen, Nan; Yuan, Shi-Jie; Wu, Chao; Cheng, Yuan-Yuan; Song, Xiang-Ning; Li, Wen-Wei; Tong, Zhong-Hua; Yu, Han-Qing

    2014-05-01

    In this study, 27 strains of electrochemically active bacteria (EAB) were rapidly isolated and their capabilities of extracellular electron transfer were identified using a photometric method based on WO3 nanoclusters. These strains caused color change of WO3 from white to blue in a 24-well agar plate within 40 h. Most of the isolated EAB strains belonged to the genera of Aeromonas and Shewanella. One isolate, Pantoea agglomerans S5-44, was identified as an EAB that can utilize acetate as the carbon source to produce electricity and reduce azo dyes under anaerobic conditions. The results confirmed the capability of P. agglomerans S5-44 for extracellular electron transfer. The isolation of this acetate-utilizing, facultative EBA reveals the metabolic diversity of environmental bacteria. Such strains have great potential for environmental applications, especially at interfaces of aerobic and anaerobic environments, where acetate is the main available carbon source.

  2. Draft genome sequence of Paenisporosarcina sp. strain TG-14, a psychrophilic bacterium isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica.

    PubMed

    Koh, Hye Yeon; Lee, Sung Gu; Lee, Jun Hyuck; Doyle, Shawn; Christner, Brent C; Kim, Hak Jun

    2012-12-01

    The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica. Here we report the draft genome sequence of this strain, which may provide useful information on the cold adaptation mechanism in extremely variable environments.

  3. Draft Genome Sequence of Paenisporosarcina sp. Strain TG-14, a Psychrophilic Bacterium Isolated from Sediment-Laden Stratified Basal Ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica

    PubMed Central

    Koh, Hye Yeon; Lee, Sung Gu; Lee, Jun Hyuck; Doyle, Shawn; Christner, Brent C.

    2012-01-01

    The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica. Here we report the draft genome sequence of this strain, which may provide useful information on the cold adaptation mechanism in extremely variable environments. PMID:23144403

  4. Gold nanoparticles synthesized by Geobacillus sp. strain ID17 a thermophilic bacterium isolated from Deception Island, Antarctica

    PubMed Central

    2013-01-01

    Background The use of microorganisms in the synthesis of nanoparticles emerges as an eco-friendly and exciting approach, for production of nanoparticles due to its low energy requirement, environmental compatibility, reduced costs of manufacture, scalability, and nanoparticle stabilization compared with the chemical synthesis. Results The production of gold nanoparticles by the thermophilic bacterium Geobacillus sp. strain ID17 is reported in this study. Cells exposed to Au3+ turned from colourless into an intense purple colour. This change of colour indicates the accumulation of intracellular gold nanoparticles. Elemental analysis of particles composition was verified using TEM and EDX analysis. The intracellular localization and particles size were verified by TEM showing two different types of particles of predominant quasi-hexagonal shape with size ranging from 5–50 nm. The mayority of them were between 10‒20 nm in size. FT-IR was utilized to characterize the chemical surface of gold nanoparticles. This assay supports the idea of a protein type of compound on the surface of biosynthesized gold nanoparticles. Reductase activity involved in the synthesis of gold nanoparticles has been previously reported to be present in others microorganisms. This reduction using NADH as substrate was tested in ID17. Crude extracts of the microorganism could catalyze the NADH-dependent Au3+ reduction. Conclusions Our results strongly suggest that the biosynthesis of gold nanoparticles by ID17 is mediated by enzymes and NADH as a cofactor for this biological transformation. PMID:23919572

  5. Antiplasmodial activity of bacilosarcin A isolated from the octocoral-associated bacterium Bacillus sp. collected in Panama

    PubMed Central

    Boya, Cristopher A.; Herrera, Liuris; Guzman, Hector M.; Gutierrez, Marcelino

    2012-01-01

    Aim: This study was designed for isolating and characterizing antiplasmodial compounds from marine octocoral-associated bacteria. Materials and Methods: The organic extract of the Bacillus sp. was subjected to purification using several chromatography techniques guided by bioassays to yield three isocoumarin derivatives (1–3). Chemical structures of the compounds were elucidated on the basis of HRMS spectra and NMR spectroscopy. The antiplasmodial activity of the isolated compounds was evaluated in vitro against the chloroquine-resistant Plasmodium falciparum strain W2. Results: Isolated compounds were identified as bacilosarcin A (1), AI77-F (2), and AI77-H (3). Bacilosarcin A (1) displayed a low micromolar activity (IC50 = 2.2 μM) against P. falciparum while compounds 2 and 3 showed no activity. Conclusions: Bacilosarcin A was found to be responsible for the antiplasmodial activity observed in the crude extract obtained from the Bacillus sp. PMID:22368402

  6. Aeromonas veronii, a tributyltin (TBT)-degrading bacterium isolated from an estuarine environment, Ria de Aveiro in Portugal.

    PubMed

    Cruz, Andreia; Caetano, Tânia; Suzuki, Satoru; Mendo, Sónia

    2007-12-01

    Organotin compounds are used in a variety of industrial processes therefore their subsequent discharge into the environment is widespread. Bacteria play an important role in biogeochemical transformations acting as natural decontamination agents. Therefore, screening for tributyltin (TBT)-resistant and -degrading bacteria is relevant for the selection of isolates with decontamination ability of these polluted areas. With this purpose, 50 strains were isolated from sediment and water from Ria de Aveiro and their tolerance to TBT, up to 3mM, was evaluated. Generally, occurrence of highly TBT-resistant bacteria was observed, and Gram negative bacteria exhibited more tolerance to TBT than Gram positive bacteria. A memory response was observed when bacteria were progressively exposed to increasingly higher TBT concentrations. One isolate, Aeromonas veronii Av27, highly resistant to TBT (3mM) uses this compound as carbon source and degrades it to less toxic compounds.

  7. Influence of probiotic bacterium Bacillus cereus isolated from the gut of wild shrimp Penaeus monodon in turn as a potent growth promoter and immune enhancer in P. monodon.

    PubMed

    NavinChandran, Manohar; Iyapparaj, Palanisamy; Moovendhan, Subramanian; Ramasubburayan, Ramasamy; Prakash, Santhiyagu; Immanuel, Grasian; Palavesam, Arunachalam

    2014-01-01

    A probiotic bacterium isolated from the gut of wild shrimp Penaeus monodon rendered maximum antagonistic activity against shrimp pathogens and was capable of producing extracellular enzymes. The probiotic bacterium was identified as Bacillus cereus through 16S rRNA sequencing. The lyophilized B. cereus was supplemented with shrimp basal diet at four different concentrations (0.1–0.4%/100 g feed) in D1–D4 diets. The viability of probiotic bacterium in the test diets was evaluated during the study period at various time intervals. The viability ranged from 50.24 ± 1.42 to 180.34 ± 1.30 CFU/g in D1 to D3 diets on the 30th day, whereas it was slightly declined from 45.23 ± 1.30 to 169.13 ± 1.18 CFU/g during the 90th day of storage. A control diet (C), devoid of probiotic supplementation was also simultaneously prepared. During experimentation, P. monodon postlarvae (PL-15) were cultured in individual one tonne capacity FRP tanks in triplicates provided with equal amount of substratum (clay soil) and fed with these respective diets at ad libitum for 90 days. Survival was high (82.0 ± 1.60%) in D4 diet fed shrimp as against a low survival of 65.0 ± 1.33% displayed by control diet fed shrimp. Overall growth responses inferred that a maximum production of 10.45 ± 0.275 g, SGR of 4.40 ± 0.179% and a better FCR of 1.27 ± 0.081 were obtained in D4 diet fed shrimp. However, the water quality parameters showed nonsignificant (P > 0.05) variations among the control and the probiotic treated groups. The tested immunological parameters such as Total haemocyte count, phenoloxidase activity, respiratory burst activity, lysozyme activity, plasma protein concentration and bactericidal activity were higher in D4 diet fed P. monodon, when compared to that of other diets fed shrimp. It is therefore suggested that lyophilized probiotic B. cereus at a concentration of 0.4%/100 g feed was efficient in stimulating the growth and immunity in shrimp.

  8. Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo.

    PubMed

    Ouoba, Labia Irène I; Vouidibio Mbozo, Alain B; Thorsen, Line; Anyogu, Amarachukwu; Nielsen, Dennis S; Kobawila, Simon C; Sutherland, Jane P

    2015-11-01

    Investigation of the microbial diversity of Ntoba Mbodi, an African food made from the alkaline fermentation of cassava leaves, revealed the presence of a Gram-positive, catalase-positive, aerobic, motile and rod-shaped endospore-forming bacterium (NM73) with unusual phenotypic and genotypic characteristics. The analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Lysinibacillus meyeri WS 4626T (98.93%), Lysinibacillus xylanilyticus XDB9T (96.95%) and Lysinibacillus odysseyi 34hs-1T (96.94%). The DNA-DNA relatedness of the isolate with L. meyeri LMG 26643T, L. xylanilyticus DSM 23493T and L. odysseyi DSM 18869T was 41%, 16% and 15%, respectively. The internal transcribed spacer-PCR profile of the isolate was different from those of closely related bacteria. The cell-wall peptidoglycan type was A4α, L-Lys-D-Asp and the major fatty acids were iso-C15:0, anteiso-C15:0, anteiso-C17:0 and iso-C17:0 and iso-C17:1ω10c. The polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphoaminolipid, aminolipid, two phospholipids and two unknown lipids. The predominant menaquinones were MK-7 and MK-6. Ribose was the only whole-cell sugar detected. The DNA G+C content was 38 mol%. Based on the results of the phenotypic and genotypic characterization, it was concluded that the isolate represents a novel species of the genus Lysinibacillus, for which the name of Lysinibacillus louembei sp. nov. is proposed. NM73T ( = DSM 25583T = LMG 26837T) represents the type strain.

  9. Isolation and Characterization of Burkholderia rinojensis sp. nov., a Non-Burkholderia cepacia Complex Soil Bacterium with Insecticidal and Miticidal Activities

    PubMed Central

    Fernandez, Lorena E.; Koivunen, Marja; Yang, April; Flor-Weiler, Lina; Marrone, Pamela G.

    2013-01-01

    Isolate A396, a bacterium isolated from a Japanese soil sample demonstrated strong insecticidal and miticidal activities in laboratory bioassays. The isolate was characterized through biochemical methods, fatty acid methyl ester (FAME) analysis, sequencing of 16S rRNA, multilocus sequence typing and analysis, and DNA-DNA hybridization. FAME analysis matched A396 to Burkholderia cenocepacia, but this result was not confirmed by 16S rRNA or DNA-DNA hybridization. 16S rRNA sequencing indicated closest matches with B. glumae and B. plantarii. DNA-DNA hybridization experiments with B. plantarii, B. glumae, B. multivorans, and B. cenocepacia confirmed the low genetic similarity (11.5 to 37.4%) with known members of the genus. PCR-based screening showed that A396 lacks markers associated with members of the B. cepacia complex. Bioassay results indicated two mechanisms of action: through ingestion and contact. The isolate effectively controlled beet armyworms (Spodoptera exigua; BAW) and two-spotted spider mites (Tetranychus urticae; TSSM). In diet overlay bioassays with BAW, 1% to 4% (vol/vol) dilution of the whole-cell broth caused 97% to 100% mortality 4 days postexposure, and leaf disc treatment bioassays attained 75% ± 22% mortality 3 days postexposure. Contact bioassays led to 50% larval mortality, as well as discoloration, stunting, and failure to molt. TSSM mortality reached 93% in treated leaf discs. Activity was maintained in cell-free supernatants and after heat treatment (60°C for 2 h), indicating that a secondary metabolite or excreted thermostable enzyme might be responsible for the activity. Based on these results, we describe the novel species Burkholderia rinojensis, a good candidate for the development of a biocontrol product against insect and mite pests. PMID:24096416

  10. Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea.

    PubMed

    Tanaka, Reiji; Cleenwerck, Ilse; Mizutani, Yukino; Iehata, Shunpei; Shibata, Toshiyuki; Miyake, Hideo; Mori, Tetsushi; Tamaru, Yutaka; Ueda, Mitsuyoshi; Bossier, Peter; Vandamme, Peter

    2015-12-01

    Four brown-alga-degrading, Gram-stain-negative, aerobic, non-flagellated, gliding and rod-shaped bacteria, designated LMG 28520T, LMG 28521, LMG 28522 and LMG 28523, were isolated from the gut of the abalone Haliotis gigantea obtained in Japan. The four isolates had identical random amplified polymorphic DNA patterns and grew optimally at 25 °C, at pH 6.0-9.0 and in the presence of 1.0-4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences placed the isolates in the genus Formosa with Formosa algae and Formosa arctica as closest neighbours. LMG 28520T and LMG 28522 showed 100 % DNA-DNA relatedness to each other, 16-17 % towards F. algae LMG 28216T and 17-20 % towards F. arctica LMG 28318T; they could be differentiated phenotypically from these established species. The predominant fatty acids of isolates LMG 28520T and LMG 28522 were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G and iso-C15 : 0. Isolate LMG 28520T contained menaquinone-6 (MK-6) as the major respiratory quinone and phosphatidylethanolamine, two unknown aminolipids and an unknown lipid as the major polar lipids. The DNA G+C content was 34.4 mol% for LMG 28520T and 35.5 mol% for LMG 28522. On the basis of their phylogenetic and genetic distinctiveness, and differential phenotypic properties, the four isolates are considered to represent a novel species of the genus Formosa, for which the name Formosa haliotis sp. nov. is proposed. The type strain is LMG 28520T ( = NBRC 111189T).

  11. Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill.

    PubMed

    Ekman, Jaakko V; Raulio, Mari; Busse, Hans-Jürgen; Fewer, David P; Salkinoja-Salonen, Mirja

    2011-03-01

    A rod-shaped, non-spore-forming, non-motile, aerobic, oxidase and catalase-positive and radiation-resistant bacterium (designated strain K4.1(T)) was isolated from biofilm collected from a Finnish paper mill. The bacterium grew as pale pink colonies on oligotrophic medium at 12 to 50 °C (optimum 37 to 45 °C) and at pH 6 to 10.3. The DNA G+C content of the strain was 66.8 l%. According to 16S rRNA gene sequence analysis, strain K4.1(T) was distantly related to the genus Deinococcus, sharing highest similarity with Deinococcus pimensis (90.0  %). In the phylogenetic tree, strain K4.1(T) formed a separate branch in the vicinity of the genus Deinococcus. The peptidoglycan type was A3β with L-Orn-Gly-Gly and the quinone system was determined to be MK-8. The polar lipid profile of strain K4.1(T) differed markedly from that of the genus Deinococcus. The predominant lipid of strain K4.1(T) was an unknown aminophospholipid and it did not contain the unknown phosphoglycolipid predominant in the polar lipid profiles of deinococci analysed to date. Two of the predominant fatty acids of the strain, 15 : 0 anteiso and 17 : 0 anteiso, were lacking or present in small amounts in species of the genus Deinococcus. Phylogenetic distinctness and significant differences in the polar lipid and fatty acid profiles suggest classification of strain K4.1(T) as a novel genus and species in the family Deinococcaceae, for which we propose the name Deinobacterium chartae gen. nov., sp. nov. The type strain is K4.1(T) (=DSM 21458(T) =HAMBI 2721(T)).

  12. Savagea faecisuis gen. nov., sp. nov., a tylosin- and tetracycline-resistant bacterium isolated from a swine-manure storage pit.

    PubMed

    Whitehead, Terence R; Johnson, Crystal N; Patel, Nisha B; Cotta, Michael A; Moore, Edward R B; Lawson, Paul A

    2015-07-01

    A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular methods was performed on three strains of a Gram-stain positive, non-sporeforming, motile aerobic rod-shaped bacterium resistant to tylosin and tetracycline isolated from a swine-manure storage pit. On the basis of 16S rRNA gene sequence analyses, it was confirmed that these isolates are highly related to each other and form a hitherto unknown lineage within the Planococcaceae. In particular, pairwise analysis of the 16S rRNA gene sequence demonstrated that the novel organism is closely related to members of the genus Sporosarcina (92.8-94.5 %), Pyschrobacillus (93.5-93.9 %) and Paenisporosarcina (93.3-94.5 %). The predominant fatty acids were found to consist of iso-C15:0 and iso-C17:1 ω10c and the G+C mol% was determined to be 41.8. Based on biochemical, chemotaxonomic, and phylogenetic evidence, it is proposed that these novel strains be classified as a novel genus and species, Savagea faecisuis gen nov., sp. nov. The type strain is Con12(T) (=CCUG 63563(T) = NRRL B-59945(T) = NBRC 109956(T)).

  13. Characterization of Fe (III)-reducing enrichment culture and isolation of Fe (III)-reducing bacterium Enterobacter sp. L6 from marine sediment.

    PubMed

    Liu, Hongyan; Wang, Hongyu

    2016-07-01

    To enrich the Fe (III)-reducing bacteria, sludge from marine sediment was inoculated into the medium using Fe (OH)3 as the sole electron acceptor. Efficiency of Fe (III) reduction and composition of Fe (III)-reducing enrichment culture were analyzed. The results indicated that the Fe (III)-reducing enrichment culture with the dominant bacteria relating to Clostridium and Enterobact