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Sample records for bacterium rhodospirillum rubrum

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

    OpenAIRE

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

    2012-01-01

    The biosynthesis of the major carotenoid spirilloxanthin by the purple nonsulfur bacterium Rhodospirillum rubrum is thought to occur via a linear pathway proceeding through phytoene and, later, lycopene as intermediates. This assumption is based solely on early chemical evidence (B. H. Davies, Biochem. J. 116:93–99, 1970). In most purple bacteria, the desaturation of phytoene, catalyzed by the enzyme phytoene desaturase (CrtI), leads to neurosporene, involving only three dehydrogenation steps...

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

    Science.gov (United States)

    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.

  3. Fructose metabolism of the purple non-sulfur bacterium Rhodospirillum rubrum: effect of carbon dioxide on growth, and production of bacteriochlorophyll and organic acids.

    Science.gov (United States)

    Rudolf, Christiane; Grammel, Hartmut

    2012-04-05

    During fermentative metabolism, carbon dioxide fixation plays a key role in many bacteria regarding growth and production of organic acids. The present contribution, dealing with the facultative photosynthetic bacterium Rhodospirillum rubrum, reveals not only the strong influence of ambient carbon dioxide on the fermentative break-down of fructose but also a high impact on aerobic growth with fructose as sole carbon source. Both growth rates and biomass yield increased with increasing carbon dioxide supply in chemoheterotrophic aerobic cultures. Furthermore, intracellular metabolite concentration measurements showed almost negligible concentrations of the tricarboxylic acid cycle intermediates succinate, fumarate and malate under aerobic growth, in contrast to several metabolites of the glycolysis. In addition, we present a dual phase fed-batch process, where an aerobic growth phase is followed by an anaerobic production phase. The biosynthesis of bacteriochlorophyll and the secretion of organic acids were both affected by the carbon dioxide supply, the pH value and by the cell density at the time of switching from aerobic to anaerobic conditions. The formation of pigmented photosynthetic membranes and the amount of bacteriochlorophyll were inversely correlated to the secretion of succinate. Accounting the high biotechnological potential of R. rubrum, optimization of carbon dioxide supply is important because of the favored application of fructose-containing fermentable feedstock solutions in bio-industrial processes. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Insight into the radiotolerance of the life support bacterium Rhodospirillum rubrum S1H by means of phenotypic and transcriptomic methods

    Science.gov (United States)

    Mastroleo, Felice; Monsieurs, Pieter; Leys, Natalie

    The MELiSSA life support system from the European Space Agency is targeting the produc-tion of oxygen, water and food by recycling organic waste. Among different types of pro-cesses, MELiSSA uses several interconnected bioreactors inhabited by microorganisms and higher plants (Hendrickx et al., 2006; Mergeay et al., 1988). Because this loop is foreseen to be functional in space where it will be exposed to higher doses and different spectra of ionizing radiation, it was decided to screen the radiotolerance of the organisms used. In this study, the radiotolerance (i.e. tolerance to ionizing radiation) of the photosynthetic bacterium Rho-dospirillum rubrum S1H was investigated. In this test, first the effect of low energy Cobalt-60 gamma rays, were tested. To assess the radiotolerance of bacterium S1H, the survival rate after increasing exposure was determined. R. rubrum S1H appeared relatively radiosensitive, as the radiation dose at which 90% of the population was killed (D10 value) was 4 times lower than the model bacterium Escherichia coli. It was demonstrate that the culture medium has an impact on radiation tolerance. This survival curve also permitted to select a number of sub-lethal ionizing radiation doses (¡ D10 ), that were used to analyze the gene expression response of R. rubrum S1H after gamma irradiation. The microarray transcriptome analysis results ob-tained from different doses and different culture medium showed a significant response of the bacterium to sublethal doses. Potential marker genes for ionizing radiation stress in R. rubrum S1H were identified. By quantitative PCR, it was shown that the expression of these marker genes increased with the recovery time after exposure to ionizing radiation. In other words, the radiation tolerance and the response of R. rubrum S1H to low energy Cobalt-60 gamma ionizing radiation was characterized. Therefore to ensure MELiSSA process robustness during extended space exploration mission, it is advised that

  5. Carbon roadmap from syngas to polyhydroxyalkanoates in Rhodospirillum rubrum.

    Science.gov (United States)

    Revelles, O; Tarazona, N; García, J L; Prieto, M A

    2016-02-01

    The gasification of organic waste materials to synthesis gas (syngas), followed by microbial fermentation, provides a significant resource for generating bioproducts such as polyhydroxyalkanoates (PHA). The anaerobic photosynthetic bacterium, Rhodospirillum rubrum, is an organism particularly attractive for the bioconversion of syngas into PHAs. In this study, a quantitative physiological analysis of R. rubrum was carried out by implementing GC-MS and HPLC techniques to unravel the metabolic pathway operating during syngas fermentation that leads to PHA production. Further, detailed investigations of the central carbon metabolites using (13) C-labelled substrate showed significant CO2 assimilation (of 40%) into cell material and PHA from syngas carbon fraction. By a combination of quantitative gene expression and enzyme activity analyses, the main role of carboxylases from the central carbon metabolism in CO2 assimilation was shown, where the Calvin-Benson-Bassham cycle (CBB) played a minor role. This knowledge sheds light about the biochemical pathways that contribute to synthesis of PHA during syngas fermentation being valuable information to further optimize the fermentation process. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Whole-genome shotgun optical mapping of Rhodospirillum rubrum

    Energy Technology Data Exchange (ETDEWEB)

    Reslewic, S. [Univ. Wisc.-Madison; Zhou, S. [Univ. Wisc.-Madison; Place, M. [Univ. Wisc.-Madison; Zhang, Y. [Univ. Wisc.-Madison; Briska, A. [Univ. Wisc.-Madison; Goldstein, S. [Univ. Wisc.-Madison; Churas, C. [Univ. Wisc.-Madison; Runnheim, R. [Univ. Wisc.-Madison; Forrest, D. [Univ. Wisc.-Madison; Lim, A. [Univ. Wisc.-Madison; Lapidus, A. [Univ. Wisc.-Madison; Han, C. S. [Univ. Wisc.-Madison; Roberts, G. P. [Univ. Wisc.-Madison; Schwartz, D. C. [Univ. Wisc.-Madison

    2005-09-01

    Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII map acted as a scaffold for high-resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and confirmation of genome sequence, this work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a "molecular cytogenetics" approach to solving problems in genomic analysis.

  7. On the relation between phototaxis and photosynthesis in Rhodospirillum Rubrum

    NARCIS (Netherlands)

    Thomas, J.B.; Nijenhuis, L.E.

    1950-01-01

    The relation between phototaxis and photosynthesis in Rhodospirillum rubrum has been studied. The light intensity at which saturation is reached in photosynthesis proved to coincide with that at which the contrast sensitivity starts to decrease. Potassium cyanide, which preferably inhibits the

  8. Understanding the physiological roles of polyhydroxybutyrate (PHB) in Rhodospirillum rubrum S1 under aerobic chemoheterotrophic conditions.

    Science.gov (United States)

    Narancic, Tanja; Scollica, Elisa; Kenny, Shane T; Gibbons, Helena; Carr, Eibhlin; Brennan, Lorraine; Cagney, Gerard; Wynne, Kieran; Murphy, Cormac; Raberg, Matthias; Heinrich, Daniel; Steinbüchel, Alexander; O'Connor, Kevin E

    2016-10-01

    Polyhydroxybutyrate (PHB) is an important biopolymer accumulated by bacteria and associated with cell survival and stress response. Here, we make two surprising findings in the PHB-accumulating species Rhodospirillum rubrum S1. We first show that the presence of PHB promotes the increased assimilation of acetate preferentially into biomass rather than PHB. When R. rubrum is supplied with (13)C-acetate as a PHB precursor, 83.5 % of the carbon in PHB comes from acetate. However, only 15 % of the acetate ends up in PHB with the remainder assimilated as bacterial biomass. The PHB-negative mutant of R. rubrum assimilates 2-fold less acetate into biomass compared to the wild-type strain. Acetate assimilation proceeds via the ethylmalonyl-CoA pathway with (R)-3-hydroxybutyrate as a common intermediate with the PHB pathway. Secondly, we show that R. rubrum cells accumulating PHB have reduced ribulose 1,5-bisphosphate carboxylase (RuBisCO) activity. RuBisCO activity reduces 5-fold over a 36-h period after the onset of PHB. In contrast, a PHB-negative mutant maintains the same level of RuBisCO activity over the growth period. Since RuBisCO controls the redox potential in R. rubrum, PHB likely replaces RuBisCO in this role. R. rubrum is the first bacterium found to express RuBisCO under aerobic chemoheterotrophic conditions.

  9. Melatonin immunoreactivity in the photosynthetic prokaryote Rhodospirillum rubrum: implications for an ancient antioxidant system.

    Science.gov (United States)

    Manchester, L C; Poeggeler, B; Alvares, F L; Ogden, G B; Reiter, R J

    1995-01-01

    Rhodospirillum rubrum is a spiral anoxygenic photosynthetic bacterium that can exist under either aerobic or anaerobic conditions. The organism thrives in the presence of light or complete darkness and represents one of the oldest species of living organisms, possibly 2-3.5 billion years old. The success of this prokaryotic species may be attributed to the evolution of certain indole compounds that offer protection against life-threatening oxygen radicals produced by an evolutionary harsh environment. Melatonin, N-acetyl-5-methoxytryptamine, is an indolic highly conserved molecule that exists in protists, plants, and animals. This study was undertaken to determine the presence of an immunoreactive melatonin in the kingdom Monera and particularly in the photosynthetic bacterium, R. rubrum, under conditions of prolonged darkness or prolonged light. Immunoreactive melatonin was measured during both the extended day and extended night. Significantly more melatonin was observed during the scotophase than the photophase. This study marks the first demonstration of melatonin in a bacterium. The high level of melatonin observed in bacteria may provide on-site protection of bacterial DNA against free radical attack.

  10. Microaerophilic cooperation of reductive and oxidative pathways allows maximal photosynthetic membrane biosynthesis in Rhodospirillum rubrum.

    Science.gov (United States)

    Grammel, Hartmut; Gilles, Ernst-Dieter; Ghosh, Robin

    2003-11-01

    The purple nonsulfur bacterium Rhodospirillum rubrum has been employed to study physiological adaptation to limiting oxygen tensions (microaerophilic conditions). R. rubrum produces maximal levels of photosynthetic membranes when grown with both succinate and fructose as carbon sources under microaerophilic conditions in comparison to the level (only about 20% of the maximum) seen in the absence of fructose. Employing a unique partial O(2) pressure (pO(2)) control strategy to reliably adjust the oxygen tension to values below 0.5%, we have used bioreactor cultures to investigate the metabolic rationale for this effect. A metabolic profile of the central carbon metabolism of these cultures was obtained by determination of key enzyme activities under microaerophilic as well as aerobic and anaerobic phototrophic conditions. Under aerobic conditions succinate and fructose were consumed simultaneously, whereas oxygen-limiting conditions provoked the preferential breakdown of fructose. Fructose was utilized via the Embden-Meyerhof-Parnas pathway. High levels of pyrophosphate-dependent phosphofructokinase activity were found to be specific for oxygen-limited cultures. No glucose-6-phosphate dehydrogenase activity was detected under any conditions. We demonstrate that NADPH is supplied mainly by the pyridine-nucleotide transhydrogenase under oxygen-limiting conditions. The tricarboxylic acid cycle enzymes are present at significant levels during microaerophilic growth, albeit at lower levels than those seen under fully aerobic growth conditions. Levels of the reductive tricarboxylic acid cycle marker enzyme fumarate reductase were also high under microaerophilic conditions. We propose a model by which the primary "switching" of oxidative and reductive metabolism is performed at the level of the tricarboxylic acid cycle and suggest how this might affect redox signaling and gene expression in R. rubrum.

  11. MESSAGE 2 space experiment with Rhodospirillum rubrum S1H

    Data.gov (United States)

    National Aeronautics and Space Administration — R. rubrum S1H inoculated on solid agar rich media was sent to the ISS in October 2003 (MESSAGE-part 2 experiment). After 10 days flight R. rubrum cultures returned...

  12. Model-based high cell density cultivation of Rhodospirillum rubrum under respiratory dark conditions.

    Science.gov (United States)

    Zeiger, Lisa; Grammel, Hartmut

    2010-03-01

    The potential of facultative photosynthetic bacteria as producers of photosynthetic pigments, vitamins, coenzymes and other valuable products has been recognized for decades. However, mass cultivation under photosynthetic conditions is generally inefficient due to the inevitable limitation of light supply when cell densities become very high. The previous development of a new cultivation process for maximal expression of photosynthetic genes under semi-aerobic dark conditions in common bioreactors offers a new perspective for utilizing the facultative photosynthetic bacterium Rhodospirillum rubrum for large-scale applications. Based on this cultivation system, the present study aimed in determining the maximal achievable cell density of R. rubrum in a bioreactor, thereby providing a major milestone on the way to industrial bioprocesses. As a starting point, we focus on aerobic growth due to higher growth rates and more facile process control under this condition, with the option to extend the process by an anaerobic production phase. Process design and optimization were supported by an unstructured computational process model, based on mixed-substrate kinetics. Key parameters for growth and process control were determined in shake-flask experiments or estimated by simulation studies. For fed-batch cultivation, a computer-controlled exponential feed algorithm in combination with a pH-stat element was implemented. As a result, a maximal cell density of 59 g cell dry weight (CDW) L(-1) was obtained, representing so far not attainable cell densities for photosynthetic bacteria. The applied exponential fed-batch methodology therefore enters a range which is commonly employed for industrial applications with microbial cells. The biochemical analysis of high cell density cultures revealed metabolic imbalances, such as the accumulation and excretion of tetrapyrrole intermediates of the bacteriochlorophyll biosynthetic pathway. (c) 2009 Wiley Periodicals, Inc.

  13. Synthesis Gas (Syngas)-Derived Medium-Chain-Length Polyhydroxyalkanoate Synthesis in Engineered Rhodospirillum rubrum.

    Science.gov (United States)

    Heinrich, Daniel; Raberg, Matthias; Fricke, Philipp; Kenny, Shane T; Morales-Gamez, Laura; Babu, Ramesh P; O'Connor, Kevin E; Steinbüchel, Alexander

    2016-10-15

    utilization of cheap substrates for the microbial production of PHAs is crucial to lower production costs. Feedstock not competing with human nutrition is highly favorable. Syngas, a mixture of carbon monoxide, carbon dioxide, and hydrogen, can be obtained by pyrolysis of organic waste and can be utilized for PHA synthesis by several kinds of bacteria. Up to now, the biosynthesis of PHAs from syngas has been limited to short-chain-length PHAs, which results in a stiff and brittle material. In this study, the syngas-utilizing bacterium Rhodospirillum rubrum was genetically modified to synthesize a polymer which consisted of medium-chain-length constituents, resulting in a rubber-like material. This study reports the establishment of a microbial synthesis of these so-called medium-chain-length PHAs from syngas and therefore potentially extends the applications of syngas-derived PHAs. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  14. Quorum sensing influences growth and photosynthetic membrane production in high-cell-density cultivations of Rhodospirillum rubrum.

    Science.gov (United States)

    Carius, Lisa; Carius, Anke B; McIntosh, Matthew; Grammel, Hartmut

    2013-08-08

    The facultative anoxygenic photosynthetic bacterium Rhodospirillum rubrum exhibits versatile metabolic activity allowing the adaptation to rapidly changing growth conditions in its natural habitat, the microaerobic and anoxic zones of stagnant waters. The microaerobic growth mode is of special interest as it allows the high-level expression of photosynthetic membranes when grown on succinate and fructose in the dark, which could significantly simplify the industrial production of compounds associated with PM formation. However, recently we showed that PM synthesis is no longer inducible when R. rubrum cultures are grown to high cell densities under aerobic conditions. In addition a reduction of the growth rate and the continued accumulation of precursor molecules for bacteriochlorophyll synthesis were observed under high cell densities conditions. In the present work, we demonstrate that the cell density-dependent effects are reversible if the culture supernatant is replaced by fresh medium. We identified six N-acylhomoserine lactones and show that four of them are produced in varying amounts according to the growth phase and the applied growth conditions. Further, we demonstrate that N-acylhomoserine lactones and tetrapyrrole compounds released into the growth medium affect the growth rate and PM expression in high cell density cultures. In summary, we provide evidence that R. rubrum possesses a Lux-type quorum sensing system which influences the biosynthesis of PM and the growth rate and is thus likely to be involved in the phenotypes of high cell density cultures and the rapid adaptation to changing environmental conditions.

  15. Tailor-made PAT platform for safe syngas fermentations in batch, fed-batch and chemostat mode with Rhodospirillum rubrum.

    Science.gov (United States)

    Karmann, Stephanie; Follonier, Stéphanie; Egger, Daniel; Hebel, Dirk; Panke, Sven; Zinn, Manfred

    2017-11-01

    Recently, syngas has gained significant interest as renewable and sustainable feedstock, in particular for the biotechnological production of poly([R]-3-hydroxybutyrate) (PHB). PHB is a biodegradable, biocompatible polyester produced by some bacteria growing on the principal component of syngas, CO. However, working with syngas is challenging because of the CO toxicity and the explosion danger of H 2 , another main component of syngas. In addition, the bioprocess control needs specific monitoring tools and analytical methods that differ from standard fermentations. Here, we present a syngas fermentation platform with a focus on safety installations and process analytical technology (PAT) that serves as a basis to assess the physiology of the PHB-producing bacterium Rhodospirillum rubrum. The platform includes (i) off-gas analysis with an online quadrupole mass spectrometer to measure CO consumption and production rates of H 2 and CO 2 , (ii) an at-line flow cytometer to determine the total cell count and the intracellular PHB content and (iii) different online sensors, notably a redox sensor that is important to confirm that the culture conditions are suitable for the CO metabolization of R. rubrum. Furthermore, we present as first applications of the platform a fed-batch and a chemostat process with R. rubrum for PHB production from syngas. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  16. Syngas obtained by microwave pyrolysis of household wastes as feedstock for polyhydroxyalkanoate production in Rhodospirillum rubrum

    OpenAIRE

    Revelles, Olga; Beneroso, Daniel; Menéndez, J. Angel; Arenillas, Ana; García, J. Luis; Prieto, M. Auxiliadora

    2016-01-01

    Summary The massive production of urban and agricultural wastes has promoted a clear need for alternative processes of disposal and waste management. The potential use of municipal solid wastes (MSW) as feedstock for the production of polyhydroxyalkanoates (PHA) by a process known as syngas fermentation is considered herein as an attractive bio‐economic strategy to reduce these wastes. In this work, we have evaluated the potential of Rhodospirillum rubrum as microbial cell factory for the syn...

  17. Bakteriochlorophyllvorstufen und Pigment-Protein-Komplexe in Rhodospirillum rubrum ST3 und GN11

    OpenAIRE

    Hammel, Jörg U.

    2006-01-01

    In der vorliegenden Arbeit wurden zwei Mutanten des Alpha-Proteobakteriums Rhodospirillum rubrum untersucht, die im Bakteriochlorophyll-Biosyntheseweg unterbrochen sind, um einen Beitrag zum genaueren Verständnis der Biosynthese dieser Moleküle und der einzelnen daran beteiligten Schritte zu liefern. Von den beiden Stämmen ST3 und GN11 wurden die ins Kulturmedium ausgeschiedenen Pigmente aufgereinigt und spektroskopisch analysiert. Ebenfalls wurden sowohl von ST3, als auch von GN11 die in int...

  18. Two types of essential carboxyl groups in Rhodospirillum rubrum proton ATPase

    International Nuclear Information System (INIS)

    Ceccarelli, E.; Vallejos, R.H.

    1983-01-01

    Two different types of essential carboxyl groups were detected in the extrinsic component of the proton ATPase of Rhodospirillum rubrum. Chemical modification of R. rubrum chromatophores or its solubilized ATPase by Woodward's reagent K resulted in inactivation of photophosphorylating and ATPase activities. The apparent order of reaction was nearly 1 with respect to reagent concentration and similar K1 were obtained for the soluble and membrane-bound ATPases suggesting that inactivation was associated with modification of one essential carboxyl group located in the soluble component of the proton ATPase. Inactivation was prevented by adenine nucleotides but not by divalent cations. Dicyclohexylcarbodiimide completely inhibited the solubilized ATPase with a K1 of 5.2 mM and a K2 of 0.81 min-1. Mg2+ afforded nearly complete protection with a Kd of 2.8 mM. Two moles of [14C]dicyclohexylcarbodiimide were incorporated per mole of enzyme for complete inactivation but in the presence of 30 mM MgCl2 only one mole was incorporated and there was no inhibition. The labeling was recovered mostly from the beta subunit. The incorporation of the labeled reagent into the ATPase was not prevented by previous modification with Woodward's reagent K. It is concluded that both reagents modified two different essential carboxyl groups in the soluble ATPase from R. rubrum

  19. A glutathione redox effect on photosynthetic membrane expression in Rhodospirillum rubrum.

    Science.gov (United States)

    Carius, Anke Berit; Henkel, Marius; Grammel, Hartmut

    2011-04-01

    The formation of intracytoplasmic photosynthetic membranes by facultative anoxygenic photosynthetic bacteria has become a prime example for exploring redox control of gene expression in response to oxygen and light. Although a number of redox-responsive sensor proteins and transcription factors have been characterized in several species during the last several years in some detail, the overall understanding of the metabolic events that determine the cellular redox environment and initiate redox signaling is still poor. In the present study we demonstrate that in Rhodospirillum rubrum, the amount of photosynthetic membranes can be drastically elevated by external supplementation of the growth medium with the low-molecular-weight thiol glutathione. Neither the widely used reductant dithiothreitol nor oxidized glutathione caused the same response, suggesting that the effect was specific for reduced glutathione. By determination of the extracellular and intracellular glutathione levels, we correlate the GSH/GSSG redox potential to the expression level of photosynthetic membranes. Possible regulatory interactions with periplasmic, membrane, and cytosolic proteins are discussed. Furthermore, we found that R. rubrum cultures excrete substantial amounts of glutathione to the environment.

  20. Molecular cloning and sequence of the B880 holochrome gene from Rhodospirillum rubrum

    International Nuclear Information System (INIS)

    Anon.

    1986-01-01

    Restriction fragments of genomic Rhodospirillum rubrum DNA were selected according to size by electrophoresis followed by hybridization with [ 32 P]mRNA encoding the two B880 holochrome polypeptides. The fragments were cloned into Escherchia coli C600 with plasmid pBR327 as a vector. The clones were selected by colony hybridization with 32 P-holochrome-mRNA and counter selected by hybridization with Rs. rubrum ribosomal RNA, a minor contaminant of the mRNA preparation. Chimeric plasmid pRR22 was shown to contain the B880 genes by hybrid selection of B880 holochrome-mRNA. A restriction map of its 2.2-kilobase insert and the sequence of a 430 base pair fragment thereof is reported. Genes α and β are nearly contiguous, indicating that they are transcribed as a single operon. The predicted amino acid sequences coincide with the sequences of the α and β polypeptides established in other laboratories, except for additional C-terminal tails of 10 and 13 amino acid residues, respectively

  1. Syngas obtained by microwave pyrolysis of household wastes as feedstock for polyhydroxyalkanoate production in Rhodospirillum rubrum.

    Science.gov (United States)

    Revelles, Olga; Beneroso, Daniel; Menéndez, J Angel; Arenillas, Ana; García, J Luis; Prieto, M Auxiliadora

    2017-11-01

    The massive production of urban and agricultural wastes has promoted a clear need for alternative processes of disposal and waste management. The potential use of municipal solid wastes (MSW) as feedstock for the production of polyhydroxyalkanoates (PHA) by a process known as syngas fermentation is considered herein as an attractive bio-economic strategy to reduce these wastes. In this work, we have evaluated the potential of Rhodospirillum rubrum as microbial cell factory for the synthesis of PHA from syngas produced by microwave pyrolysis of the MSW organic fraction from a European city (Seville). Growth rate, uptake rate, biomass yield and PHA production from syngas in R. rubrum have been analysed. The results revealed the strong robustness of this syngas fermentation where the purity of the syngas is not a critical constraint for PHA production. Microwave-induced pyrolysis is a tangible alternative to standard pyrolysis, because it can reduce cost in terms of energy and time as well as increase syngas production, providing a satisfactory PHA yield. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  2. Metabolic Regulation as a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum rubrum

    Directory of Open Access Journals (Sweden)

    Justin A. North

    2016-07-01

    Full Text Available Rhodospirillum rubrum possesses a novel oxygen-independent, aerobic methionine salvage pathway (MSP for recycling methionine from 5-methylthioadenosine (MTA, the MTA-isoprenoid shunt. This organism can also metabolize MTA as a sulfur source under anaerobic conditions, suggesting that the MTA-isoprenoid shunt may also function anaerobically as well. In this study, deep proteomics profiling, directed metabolite analysis, and reverse transcriptase quantitative PCR (RT-qPCR revealed metabolic changes in response to anaerobic growth on MTA versus sulfate as sole sulfur source. The abundance of protein levels associated with methionine transport, cell motility, and chemotaxis increased in the presence of MTA over that in the presence of sulfate. Purine salvage from MTA resulted primarily in hypoxanthine accumulation and a decrease in protein levels involved in GMP-to-AMP conversion to balance purine pools. Acyl coenzyme A (acyl-CoA metabolic protein levels for lipid metabolism were lower in abundance, whereas poly-β-hydroxybutyrate synthesis and storage were increased nearly 10-fold. The known R. rubrum aerobic MSP was also shown to be upregulated, to function anaerobically, and to recycle MTA. This suggested that other organisms with gene homologues for the MTA-isoprenoid shunt may also possess a functioning anaerobic MSP. In support of our previous findings that ribulose-1,5-carboxylase/oxygenase (RubisCO is required for an apparently purely anaerobic MSP, RubisCO transcript and protein levels both increased in abundance by over 10-fold in cells grown anaerobically on MTA over those in cells grown on sulfate, resulting in increased intracellular RubisCO activity. These results reveal for the first time global metabolic responses as a consequence of anaerobic MTA metabolism compared to using sulfate as the sulfur source.

  3. Anaerobic detoxification fermentation by Rhodospirillum rubrum for rice straw as feed with moderate pretreatment.

    Science.gov (United States)

    Zhang, Jian; Yuan, Jie; Zhang, Wen-Xue; Tu, Fang; Jiang, Ya; Sun, Chuan-Ze

    2018-01-02

    A novel and effective process was put forward for converting rice straw into feed by combining diluted acid hydrolysis and ammonization with Rhodospirillum rubrum fermentation. After pretreatment with dilute sulfuric or phosphoric acid (1%, w/w) at 100°C, materials were subjected to fermentation under several gases (N 2 , CO 2 , and air) and different light intensities in a 2-L fermentor. The key indexes of feed for fermented materials were estimated and several toxic substances were investigated during the fermentation. Following sulfuric acid treatment, the true protein of rice straw increased from 29 to 143 g kg -1 and the crude fiber decreased from 359 to 136 g kg -1 after fermentation at 0.3 L min -1  L -1 of N 2 flow and a light intensity of 3400 lux; and following phosphoric acid treatment, the true protein increased by 286% and the crude fiber decreased by 52% after fermentation at 0.4 L min -1  L -1 of N 2 flow and a light intensity of 3000 lux. Other key contents were also improved for use as feed, and some toxic substances (i.e., furfural, hydroxymethylfurfural, acetic acid, phenol, cresol) produced by the pretreatments could be removed at low levels during the fermentations.

  4. [Intermediate states formed during discharge separation in the reaction centers of Rhodospirillum rubrum in the presence of a low-redox potential].

    Science.gov (United States)

    Godik, V I; Samuilov, V D; Borisov, A Iu

    1978-01-01

    The intermediate short-lived states arising in reaction centre preparations (RC) of purple bacterium Rhodospirillum rubrum are investigated under the conditions of low redox potential. Excitation by 353 and 530 nm laser pulses produced two states characterized by optical absorption changes in the range of 350--650 nm and lifetimes: 10--30 ns for the first state and 2.5 +/- 0.5 microseconds for the second one. The first state is similar to the state PF, described previously by Parson et al. for RC from Rps. sphaeroides. Carotenoid extraction with isooctane resulted in changing the spectrum with tau = 2.5 microseconds and in the appearance of new absorption changes similar to those for the R state observed before in carotenoidless bacterial strains within microsecond time range. The comparison of the microsecond spectra with difference spectra (continuous light minus dark) of RC from R. rubrum in the range of 350--650 nm made it possible to identify the states with tau = 2.5 microseconds as carotenoid triplet states. The ratio of quantum yields of PR and carotenoid triplet states production was determined as being 1 : 1. The conclusion was made that triplet-triplet energy transfer from state PR to carotenoid is responsible for the production of carotenoid triplet states.

  5. BASE-A space experiment with Rhodospirillum rubrum S1H

    Data.gov (United States)

    National Aeronautics and Space Administration — R. rubrum S1H inoculated on solid minimal media was sent to the ISS in September 2006 (BASE-A experiment). After 10 days flight R. rubrum cultures returned back to...

  6. Stepwise reduction of the culture redox potential allows the analysis of microaerobic metabolism and photosynthetic membrane synthesis in Rhodospirillum rubrum.

    Science.gov (United States)

    Carius, Lisa; Hädicke, Oliver; Grammel, Hartmut

    2013-02-01

    Bacterial growth under oxygen-limited (microaerobic) conditions is often accompanied by phenomena of great interest for fundamental research and industrial application. The microaerobic lifestyle of anoxygenic photosynthetic bacteria like Rhodospirillum rubrum harbors such a phenomenon, as it allows the formation of photosynthetic membranes and related interesting products without light. However, due to the technical difficulties in process control of microaerobic cultivations and the limited sensitivity of available oxygen sensors, the analysis of microaerobic growth and physiology is still underrepresented in current research. The main focus of the present study was to establish an experimental set-up for the systematic study of physiological processes, associated with the growth of R. rubrum under microaerobic conditions in the dark. For this purpose, we introduce a robust and reliable microaerobic process control strategy, which applies the culture redox potential (CRP) for assessing different degrees of oxygen limitation in bioreactor cultivations. To describe the microaerobic growth behavior of R. rubrum cultures for each of these defined CRP reduction steps, basic growth parameters were experimentally determined. Flux variability analysis provided an insight into the metabolic activity of the TCA cycle and implied its connection to the respiratory capacity of the cells. In this context, our results suggest that microaerobic growth of R. rubrum can be described as an oxygen-activated cooperative mechanism. The present study thus contributes to the investigation of metabolic and regulatory events responsible for the redox-sensitive formation of photosynthetic membranes in facultative photosynthetic bacteria. Furthermore, the introduced microaerobic cultivation setup should be generally applicable for any microbial system of interest which can be cultivated in common stirred-tank bioreactors. Copyright © 2012 Wiley Periodicals, Inc.

  7. Model-based derivation, analysis and control of unstable microaerobic steady-states--considering Rhodospirillum rubrum as an example.

    Science.gov (United States)

    Carius, Lisa; Rumschinski, Philipp; Faulwasser, Timm; Flockerzi, Dietrich; Grammel, Hartmut; Findeisen, Rolf

    2014-04-01

    Microaerobic (oxygen-limited) conditions are critical for inducing many important microbial processes in industrial or environmental applications. At very low oxygen concentrations, however, the process performance often suffers from technical limitations. Available dissolved oxygen measurement techniques are not sensitive enough and thus control techniques, that can reliable handle these conditions, are lacking. Recently, we proposed a microaerobic process control strategy, which overcomes these restrictions and allows to assess different degrees of oxygen limitation in bioreactor batch cultivations. Here, we focus on the design of a control strategy for the automation of oxygen-limited continuous cultures using the microaerobic formation of photosynthetic membranes (PM) in Rhodospirillum rubrum as model phenomenon. We draw upon R. rubrum since the considered phenomenon depends on the optimal availability of mixed-carbon sources, hence on boundary conditions which make the process performance challenging. Empirically assessing these specific microaerobic conditions is scarcely practicable as such a process reacts highly sensitive to changes in the substrate composition and the oxygen availability in the culture broth. Therefore, we propose a model-based process control strategy which allows to stabilize steady-states of cultures grown under these conditions. As designing the appropriate strategy requires a detailed knowledge of the system behavior, we begin by deriving and validating an unstructured process model. This model is used to optimize the experimental conditions, and identify properties of the system which are critical for process performance. The derived model facilitates the good process performance via the proposed optimal control strategy. In summary the presented model-based control strategy allows to access and maintain microaerobic steady-states of interest and to precisely and efficiently transfer the culture from one stable microaerobic steady

  8. An aerobic detoxification photofermentation by Rhodospirillum rubrum for converting soy sauce residue into feed with moderate pretreatment.

    Science.gov (United States)

    Zhang, Jian; Yuan, Jie; Zhang, Wen-Xue; Zhu, Wen-You; Tu, Fang; Jiang, Ya; Sun, Chuan-Ze

    2017-09-25

    This paper reports an effective process for converting soy sauce residue into feeds by combining moderate acid hydrolysis and ammonization with Rhodospirillum rubrum fermentation. After pretreatment with dilute sulfuric or phosphoric acid (1%, w/w) at 100 °C, materials were subjected to fermentation under several gases (N 2 , CO 2 , and air) and different light intensities in a 2-L fermentor. Following sulfuric acid treatment, the true protein increased from 188 to 362 g kg -1 and the crude fiber decreased from 226 to 66 g kg -1 after fermentation at 0.5 L min -1  L -1 of air flow and a light intensity of 750 lx and following phosphoric acid treatment, the true protein increased by 90% and the crude fiber decreased by 67% after fermentation at 0.6 L min -1  L -1 of air flow and a light intensity of 600 lx Other contents, including crude fat, crude ash, phosphorus, sulfur, sulfur-containing amino acids, sodium chloride, and calcium, were also improved for use as feed. Meantime, some toxic substances, including furfural, hydroxymethylfurfural (5-HMF), acetic acid, phenol, and cresol, which were produced by the pretreatments, could be removed by 12-32, 5-8, 49-53, 7-8, and 7-8%, respectively; and total sugars, glucose, and xylose could be utilized by 68-69, 71-72, and 63-67% respectively. The quality of soy sauce residue is improved for use as feed and some toxic substances can be decreased via the R. rubrum fermentation.

  9. Redox-state dynamics of ubiquinone-10 imply cooperative regulation of photosynthetic membrane expression in Rhodospirillum rubrum.

    Science.gov (United States)

    Grammel, Hartmut; Ghosh, Robin

    2008-07-01

    It is now well established that, for photosynthetic bacteria, the aerobic-to-microaerophilic transition activates the membrane-bound sensor kinase RegB, which subsequently phosphorylates the transcriptional activator RegA, thereby inducing elevated levels of intracellular photosynthetic membranes. The mechanism of RegB activation--in particular, the role of ubiquinone-10--is controversial at present. One problem here is that very limited quantitative in vivo data for the response of the ubiquinone redox state to different cultivation conditions exist. Here, we utilize Rhodospirillum rubrum to study the correlation of the quinone redox state to the expression level of photosynthetic membranes and determine an effective response function directly. Our results show that changes in the photosynthetic membrane levels between 50 and 95% of that maximally attainable are associated with only a twofold change in the ubiquinol/ubiquinone ratio and are not necessarily proportional to the total levels of either quinone or [NAD(+) + NADH]. There is no correlation between the redox potentials of the quinone and pyridine nucleotide pools. Hill function analysis of the photosynthetic membrane induction in response to the quinone redox state suggests that the induction process is highly cooperative. Our results are probably generally applicable to quinone redox regulation in bacteria.

  10. Three novel proteins co-localise with polyhydroxybutyrate (PHB) granules in Rhodospirillum rubrum S1.

    Science.gov (United States)

    Narancic, Tanja; Scollica, Elisa; Cagney, Gerard; O'Connor, Kevin E

    2018-04-01

    Polyhydroxybutyrate (PHB), a biodegradable polymer accumulated by bacteria is deposited intracellularly in the form of inclusion bodies often called granules. The granules are supramolecular complexes harbouring a varied number of proteins on their surface, which have specific but incompletely characterised functions. By comparison with other organisms that produce biodegradable polymers, only two phasins have been described to date for Rhodosprillum rubrum, raising the possibility that more await discovery. Using a comparative proteomics strategy to compare the granules of wild-type R. rubrum with a PHB-negative mutant housing artificial PHB granules, we identified four potential PHB granules' associated proteins. These were: Q2RSI4, an uncharacterised protein; Q2RWU9, annotated as an extracellular solute-binding protein; Q2RQL4, annotated as basic membrane lipoprotein; and Q2RQ51, annotated as glucose-6-phosphate isomerase. In silico analysis revealed that Q2RSI4 harbours a Phasin_2 family domain and shares low identity with a single-strand DNA-binding protein from Sphaerochaeta coccoides. Fluorescence microscopy found that three proteins Q2RSI4, Q2EWU9 and Q2RQL4 co-localised with PHB granules. This work adds three potential new granule associated proteins to the repertoire of factors involved in bacterial storage granule formation, and confirms that proteomics screens are an effective strategy for discovery of novel granule associated proteins.

  11. Tryptophan phosphorescence spectroscopy reveals that a domain in the NAD(H)-binding component (dI) of transhydrogenase from Rhodospirillum rubrum has an extremely rigid and conformationally homogeneous protein core

    NARCIS (Netherlands)

    Broos, J; Gabellieri, E; van Boxel, GI; Jackson, JB; Strambini, GB; Strambini, Giovanni B.

    2003-01-01

    The characteristics of tryptophan phosphorescence from the NAD(H)-binding component (dI) component of Rhodospirillum rubrum transhydrogenase are described. This enzyme couples hydride transfer between NAD( H) and NADP( H) to proton translocation across a membrane and is only active as a dimer.

  12. Low Earth orbit journey and ground simulations studies point out metabolic changes in the ESA life support organism Rhodospirillum rubrum

    Science.gov (United States)

    Mastroleo, Felice; Leys, Natalie; Benotmane, Rafi; Vanhavere, Filip; Janssen, Ann; Hendrickx, Larissa; Wattiez, Ruddy; Mergeay, Max

    MELiSSA (Micro-Ecological Life Support System Alternative) is a project of closed regenerative life support system for future space flights developed by the European Space Agency. It consists of interconnected processes (i.e. bioreactors, higher plant compartments, filtration units,..) targeting the total recycling of organic waste into oxygen, water and food. Within the MELiSSA loop, the purple non-sulfur alpha-proteobacterium R. rubrum ATCC25903 is used to convert fatty acids released from the upstream raw waste digesting reactor to CO2 and biomass, and to complete the mineralization of aminoacids into NH4+ that will be forwarded to the nitrifying compartment. Among the numerous challenges of the project, the functional stability of the bioreactors in long term and under space flight conditions is of paramount importance for the efficiency of the life support system and consequently the crew safety. Therefore, the physiological and metabolic changes induced by space flight were investigated for R. rubrum. The bacterium grown on solid medium during 2 different 10-day space flights to the ISS (MES- SAGE2, BASE-A experiments) were compared to cells grown on Earth 1 g gravity or modeled microgravity and normal Earth radiation or simulated space flight radiation conditions in order to relate each single stress to its respective cellular response. For simulating the radiation environment, pure gamma and neutron sources were combined, while simulation of changes in gravity where performed using the Random Positioning Machine technology. Transcriptome analysis using R. rubrum total genome DNA-chip showed up-regulation of genes involved in oxidative stress response after a 10-day mission inside the ISS, without loss of viability. As an example, alkyl hydroperoxide reductase, thioredoxin reductase and bacterioferritin genes are least 2 fold induced although the radiation dose experienced by the bacterium (4 mSv) is very low compared to its radiotolerance (D10 = 100 Sv

  13. Rhodospirillum rubrum CO-dehydrogenase. Part 2: Spectroscopic investigation and assignment of spin-spin coupling signals

    Energy Technology Data Exchange (ETDEWEB)

    Heo, J.; Staples, C.R.; Telser, J.; Ludden, P.W.

    1999-12-08

    The carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum was examined at several potentials. The electron paramagnetic resonance (EPR) spectrum of CODH poised at approximately {minus}295 mV exhibits a species (referred to as C{sub red1}) that was previously attributed to [Fe{sub 4}S{sub 4}]{sub C}{sup 1+} (S = 1/2) weakly exchange-coupling with Ni{sup 2+} (S = 1) to yield apparent g-values of (G{sub z,y,x} = 2.03, 1.88, 1.71). UV-visible absorption spectroscopy showed only one [Fe{sub 4}S{sub 4}] cluster to be reduced at {minus}295 mV. Based upon the assignment of S = 1/2 resonances in indigo carmine-poised C531A CODH to a [(CO{sub L})Fe{sup 3+}-Ni{sup 2+}-H{minus}]{sup 4+} cluster, a careful search for similar resonances in the EPR spectrum of the enzyme state of wild-type CODH producing C{sub red1} was undertaken. Coupled putative [(CO{sub L})Fe{sup 3+}-Ni{sup 2+}-H{minus}]{sup 4+} signals were observed in low intensity, which, in conjunction with the other assignments, prompted a reinterpretation of the redox state of the enzyme producing C{sub red1}. instead of coupling with Ni{sup 2+} (S = 1), the authors propose [Fe{sub 4}S{sub 4}]{sub C}{sup 1+} (S = 1/2) couples with [(CO{sub L})-Fe{sup 3+}-Ni{sup 2+}-H{minus}]{sup 4+} (S = 1/2). The putative [FeNi] signals were heterogeneous, but this heterogeneity could be removed by preincubation with CO prior to subsequent poising. They propose that an unreactive CO molecule (CO{sub L}) is bound to the [FeNi] cluster, possibly modulating the reduction potential and activating the [FeNi] cluster for catalysis of a substrate CO molecule (CO{sub S}). Either Zn{sup 2+} or Co{sup 2+} was incorporated into purified, Ni-deficient CODH. The EPR spectra of reduced Zn-CODH and Co-CODH contain resonances in the g = 1.73--1.76 region (which they call C{sub red2A}), and an upfield wing (shoulder) near g = 2.09. That these features are observed without a paramagnetic heterometal present indicates that they are derived

  14. Pigment exchange in the light collecting complex of Rhodospirillum rubrum purple bacteria and Fourier transform Raman spectroscopy on metallo-bacterio-pheophytins a

    International Nuclear Information System (INIS)

    Naveke, Arne

    1998-03-01

    Light collecting complexes (antennas) in membranes of photosynthetic bacteria and plants capture solar light during photosynthesis and transmit the excitation energy to the reaction centre where it is transformed into energy which can be used by the organism. Antennas and reaction centres are made of polypeptides and pigments (bacterio-chlorophylls) which have a crucial role in solar energy capture, but also in subsequent energy transfers. Whereas three-dimensional structures of some antennas and reaction centres are already known with a high resolution, there is almost no quantitative data on interactions between polypeptides and pigments which however confer their specificity to these complexes. A possibility to obtain such data is to introduce chemically modified pigments within antennas and reaction centres. In this research thesis, some metallo-bacteriopheophytins a have been synthesized and studied by Fourier transform Raman spectroscopy. Vibrations modes have been studied. A process of exchange of the bacterio-chlorophyll a in the LHI antenna of the Rhodospirillum rubrum purple bacteria has been developed to obtain a good efficiency in antennas containing zinc-bacterio-pheophytin a and nickel-bacterio-pheophytin a, as well as bacterio-pheophytin a. Absorption spectra are discussed as well as the occurring relationships between complexes, and the extent of the occurring exchange [fr

  15. Inhibition of telomerase activity and induction of apoptosis by Rhodospirillum rubrum L-asparaginase in cancer Jurkat cell line and normal human CD4+ T lymphocytes.

    Science.gov (United States)

    Zhdanov, Dmitry D; Pokrovsky, Vadim S; Pokrovskaya, Marina V; Alexandrova, Svetlana S; Eldarov, Mikhail A; Grishin, Dmitry V; Basharov, Marsel M; Gladilina, Yulia A; Podobed, Olga V; Sokolov, Nikolai N

    2017-11-01

    Rhodospirillum rubrum L-asparaginase mutant E149R, V150P, F151T (RrA) down-regulates telomerase activity due to its ability to inhibit the expression of telomerase catalytic subunit hTERT. The aim of this study was to define the effect of short-term and long-term RrA exposure on proliferation of cancer Jurkat cell line and normal human CD4 + T lymphocytes. RrA could inhibit telomerase activity in dose- and time-dependent manner in both Jurkat and normal CD4 + T cells. Continuous RrA exposure of these cells resulted in shortening of telomeres followed by cell cycle inhibition, replicative senescence, and development of apoptosis. Complete death of Jurkat cells was observed at the day 25 of RrA exposure while normal CD4 + T cells died at the day 50 due to the initial longer length of telomeres. Removal of RrA from senescent cells led to a reactivation of hTERT expression, restoration telomerase activity, re-elongation of telomeres after 48 h of cultivation, and survival of cells. These findings demonstrate that proliferation of cancer and normal telomerase-positive cells can be limited by continuous telomerase inhibition with RrA. Longer telomeres of normal CD4 + T lymphocytes make such cells more sustainable to RrA exposure that could give them an advantage during anti-telomerase therapy. These results should facilitate further investigations of RrA as a potent anti-telomerase therapeutic protein. © 2017 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  16. A Glutathione Redox Effect on Photosynthetic Membrane Expression in Rhodospirillum rubrum▿†

    Science.gov (United States)

    Carius, Anke Berit; Henkel, Marius; Grammel, Hartmut

    2011-01-01

    The formation of intracytoplasmic photosynthetic membranes by facultative anoxygenic photosynthetic bacteria has become a prime example for exploring redox control of gene expression in response to oxygen and light. Although a number of redox-responsive sensor proteins and transcription factors have been characterized in several species during the last several years in some detail, the overall understanding of the metabolic events that determine the cellular redox environment and initiate redox signaling is still poor. In the present study we demonstrate that in Rhodospirillum rubrum, the amount of photosynthetic membranes can be drastically elevated by external supplementation of the growth medium with the low-molecular-weight thiol glutathione. Neither the widely used reductant dithiothreitol nor oxidized glutathione caused the same response, suggesting that the effect was specific for reduced glutathione. By determination of the extracellular and intracellular glutathione levels, we correlate the GSH/GSSG redox potential to the expression level of photosynthetic membranes. Possible regulatory interactions with periplasmic, membrane, and cytosolic proteins are discussed. Furthermore, we found that R. rubrum cultures excrete substantial amounts of glutathione to the environment. PMID:21317329

  17. Ultra-broadband 2D electronic spectroscopy of carotenoid-bacteriochlorophyll interactions in the LH1 complex of a purple bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Maiuri, Margherita [CNR-IFN, Dipartimento di Fisica, Politecnico di Milano, P.zza L. da Vinci 32, Milano 20133 (Italy); Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08544 (United States); Réhault, Julien; Polli, Dario; Cerullo, Giulio, E-mail: giulio.cerullo@polimi.it [CNR-IFN, Dipartimento di Fisica, Politecnico di Milano, P.zza L. da Vinci 32, Milano 20133 (Italy); Carey, Anne-Marie; Hacking, Kirsty; Cogdell, Richard J. [Glasgow Biomedical Research Centre, IBLS, University of Glasgow, 126 Place, Glasgow G12 8TA, Scotland (United Kingdom); Garavelli, Marco [Dipartimento di Chimica “G. Ciamician,” Università di Bologna, Via Selmi 2, IT-40126 Bologna (Italy); CNRS, Institut de Chimie de Lyon, École Normale Supérieure de Lyon, Université de Lyon, 46 Allée d’Italie, F-69364 Lyon Cedex 07 (France); Lüer, Larry [Madrid Institute for Advanced Studies, IMDEA Nanociencia, Madrid (Spain)

    2015-06-07

    We investigate the excitation energy transfer (EET) pathways in the photosynthetic light harvesting 1 (LH1) complex of purple bacterium Rhodospirillum rubrum with ultra-broadband two-dimensional electronic spectroscopy (2DES). We employ a 2DES apparatus in the partially collinear geometry, using a passive birefringent interferometer to generate the phase-locked pump pulse pair. This scheme easily lends itself to two-color operation, by coupling a sub-10 fs visible pulse with a sub-15-fs near-infrared pulse. This unique pulse combination allows us to simultaneously track with extremely high temporal resolution both the dynamics of the photoexcited carotenoid spirilloxanthin (Spx) in the visible range and the EET between the Spx and the B890 bacterio-chlorophyll (BChl), whose Q{sub x} and Q{sub y} transitions peak at 585 and 881 nm, respectively, in the near-infrared. Global analysis of the one-color and two-color 2DES maps unravels different relaxation mechanisms in the LH1 complex: (i) the initial events of the internal conversion process within the Spx, (ii) the parallel EET from the first bright state S{sub 2} of the Spx towards the Q{sub x} state of the B890, and (iii) the internal conversion from Q{sub x} to Q{sub y} within the B890.

  18. Polyploidy in Acer rubrum L.

    Science.gov (United States)

    John W. Duffield

    1943-01-01

    Acer rubrum L. is a highly polymorphic species occupying a range which includes almost all of the United States east of the prairies, southeastern Canada, and a portion of Newfoundland. The range of habitats occupied is equally impressive. Cytological study of this species was first undertaken by Mottier in 1893, but the first indication of...

  19. Hydrogen as clean fuel via continuous fermentation by anaerobic ...

    African Journals Online (AJOL)

    free and oxidized to water as a combustion product. Bioconversion of synthesis gas to hydrogen was demonstrated in a continuous fermentation utilizing malate as a carbon source. Rhodospirillum rubrum, an anaerobic photosynthetic bacterium ...

  20. Identification of chromatophore membrane protein complexes formed under different nitrogen availability conditions in Rhodospirillum rubrum

    DEFF Research Database (Denmark)

    Selao, Tiago Toscano; Branca, Rui; Chae, Pil Seok

    2011-01-01

    of two-dimensional Blue Native/SDS-PAGE and NSI-LC-LTQ-Orbitrap mass spectrometry. We have identified several membrane protein complexes, including components of the ATP synthase, reaction center, light harvesting, and NADH dehydrogenase complexes. Additionally, we have identified differentially...

  1. Cultivo en biorreactores de rhodospirillum rubrum en condiciones fotoheterotróficas

    OpenAIRE

    Cabello Bergillos, Fernando

    2007-01-01

    Consultable des del TDX Títol obtingut de la portada digitalitzada La presente tesis está enmarcada en el desarrollo de los sistemas de soporte de vida biológicos, de especial aplicación para los viajes espaciales tripulados de larga duración. Concretamente, este trabajo se centra en el estudio, análisis, modelización y escalado de uno de los cinco compartimentos que integran el bucle MELiSSA, el compartimento fotoheterotrófico. Los experimentos han sido encaminados a determinar la infl...

  2. Redox-State Dynamics of Ubiquinone-10 Imply Cooperative Regulation of Photosynthetic Membrane Expression in Rhodospirillum rubrum▿

    Science.gov (United States)

    Grammel, Hartmut; Ghosh, Robin

    2008-01-01

    It is now well established that, for photosynthetic bacteria, the aerobic-to-microaerophilic transition activates the membrane-bound sensor kinase RegB, which subsequently phosphorylates the transcriptional activator RegA, thereby inducing elevated levels of intracellular photosynthetic membranes. The mechanism of RegB activation—in particular, the role of ubiquinone-10—is controversial at present. One problem here is that very limited quantitative in vivo data for the response of the ubiquinone redox state to different cultivation conditions exist. Here, we utilize Rhodospirillum rubrum to study the correlation of the quinone redox state to the expression level of photosynthetic membranes and determine an effective response function directly. Our results show that changes in the photosynthetic membrane levels between 50 and 95% of that maximally attainable are associated with only a twofold change in the ubiquinol/ubiquinone ratio and are not necessarily proportional to the total levels of either quinone or [NAD+ + NADH]. There is no correlation between the redox potentials of the quinone and pyridine nucleotide pools. Hill function analysis of the photosynthetic membrane induction in response to the quinone redox state suggests that the induction process is highly cooperative. Our results are probably generally applicable to quinone redox regulation in bacteria. PMID:18487324

  3. In vitro Antifungal Activity of Limonene against Trichophyton rubrum

    OpenAIRE

    Chee, Hee Youn; Kim, Hoon; Lee, Min Hee

    2009-01-01

    In this study, the antifungal activities of limonene against Trichophyton rubrum were evaluated via broth microdilution and vapor contact assays. In both assays, limonene was shown to exert a potent antifungal effect against T. rubrum. The volatile vapor of limonene at concentrations above 1 ?l/800 ml air space strongly inhibited the growth of T. rubrum. The MIC value was 0.5% v/v in the broth microdilution assay. The antifungal activity of limonene against T. rubrum was characterized as a fu...

  4. Evaluating PHA productivity of bioengineered Rhodosprillum rubrum.

    Directory of Open Access Journals (Sweden)

    Huanan Jin

    Full Text Available This study explored the potential of using Rhodosprillum rubrum as the biological vehicle to convert chemically simple carbon precursors to a value-added bio-based product, the biopolymer PHA. R. rubrum strains were bioengineered to overexpress individually or in various combinations, six PHA biosynthetic genes (phaC1, phaA, phaB, phaC2, phaC3, and phaJ, and the resulting nine over-expressing strains were evaluated to assess the effect on PHA content, and the effect on growth. These experiments were designed to genetically evaluate: 1 the role of each apparently redundant PHA polymerase in determining PHA productivity; 2 identify the key gene(s within the pha biosynthetic operon that determines PHA productivity; and 3 the role of phaJ to support PHA productivity. The result of overexpressing each PHA polymerase-encoding gene indicates that phaC1 and phaC2 are significant contributors to PHA productivity, whereas phaC3 has little effect. Similarly, over-expressing individually or in combination the three PHA biosynthesis genes located in the pha operon indicates that phaB is the key determinant of PHA productivity. Finally, analogous experiments indicate that phaJ does not contribute significantly to PHA productivity. These bioengineering strains achieved PHA productivity of up to 30% of dry biomass, which is approximately 2.5-fold higher than the non-engineered control strain, indicating the feasibility of using this approach to produce value added bio-based products.

  5. Dynamics of sequestered cryptophyte nuclei in Mesodinium rubrum during starvation and refeeding

    DEFF Research Database (Denmark)

    Kim, Miran; Drumm, Kirstine; Daugbjerg, Niels

    2017-01-01

    nucleus in M. rubrum. Here, we conducted starvation and refeeding studies to monitor the fate of prey nuclei acquired by M. rubrum when feeding on Teleaulax amphioxeia and to explore the influence of the retained prey nucleus on photosynthesis of M. rubrum. Results indicate that enlargement of the prey...... on rate of carbon fixation. We interpret results within the context of a model that considers the dynamics of ingested prey nuclei during division of M. rubrum....

  6. A Trichophyton Rubrum Infection Model Based on the Reconstructed Human Epidermis - Episkin®.

    Science.gov (United States)

    Liang, Pan-Pan; Huang, Xin-Zhu; Yi, Jin-Ling; Chen, Zhi-Rui; Ma, Han; Ye, Cong-Xiu; Chen, Xian-Yan; Lai, Wei; Chen, Jian

    2016-01-05

    Trichophyton rubrum represents the most common infectious fungus responsible for dermatophytosis in human, but the mechanism involved is still not completely understood. An appropriate model constructed to simulate host infection is the prerequisite to study the pathogenesis of dermatophytosis caused by T. rubrum. In this study, we intended to develop a new T. rubrum infection model in vitro, using the three-dimensional reconstructed epidermis - EpiSkin ®, and to pave the way for further investigation of the mechanisms involved in T. rubrum infection. The reconstructed human epidermis (RHE) was infected by inoculating low-dose (400 conidia) and high-dose (4000 conidia) T. rubrum conidia to optimize the infection dose. During the various periods after infection, the samples were processed for pathological examination and scanning electron microscopy (SEM) observation. The histological analysis of RHE revealed a fully differentiated epidermis with a functional stratum corneum, which was analogous to the normal human epidermis. The results of hematoxylin and eosin staining and the periodic acid-Schiff staining showed that the infection dose of 400 conidia was in accord with the pathological characteristics of host dermatophytosis caused by T. rubrum. SEM observations further exhibited the process of T. rubrum infection in an intuitionistic way. We established the T. rubrum infection model on RHE in vitro successfully. It is a promising model for further investigation of the mechanisms involved in T. rubrum infection.

  7. Trichophyton rubrum onychomycosis in an 8-week-old infant

    Directory of Open Access Journals (Sweden)

    Vinod K Khurana

    2011-01-01

    Full Text Available An 8-week-old infant presented with 7 weeks history of nail involvement and discoloration. Lesions started over the middle fingernail of right hand at 1 week of age, spreading over to other nails within 2 weeks. Only two nails of the feet were spared. On KOH examination, fungal hyphae were seen and culture showed growth of Trichophyton rubrum. The purpose is to report the earliest case of onychomycosis having multiple nail involvement of fingers and toes (18 nails.

  8. The marine mixotroph, Mesodinium rubrum is far more than a greenhouse ciliate

    Science.gov (United States)

    Yih, W.; Myung, G.; Kim, H. S.; Yoo, Y. D.; Rho, J. R.

    2016-02-01

    Permanent symbiosis between the mixotrophic ciliate Mesodinium rubrum and the cryptomonad symbionts has long been assumed since 1908, when Hans Lohmann firstly described the reddish-brown globules inside M. rubrum ("Halteria rubra") cells as symbiotic algae ("Erythromonas haltericola"). Thus, M. rubrum was envisioned as a host greenhouse where numerous cryptomonad symbionts could be farmed. During last two decades, however, information on the species interaction among marine protists including M. rubrum was so impressively accumulated that the more real picture of the `symbiotic relationship' could be revealed. In addition to the obligate replacement of the selected organelles from a `symbiont', multiple donor strains for the klepto-organelles of M. rubrum was also explored. Hence, experimentally designed organelle trades for M. rubrum is not impossible today. This unique mixotrophic ciliate must be a pivotal member of marine plankton ecosystem with its superior klepto-organelles, motility, growth rate, and linkablilty to higher trophic levels. M. rubrum can link marine heterotrophic bacteria and cyanobacteria to its own predators which in turn could be consumed by other carnivores. Supported by the klepto-organelles and vitamins from prey cryptomonads as well as N(from cyanobacteria) and P(from heterotrophic bacteria) nutrients, M. rubrum thrives at diverse marine environments. Bacterivory by the protistan members of `Mesodinium food chain' may need to be further studied before we can better understand the superiority of the unique ciliate species in the sea.

  9. Interaction between Mesodinium rubrum and its prey: importance of prey concentration, irradiance and pH

    DEFF Research Database (Denmark)

    Moldrup, Morten; Hansen, Per Juel

    2007-01-01

    ABSTRACT: The functional and numerical responses for the marine obligate mixotrophic ciliate Mesodinium rubrum Lohmann, 1908 (=Myrionecta rubra Jankowsky, 1976) were studied at 2 irradiances (20 and 100 µE m2 s-1). Furthermore, its tolerance to high pH levels and response to starvation were studied...... was sufficient for maximum growth, but carbon contributions as high as 22% were observed to have no effect on growth. The pH experiments revealed that the growth of M. rubrum and Teleaulax sp. was impeded at pH levels in excess of 8.5 and 8.8, respectively. Experiments to reveal M. rubrum's response...... to starvation showed that M. rubrum could survive for around 50 d without prey. These results are all discussed with respect to M. rubrum's adaptation to its environment....

  10. TrED: the Trichophyton rubrum Expression Database

    Directory of Open Access Journals (Sweden)

    Liu Tao

    2007-07-01

    Full Text Available Abstract Background Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It's a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. Description All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. Conclusion TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes. TrED is available from URL: http://www.mgc.ac.cn/TrED/.

  11. Photoresponses of the purple nonsulfur bacteria Rhodospirillum centenum and Rhodobacter sphaeroides.

    OpenAIRE

    Sackett, M J; Armitage, J P; Sherwood, E E; Pitta, T P

    1997-01-01

    We have measured the photoresponse of two purple nonsulfur bacteria, Rhodobacter sphaeroides and Rhodospirillum centenum, under defined conditions in a light beam propagating at 90 degrees to the optical axis of the microscope. This beam presented cells with a steep gradient of intensity perpendicular to the direction of propagation and a shallow gradient in the direction of light propagation. R. centenum, a species that reverses to change direction, accumulated in the light beam, as expected...

  12. Mass entrapment and lysis of Mesodinium rubrum cells in mucus threads observed in cultures with Dinophysis

    DEFF Research Database (Denmark)

    Ojamäe, Karin; Hansen, Per Juel; Lips, Inga

    2016-01-01

    The entrapment and death of the ciliate Mesodinium rubrum in the mucus threads in cultures with Dinophysis is described and quantified. Feeding experiments with different concentrations and predator–prey ratios of Dinophysis acuta, Dinophysis acuminata and M. rubrum to study the motility loss...... and aggregate formation of the ciliates and the feeding behaviour of Dinophysis were carried out. In cultures of either Dinophysis species, the ciliates became entrapped in the mucus, which led to the formation of immobile aggregates of M. rubrum and subsequent cell lysis. The proportion of entrapped ciliates...... was influenced by the concentration of Dinophysis and the ratio of predator and prey in the cultures. At high cell concentrations of prey (136 cells mL−1) and predator (100 cells mL−1), a maximum of 17% of M. rubrum cells became immobile and went through cell lysis. Ciliates were observed trapped in the mucus...

  13. Factors affecting griseofulvin susceptibility testing of Trichophyton rubrum in microcultures.

    Science.gov (United States)

    Granade, T C; Artis, W M

    1982-01-01

    A microculture broth assay system for griseofulvin susceptibility testing of Trichophyton rubrum was further characterized. The effects of mass and number of colony-forming units of a fragmented mycelial inoculum, 5- or 8-day incubation periods, 25 or 32 degrees C incubation temperatures, and the solvents used to dissolve griseofulvin on the minimal inhibitory concentration (MIC) of griseofulvin were determined. An inoculum density with an absorbance of 0.600 at 450 nm ensured successful inoculation of all microcultures. Reduction of the inoculum mass to an absorbance of 0.200 lowered the number of colony-forming units in the inoculum by 60 to 80%. This decreased the efficiency of inoculation but did not alter the resulting MIC. There was no correlation between MIC and the number of colony-forming units used to initiate growth. Neither incubation temperature nor the length of incubation affected the MIC. The use of either acetone or ethanol to solubilize griseofulvin likewise had no effect on the MIC. The mean reproducibility of the MICs determined with the microculture method was 96%. Images PMID:7161372

  14. Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy.

    Science.gov (United States)

    Poli, Annarita; Romano, Ida; Mastascusa, Vincenza; Buono, Lorena; Orlando, Pierangelo; Nicolaus, Barbara; Leone, Luigi; Hong, Kar Wai; Chan, Kok-Gan; Goh, Kian Mau; Pascual, Javier

    2018-01-03

    Strain Corallo1 T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1 T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1 T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1 T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1 T . A draft genome sequence of strain Corallo1 T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1 T are C 16:1 , n-C 16:0 and C 18:1 , and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1 T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1 T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1 T (= DSM 27495 T  = CIP 110630 T ).

  15. In vitro activities of four antifungal drugs against Trichophyton rubrum isolates exhibiting resistance to fluconazole.

    Science.gov (United States)

    Santos, D A; Hamdan, J S

    2007-07-01

    Thirty-two clinical isolates of Trichophyton rubrum exhibiting resistance to fluconazole [minimum inhibitory concentrations (MICs) > or = 64 microg ml(-1)] were selected to test the antifungal activity of ketoconazole, itraconazole, griseofulvin and terbinafine. We followed the guidelines of the National Committee for Clinical Laboratory Standards for testing filamentous fungi. The strains Candida parapsilosis (ATCC 22019), Candida krusei (ATCC 6258), T. rubrum (ATCC 40051) and Trichophyton mentagrophytes (ATCC 40004) were included for quality control. The microdilution plates were incubated at 28 degrees C and were read visually after 7 days of incubation and endpoint determination readings were performed visually. The MIC ranges for the four antifungals were: 0.0625-2 microg ml(-1) for ketoconazole, 0.25-2.0 microg ml(-1) for griseofulvin, < or =0.031-1.0 microg ml(-1) for itraconazole and < or =0.031 microg ml(-1) for terbinafine (for all tested isolates). Terbinafine was the most potent drug against T. rubrum, in vitro, followed by itraconazole, ketoconazole and griseofulvin. Much work is still needed to correlate the MICs of these drugs with clinical outcomes to develop interpretative breakpoints for T. rubrum and other dermatophytes.

  16. Daily profile of melatonin levels in Chenopodium rubrum L. depends on photoperiod

    Czech Academy of Sciences Publication Activity Database

    Wolf, Karel; Kolář, Jan; Witters, E.; Dongen, W.; Onckelen, H.; Macháčková, Ivana

    2001-01-01

    Roč. 158, č. 11 (2001), s. 1491-1493 ISSN 0176-1617 R&D Projects: GA ČR GA206/00/1354 Institutional research plan: CEZ:AV0Z5038910 Keywords : Chenopodium rubrum * circadian rhythms * melatonin Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.018, year: 2001

  17. Comparison of the In Vitro Activities of Newer Triazoles and Established Antifungal Agents against Trichophyton rubrum

    NARCIS (Netherlands)

    Deng, S.; Zhang, C.; Seyedmousavi, S.; Zhu, S.; Tan, X.; Wen, Y.; Huang, X.; Lei, W.; Zhou, Z.; Fang, W.; Shen, S.; Deng, D.; Pan, W.; Liao, W.

    2015-01-01

    One hundred eleven clinical Trichophyton rubrum isolates were tested against 7 antifungal agents. The geometric mean MICs of all isolates were, in increasing order: terbinafine, 0.03 mg/liter; voriconazole, 0.05 mg/liter; posaconazole, 0.11 mg/liter; isavuconazole, 0.13 mg/liter; itraconazole, 0.26

  18. Gene Expression Response of Trichophyton rubrum during Coculture on Keratinocytes Exposed to Antifungal Agents

    Directory of Open Access Journals (Sweden)

    Tatiana Takahasi Komoto

    2015-01-01

    Full Text Available Trichophyton rubrum is the most common causative agent of dermatomycoses worldwide, causing infection in the stratum corneum, nails, and hair. Despite the high prevalence of these infections, little is known about the molecular mechanisms involved in the fungal-host interaction, particularly during antifungal treatment. The aim of this work was to evaluate the gene expression of T. rubrum cocultured with keratinocytes and treated with the flavonoid trans-chalcone and the glycoalkaloid α-solanine. Both substances showed a marked antifungal activity against T. rubrum strain CBS (MIC = 1.15 and 17.8 µg/mL, resp.. Cytotoxicity assay against HaCaT cells produced IC50 values of 44.18 to trans-chalcone and 61.60 µM to α-solanine. The interaction of keratinocytes with T. rubrum conidia upregulated the expression of genes involved in the glyoxylate cycle, ergosterol synthesis, and genes encoding proteases but downregulated the ABC transporter TruMDR2 gene. However, both antifungals downregulated the ERG1 and ERG11, metalloprotease 4, serine proteinase, and TruMDR2 genes. Furthermore, the trans-chalcone downregulated the genes involved in the glyoxylate pathway, isocitrate lyase, and citrate synthase. Considering the urgent need for more efficient and safer antifungals, these results contribute to a better understanding of fungal-host interactions and to the discovery of new antifungal targets.

  19. Growth Inhibition and Morphological Alterations of Trichophyton Rubrum Induced by Essential oil from Cymbopogon Winterianus Jowitt Ex Bor

    OpenAIRE

    de Oliveira Pereira, Fillipe; Alves Wanderley, Paulo; Cavalcanti Viana, Fernando Ant?nio; Baltazar de Lima, Rita; Barbosa de Sousa, Frederico; de Oliveira Lima, Edeltrudes

    2011-01-01

    Trichophyton rubrum is one of the most common fungi causer of dermatophytosis, mycosis that affect humans and animals around the world. Researches aiming new products with antifungal activity become necessary to overcome difficulties on treatment of these infections. Accordingly, this study aimed to investigate the antifungal activity of essential oil from Cymbopogon winterianus against the dermatophyte T. rubrum. The antifungal screening was performed by solid medium diffusion method with 16...

  20. Transcriptional profiling reveals the expression of novel genes in response to various stimuli in the human dermatophyte Trichophyton rubrum

    Directory of Open Access Journals (Sweden)

    Aquino-Ferreira Roseli

    2010-02-01

    Full Text Available Abstract Background Cutaneous mycoses are common human infections among healthy and immunocompromised hosts, and the anthropophilic fungus Trichophyton rubrum is the most prevalent microorganism isolated from such clinical cases worldwide. The aim of this study was to determine the transcriptional profile of T. rubrum exposed to various stimuli in order to obtain insights into the responses of this pathogen to different environmental challenges. Therefore, we generated an expressed sequence tag (EST collection by constructing one cDNA library and nine suppression subtractive hybridization libraries. Results The 1388 unigenes identified in this study were functionally classified based on the Munich Information Center for Protein Sequences (MIPS categories. The identified proteins were involved in transcriptional regulation, cellular defense and stress, protein degradation, signaling, transport, and secretion, among other functions. Analysis of these unigenes revealed 575 T. rubrum sequences that had not been previously deposited in public databases. Conclusion In this study, we identified novel T. rubrum genes that will be useful for ORF prediction in genome sequencing and facilitating functional genome analysis. Annotation of these expressed genes revealed metabolic adaptations of T. rubrum to carbon sources, ambient pH shifts, and various antifungal drugs used in medical practice. Furthermore, challenging T. rubrum with cytotoxic drugs and ambient pH shifts extended our understanding of the molecular events possibly involved in the infectious process and resistance to antifungal drugs.

  1. Molecular Strain Typing of Clinical Isolates, Trichophyton rubrum using Non Transcribed Spacer (NTS) Region as a Molecular Marker.

    Science.gov (United States)

    Ramaraj, Vijayakumar; Vijayaraman, Rajyoganandh S; Elavarashi, Elangovan; Rangarajan, Sudha; Kindo, Anupma Jyoti

    2017-05-01

    Dermatophytes are a group of fungi which infect keratinized tissues and causes superficial mycoses in humans and animals. The group comprises of three major genera, Trichophyton , Microsporum and Epidermophyton . Among them Trichophyton rubrum is a predominant anthropophilic fungi which causes chronic infections. Although, the infection is superficial and treatable, reinfection/coinfection causes inflation in the treatment cost. Identifying the source and mode of transmission is essential to prevent its transmission. Accurate discrimination is required to understand the clinical (relapse or reinfection) and epidemiological implications of the genetic heterogeneity of this species. Polymorphism in the Non Transcribed Spacer (NTS) region of ribosomal DNA (rDNA) clusters renders an effective way to discriminate strains among T. rubrum . To carry out the strain typing of the clinical isolates, Trichophyton rubrum using NTS as a molecular marker. Seventy T.rubrum clinical isolates obtained from April-2011-March 2013, from Sri Ramachandra Medical Centre, Chennai, Tamil Nadu, India, were identified by conventional phenotypic methods and included in this prospective study. The isolates were then subjected to Polymerase Chain Reaction (PCR) targeting two subrepeat elements (SREs), TRS-1 and TRS-2 of the NTS region. Strain-specific polymorphism was observed in both subrepeat loci. Total, nine different strains were obtained on combining both TRS-1 and TRS-2, SREs. The outcome has given a strong representation for using NTS region amplification in discriminating the T. rubrum clinical isolates. The method can be adapted as a tool for conducting epidemiology and population based study in T. rubrum infections. This will help in future exploration of the epidemiology of T. rubrum .

  2. Forty-Eight-Hour Diagnosis of Onychomycosis with Subtyping of Trichophyton rubrum Strains

    Science.gov (United States)

    Kardjeva, V.; Summerbell, R.; Kantardjiev, T.; Devliotou-Panagiotidou, D.; Sotiriou, E.; Gräser, Y.

    2006-01-01

    A novel strategy for the molecular identification of fungal agents of onychomycosis (including Trichophyton rubrum) has been designed based on the use of species-specific and universal primers in conjunction with a commercial kit that allows the extraction of DNA directly from the nail specimens. The microsatellite marker T1, which is based on a (GT)n repeat, was applied for the species-specific identification of Trichophyton rubrum. To evaluate how often Scopulariopsis spp. are detected in nail specimens, a second primer pair was designed to amplify specifically a 336-bp DNA fragment of the 28S region of the nuclear rRNA gene of S. brevicaulis and closely related species. Other fungal species were identified using amplification of the internal transcribed spacer (ITS) region of the rRNA gene, followed by restriction fragment length polymorphism analysis or sequencing. In addition, polyacrylamide gel separation of the T1-PCR product allowed subtyping of T. rubrum strains. We studied 195 nail specimens (the “nail sample”) and 66 previously collected etiologic strains (the “strain sample”) from 261 onychomycosis patients from Bulgaria and Greece. Of the etiologic agents obtained from both samples, T. rubrum was the most common organism, confirmed to be present in 76% of all cases and serving as the sole or (rarely) mixed etiologic agent in 199 of 218 cases (91%) where the identity of the causal organism(s) was confirmed. Other agents seen included molds (6% of cases with identified etiologic agents; mainly S. brevicaulis) and other dermatophyte species (4%; most frequently Trichophyton interdigitale). Simultaneous infections with two fungal species were confirmed in a small percentage of cases (below 1%). The proportion of morphologically identified cultures revealed by molecular study to have been misidentified was 6%. Subtyping revealed that all but five T. rubrum isolates were of the common type B that is prevalent in Europe. In comparison to microscopy

  3. Biological conversion of synthesis gas. Final report, August 31, 1990--September 3, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Basu, R.; Klasson, K.T.; Johnson, E.R.; Takriff, M.; Clausen, E.C.; Gaddy, J.L.

    1993-09-01

    Based upon the results of this culture screening study, Rhodospirillum rubrum is recommended for biocatalysis of the water gas shift reaction and Chlorobium thiosulfatophilum is recommended for H{sub 2}S conversion to elemental sulfur. Both bacteria require tungsten light for growth and can be co-cultured together if H{sub 2}S conversion is not complete (required concentration of at least 1 ppM), thereby presenting H{sub 2} uptake by Chlorobium thiosulfatophilum. COS degradation may be accomplished by utilizing various CO-utilizing bacteria or by indirectly converting COS to elemental sulfur after the COS first undergoes reaction to H{sub 2} in water. The second alternative is probably preferred due to the low expected concentration of COS relative to H{sub 2}S. Mass transfer and kinetic studies were carried out for the Rhodospirillum rubrum and Chlorobium thiosulfatophilum bacterial systems. Rhodospirillum rubrum is a photosynthetic anaerobic bacterium which catalyzes the biological water gas shift reaction: CO + H{sub 2}O {yields} CO{sub 2} + H{sub 2}. Chlorobium thiosulfatophilum is also a photosynthetic anaerobic bacteria, and converts H{sub 2}S and COS to elemental sulfur.

  4. Monocyte-derived dendritic cells from patients with dermatophytosis restrict the growth of Trichophyton rubrum and induce CD4-T cell activation.

    Directory of Open Access Journals (Sweden)

    Karla Santiago

    Full Text Available Dermatophytes are the most common agents of superficial mycoses that are caused by mold fungi. Trichophyton rubrum is the most common pathogen causing dermatophytosis. The immunology of dermatophytosis is currently poorly understood. Recently, our group investigated the interaction of T. rubrum conidia with peritoneal mouse macrophages. We found that macrophages phagocytose T. rubrum conidia resulted in a down-modulation of class II major histocompatibility complex (MHC antigens and in the expression of co-stimulatory molecules. Furthermore, it induced the production of IL-10, and T. rubrum conidia differentiated into hyphae that grew and killed the macrophages after 8 hrs of culture. This work demonstrated that dendritic cells (DCs and macrophages, from patients or normal individuals, avidly interact with pathogenic fungus T. rubrum. The dermatophyte has two major receptors on human monocyte-derived DC: DC-SIGN and mannose receptor. In contrast macrophage has only mannose receptor that participates in the phagocytosis or bound process. Another striking aspect of this study is that unlike macrophages that permit rapid growth of T. rubrum, human DC inhibited the growth and induces Th activation. The ability of DC from patients to interact and kill T. rubrum and to present Ags to T cells suggests that DC may play an important role in the host response to T. rubrum infection by coordinating the development of cellular immune response.

  5. Lactococcus lactis - a diploid bacterium

    DEFF Research Database (Denmark)

    Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

    the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...... milk products, is born with two complete non-replicating chromosomes. L. lactis therefore remain diploid throughout its entire life cycle....

  6. Trichophyton rubrum is inhibited by free and nanoparticle encapsulated curcumin by induction of nitrosative stress after photodynamic activation.

    Science.gov (United States)

    Baltazar, Ludmila Matos; Krausz, Aimee E; Souza, Ana Camila Oliveira; Adler, Brandon L; Landriscina, Angelo; Musaev, Tagai; Nosanchuk, Joshua D; Friedman, Adam J

    2015-01-01

    Antimicrobial photodynamic inhibition (aPI) utilizes radical stress generated from the excitation of a photosensitizer (PS) with light to destroy pathogens. Its use against Trichophyton rubrum, a dermatophytic fungus with increasing incidence and resistance, has not been well characterized. Our aim was to evaluate the mechanism of action of aPI against T. rubrum using curcumin as the PS in both free and nanoparticle (curc-np) form. Nanocarriers stabilize curcumin and allow for enhanced solubility and PS delivery. Curcumin aPI, at optimal conditions of 10 μg/mL of PS with 10 J/cm² of blue light (417 ± 5 nm), completely inhibited fungal growth (paPI efficacy, suggesting that curcumin acts potently via a nitrosative pathway. The curc-np induced greater NO˙ expression and enhanced apoptosis of fungal cells, highlighting curc-np aPI as a potential treatment for T. rubrum skin infections.

  7. Evaluation of semisolid agar method for antifungal susceptibility test of T. rubrum

    Directory of Open Access Journals (Sweden)

    Sultana Razia

    2016-08-01

    Full Text Available Background: With increasing fungal disease many newer antifungal drugs are available with different spectrum of activ­ity. Antifungal susceptibility test will help clinicians for selection of effective drug and thereby treatment of patient. Objective: The study was undertaken to perform a simple screening drug susceptibility test of T. rnbrum by Semi Solid Agar Antifungal Susceptibility (SAAS Method: Perfonnance of susceptibility method was assessed by comparing the MICs of three commonly prescribed antifungal agents namely- tluconazole (FCZ, itraconazole (ITZ and terbinafine (TER to the CLSI (Clinical and Laboratory Standard Institute recommended M-38, a broth microdilution method. Results: In SAAS method, among twenty nine T. rubrum, twenty five (86.2% were susceptible (MIC range 0.5-64 µg/ml to Fluconazole (FCZ and four (13.7% were resistant (MIC value >64 µg/ml. In broth microdilution method, among twenty nine T. rubrum, twenty six (89.6% were susceptible (MIC range 0.3-64 µg/ml to FCZ and three (10.3% were resistant (MIC value >64 µg/ml. In case of both ITZ and TER, all were susceptible (MIC range 0.3-64 µg/ml to both methods. The SAAS method demonstrated the susceptibility pattern of T. rubrum against FCZ, ITZ and TER usually within 72 to 96 hours after organism isolation and results were concordance with the results of CLSI broth microdilution method. Conclusion: Though it is a newer method with proper standardization of the test method, SAAS method is simple and easily applicable screening method for susceptibility testing of antifungal agents against dermatophytes in any microbiology laboratories.

  8. Carum copticum and Thymus vulgaris oils inhibit virulence in Trichophyton rubrum and Aspergillus spp.

    Science.gov (United States)

    Khan, Mohd Sajjad Ahmad; Ahmad, Iqbal; Cameotra, Swaranjit Singh

    2014-01-01

    Emergence of drug-resistant strains has demanded for alternative means of combating fungal infections. Oils of Carum copticum and Thymus vulgaris have long been used in ethnomedicine for ailments of various fungal infections. Since their activity has not been reported in particular against drug-resistant fungi, this study was aimed to evaluate the effects of oils of C. copticum and T. vulgaris on the growth and virulence of drug-resistant strains of Aspergillus spp. and Trichophyton rubrum. The gas chromatography-mass spectrometry analysis revealed thymol constituting 44.71% and 22.82% of T. vulgaris and C. copticum, respectively. Inhibition of mycelial growth by essential oils was recorded in the order of thymol > T. vulgaris > C. copticum against the tested strains. RBC lysis assay showed no tested oils to be toxic even up to concentration two folds higher than their respective MFCs. Thymol exhibited highest synergy in combination with fluconazole against Aspergillus fumigatus MTCC2550 (FICI value 0.187) and T. rubrum IOA9 (0.156) as determined by checkerboard method. Thymol and T. vulgaris essential oil were equally effective against both the macro and arthroconidia growth (MIC 72 μg/mL). A > 80% reduction in elastase activity was recorded for A. fumigatus MTCC2550 by C. copticum, T. vulgaris oils and thymol. The effectiveness of these oils against arthroconidia and synergistic interaction of thymol and T. vulgaris with fluconazole can be exploited to potentiate the antifungal effects of fluconazole against drug-resistant strains of T. rubrum and Aspergillus spp.

  9. Investigation of the antifungal potential of linalool against clinical isolates of fluconazole resistant Trichophyton rubrum.

    Science.gov (United States)

    de Oliveira Lima, M I; Araújo de Medeiros, A C; Souza Silva, K V; Cardoso, G N; de Oliveira Lima, E; de Oliveira Pereira, F

    2017-06-01

    The aim of this study was to investigate the activity of the monoterpene linalool against clinical isolates of Trichophyton rubrum. Initially, a sensitivity assay for commercial antifungals with solid disks in diffusion medium was performed. Minimum inhibitory concentration (MIC) of linalool and ketoconazole (positive control) were determined by microdilution in RPMI 1640 medium (CLSI M38-A2). We then evaluated the action of linalool and ketoconazole at different concentrations (1/2MIC, MIC and 2×MIC) on mycelial growth (radial mycelial growth), conidia production and conidia germination using a hemacytometer. The effects on cell membrane (release of intracellular material) were also investigated. Finally, changes in fungal morphology as induced by the test drugs were analyzed. Based on the sensitivity tests, the fungal strains showed resistance to 5-fluorocytosine and fluconazole. The linalool MIC values ranged from 256μg/mL to 512μg/mL, whereas ketoconazole showed values of 4μg/mL to 8μg/mL. For the LM 305 strain, the test drugs showed the following MIC values: linalool 256μg/mL and ketoconazole 8μg/mL. The mycelial growth of T. rubrum LM 305 was inhibited by linalool (2×MIC) and ketoconazole (1/2MIC, MIC, 2×MIC), in 7 days of treatment (PLinalool also caused leakage of intracellular material (Plinalool and ketoconazole to induce micro-morphological changes, forming abnormal, wide, short and crooked hyphae. Based on these results, we conclude that linalool presents as an antifungal agent with anti-Trichophyton rubrum potential, an important dermatophytosis agent. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  10. Efek Antijamur Minyak Atsiri Jahe Merah (Zingiber officinale Var. Rubrum terhadap Candida albicans

    Directory of Open Access Journals (Sweden)

    Hermina Karuna Atmaja

    2015-10-01

    Full Text Available The prevalence of Candida albicans infections is increasing in the society. Therefore, an effective and affordable antifungal drug with minimal side effect is needed. Ginger (Zingiber officinale is a traditional herb which has an antifungal effect in its volatile oil. Objective: To investigate antifungal effect of volatile oil from Zingiber officinale var rubrum against C. albicans in vitro, to determine the optimum concentration, and finally to determine the correlation between the various concentrations of the oil and the inhibition zone. Material and method: Strain C. albicans tested was obtained from the Department of Parasitology, Medical Faculty, University of Indonesia. Volatile oil of Zingiber officinale var. rubrum was produced from water and steam distillation of fresh ginger in BALLITRO, Bogor. Concentrations of the volatile oil used were 100%, 50%, 25%, 12,5% 6.25%, 3.125%, 1.56% and 0.78%. Methods used were colony counting and disk diffusion method (by using 6 mm blank disk. The specimens were divided into two groups, treatment group (C. albicans with application of volatile oil and control group (C. albicans without application of volatile oil. Result: There was a significant decrease in the amount of C. albicans colonies from 3.125% to 6.25% of concentration. The amount of C. albicans colonies at concentration 6.25% was also significantly lower than in the control group. Moreover, there was strong and positive correlation between the concentration of the volatile oil and the inhibition zone. Conclusion: Volatile oil from Zingiber officinale var. rubrum has an antifungal effect against C. albicans in vitro with optimum concentration at 6.25%. Increasing concentrations of the oil correlates with increasing inhibition zome.

  11. In vitro drug sensitivity of trichophyton rubrum against griseofulvin, ketoconazole and fluconazole

    Directory of Open Access Journals (Sweden)

    Tandon S

    1996-01-01

    Full Text Available The invitro activity of griseofulvin, ketoconazole and fiuconazole was investigated against 50 isolates of Trichophyton rubrum. Ketoconazole was more active, inhibiting all the 50 isolates at a concentration of 5 μgm/ml (MIC range 0.5-5 μgm/ml. Griseofulvin (MIC range 2.5-20 μgm/ml required 20 μgm/ml of the drug for inhibition of all the isolates. Fluconazole was least active as it inhibited only 2 isolates at a concentration of 20 μgm/ml, which was the upper limit of the test system.

  12. Dermatofitose por Tricophyton rubrum como infecção oportunista em pacientes com doença de Cushing Dermatophytosis caused by Tricophyton rubrum as an opportunistic infection in patients with Cushing disease

    Directory of Open Access Journals (Sweden)

    Isy Peixoto

    2010-12-01

    Full Text Available O dermatófito Trichophyton rubrum é um agente comum nas micoses superficiais, podendo apresentar lesões extensas pauci-inflamatórias de evolução crônica, especialmente em imunocomprometidos. O hipercortisolismo, na síndrome de Cushing, aumenta o risco de infecções, resultado do efeito imunossupressor dos glicocorticóides. Os casos relatados apresentam duas formas distintas de dermatofitose, em pacientes com doença de Cushing, causadas por Tricophyton rubrum e posterior remissão após normalização da cortisolemia.Trichophyton rubrum is a common agent found in superficial mycoses, which present ample nonin?ammatory lesions, with chronic evolution, especially in immunocompromised patients. The hypercortisolism in Cushing's syndrome increases the risk of infections as a result of the immunosuppressive effect of glucocorticoids. The reported cases here refer to two different types of dermatophytosis caused by Trichophyton rubrum in patients with Cushing's disease, resistant to antifungal treatment. The disease remitted after the levels of cortisol went back to normal.

  13. Phenotypic plasticity of leaf shape along a temperature gradient in Acer rubrum.

    Directory of Open Access Journals (Sweden)

    Dana L Royer

    2009-10-01

    Full Text Available Both phenotypic plasticity and genetic determination can be important for understanding how plants respond to environmental change. However, little is known about the plastic response of leaf teeth and leaf dissection to temperature. This gap is critical because these leaf traits are commonly used to reconstruct paleoclimate from fossils, and such studies tacitly assume that traits measured from fossils reflect the environment at the time of their deposition, even during periods of rapid climate change. We measured leaf size and shape in Acer rubrum derived from four seed sources with a broad temperature range and grown for two years in two gardens with contrasting climates (Rhode Island and Florida. Leaves in the Rhode Island garden have more teeth and are more highly dissected than leaves in Florida from the same seed source. Plasticity in these variables accounts for at least 6-19% of the total variance, while genetic differences among ecotypes probably account for at most 69-87%. This study highlights the role of phenotypic plasticity in leaf-climate relationships. We suggest that variables related to tooth count and leaf dissection in A. rubrum can respond quickly to climate change, which increases confidence in paleoclimate methods that use these variables.

  14. Trichophyton rubrum osteomyelitis after calcaneus external fixation pin stabilization of a pilon fracture.

    Science.gov (United States)

    Waryasz, Gregory R; Bariteau, Jason T

    2014-01-01

    Fungal organisms are an uncommon cause of osteomyelitis, and no dermatophyte osteomyelitis infections have been reported in published studies. We present the case of Trichophyton rubrum osteomyelitis of the calcaneus. Our patient initially presented with a pilon fracture requiring temporary external fixation while awaiting definitive fixation. From our review of the published data, the present case is the first of this type of fungal osteomyelitis to be reported. The patient was evaluated for a left neck mass during his hospitalization that was later found to be consistent with salivary duct carcinoma of the tail of the parotid gland. A left neck dissection and superficial excision of the parotid gland was performed after fixation of his pilon fracture. Subsequently, he developed an increasing lucency in the calcaneus and symptoms of pain and erythema months after the calcaneus pin had been removed. The osteomyelitis was treated with surgical debridement and 3 months of itraconazole once cultures had definitively grown T. rubrum. Copyright © 2014 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  15. Overexpression, purification, crystallization and preliminary diffraction studies of the Protaminobacter rubrum sucrose isomerase SmuA

    International Nuclear Information System (INIS)

    Ravaud, Stéphanie; Watzlawick, Hildegard; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2005-01-01

    The P. rubrum sucrose isomerase SmuA, a key enzyme in the industrial production of isomaltulose, was crystallized and diffraction data were collected to 1.95 Å resolution. Palatinose (isomaltulose, α-d-glucosylpyranosyl-1,6-d-fructofuranose), a nutritional and acariogenic reducing sugar, is industrially obtained from sucrose by using immobilized cells of Protaminobacter rubrum that produce the sucrose isomerase SmuA. The isomerization of sucrose catalyzed by this enzyme also results in the formation of trehalulose (α-d-glucosylpyranosyl-1,1-d-fructofuranose) in smaller amounts and glucose, fructose and eventually isomaltose as by-products, which lower the yield of the reaction and complicate the recovery of palatinose. The determination of the three-dimensional structure of SmuA will provide a basis for rational protein-engineering studies in order to optimize the industrial production of palatinose. A recombinant form of the 67.3 kDa SmuA enzyme has been crystallized in the native state by the vapour-diffusion method. Crystals belong to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 61.6, b = 81.4, c = 135.6 Å, and diffract to 1.95 Å resolution on a synchrotron-radiation source

  16. Red Maple (Acer rubrum L.) Growth and Foliar Nutrient Responses to Soil Fertility Level and Water Regime

    Science.gov (United States)

    C. H. Pham; Howard G. Halverson; Gordon M. Heisler

    1978-01-01

    Red maple (Acer rubrum L.) seedlings were grown in a greenhouse using three treatments: two soil horizons, two soil moisture regimes, and three nutrient levels. Fertilization increased growth under moist conditions on the more fertile topsoil. Under dry conditions, fertilization had no effect on growth in subsoil, and slightly increased growth in...

  17. Effect of planting procedures in initial growth of Acer rubrum L. and Fraxinus pennsylvanicum L. in a parking lot

    Science.gov (United States)

    Gordon M. Heisler; Robert E. Schutzki; Robert P. Zisa; Howard G. Halverson; Bruce A. Hamilton

    1982-01-01

    Five-year old red maples, Acer rubrum L. 'October Glory', and green ash, Fraxinus pennsylvanicum L. 'Marshall Seedless', were planted in 8 ft x 8 ft openings in an asphalt parking lot with two planting stocks (bare-root, BR, and balled and burlapped, B&B) and two fertilizer levels (a control and 1.36 kg of...

  18. A new biosorbent for the removal of Cu(II from aqueous solution; red marine alga, Ceramium rubrum

    Directory of Open Access Journals (Sweden)

    Ege A.

    2013-04-01

    Full Text Available Biosorption is an effective technique for the removal of heavy metals from wastewater. In this study, dried, sodium hydroxide and formaldehyde modified red alga, Ceramium rubrum were used for the biosorption of copper from aqueous solution. The biosorption characteristics such as pH, biomass dosage, temperature and contact time were investigated. Also, Fourier Transform Infrared Spectrophotemetric analysis of C.rubrum was performed to identify its structure. Langmuir and Freundlich isotherm models were applied to describe the biosorption of Cu2+ onto C.rubrum biomass at the equilibrium. Langmuir model fitted well the equilibrium data for all biosorbents. Maximum biosorption capacity of dried biomass was calculated 25.51 mg/g, while it was calculated 42.92 mg/g and 30.03 mg/g for sodium hydroxide modified and formaldehyde modified biomass, respectively. Modified biomasses have higher maximum biosorption capacities indicating that modification of biomass with NaOH and HCHOH may increase responsible active sites for biosorption on the C.rubrum.

  19. Analysis of stand basal area development of thinned and unthinned Acer rubrum forests in the upper Great Lakes region, USA

    Science.gov (United States)

    Justin L. Pszwaro; Anthony W. D' Amato; Thomas E. Burk; Matthew B. Russell; Brian J. Palik; Terry F. Strong

    2016-01-01

    Red maple (Acer rubrum L.), historically a common but not abundant tree species in North America, has increased in abundance throughout its range over the last several decades; however, it has received little attention in growth and yield studies. The objectives of this study were to (i) evaluate the effects of stocking level and stand density on...

  20. Molecular identification of phosphate solubilizing bacterium ...

    African Journals Online (AJOL)

    A phosphate solubilizing bacterium was isolated from the rhizosphere soil of upland rice and identified by 16S rRNA gene sequencing. The gene sequence showed 99% homology with Alcaligenes faecalis. Based on the gene sequence homology, it was identified as A. faecalis. Interaction effect of this bacterium on growth ...

  1. Novel antimicrobial activity of a dichloromethane extract obtained from red seaweed Ceramium rubrum (Hudson (Rhodophyta: Florideophyceae against Yersinia ruckeri and Saprolegnia parasitica, agents that cause diseases in salmonids

    Directory of Open Access Journals (Sweden)

    Yurima Cortés

    2014-05-01

    Conclusions: These results may constitute a basis for promising future applied research that could investigate the use of C. rubrum seaweed as a source of antimicrobial compounds against fish pathogens.

  2. Characterization of Rubisco activase from thermally contrasting genotypes of Acer rubrum (Aceraceae).

    Science.gov (United States)

    Weston, David J; Bauerle, William L; Swire-Clark, Ginger A; Moore, Brandon D; Baird, Wm Vance

    2007-06-01

    The lability of Rubisco activase function is thought to have a major role in the decline of leaf photosynthesis under moderate heat (RCA1 and RCA2 proteins increased modestly in FL plants under warmer temperature, while only RCA2 protein increased in MN plants. Rubisco large subunit (RbsL) protein abundance was relatively unaffected in either genotype by temperature. These results support the idea that Rubisco activase, particularly the ratio of Rubisco activase to Rubisco, may play a role in the photosynthetic heat acclimation in A. rubrum and may have adaptive significance. This mechanism alone is not likely to entirely explain the thermotolerance in the FL genotype, and future research on adaptive mechanisms to high temperatures should consider activase function in a multipathway framework.

  3. The effect of ionizing radiation on the structural and ultrastructural organization of Mycobacterium rubrum

    International Nuclear Information System (INIS)

    Poglazova, M.N.; Biryuzova, V.I.; Gromova, L.A.

    1979-01-01

    A description of a structural and ultrastructural organization of a normally developing and irradiated cell of Mycobacterium rubrum is given. The cytomorphological differentiation of membrane bacterial structures and radiation their functional role are shown. When ionizing role of membrane is used as a tool for decoding the structures their relationship with a certain cell function is confirmed. A description of damages of different individually functioning membrane systems under cell irradiation is given. It is shown that at suppression of peptidoglycane synthesis the mesosomes are absent in the cells, at their hypertrophy the hypersynthesis of cell wall material is observed. An increase in the level of cell metabolic processes results in an increase of the number of mitochondrial analogs. It is shown that the disturbance of the cell division function is caused by the damage of nucleoid DNA structure and degradation of nucleidosomes. Changes in carbohydrate and lipide metabolisms are observed

  4. Growth inhibition and morphological alterations of Trichophyton rubrum induced by essential oil from Cymbopogon winterianus Jowitt ex Bor

    Directory of Open Access Journals (Sweden)

    Fillipe de Oliveira Pereira

    2011-03-01

    Full Text Available Trichophyton rubrum is one of the most common fungi causer of dermatophytosis, mycosis that affect humans and animals around the world. Researches aiming new products with antifungal activity become necessary to overcome difficulties on treatment of these infections. Accordingly, this study aimed to investigate the antifungal activity of essential oil from Cymbopogon winterianus against the dermatophyte T. rubrum. The antifungal screening was performed by solid medium diffusion method with 16 T. rubrum strains, minimum inhibitory concentration (MIC and minimum fungicide concentration (MFC were determined using the microdilution method. The effects on mycelial dry weight and morphology were also observed. Screening showed essential oil in natura inhibited all the tested strains, with inhibition zones between 24-28 mm diameter. MIC50 and MIC90 values of the essential oil were 312 µg/mL for nearly all the essayed strains (93.75 % while the MFC50 and MFC90 values were about eight times higher than MIC for all tested strains. All tested essential oil concentrations managed to inhibit strongly the mycelium development. Main morphological changes on the fungal strains observed under light microscopy, which were provided by the essential oil include loss of conidiation, alterations concerning form and pigmentation of hyphae. In the oil presence, colonies showed folds, cream color and slightly darker than the control, pigment production was absent on the reverse and with evident folds. It is concluded that C. winterianus essential oil showed activity against T. rubrum. Therefore, it could be known as potential antifungal compound especially for protection against dermatophytosis.

  5. Growth Inhibition and Morphological Alterations of Trichophyton Rubrum Induced by Essential oil from Cymbopogon Winterianus Jowitt Ex Bor.

    Science.gov (United States)

    de Oliveira Pereira, Fillipe; Alves Wanderley, Paulo; Cavalcanti Viana, Fernando Antônio; Baltazar de Lima, Rita; Barbosa de Sousa, Frederico; de Oliveira Lima, Edeltrudes

    2011-01-01

    Trichophyton rubrum is one of the most common fungi causer of dermatophytosis, mycosis that affect humans and animals around the world. Researches aiming new products with antifungal activity become necessary to overcome difficulties on treatment of these infections. Accordingly, this study aimed to investigate the antifungal activity of essential oil from Cymbopogon winterianus against the dermatophyte T. rubrum. The antifungal screening was performed by solid medium diffusion method with 16 T. rubrum strains, minimum inhibitory concentration (MIC) and minimum fungicide concentration (MFC) were determined using the microdilution method. The effects on mycelial dry weight and morphology were also observed. Screening showed essential oil in natura inhibited all the tested strains, with inhibition zones between 24-28 mm diameter. MIC50 and MIC90 values of the essential oil were 312 μg/mL for nearly all the essayed strains (93.75 %) while the MFC50 and MFC90 values were about eight times higher than MIC for all tested strains. All tested essential oil concentrations managed to inhibit strongly the mycelium development. Main morphological changes on the fungal strains observed under light microscopy, which were provided by the essential oil include loss of conidiation, alterations concerning form and pigmentation of hyphae. In the oil presence, colonies showed folds, cream color and slightly darker than the control, pigment production was absent on the reverse and with evident folds. It is concluded that C. winterianus essential oil showed activity against T. rubrum. Therefore, it could be known as potential antifungal compound especially for protection against dermatophytosis.

  6. Growth Inhibition and Morphological Alterations of Trichophyton Rubrum Induced by Essential oil from Cymbopogon Winterianus Jowitt Ex Bor

    Science.gov (United States)

    de Oliveira Pereira, Fillipe; Alves Wanderley, Paulo; Cavalcanti Viana, Fernando Antônio; Baltazar de Lima, Rita; Barbosa de Sousa, Frederico; de Oliveira Lima, Edeltrudes

    2011-01-01

    Trichophyton rubrum is one of the most common fungi causer of dermatophytosis, mycosis that affect humans and animals around the world. Researches aiming new products with antifungal activity become necessary to overcome difficulties on treatment of these infections. Accordingly, this study aimed to investigate the antifungal activity of essential oil from Cymbopogon winterianus against the dermatophyte T. rubrum. The antifungal screening was performed by solid medium diffusion method with 16 T. rubrum strains, minimum inhibitory concentration (MIC) and minimum fungicide concentration (MFC) were determined using the microdilution method. The effects on mycelial dry weight and morphology were also observed. Screening showed essential oil in natura inhibited all the tested strains, with inhibition zones between 24-28 mm diameter. MIC50 and MIC90 values of the essential oil were 312 μg/mL for nearly all the essayed strains (93.75 %) while the MFC50 and MFC90 values were about eight times higher than MIC for all tested strains. All tested essential oil concentrations managed to inhibit strongly the mycelium development. Main morphological changes on the fungal strains observed under light microscopy, which were provided by the essential oil include loss of conidiation, alterations concerning form and pigmentation of hyphae. In the oil presence, colonies showed folds, cream color and slightly darker than the control, pigment production was absent on the reverse and with evident folds. It is concluded that C. winterianus essential oil showed activity against T. rubrum. Therefore, it could be known as potential antifungal compound especially for protection against dermatophytosis. PMID:24031626

  7. Trichophyton rubrum is inhibited by free and nanoparticle encapsulated curcumin by induction of nitrosative stress after photodynamic activation.

    Directory of Open Access Journals (Sweden)

    Ludmila Matos Baltazar

    Full Text Available Antimicrobial photodynamic inhibition (aPI utilizes radical stress generated from the excitation of a photosensitizer (PS with light to destroy pathogens. Its use against Trichophyton rubrum, a dermatophytic fungus with increasing incidence and resistance, has not been well characterized. Our aim was to evaluate the mechanism of action of aPI against T. rubrum using curcumin as the PS in both free and nanoparticle (curc-np form. Nanocarriers stabilize curcumin and allow for enhanced solubility and PS delivery. Curcumin aPI, at optimal conditions of 10 μg/mL of PS with 10 J/cm² of blue light (417 ± 5 nm, completely inhibited fungal growth (p<0.0001 via induction of reactive oxygen (ROS and nitrogen species (RNS, which was associated with fungal death by apoptosis. Interestingly, only scavengers of RNS impeded aPI efficacy, suggesting that curcumin acts potently via a nitrosative pathway. The curc-np induced greater NO˙ expression and enhanced apoptosis of fungal cells, highlighting curc-np aPI as a potential treatment for T. rubrum skin infections.

  8. The Role of NADPH Oxidase in the Inhibition of Trichophyton rubrum by 420-nm Intense Pulsed Light

    Directory of Open Access Journals (Sweden)

    Hao Huang

    2018-01-01

    Full Text Available Objectives: To evaluate the effect of intense pulsed light (IPL on Trichophyton rubrum and investigate its mechanism of action.Methods: The viability of fungi treated with IPL alone and with IPL combined with an NADPH oxidase inhibitor (DPI pretreatment was determined by MTT assays. The reactive oxygen species (ROS were quantified with a DCFH-DA fluorescent probe. Malondialdehyde (MDA content and superoxide dismutase (SOD and glutathione peroxidase (GSH-Px activities were determined by commercial kits. The transcription of the Nox gene was quantified using quantitative real-time PCR (qRT-PCR analysis, and micromorphology was observed using scanning electron microscopy (SEM. In addition, fungal keratinase activity was detected by measuring dye release from keratin azure.Results: The growth declined with statistical significance after 6 h of treatment (P < 0.001. The ROS and MDA content increased after IPL treatment, whereas the SOD and GSH-Px activity decreased. Nox gene expression was upregulated, and the micromorphology was damaged. Keratinase activity decreased. Fungi that received DPI pretreatment exhibited contrasting outcomes.Conclusion: We found that 420-nm IPL significantly inhibited the growth and pathogenicity of T. rubrum in vitro. A suggested mechanism involves Nox as a factor that mediates 420-nm IPL-induced oxidative damage of T. rubrum.

  9. Root - shoot - signaling in Chenopodium rubrum L. as studied by 15O labeled water uptake

    International Nuclear Information System (INIS)

    Ohya, T.; Hayashi, Y.; Tanoi, K.; Rai, H.; Nakanishi, T.M.; Suzuki, K.; Albrechtova, J.T.P.; Wagner, E.

    2005-01-01

    Full text: It has been demonstrated with C. rubrum that the different organ systems are transmitting surface action potentials which might be the basis for systemic signal transduction. Shoot tip respectively root generated action potentials travel along the stem axis. Shoot tip generated action potentials arriving at the basis can be reflected and travel upwards. The radioactive labeling technique was established at the NIRS in Inage, Japan. About 2 GBq of 15 O labeled Hoagland's solution was supplied to the plant root or cut stem in a phytotron at 25 o C with 45 % of relative humidity and continuous light. By cutting the shoot apical bud and the apices of main side branches the uptake of 15 O labeled water was inhibited in plants with intact roots but not in plants with roots cut. Because of the short half-life of 15 O (2 min), experiments could be repeated in hourly intervals. Cutting the apex probably limits root water uptake via a hydraulic-electrochemical signal. The results are discussed with respect to the significance of a continuous communication between the root system and the shoot apical meristem(s) in the adaptation of plants to their environment. (author)

  10. Susceptibility of Trichophyton quinckeanum and Trichophyton rubrum to products of oxidative metabolism.

    Science.gov (United States)

    Calderon, R A; Shennan, G I

    1987-01-01

    Two dermatophyte strains, Trichophyton quinckeanum and Trichophyton rubrum, were highly susceptible to in vitro killing by components of the H2O2-peroxidase-halide system. Both strains were, however, resistant to relatively high concentrations of reagent H2O2 or H2O2 enzymatically generated by glucose and glucose oxidase, KI, or lactoperoxidase (LPO) alone. Resistance to hydrogen peroxidase killing was found to be in part due to the presence of endogenous catalase in the fungi; susceptibility was increased by pretreatment of the fungi with a catalase inhibitor. Kinetic studies using small quantities of reagent or enzymatically generated H2O2 and LPO-KI showed that the system was lethal for both fungal strains within 1 min. Furthermore, using the glucose-glucose oxidase-LPO-KI system, it was shown that catalase, superoxide dismutase and histidine scavengers of H2O2, superoxide anion and singlet oxygen, respectively, prevented the killing of fungus, whereas scavengers of hydroxyl radicals such as benzoate and mannitol had no effect. T. quinckeanum was found to contain large quantities of superoxide anion, as judged by the nitroblue-tetrazolium test. Consequently, the xanthine (or hypoxanthine) and xanthine oxidase system in which the main product is superoxide anion had no toxic effect on the fungus. The high sensitivity of dermatophytes to killing by the H2O2-peroxidase-halide system active in polymorphonuclear neutrophils and macrophages may account in part for fungal toxicity in vivo. PMID:3610210

  11. Producing armyworm (spodoptera sp.) Bioinsecticide based on cysteine protease of red ginger (zingiber officinale var. Rubrum)

    Science.gov (United States)

    Afnan, N. T.; Nur, D. F.; Utami, T. S.; Sahlan, M.; Wijanarko, A.; Hermansyah, H.

    2018-03-01

    Armyworm (Spodoptera sp.) is highly polyphagous defoliator on various horticulture and grain plants. Various chemical insecticides have been created to control it. There is a need to create an eco-friendly and specific insecticide which only affect armyworm’s nervous system. This research investigates cysteine-protease’s enzyme activity of red ginger (Zingiber officinale var. Rubrum) which is called zingibain. Its catalytic site matches with residue site in armyworm’s body so it can be used as bioinsecticide raw material which meets the criterias above. Fresh red ginger rhizomes were washed and extracted. The juice was then deposited in low temperature and centrifuged to get rid of its starch content. It was filtrated to remove large contaminants and poured into Potassium Phospate buffer. The liquid was then centrifuged again for 30 minutes before collecting the supernatant. Fresh leaves were then dipped into crude ginger protease extract and fed to fourth instar-armyworms. Leaves dipped into non-diluted extract were barely eaten by armyworm while the 50% and 25% dilution was half eaten and most eaten. The crude red ginger extract was not strong enough to kill them although the research showed its enzymatic activity reaches up to 169 PU. It still needs improvement to be produced as commercial bioinsecticide.

  12. Biodegradation of endosulfan by a soil bacterium.

    Science.gov (United States)

    Shivaramaiah, H M; Kennedy, I R

    2006-01-01

    A bacterium capable of metabolizing endosulfan (6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepine3-oxide) was isolated from cotton-growing soil and effectively shown to degrade endosulfan into endosulfan sulfate. The bacterium degraded 50% of the compound within 3 days of incubation. Endosulfan sulfate was the only terminal product and no other metabolites were formed during the incubation. Endosulfan and its metabolites were analyzed by gas chromatography. The metabolites formed indicated that the organism follows an oxidative pathway for metabolism of this pesticide. Therefore, the present study, microbial degradation of endosulfan by a soil bacterium, may provide a basis for the development of bioremediation strategies to remediate the pollutants in the environment.

  13. Microbial treatment of aqueous wastes

    International Nuclear Information System (INIS)

    Lee, Kang Suk; Chun, Ki Jung; Kim, Kug Chan; Choi, Yong Ho; Kim, Jin Kyu; Kim, In Gyu; Park, Hyo Koo; Lee, Keun Bae

    1992-01-01

    Uranium accumulated extracellularly on the surface of Rhodobacter capsulata and Rhodospirillum rubrum cells. The rate and extent accumulation were subject to environmental parameter such as pH, temperature, carbon source, trace element and interference by certain cations. Uranium accumulation by the cells was rapid and metabolism was not required for uranium uptake by both organism. Cell-bound uranium reached concentration of 22% (Rhodospirillum rubrum) and 24% (Rhdobacter capsulata)of the dry cell weight, but in the cells grown in the presence of inhibitory concentration of CoCl 2 , cell-bound uranium reached concentration of 27% (Rhodospirillum rubrum) and 29% (Rhodobacter capsulata) of dry cell weight. (Author)

  14. Zymomonas mobilis: a bacterium for ethanol production

    Energy Technology Data Exchange (ETDEWEB)

    Baratti, J.C.; Bu' Lock, J.D.

    1986-01-01

    Zymomonas mobilis is a facultative anaerobic gram negative bacterium first isolated in tropical countries from alcoholic beverages like the African palm wine, the Mexican pulque and also as a contaminant of cider (cider sickness) or beer in the European countries. It is one of the few facultative anaerobic bacteria degrading glucose by the Entner-Doudoroff pathway usually found in strictly aerobic microorganisms. Some work was devoted to this bacterium in the 50s and 60s and was reviewed by Swings and De Ley in their classical paper published in 1977. During the 70s there was very little work on the bacterium until 1979 and the first report by the Australian group of P.L. Rogers on the great potentialities of Z. mobilis for ethanol production. At that time the petroleum crisis had led the developed countries to search for alternative fuel from renewable resources. The Australian group clearly demonstrated the advantages of the bacterium compared to the yeasts traditionally used for the alcoholic fermentation. As a result, there was a considerable burst in the Zymomonas literature which started from nearly zero in the late 70s to attain 70 papers published in the field in 1984. In this article, papers published from 1982 to 1986 are reviewed.

  15. Gender-related traits in the dioecious shrub Empetrum rubrum in two plant communities in the Magellanic steppe

    Science.gov (United States)

    Díaz-Barradas, Mari Cruz; Zunzunegui, María; Collantes, Marta; Álvarez-Cansino, Leonor; García Novo, Francisco

    2014-10-01

    Following the theory on costs of reproduction, sexually dimorphic plants may exhibit several trade-offs in energy and resources that can determine gender dimorphism in morphological or physiological traits, especially during the reproductive period. In this study we assess whether the sexes of the dioecious species Empetrum rubrum differ in morphological and ecophysiological traits related to water economy and photochemical efficiency and whether these differences change in nearby populations with contrasting plant communities. We conducted physiological, morphological, sex ratio, and cover measurements in E. rubrum plants in the Magellanic steppe, North-Eastern part of Tierra del Fuego (Argentina), from two types of heathlands with differing community composition. We found differences between sites in soil pH and wind speed at the canopy level. E. rubrum plants exhibited lower photosynthetic height and higher LAI (leaf area index), lower RWC (relative water content) and higher water-use efficiency (lower Δ13C) in the heathland with harsher environmental conditions. Gender dimorphism in the physiological response was patent for photochemical efficiency and water use (RWC and Δ13C discrimination), with males showing a more conservative strategy in relation to females. Accordingly, male-biased sex ratio in the stress-prone community suggested a better performance of male plants under stressful environmental conditions. The integrated analysis of all variables (photochemical efficiency, RWC, leaf dry matter content (LDMC), pigments, and Δ13C) indicated an interaction between gender and heathland community effects in the physiological response. We suggest that female plants may exhibit compensatory mechanisms to face their higher reproductive costs.

  16. Photodynamic inhibition of Trichophyton rubrum: in vitro activity and the role of oxidative and nitrosative bursts in fungal death.

    Science.gov (United States)

    Baltazar, Ludmila de Matos; Soares, Betânia Maria; Carneiro, Hellem Cristina Silva; Avila, Thiago Vinícius; Gouveia, Ludmila Ferreira; Souza, Danielle G; Ferreira, Marcus Vinícius Lucas; Pinotti, Marcos; Santos, Daniel de Assis; Cisalpino, Patrícia Silva

    2013-02-01

    Antimicrobial photodynamic inhibition (aPI) is based on the use of a light source and a photosensitizer to kill pathogens. Little is known about aPI of dermatophytic fungi and its mechanism of action. We aimed to evaluate aPI of Trichophyton rubrum. We performed tests using toluidine blue (TBO) as a photosensitizer and a 630 nm light-emitting diode (LED) as a source of light to target 12 T. rubrum isolates. Susceptibility testing with cyclopiroxolamine, time-kill curves and quantification of reactive oxygen species (ROS), peroxynitrite (ONOO·) and nitric oxide (NO·) were performed. The optimal conditions for in vitro aPI were 10 mg/L for TBO and 48 J/cm(2) for LED; these conditions were fungicidal or inhibited >98% of fungal growth depending on the strain tested. LED or TBO treatment alone did not inhibit growth. The MICs of cyclopiroxolamine were 2.0 mg/L for 90% of the strains. Analysis of time-kill curves revealed that pathogen death occurred 24 h post-treatment. Quantification of ROS, ONOO· and NO· revealed improvement after aPI. Photodynamic inhibition was more efficient in promoting cell death than the antifungal cyclopiroxolamine against T. rubrum. ROS, ONOO· and NO· were important in the fungicidal activity of aPI. A suggested mechanism for this activity is that TBO is excited by LED light (630 nm), reacts with biomolecules and increases the availability of transition electrons and substrates for nitric oxide synthase, thereby increasing the oxidative and nitrosative bursts in the fungal cell.

  17. Phototoxic action of light emitting diode in the in vitro viability of Trichophyton rubrum Ação fototóxica do diodo emissor de luz na viabilidade de Trichophyton rubrum in vitro

    Directory of Open Access Journals (Sweden)

    José Cláudio Faria Amorim

    2012-04-01

    Full Text Available BACKGROUND: Trichophyton rubrum is the most common agent of superficial mycosis of the skin and nails causing long lasting infections and high recurrence rates. Current treatment drawbacks involve topical medications not being able to reach the nail bed at therapeutic concentrations, systemic antifungal drugs failing to eradicate the fungus before the nails are renewed, severe side effects and selection of resistant fungal isolates. Photodynamic therapy (PDT has been a promising alternative to conventional treatments. OBJECTIVES: This study evaluated the in vitro effectiveness of toluidine blue O (TBO irradiated by Light emitting diode (LED in the reduction of T. rubrum viability. METHODS: The fungal inoculums' was prepared and exposed to different TBO concentrations and energy densities of Light emitting diode for evaluate the T. rubrum sensibility to PDT and production effect fungicidal after photodynamic treatment. In addition, the profiles of the area and volume of the irradiated fungal suspensions were also investigated. RESULTS: A small reduction, in vitro, of fungal cells was observed after exposition to 100 µM toluidine blue O irradiated by 18 J/cm² Light emitting diode. Fungicidal effect occurred after 25 µM toluidine blue O irradiation by Light emitting diode with energy density of 72 J/cm². The analysis showed that the area and volume irradiated by the Light emitting diode were 52.2 mm² and 413.70 mm³, respectively. CONCLUSION: The results allowed to conclude that Photodynamic therapy using Light emitting diode under these experimental conditions is a possible alternative approach to inhibit in vitro T. rubrum and may be a promising new treatment for dermatophytosis caused by this fungus.FUNDAMENTOS: Trichophyton rubrum é o agente mais comum das micoses superficiais de pele e unhas causando infecções de longa duração e altas taxas de recidiva. As desvantagens do tratamento atual envolvem medicações tópicas as quais n

  18. A darklight transition triggers expression of the floral promoter CrFTL1 and downregulates CONSTANS-like genes in a short-day plant Chenopodium rubrum

    Czech Academy of Sciences Publication Activity Database

    Drabešová, Jana; Cháb, David; Kolář, Jan; Haškovcová, Kateřina; Štorchová, Helena

    2014-01-01

    Roč. 65, č. 8 (2014), s. 2137-2146 ISSN 0022-0957 R&D Projects: GA ČR GA522/05/0300; GA ČR(CZ) GAP506/12/1359 Institutional support: RVO:61389030 Keywords : Chenopodium rubrum * CONSTANS-like * flowering Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.526, year: 2014

  19. Evaluation of a single application of Neonicotnoid and multi-application contact insecticides for flatheaded borer management in field grown Acer rubrum L. cultivars

    Science.gov (United States)

    Two trials evaluated insecticides for flatheaded borer (Chrysobothris femorata [Olivier]) control and red maple (Acer rubrum L.) cultivar growth over a 4-year period. Soil-applied systemic insecticides (acephate, imidacloprid, clothianidin, dinotefuran, and thiamethoxam) and trunk-applied contact i...

  20. Discovery of a sexual stage in Trichophyton onychocola, a presumed geophilic dermatophyte isolated from toenails of patients with a history of T. rubrum onychomycosis

    DEFF Research Database (Denmark)

    Hubka, Vit; Nissen, Christoffer V; Jensen, Rasmus Hare

    2015-01-01

    Trichophyton onychocola is a recently described geophilic dermatophyte that has been isolated from a toenail of Czech patient with a history of onychomycosis due to T. rubrum and clinical suspicion of relapse. In this study, we report a similar case from Denmark in an otherwise healthy 56-year-ol...

  1. The identification and characteristics of Echinoparyphium rubrum (Cort. 1914) new comb. (Trematoda, Echinostomatidae) based on experimental evidence of the life cycle

    Science.gov (United States)

    Kanev, I.; Sorensen, R.; Sterner, M.; Cole, Rebecca A.; Fried, B.

    1998-01-01

    The life cycle of Echinoparyphium rubrum (Cort, 1914) comb. n. has been completed experimentally. All of the developmental stages egg, miracidium, sporocyst, mother and daughter rediae, cercaria, metacercaria, and adult were examined and described. The miracidia infected freshwater snails of the genus Physa , P. gyrina and P. occidentalis. Attempts to infect snails of the genera Lymnaea, L. auricularis, L. peregra, L. truncatula and Bulinus, B. truncatus failed. Cercariae infected various pulmonate and prosobranch freshwater snails, mussels, frogs, water turtles and planarians. The adults developed in the small intestine of birds and mammals. The identity and major characteristics of Echinoparyphium rubrum are discussed. Synonyms of E. rubrum are Cercaria rubra Cort, 1914; Cercaria biflexa Faust, 1917; Cercaria chisolenata Faust, 1918; Echinostoma callawayensis Barker et Noll, 1915; Echinostoma revolutum of Johnson (1920); Echinoparyphium elegans of Cannon (1938), of Bain and Trelfall (1977), of Mahoney and Trelfall (1977); and Echinoparyphium recurvatum of Jilek (1977), Harley (1972), Sankurathri and Holmes (1976). Comparisons are made between E. rubrum and its 43-collar-spined allies: E. flexum from North America, E. cinctum from Europe, E. dunni from Asia and E. elegans from Africa.

  2. Ciliary-propelling mechanism, effect of temperature and viscosity on swimming speed, and adaptive significance of ‘jumping’ in the ciliate Mesodinium rubrum

    DEFF Research Database (Denmark)

    Riisgård, Hans Ulrik; Larsen, Poul Scheel

    2009-01-01

    . The results, supplemented with an analysis of a hydrodynamic model for self-propagation of an idealized micro-organism, support the hypothesis that the response is mainly physical/mechanical rather than biological. Since the jump-speed of M. rubrum is nearly the same for all tracks of varying jumplengths...

  3. Halorubrum rubrum sp. nov., an extremely halophilic archaeon from a Chinese salt lake.

    Science.gov (United States)

    Qiu, Xing-Xing; Zhao, Mei-Lin; Han, Dong; Zhang, Wen-Jiao; Cui, Heng-Lin

    2013-11-01

    genus Halorubrum, for which the name Halorubrum rubrum sp. nov. is proposed. The type strain is YC87(T) (=CGMCC 1.12124(T) = JCM 18365(T)).

  4. Extracellular Production of Silver Nanoparticles by Using Three Common Species of Dermatophytes: Trichophyton rubrum, Trichophyton mentagrophytes and Microsporum canis

    International Nuclear Information System (INIS)

    Moazeni, M.; Rashidi, N.; Shahverdi, Ahmad R.; Noorbakhsh, F.; Rezaie, S.

    2012-01-01

    To develop a new green approach for biosynthesis of silver nanoparticles, myconanotechnology has been represented as a novel field of study in nano technology. In this study, we have reported the extracellular synthesis of highly stable silver nanoparticles using three species of dermatophytes: Trichophyton rubrum, Trichophyton mentagrophytes and Microsporum canis. Methods: Clinical strains of these species were grown in a liquid medium containing mineral salt and incubated at 25 d egree C for 5-7 days. The cell-free filtrate of each culture was obtained and subjected to synthesize silver nanoparticles in the presence of 1 m M AgNO 3 . Results: The reduction of Ag + ions in metal nanoparticles was investigated virtually by tracing the solution color which was switched into reddish-light brown after 72 h. For T. mentagrophytes, a UV-visible spectra demonstrating a strong, quite narrow peak located between 422 and 425 nm was obtained. For M. canis, a fairly wide peak centering at 441 nm and for T. rubrum, a weak spectrum to decipher were observed. According to transmission electron microscopy results, fairly uniform, spherical, and small in size with almost less than 50 nm particles were forms in case of T. mentagrophytes. For the other two species, transmission electron microscopy images showed existence of small spherical nano silvers but not as small as nanoparticles synthesized by T. mentagrophytes. Conclusion: We observed that species belong to a single genus of the fungi have variable ability to synthesize silver nanoparticles extracellulary with different efficiency. Furthermore, the extracellular synthesis may make the process simpler and easier for following processes.

  5. Agrobacterium tumefaciens is a diazotrophic bacterium

    International Nuclear Information System (INIS)

    Kanvinde, L.; Sastry, G.R.K.

    1990-01-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate 15 N supplied as 15 N 2 . As with most other well-characterized diazotrophic bacteria, the presence of NH 4 + in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship

  6. The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination

    Directory of Open Access Journals (Sweden)

    Ding Guohui

    2007-04-01

    Full Text Available Abstract Background Conidia are considered to be the primary cause of infections by Trichophyton rubrum. Results We have developed a cDNA microarray containing 10250 ESTs to monitor the transcriptional strategy of conidial germination. A total of 1561 genes that had their expression levels specially altered in the process were obtained and hierarchically clustered with respect to their expression profiles. By functional analysis, we provided a global view of an important biological system related to conidial germination, including characterization of the pattern of gene expression at sequential developmental phases, and changes of gene expression profiles corresponding to morphological transitions. We matched the EST sequences to GO terms in the Saccharomyces Genome Database (SGD. A number of homologues of Saccharomyces cerevisiae genes related to signalling pathways and some important cellular processes were found to be involved in T. rubrum germination. These genes and signalling pathways may play roles in distinct steps, such as activating conidial germination, maintenance of isotropic growth, establishment of cell polarity and morphological transitions. Conclusion Our results may provide insights into molecular mechanisms of conidial germination at the cell level, and may enhance our understanding of regulation of gene expression related to the morphological construction of T. rubrum.

  7. The agony of choice in dermatophyte diagnostics-performance of different molecular tests and culture in the detection of Trichophyton rubrum and Trichophyton interdigitale.

    Science.gov (United States)

    Kupsch, C; Ohst, T; Pankewitz, F; Nenoff, P; Uhrlaß, S; Winter, I; Gräser, Y

    2016-08-01

    Dermatophytosis caused by dermatophytes of the genera Trichophyton and Microsporum belong to the most frequent mycoses worldwide. Molecular detection methods proved to be highly sensitive and enable rapid and accurate detection of dermatophyte species from clinical specimens. For the first time, we compare the performance of different molecular methods with each other and with conventional diagnostics in the detection of dermatophytoses caused by Trichophyton rubrum and Trichophyton interdigitale in clinical specimens (nail, skin and hair). The compared molecular methods comprise two already published PCR-ELISAs, a published quantitative RT-PCR as well as a newly developed PCR-ELISA targeting the internal transcribed spacer region. We investigated the sensitivity of the assays by analysing 375 clinical samples. In 148 specimens (39.5%) a positive result was gained in at least one of the four molecular tests or by culture, but the number of detected agents differed significantly between some of the assays. The most sensitive assay, a PCR-ELISA targeting a microsatellite region, detected 81 T. rubrum infections followed by an internal transcribed spacer PCR-ELISA (60), quantitative RT-PCR (52) and a topoisomerase II PCR-ELISA (51), whereas cultivation resulted in T. rubrum identification in 37 samples. The pros and cons of all four tests in routine diagnostics are discussed. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  8. Experimental evolution of aging in a bacterium

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    Stearns Stephen C

    2007-07-01

    Full Text Available Abstract Background Aging refers to a decline in reproduction and survival with increasing age. According to evolutionary theory, aging evolves because selection late in life is weak and mutations exist whose deleterious effects manifest only late in life. Whether the assumptions behind this theory are fulfilled in all organisms, and whether all organisms age, has not been clear. We tested the generality of this theory by experimental evolution with Caulobacter crescentus, a bacterium whose asymmetric division allows mother and daughter to be distinguished. Results We evolved three populations for 2000 generations in the laboratory under conditions where selection was strong early in life, but very weak later in life. All populations evolved faster growth rates, mostly by decreasing the age at first division. Evolutionary changes in aging were inconsistent. The predominant response was the unexpected evolution of slower aging, revealing the limits of theoretical predictions if mutations have unanticipated phenotypic effects. However, we also observed the spread of a mutation causing earlier aging of mothers whose negative effect was reset in the daughters. Conclusion Our results confirm that late-acting deleterious mutations do occur in bacteria and that they can invade populations when selection late in life is weak. They suggest that very few organisms – perhaps none- can avoid the accumulation of such mutations over evolutionary time, and thus that aging is probably a fundamental property of all cellular organisms.

  9. Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea

    KAUST Repository

    van de Water, Jeroen A. J. M.

    2017-07-05

    Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same \\'core microbiome\\' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of \\'core\\' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.

  10. Disparate SAR data of griseofulvin analogues for the dermatophytes Trichophyton mentagrophytes, T. rubrum, and MDA-MB-231 cancer cells.

    Science.gov (United States)

    Rønnest, Mads H; Raab, Marc S; Anderhub, Simon; Boesen, Sven; Krämer, Alwin; Larsen, Thomas O; Clausen, Mads H

    2012-01-26

    Griseofulvin and 53 analogues of this compound have been tested against the pathogenic dermatophytes Trichophyton rubrum and Trichophyton mentagrophytes as well as against the breast cancer cell line MDA-MB-231. The modifications to griseofulvin include the 4, 5, 6, 2', 3', and 4' positions. The SAR of the griseofulvin analogues toward the two fungi followed the same trend with the majority being less active than griseofulvin and none had more than twice the potency of the parent compound. A comparison of the antifungal and the anticancer SAR revealed distinct differences, as the majority of analogues showed increased activity against the cancer cell line MDA-MB-231, highlighted by 2'-benzyloxy-2'-demethoxy-griseofulvin, which showed low activity against both fungi but was among the most potent compounds against MDA-MB-231 cancer cells. Tubulin has been proposed as the target of griseofulvin in both fungal and mammalian cells, but the differences revealed by this SAR study strongly suggest that the mode-of-action of the compound class toward fungi and mammalian cancer cells is different.

  11. Physiological and foliar injury responses of Prunus serotina, Fraxinus americana, and Acer rubrum seedlings to varying soil moisture and ozone

    International Nuclear Information System (INIS)

    Schaub, M.; Skelly, J.M.; Steiner, K.C.; Davis, D.D.; Pennypacker, S.P.; Zhang, J.; Ferdinand, J.A.; Savage, J.E.; Stevenson, R.E.

    2003-01-01

    High soil water availability favors ozone uptake, increases foliar injury, and exacerbates the negative ozone effect on gas exchange of seedlings of deciduous tree species. - Sixteen black cherry (Prunus serotina, Ehrh.), 10 white ash (Fraxinus americana, L.) and 10 red maple (Acer rubrum, L.) 1-year old seedlings were planted per plot in 1997 on a former nursery bed within 12 open-top chambers and six open plots. Seedlings were exposed to three different ozone scenarios (ambient air: 100% O 3 ; non-filtered air: 98% ambient O 3 ; charcoal-filtered air: 50% ambient O 3 ) within each of two different water regimes (nine plots irrigated, nine plots non-irrigated) during three growing seasons. During the 1998 and 1999 growing season, leaf gas exchange, plant water relations, and foliar injury were measured. Climatic data, ambient- and chamber-ozone-concentrations were monitored. We found that seedlings grown under irrigated conditions had similar (in 1998) but significantly higher gas exchange rates (in 1999) than seedlings grown within non-irrigated plots among similar ozone exposures. Cherry and ash had similar ozone uptake but cherry developed more ozone-induced injury (<34% affected leaf area, LAA) than ash (<5% LAA), while maple rarely showed foliar injury, indicating the species differed in ozone sensitivity. Significantly more severe injury on seedlings grown under irrigated conditions than seedlings grown under non-irrigated conditions demonstrated that soil moisture altered seedling responses to ambient ozone exposures

  12. Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale

    KAUST Repository

    van de Water, Jeroen A. J. M.

    2016-06-06

    Mass mortality events in populations of the iconic red coral Corallium rubrum have been related to seawater temperature anomalies that may have triggered microbial disease development. However, very little is known about the bacterial community associated with the red coral. We therefore aimed to provide insight into this species’ bacterial assemblages using Illumina MiSeq sequencing of 16S rRNA gene amplicons generated from samples collected at five locations distributed across the western Mediterranean Sea. Twelve bacterial species were found to be consistently associated with the red coral, forming a core microbiome that accounted for 94.6% of the overall bacterial community. This core microbiome was particularly dominated by bacteria of the orders Spirochaetales and Oceanospirillales, in particular the ME2 family. Bacteria belonging to these orders have been implicated in nutrient cycling, including nitrogen, carbon and sulfur. While Oceanospirillales are common symbionts of marine invertebrates, our results identify members of the Spirochaetales as other important dominant symbiotic bacterial associates within Anthozoans.

  13. Isolation of flavonoids from Anemopaegma arvense (Vell Stellf. ex de Souza and their antifungal activity against Trichophyton rubrum

    Directory of Open Access Journals (Sweden)

    Camila Di Giovane Costanzo

    2013-09-01

    Full Text Available Anemopaegma arvense (Vell Stellf. ex de Souza belongs to the family Bignoniaceae, and is popularly known as catuaba. To evaluate the cytotoxic and antimicrobial activity of A. arvense, fraction F3 and flavonoids 1 (quercetin 3-O-α-L-rhamnopyranosyl-(1→6-β-D-glucopyranoside (rutin and flavonoid 2 (quercetin 3-O-α-L-rhamnopyranosyl-(1→6-β-D-galactopyranoside were isolated from the leaves of this plant. Fraction F3 and flavonoids 1 and 2 exhibited no antibacterial activity. Furthermore, no cytotoxic activity of fraction 3 or flavonoids 1 and 2 was observed against the tumor cells tested. However, analysis of the antifungal activity of flavonoids 1 and 2 revealed minimum inhibitory concentrations of 0.5 and 0.25 mg/mL, respectively, against the Trichophyton rubrum strains tested (wild type and mutant. This study demonstrates for the first time the antifungal activity of isolated flavonoids, validating the same activity for A. arvense.

  14. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    Energy Technology Data Exchange (ETDEWEB)

    Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  15. A Rapid Method for the Extraction and Analysis of Carotenoids and Other Hydrophobic Substances Suitable for Systems Biology Studies with Photosynthetic Bacteria

    Directory of Open Access Journals (Sweden)

    Oliver Sawodny

    2013-10-01

    Full Text Available A simple, rapid, and inexpensive extraction method for carotenoids and other non-polar compounds present in phototrophic bacteria has been developed. The method, which has been extensively tested on the phototrophic purple non-sulphur bacterium Rhodospirillum rubrum, is suitable for extracting large numbers of samples, which is common in systems biology studies, and yields material suitable for subsequent analysis using HPLC and mass spectroscopy. The procedure is particularly suitable for carotenoids and other terpenoids, including quinones, bacteriochlorophyll a and bacteriopheophytin a, and is also useful for the analysis of polar phospholipids. The extraction procedure requires only a single step extraction with a hexane/methanol/water mixture, followed by HPLC using a Spherisorb C18 column, with a mobile phase consisting of acetone-water and a non-linear gradient of 50%–100% acetone. The method was employed for examining the carotenoid composition observed during microaerophilic growth of R. rubrum strains, and was able to determine 18 carotenoids, 4 isoprenoid-quinones, bacteriochlorophyll a and bacteriopheophytin a as well as four different phosphatidylglycerol species of different acyl chain compositions. The analytical procedure was used to examine the dynamics of carotenoid biosynthesis in the major and minor pathways operating simultaneously in a carotenoid biosynthesis mutant of R. rubrum.

  16. Effect of Culture Supernatant Derived from Trichophyton Rubrum Grown in the Nail Medium on the Innate Immunity-related Molecules of HaCaT

    Directory of Open Access Journals (Sweden)

    Xin-Zhu Huang

    2015-01-01

    Full Text Available Background: Trichophyton rubrum is superficial fungi characteristically confined to dead keratinized tissues. These observations suggest that the soluble components released by the fungus could influence the host immune response in a cell in contact-free manner. Therefore, this research aimed to analyze whether the culture supernatant derived from T. rubrum grown in the nail medium could elicit the immune response of keratinocyte effectively. Methods: The culture supernatants of two strains (T1a, T XHB were compared for the β-glucan concentrations and their capacity to impact the innate immunity of keratinocytes. The β-glucan concentrations in the supernatants were determined with the fungal G-test kit and protein concentrations with bicinchoninic acid protein quantitative method, then HaCaT was stimulated with different concentrations of culture supernatants by adopting morphological method to select a suitable dosage. Expressions of host defense genes were assessed by quantitative polymerase chain reaction after the HaCaT was stimulated with the culture supernatants. Data were analyzed with one-way analysis of variance, followed by the least significant difference test. Results: The T. rubrum strains (T1a and T XHB released β-glucan of 87.530 ± 37.581 pg/ml and 15.747 ± 6.453 pg/ml, respectively into the media. The messenger RNA (mRNA expressions of toll-like receptor-2 (TLR2, TLR4, and CARD9 were moderately up-regulated in HaCaT within 6-h applications of both supernatants. HaCaT cells were more responsive to T1a than T XHB . The slight increase of dendritic cells-specific intercellular adhesion molecule 3-grabbing nonintegrin expression was faster and stronger, induced by T1a supernatant than T XHB . The moderate decreases of RNase 7, the slight up-regulations of Dectin-1 and interleukin-8 at the mRNA level were detected only in response to T1a rather than T XHB . After a long-time contact, all the elevated defense genes decreased after

  17. Fast-growing Acer rubrum differs from slow-growing Quercus alba in leaf, xylem and hydraulic trait coordination responses to simulated acid rain.

    Science.gov (United States)

    Medeiros, Juliana S; Tomeo, Nicholas J; Hewins, Charlotte R; Rosenthal, David M

    2016-08-01

    We investigated the effects of historic soil chemistry changes associated with acid rain, i.e., reduced soil pH and a shift from nitrogen (N)- to phosphorus (P)-limitation, on the coordination of leaf water demand and xylem hydraulic supply traits in two co-occurring temperate tree species differing in growth rate. Using a full-factorial design (N × P × pH), we measured leaf nutrient content, water relations, leaf-level and canopy-level gas exchange, total biomass and allocation, as well as stem xylem anatomy and hydraulic function for greenhouse-grown saplings of fast-growing Acer rubrum (L.) and slow-growing Quercus alba (L.). We used principle component analysis to characterize trait coordination. We found that N-limitation, but not P-limitation, had a significant impact on plant water relations and hydraulic coordination of both species. Fast-growing A. rubrum made hydraulic adjustments in response to N-limitation, but trait coordination was variable within treatments and did not fully compensate for changing allocation across N-availability. For slow-growing Q. alba, N-limitation engendered more strict coordination of leaf and xylem traits, resulting in similar leaf water content and hydraulic function across all treatments. Finally, low pH reduced the propensity of both species to adjust leaf water relations and xylem anatomical traits in response to nutrient manipulations. Our data suggest that a shift from N- to P-limitation has had a negative impact on the water relations and hydraulic function of A. rubrum to a greater extent than for Q. alba We suggest that current expansion of A. rubrum populations could be tempered by acidic N-deposition, which may restrict it to more mesic microsites. The disruption of hydraulic acclimation and coordination at low pH is emphasized as an interesting area of future study. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. The Evolution of the FT/TFL1 Genes in Amaranthaceae and Their Expression Patterns in the Course of Vegetative Growth and Flowering in Chenopodium rubrum

    Czech Academy of Sciences Publication Activity Database

    Drabešová, Jana; Černá, Lucie; Mašterová, Helena; Koloušková, Pavla; Potocký, Martin; Štorchová, Helena

    2016-01-01

    Roč. 6, č. 10 (2016), s. 3065-3076 ISSN 2160-1836 R&D Projects: GA ČR(CZ) GAP506/12/1359; GA ČR GA13-02290S Institutional support: RVO:61389030 Keywords : rna-seq data * locus-t * ft homologs * functional evolution * floral initiation * reference genome * arabidopsis * protein * quantification * activation * transcriptome * flowering locus t * TERMINAL FLOWER1 gene family * evolution * flowering * gene rearrangement * Amaranthaceae * Chenopodium rubrum Subject RIV: EF - Botanics Impact factor: 2.861, year: 2016

  19. OPTIMASI SABUN CAIR EKSTRAK ETANOL RIMPANG Zingiber officinale Rosc. var.rubrum DENGAN VARIASI MINYAK JARAK DAN KALIUM HIDROKSIDA

    Directory of Open Access Journals (Sweden)

    Nanda Paramita

    2014-12-01

    Full Text Available One of the causes of skin diseases are bacterial infections, such as Staphylococcus aureus and Staphylococcus epidermidis. Based on previous studies of red ginger (Zingiber officinale Rosc var.rubrum have antibacterial activity. The aimed of this research was to find the optimum concentration of castor oil and potassium hydroxide (KOH with good physicochemical properties with Simplex Lattice Design method, and determine the effectiveness of liquid soap against Staphylococcus aureus and Staphylococcus epidermidis with disc diffusion test. Extraction of red ginger with shoxletation and 96% ethanol. The optimization liquid soap design was using Simplex Lattice Design. The basic liquid soap composition was used to predict the optimum formula contain castor oil and KOH for comparasion (0: 100, (25:75, (50:50, (75:25, (100: 0. The research showed optimum consentration value of red ginger ethanol extract is 5%. The optimum formulas contained of 40,035 g of castor oil and 10,875 g KOH. The optimum liquid soap’s colour was brown, charateristic smell of ginger, stiff, with a pH value of 9,4, viscosity of 1233 cP, 1,14% free fatty acids and alkali-free 0%. The independent T test result by using the R-2.14.1 program was p values > 0.05 against S. epidermidis and p 0,05 terhadap S. epidermidis dan p<0,05 terhadap S.aureus. Hasil penelitian menyimpulkan bahwa metode Simplex Lattice Design dapat menghasilkan formula sabun cair yang optimum dan memiliki efektivitas sebagai antibakteri. Kata kunci: Minyak Jarak, KOH, Simplex Lattice Design, Rimpang Jahe Merah

  20. Daya Simpan Susu Kacang Hijau (Phaseolus radiatus L. dengan Persentase Penambahan Sari Jahe Merah (Zingiber officinale var. Rubrum

    Directory of Open Access Journals (Sweden)

    Meilla Dwi Andrestian

    2015-06-01

    Mung bean milk is one of the diversification of processed mung beans. The process of making mung bean milk using Ultra High Temperature (UHT is abundantly sold in the market. As another alternative to have a high shelf life, it needs the addition of natural preservatives such as red ginger. In general, this research aim was to determine the effect of addition of the percentage of red ginger extract (Zingiber officinale var. Rubrum on storability of green beans milk (Phaseolus radiatus L.. This research consisted of two phases, preliminary research and main research. The former stage was conducted to determine the best acceptability of nine treatment variations of red ginger extract addition. After preliminary research was made and it obtained the best results preferred by panelist, it was then followed by main research to determine the storability of green beans milk. From preliminary research, theres were three treatment preferred by panelists, namely P3 (0.75%, P5 (1.25% and P6 (1.5%. After that, those  treatments were tested for their storability in main research. From main research it showed that Q0 (control treatment can last for 0 day, Q1 treatment with the addition of red ginger extract 0,75% and Q2 (1.25% having storability for 1 day and Q3 (1.5% having the best treatment that had the longest storability (for 2 days. The more addition of red ginger extract, the longer storability of green beans milk. The best favored and longest storability of green beans milk was one added with red ginger extract of 1.5%. Keywords: Green Bean Milk, Storability, Red ginger

  1. Extreme Ionizing-Radiation-Resistant Bacterium

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2013-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein 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. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  2. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana

    Science.gov (United States)

    Pradhan, Nirakar; Dipasquale, Laura; d’Ippolito, Giuliana; Panico, Antonio; Lens, Piet N. L.; Esposito, Giovanni; Fontana, Angelo

    2015-01-01

    As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production. PMID:26053393

  3. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana

    Directory of Open Access Journals (Sweden)

    Nirakar Pradhan

    2015-06-01

    Full Text Available As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production.

  4. Comparison of the antifungal efficacy of terbinafine hydrochloride and ciclopirox olamine containing formulations against the dermatophyte Trichophyton rubrum in an infected nail plate model.

    Science.gov (United States)

    Täuber, Anja; Müller-Goymann, Christel C

    2014-07-07

    Onychomycosis is a fungal infection mostly induced by dermatophytes such as Trichophyton rubrum. Due to slow nail growth, the treatment takes 3-9 months depending on the nail size and infected area. Hence, high efficacy of the active ingredient without systemic side effects is of major interest. To test the efficacy of an antifungal formulation, an appropriate in vitro model reflecting the in vivo situation as close as possible is required. In this study, a variety of antifungal formulations, i.e., commercial ones (Ciclopoli and Lamisil cream), those used in compounding pharmacies (Pentravan) as well as poloxamer 407-based systems, have been evaluated in an infected nail plate model. The active pharmaceutical ingredients (APIs) were ciclopirox olamine and terbinafine hydrochloride. The poloxamer 407-based formulations consisted of poloxamer 407, double distilled water, propylene glycol, isopropyl alcohol, medium chain triglycerides and either 1% ciclopirox olamine or 1% terbinafine hydrochloride as API, respectively. Former studies have shown high permeation rates of terbinafine hydrochloride from similar poloxamer 407-based formulations with dimethyl isosorbide instead of propylene glycol. The present contribution shows superior inhibition of T. rubrum growth from poloxamer 407-based formulations in comparison to the commercial Lamisil cream. Moreover, poloxamer 407-based formulations were equally effective as the nail lacquer Ciclopoli even though the poloxamer formulations contained only 1% of the drug instead of 8% in the marketed lacquer. Poloxamer 407-based systems containing ciclopirox olamine proved to be about as effective as similar terbinafine hydrochloride systems.

  5. The physiology of the filamentous bacterium Microthrix parvicella

    NARCIS (Netherlands)

    Slijkhuis, H.

    1983-01-01

    A study has been made of the physiology of Microthrix parvicella. This filamentous bacterium often causes poor settleability of activated sludge in oxidation ditches supplied with domestic sewage. The organism was found to utilize only long chain fatty acids (preferably in

  6. Biosynthesis of silver nanoparticles by marine bacterium, Idiomarina ...

    Indian Academy of Sciences (India)

    Metal-tolerant microorganisms have been exploited in recent years to synthesize nanoparticles due to their potential to offer better size control through peptide binding and compartmentalization. In this paper, we report the intracellular synthesis of silver nanoparticles (SNPs) by the highly silver-tolerant marine bacterium, ...

  7. Control of magnetotactic bacterium in a micro-fabricated maze

    NARCIS (Netherlands)

    Khalil, I.S.M.; Pichel, Marc Philippe; Pichel, M.P.; Reefman, B.A.; Sardan Sukas, Ö.; Abelmann, Leon; Misra, Sarthak

    2013-01-01

    We demonstrate the closed-loop control of a magnetotactic bacterium (MTB), i.e., Magnetospirillum magnetotacticum, within a micro-fabricated maze using a magneticbased manipulation system. The effect of the channel wall on the motion of the MTB is experimentally analyzed. This analysis is done by

  8. Amylase activity of a yellow pigmented bacterium isolated from ...

    African Journals Online (AJOL)

    This study investigated the amylase activity of a yellow pigmented bacterium isolated from cassava wastes obtained from a dumpsite near a gari processing factory in Ibadan, Nigeria. Isolate was grown in nutrient broth containing 1% starch and then centrifuged at 5,000 rpm. Amylase activity was assayed using the DNSA ...

  9. Monitoring of a novel bacterium, Lactobacillus thermotolerans , in ...

    African Journals Online (AJOL)

    Abstract. We successfully established fluorescence in situ hybridization (FISH) method for specific detection and enumeration of a novel bacterium, Lactobacillus thermotolerans, in chicken feces. The specific FISH probes were designed based on the L. thermotolerans 16S rRNA gene sequences, and these sequences were ...

  10. Screening and characterization of petroleum-degrading bacterium ...

    African Journals Online (AJOL)

    Petroleum-degrading bacterium JY6 was isolated from petroleum-contaminated soils in DaQing oil field. It was identified as Bacillus cereus based on its morphological, physiological and biochemical characteristics, and analysis of its 16SrRNA gene. Biodegradation function of petroleum and oil degradation rates were ...

  11. [DNA extraction and identification of Trichophyton rubrum by real-time polymerase chain reaction from direct nail scraping specimens of patients with onycomycosis].

    Science.gov (United States)

    Berk, Elife; Kuştimur, Semra; Kalkancı, Ayşe; Oztaş, O Murat

    2011-01-01

    Trichophyton rubrum is the most frequently encountered dermatophyte species causing onichomycosis. The routine diagnosis of dermatophytes depends on the direct microscopic examination (DME) and culture methods, however due to the phenotypic identification problems related to those agents, the molecular methods come into question. The aim of this study was to evaluate the diagnostic performance of real-time polymerase chain reaction (RT-PCR) for the identification of T.rubrum by comparing to DME and culture methods, from nail samples of patients with the complaints of onychomycosis. A total of 90 patients of whom 58 were male who were admitted to the dermatology outpatients clinics of our hospital with the complaints of color/shape changes in the nails and thickening of the nail, were included in the study, together with the 20 healthy volunteer subjects as controls. The nail scraping samples obtained from the patients and controls were examined with direct microscopy using 15% potassium hydroxide, dimethyl sulphoxide and chlorazole black mixture and cultivated onto Sabouraud dextrose agar with and without cycloheximide. For DNA isolation, after the disruption of nail samples with a steel tool, phenol-chloroform-isoamyl alcohol purification method were used. The amplification and demonstration of the T.rubrum DNA have been performed by using specific primers and probes following TaqMan protocol of RT-PCR (LightCycler-Roche, USA) method. Seventy-two of the patients yielded positive and 18 yielded negative results with DME. Growth of molds was detected in the cultures of 20 (27.8%) of the 72 DME positive patients and all of the isolates were identified as T.rubrum. No fungal growth was seen in the samples of 18 patients who were DME negative. In DME positive group, 67 (93%) patients were found to be positive in RT-PCR, while 8 (44.4%) patients were RT-PCR positive in DME negative group. All of the culture positive samples (n= 20) were also found positive in RT

  12. Rubrumazines A-C, Indolediketopiperazines of the Isoechinulin Class from Eurotium rubrum MA-150, a Fungus Obtained from Marine Mangrove-Derived Rhizospheric Soil.

    Science.gov (United States)

    Meng, Ling-Hong; Du, Feng-Yu; Li, Xiao-Ming; Pedpradab, Patchara; Xu, Gang-Ming; Wang, Bin-Gui

    2015-04-24

    Three new indolediketopiperazine alkaloids of the isoechinulin type, rubrumazines A-C (1-3), each possessing an oxygenated prenyl group either at C-7 (1 and 2) or at C-5 (3), along with 13 related analogues (4-16), were isolated and identified from a culture extract of Eurotium rubrum MA-150, a fungus obtained from mangrove-derived rhizospheric soil collected from the Andaman Sea coastline, Thailand. Their structures were established by detailed interpretation of NMR spectroscopic and mass spectrometry data analysis. The structure and absolute configuration of compound 1 were confirmed by X-ray crystallographic analysis, thus providing the first characterized crystal structure of an isoechinulin-type alkaloid. All isolated compounds were evaluated for brine shrimp lethality and antibacterial activity.

  13. Biosorption of heavy metals by a marine bacterium

    International Nuclear Information System (INIS)

    Iyer, Anita; Mody, Kalpana; Jha, Bhavanath

    2005-01-01

    Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here

  14. Genome Sequence of the Milbemycin-Producing Bacterium Streptomyces bingchenggensis▿

    OpenAIRE

    Wang, Xiang-Jing; Yan, Yi-Jun; Zhang, Bo; An, Jing; Wang, Ji-Jia; Tian, Jun; Jiang, Ling; Chen, Yi-Hua; Huang, Sheng-Xiong; Yin, Min; Zhang, Ji; Gao, Ai-Li; Liu, Chong-Xi; Zhu, Zhao-Xiang; Xiang, Wen-Sheng

    2010-01-01

    Streptomyces bingchenggensis is a soil-dwelling bacterium producing the commercially important anthelmintic macrolide milbemycins. Besides milbemycins, the insecticidal polyether antibiotic nanchangmycin and some other antibiotics have also been isolated from this strain. Here we report the complete genome sequence of S. bingchenggensis. The availability of the genome sequence of S. bingchenggensis should enable us to understand the biosynthesis of these structurally intricate antibiotics bet...

  15. Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

    Directory of Open Access Journals (Sweden)

    Lukasz Makowski

    2016-11-01

    Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

  16. Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

    NARCIS (Netherlands)

    Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

    1998-01-01

    The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

  17. AÇÃO DO LASER DE BAIXA INTENSIDADE NA PRODUÇÃO DE METABÓLITOS SECUNDÁRIOS DO DERMATÓFITO TRICHOPHYTON RUBRUM

    Directory of Open Access Journals (Sweden)

    Idália Aparecida Waltrick de Brito Siqueira

    2012-12-01

    Full Text Available A ação do laser arseneto de gálio alumínio (GaAlAs nos comprimentos de onda 685nm e 830nm em cultura de Trichophyton rubrum, foi estudada visando obter  os metabólitos secundários e avaliar  a citotoxicidade dos mesmos em cultura de células. Foram utilizadas cepas do dermatófito T. rubrum provenientes do laboratório de Microbiologia da Universidade do Vale do Paraíba. O cultivo foi realizado em meio de cultura sólido de ágar Sabouraud (Merck, Alemanha em placa de Petri. A colônia de T. rubrum foi irradiada com o laser (GaAlAs a uma distância de 1cm da placa e incubadas em estufa 26ºC. Para o ensaio de citotoxicidade foi utilizada a linhagem ce-lular L929 (tecido conjuntivo de camundongo proveniente do laboratório Adolf Lutz em São Paulo. As células foram plaqueadas e incubadas com o extrato fúngico em diferentes concentrações, por 1 h. Após esta incubação foi reali-zado o teste de Metil tiazol tetrazólio (MTT para avaliação da citotoxicidade. Obteve-se uma diferença no cresci-mento das colônias controle e irradiadas a 685 nm estatisticamente significante (p<0,05. Na análise estatística com-parativa da citotoxicidade causada pelos extratos nas concentrações 2,5 mg/ml e 25x10-6 mg/ml, foi obtido p<0,05, o mesmo ocorreu entre as concentrações 25x10-2 mg/ml e 25x10-6 mg/ml. Na concentração de 25x10-2 mg/ml, observa-se uma elevação considerável (78,55% na atividade mitocondrial dos grupos com tratamento em relação ao controle. O laser GaAlAs, nas condições metodológicas deste estudo, apresentou efeitos no metabolismo celular, alteração de morfologia e da taxa de crescimento da colônia in vitro. O extrato fúngico das colônias irradiadas apre-sentou efeito bioestimulador quando comparado ao extrato obtido do grupo controle e sem tratamento com laser.

  18. Chitin utilization by the insect-transmitted bacterium Xylella fastidiosa.

    Science.gov (United States)

    Killiny, Nabil; Prado, Simone S; Almeida, Rodrigo P P

    2010-09-01

    Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa.

  19. Liver abscess associated with an oral flora bacterium Streptococcus anginosus

    Directory of Open Access Journals (Sweden)

    Hava Yılmaz

    2012-03-01

    Full Text Available Viridans group Streptococcus, a bacterium of the oral flora has a low-virulence and rarely causes liver abscess. A 40-yearoldmale patient was admitted to the hospital complaining of high fever and malaise. A physical examination revealedpoor oral hygiene; there were caries on many teeth, and he had hepatomegaly. A hepatic abscess was identified inhis abdominal tomography. Streptococcus anginosus was isolated from the drainage material, and the bile ducts werenormal in his MRI cholangiography. An immunocompetent case of liver abscess caused by Streptococcus anginosusoriginated most probably from oral flora is presented here. J Microbiol Infect Dis 2012; 2(1:33-35

  20. Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

    Energy Technology Data Exchange (ETDEWEB)

    Daniel P. Molloy

    2004-02-24

    The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

  1. Research Progress and Perspectives of Nitrogen Fixing Bacterium, Gluconacetobacter diazotrophicus, in Monocot Plants

    Directory of Open Access Journals (Sweden)

    N. Eskin

    2014-01-01

    Full Text Available Gluconacetobacter diazotrophicus is a nitrogen fixing bacterium originally found in monocotyledon sugarcane plants in which the bacterium actively fixes atmosphere nitrogen and provides significant amounts of nitrogen to plants. This bacterium mainly colonizes intercellular spaces within the roots and stems of plants and does not require the formation of the complex root organ like nodule. The bacterium is less plant/crop specific and indeed G. diazotrophicus has been found in a number of unrelated plant species. Importantly, as the bacterium was of monocot plant origin, there exists a possibility that the nitrogen fixation feature of the bacterium may be used in many other monocot crops. This paper reviews and updates the research progress of G. diazotrophicus for the past 25 years but focuses on the recent research development.

  2. Whole-genome shotgun optical mapping of rhodospirillumrubrum

    Energy Technology Data Exchange (ETDEWEB)

    Reslewic, Susan; Zhou, Shiguo; Place, Mike; Zhang, Yaoping; Briska, Adam; Goldstein, Steve; Churas, Chris; Runnheim, Rod; Forrest,Dan; Lim, Alex; Lapidus, Alla; Han, Cliff S.; Roberts, Gary P.; Schwartz,David C.

    2004-07-01

    Rhodospirillum rubrum is a phototrophic purple non-sulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems, and as a source of hydrogen and biodegradable plastics production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction maps (Xba I, Nhe I, and Hind III) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction maps from randomly sheared genomic DNA molecules extracted directly from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the Hind III map acted as a scaffold for high resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and validation of genome sequence, our work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a ''molecular cytogenetics'' approach to solving problems in genomic analysis.

  3. Biodegradation of polyethylene by the thermophilic bacterium Brevibacillus borstelensis.

    Science.gov (United States)

    Hadad, D; Geresh, S; Sivan, A

    2005-01-01

    To select a polyethylene-degrading micro-organism and to study the factors affecting its biodegrading activity. A thermophilic bacterium Brevibaccillus borstelensis strain 707 (isolated from soil) utilized branched low-density polyethylene as the sole carbon source and degraded it. Incubation of polyethylene with B. borstelensis (30 days, 50 degrees C) reduced its gravimetric and molecular weights by 11 and 30% respectively. Brevibaccillus borstelensis also degraded polyethylene in the presence of mannitol. Biodegradation of u.v. photo-oxidized polyethylene increased with increasing irradiation time. Fourier Transform Infra-Red (FTIR) analysis of photo-oxidized polyethylene revealed a reduction in carbonyl groups after incubation with the bacteria. This study demonstrates that polyethylene--considered to be inert--can be biodegraded if the right microbial strain is isolated. Enrichment culture methods were effective for isolating a thermophilic bacterium capable of utilizing polyethylene as the sole carbon and energy source. Maximal biodegradation was obtained in combination with photo-oxidation, which showed that carbonyl residues formed by photo-oxidation play a role in biodegradation. Brevibaccillus borstelensis also degraded the CH2 backbone of nonirradiated polyethylene. Biodegradation of polyethylene by a single bacterial strain contributes to our understanding of the process and the factors affecting polyethylene biodegradation.

  4. Biological Control of Meloidogyne hapla Using an Antagonistic Bacterium

    Directory of Open Access Journals (Sweden)

    Jiyeong Park

    2014-09-01

    Full Text Available We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN Meloidogyne hapla in carrot (Daucus carota subsp. sativus and tomato (Solanum lycopersicum. Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla.

  5. Isolation, structure determination, and sensory activity of mouth-drying and astringent nitrogen-containing phytochemicals isolated from red currants (Ribes rubrum).

    Science.gov (United States)

    Schwarz, Bernd; Hofmann, Thomas

    2007-02-21

    Application of chromatographic separation and taste dilution analyses recently revealed, besides a series of flavon-3-ol glycosides and (E)/(Z)-aconitic acid, four nitrogen-containing phytochemicals as the key astringent and mouth-drying compounds in red currants (Ribes rubrum). The isolation and structure determination of the astringent indoles 3-carboxymethyl-indole-1-N-beta-D-glucopyranoside (1) and 3-methylcarboxymethyl-indole-1-N-beta-D-glucopyranoside (2), as well as the astringent, noncyanogenic nitriles 2-(4-hydroxybenzoyloxymethyl)-4-beta-D-glucopyranosyloxy-2(E)-butenenitrile (3) and 2-(4-hydroxy-3-methoxybenzoyloxymethyl)-4-beta-D-glucopyranosyloxy-2(E)-butenenitrile (4) by means of 1D/2D NMR, LC-MS/MS, and UV-vis spectroscopy are reported. The structures of compounds 1 and 2 were confirmed by synthesis. Using the recently developed half-tongue test, human recognition thresholds for the astringent and mouth-drying nitrogen compounds were determined to be between 0.0003 and 5.9 micromol/L (water). In particular, the extraordinarily low threshold of 0.0003 micromol/L evaluated for the indole 1 represents the lowest recognition threshold of any astringent phytochemical reported to date.

  6. Simulated microgravity allows to demonstrate cell-to-cell communication in bacteria

    Science.gov (United States)

    Mastroleo, Felice; van Houdt, Rob; Mergeay, Max; Hendrickx, Larissa; Wattiez, Ruddy; Leys, Natalie

    Through the MELiSSA project, the European Space Agency aims to develop a closed life support system for oxygen, water and food production to support human life in space in forth-coming long term space exploration missions. This production is based on the recycling of the missions organic waste, including CO2 and minerals. The photosynthetic bacterium Rhodospir-illum rubrum S1H is used in MELiSSA to degrade organics with light energy and is the first MELiSSA organism that has been studied in space related environmental conditions (Mastroleo et al., 2009). It was tested in actual space flight to the International Space Station (ISS) as well as in ground simulations of ISS-like ionizing radiation and microgravity. In the present study, R. rubrum S1H was cultured in liquid medium in 2 devices simulating microgravity conditions, i.e. the Rotating Wall Vessel (RWV) and the Random Positioning Machine (RPM). The re-sponse of the bacterium was evaluated at both the transcriptomic and proteomic levels using respectively a dedicated whole-genome microarray and high-throughput gel-free quantitative proteomics. Both at transcriptomic and proteomic level, the bacterium showed a significant response to cultivation in simulated microgravity. The response to low fluid shear modeled microgravity in RWV was different than to randomized microgravity in RPM. Nevertheless, both tests pointed out a change in and a likely interrelation between cell-to-cell communica-tion (i.e. quorum sensing) and cell pigmentation (i.e. photosynthesis) for R. rubrum S1H in microgravity conditions. A new type of cell-to-cell communication molecule in R. rubrum S1H was discovered and characterized. It is hypothised that the lack of convection currents and the fluid quiescence in (simulated) microgravity limits communications molecules to be spread throughout the medium. Cultivation in this new artificial environment of simulated micro-gravity has showed new properties of this well know bacterium

  7. Micropollutants in closed life-support systems: the case of triclosan, a biocide excreted via urine

    Science.gov (United States)

    Mastroleo, Felice; Pycke, Benny; Boon, Nico; de Wever, Heleen; Hendrickx, Larissa; Mastroleo, Felice; Wattiez, Ruddy; Mergeay, Max; Verstraete, Willy

    OBJECTIVES: The impact of triclosan on the growth and physiology of the bacterium Rhodospirillum rubrum was studied in the frame of the regenerative life-support system, Micro- Ecological Life Support System Alternative (MELiSSA). A wide range of compounds, such as steroid hormones, pharmaceuticals and personal care products, might enter the life support system via the excrements that are to be treated and recycled. Triclosan was chosen as the first compound to be tested because MELiSSA is a closed system, which is consequently particularly sensitive to compounds inhibiting the microbial metabolism. Because triclosan is increasingly used as an antimicrobial biocide in hygienic formulations (such as toothpaste, mouthwash, deodorants, etc.) and due to its chemical stability, it is considered an emerging pollutant in terrestrial ecosystems. METHODS: In a first phase, the triclosan concentration expected in the life-support system was estimated, the Minimal Inhibitory Concentration (MIC) was determined via plating, and the effect on growth kinetics was assessed by comparing growth parameters in the Gompertz model. In a second phase, the secondary effects of triclosan on cell physiology and gene expression were studied through flow-cytometry and microarray analyses, respectively. RESULTS: Based on the pharmacokinetic data from literature, the predicted concentration range is estimated to be 6-25µg/L triclosan in the Rhodospirillum rubrum compartment of the MELiSSA. The minimal inhibitory concentration of triclosan was determined to be 71 µg/L after 7 days of exposure on Sistrom medium. Upon exposure to 50-200µg/L triclosan, triclosan-resistant mutants of Rhodospirillum rubrum arose spontaneously at high frequency (3.1 ∗ 10 - 4). Analysis of the growth kinetics of the wild-type revealed that triclosan causes an important elongation of the lag-phase and a decrease in growth rate. At concentrations higher than 75mg/L(LD = 500mg/L), triclosan is bactericidal to wild

  8. Dense populations of a giant sulfur bacterium in Namibian shelf sediments

    DEFF Research Database (Denmark)

    Schulz, HN; Brinkhoff, T.; Ferdelman, TG

    1999-01-01

    A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA...

  9. Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

    Energy Technology Data Exchange (ETDEWEB)

    Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui; Kunin, Victor; Lapidus, Alla; Hugenholtz, Philip; Patel, Bharat; Kyrpides, Nikos C.

    2008-11-03

    Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

  10. A bacterium that degrades and assimilates poly(ethylene terephthalate).

    Science.gov (United States)

    Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

    2016-03-11

    Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. Copyright © 2016, American Association for the Advancement of Science.

  11. Virtual bacterium colony in 3D image segmentation.

    Science.gov (United States)

    Badura, Pawel

    2018-04-01

    Several heuristic, biologically inspired strategies have been discovered in recent decades, including swarm intelligence algorithms. So far, their application to volumetric imaging data mining is, however, limited. This paper presents a new flexible swarm intelligence optimization technique for segmentation of various structures in three- or two-dimensional images. The agents of a self-organizing colony explore their host, use stigmergy to communicate themselves, and mark regions of interest leading to the object extraction. Detailed specification of the bacterium colony segmentation (BCS) technique in terms of both individual and social behaviour is described in this paper. The method is illustrated and evaluated using several experiments involving synthetic data, computed tomography studies, and ultrasonography images. The obtained results and observations are discussed in terms of parameter settings and potential application of the method in various segmentation tasks. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Antitrypanosomal Alkaloids from the Marine Bacterium Bacillus pumilus

    Directory of Open Access Journals (Sweden)

    Sergio Martínez-Luis

    2012-09-01

    Full Text Available Fractionation of the ethyl acetate extract of the marine bacterium Bacillus pumilus isolated from the black coral Antipathes sp. led to the isolation of five compounds: cyclo-(L-Leu-L-Pro (1, 3-hydroxyacetylindole (2, N-acetyl-b-oxotryptamine (3, cyclo-(L-Phe-L-Pro (4, and 3-formylindole (5. The structures of compounds 1−5 were established by spectroscopic analyses, including HRESITOF-MS and NMR (1H, 13C, HSQC, HMBC and COSY. Compounds 2, 3 and 5 caused the inhibition on the growth of Trypanosoma cruzi (T. cruzi, with IC50 values of 20.6, 19.4 and 26.9 μM, respectively, with moderate cytotoxicity against Vero cells. Compounds 1−5 were found to be inactive when tested against Plasmodium falciparum and Leishmania donovani, therefore showing selectivity against T. cruzi parasites.

  13. Complete genome sequence of the photoautotrophic and bacteriochlorophyll e-synthesizing green sulfur bacterium Chlorobaculum limnaeum DSM 1677T

    DEFF Research Database (Denmark)

    Tank, Marcus; Liu, Zhenfeng; Frigaard, Niels-Ulrik

    2017-01-01

    Chlorobaculum limnaeum DSM 1677T is a mesophilic, brown-colored, chlorophototrophic green sulfur bacterium that produces bacteriochlorophyll e and the carotenoid isorenieratene as major pigments. This bacterium serves as a model organism in molecular research on photosynthesis, sulfur metabolism...

  14. Physiological and foliar symptom response in the crowns of Prunus serotina, Fraxinus americana and Acer rubrum canopy trees to ambient ozone under forest conditions

    International Nuclear Information System (INIS)

    Schaub, M.; Skelly, J.M.; Zhang, J.W.; Ferdinand, J.A.; Savage, J.E.; Stevenson, R.E.; Davis, D.D.; Steiner, K.C.

    2005-01-01

    The crowns of five canopy dominant black cherry (Prunus serotina Ehrh.), five white ash (Fraxinus americana L.), and six red maple (Acer rubrum L.) trees on naturally differing environmental conditions were accessed with scaffold towers within a mixed hardwood forest stand in central Pennsylvania. Ambient ozone concentrations, meteorological parameters, leaf gas exchange and leaf water potential were measured at the sites during the growing seasons of 1998 and 1999. Visible ozone-induced foliar injury was assessed on leaves within the upper and lower crown branches of each tree. Ambient ozone exposures were sufficient to induce typical symptoms on cherry (0-5% total affected leaf area, LAA), whereas foliar injury was not observed on ash or maple. There was a positive correlation between increasing cumulative ozone uptake (U) and increasing percent of LAA for cherry grown under drier site conditions. The lower crown leaves of cherry showed more severe foliar injury than the upper crown leaves. No significant differences in predawn leaf water potential (ψ L ) were detected for all three species indicating no differing soil moisture conditions across the sites. Significant variation in stomatal conductance for water vapor (g wv ) was found among species, soil moisture, time of day and sample date. When comparing cumulative ozone uptake and decreased photosynthetic activity (P n ), red maple was the only species to show higher gas exchange under mesic vs. drier soil conditions (P wv and P n demonstrate the strong influence of heterogeneous environmental conditions within forest canopies. - Within the heterogeneous environment of a mature forest, many factors in addition to soil moisture play a significant role in determining exposure/response relationships to ozone

  15. Halosimplex pelagicum sp. nov. and Halosimplex rubrum sp. nov., isolated from salted brown alga Laminaria, and emended description of the genus Halosimplex.

    Science.gov (United States)

    Han, Dong; Cui, Heng-Lin

    2014-01-01

    Two halophilic archaeal strains, R2(T) and R27(T), were isolated from the brown alga Laminaria produced at Dalian, Liaoning Province, China. Both had pleomorphic cells that lysed in distilled water, stained Gram-negative and formed red-pigmented colonies. They grew optimally at 42 °C, pH 7.0 and in the presence of 3.1-3.4 M NaCl and 0.03-0.5 M Mg(2+). The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and four major glycolipids chromatographically identical to those of Halosimplex carlsbadense JCM 11222(T). 16S rRNA gene analysis revealed that each strain had two dissimilar 16S rRNA genes and both strains were phylogenetically related to Halosimplex carlsbadense JCM 11222(T) (92.7-98.8 % similarities). The rpoB' gene similarities between strains R2(T) and R27(T) and between these strains and Halosimplex carlsbadense JCM 11222(T) were 95.7 %, 96.1 % and 95.8 %, respectively. The DNA G+C contents of strains R2(T) and R27(T) were 62.5 mol% and 64.0 mol%, respectively. The DNA-DNA hybridization values between strains R2(T) and R27(T) and between the two strains and Halosimplex carlsbadense JCM 11222(T) were 43 %, 52 % and 47 %, respectively. It was concluded that strain R2(T) ( = CGMCC 1.10586(T) = JCM 17263(T)) and strain R27(T) ( = CGMCC 1.10591(T) = JCM 17268(T)) represent two novel species of the genus Halosimplex, for which the names Halosimplex pelagicum sp. nov. and Halosimplex rubrum sp. nov. are proposed. An emended description of the genus Halosimplex is also presented.

  16. Anti-atherosclerotic effect of Fermentum Rubrum and Gynostemma pentaphyllum mixture in high-fat emulsion- and vitamin D3-induced atherosclerotic rats.

    Science.gov (United States)

    Gou, San-Hu; Liu, Bei-Jun; Han, Xiu-Feng; Wang, Li; Zhong, Chao; Liang, Shan; Liu, Hui; Qiang, Yin; Zhang, Yun; Ni, Jing-Man

    2017-10-26

    The mixture of Hongqu and gypenosides (HG) is composed of Fermentum Rubrum (Hongqu, in Chinese) and total saponins of Gynostemma pentaphyllum (Thunb.) Makino (Jiaogulan, in Chinese) in a 3.6:1 weight ratio. Both Hongqu and Jiaogulan are considered valuable traditional Chinese medicines (TCMs); they have been commonly used in China for the treatment of hyperlipidemia and related diseases for centuries. The aim of the current study was assess the anti-atherosclerotic effect of HG. Sixty-four Wistar rats were randomly divided into eight groups: normal, model, positive control (simvastatin, 1 mg/kg), Hongqu-treated (72 mg/kg), gypenoside (total saponin)-treated (20 mg/kg), and three doses HG-treated (50, 100, and 200 mg/kg). All of the rats were fed a basal diet. Additionally, the model group rats were intragastrically administered a high-fat emulsion and intraperitoneally injected with vitamin D 3 . The serum lipid profiles, oxidative stress, inflammatory cytokine, and hepatic antioxidant levels were then determined. Furthermore, the liver histopathology and arterial tissue were analyzed, and the expression of hyperlipidemia- and atherosclerosis (AS)-related genes was measured using reverse transcription-polymerase chain reaction. The AS rat model was established after 80 days. Compared to the model group, the HG-treated groups showed an obvious improvement in the serum lipid profiles, oxidative stress, and inflammatory cytokine levels, and showed markedly increased hepatic total antioxidant capacity. Moreover, the expression of genes related to lipid synthesis and inflammation reduced and that of the genes related to lipid oxidation increased in the liver and arterial tissue, which also reflected an improved health condition. the anti-atherosclerotic effects of HG were superior to those of simvastatin, Hongqu, and the gypenosides. Therefore, HG may be a useful anti-atherosclerotic TCM preparation. Copyright © 2017. Published by Elsevier Taiwan LLC.

  17. Antifungal Effects of Bee Venom Components on Trichophyton rubrum: A Novel Approach of Bee Venom Study for Possible Emerging Antifungal Agent.

    Science.gov (United States)

    Park, Joonsoo; Kwon, Osung; An, Hyun-Jin; Park, Kwan Kyu

    2018-04-01

    Bee venom (BV) has been widely investigated for potential medical uses. Recent inadvertent uses of BV based products have shown to mitigate signs of fungal infections. However, the component mediating the antifungal effect has not been identified. This investigation compares bee venom in its whole and partial forms to evaluate the possible component responsible for the antifungal effect. Forty-eight plates inoculated with Trichophyton rubrum were allocated into four groups. The groups were treated with raw BV (RBV), melittin, apamin and BV based mist (BBM) respectively and each group was further allocated accordingly to three different concentrations. The areas were measured every other day for 14 days to evaluate the kinetic changes of the colonies. The interactions of ratio differences over interval were confirmed in groups treated with RBV and BBM. In RBV, the level of differences were achieved in groups treated with 10 mg/100 µl ( p =0.026) and 40 mg/100 µl ( p =0.000). The mean difference of ratio in groups treated with RBV was evident in day 3 and day 5. The groups that were treated with melittin or apamin did not show any significant interaction. In BBM groups, the significant levels of ratio differences over time intervals were achieved in groups treated with 200 µl/100 µl ( p =0.000) and 300 µl/100 µl ( p =0.030). The the bee venom in its whole form delivered a significant level of inhibition and we concluded that the venom in separated forms are not effective. Moreover, BV based products may exert as potential antifungal therapeutics.

  18. Characterization of the radioresistance in the radioresistant bacterium deinococcus radiodurans

    International Nuclear Information System (INIS)

    Kong Xiangrong; Du Zeji

    1999-01-01

    The radioresistance of wild type Deinococcus radiodurans KD8301 and the factors affecting the radioresistance were investigated. KH3111 which was a DNA repair mutant of KD8301 (Zeji Du, 1998) was used to be compared with KD8301. Deinococcus radiodurans was discovered by Anderson et al (1956) in X-ray sterilized canned meat that was found to have undergone spoilage. this bacterium and other species of this genus share extreme resistance to ionizing radiation and other agents that damage DNA. Wild type KD8301 and its sensitive mutant KH3111 were irradiated with 60 Co γ-ray at the dose range 0.5 ∼ 10 kGy. Dose-survival fraction curves were made and the radio resistances were determined by LD 99 . The relative contents of DNA in cells were measured by Fluorescence Spectrophotometry (Freedman and Bruce, 1971). The results indicated that wild type KD8301 possesses more radioresistant than its mutant KH3111, LD99 were 9.5 kGy and 2.4 kGy respectively. KD8301 grown at exponential phase showed a decreased resistance to radiation, and the LD99 was 5.1 kGy. No differences of DNA/protein in cells were found between the exponential phase and the stationary phase. The results could be concluded that wild type KD8301 possesses remarkable radioresistance, but this ability was decreased or disappeared after mutation (in KH3111). None DNA relative content other than the growth stages were determinant factors of radioresistance in Deinococcus radiodurans. This results were different from other report (Dickie N et al, 1990). The cellular mechanisms might be the deference's of the bacterium cell morphology between the exponential phase and the stationary phase. Recently, the mutation site of KH3111 which was mutated chemically from wild type KD8301 was identified (Zeji Du, 1998). One base pair changed in the novel gene pprA which was isolated from KD8301 genomic DNA. This point mutation was confirmed to be responsible for the sensitivity of KH3111 to γ-ray and other DNA

  19. Tropheryma whipplei: a common bacterium in rural Senegal.

    Directory of Open Access Journals (Sweden)

    Alpha Kabinet Keita

    2011-12-01

    Full Text Available BACKGROUND: Tropheryma whipplei is known as the cause of Whipple's disease, but it is also an emerging pathogen, detected in stool, that causes various chronic localized infections without histological digestive involvement and is associated with acute infections, including gastroenteritis and bacteremia. METHODS/PRINCIPAL FINDINGS: We conducted a study in 2008 and 2009 using 497 non-diarrheic and diarrheic stool samples, 370 saliva samples, 454 sera samples and 105 samples obtained from water samples in two rural Sine-Saloum villages (Dielmo and Ndiop in Senegal. The presence of T. whipplei was investigated by using specific quantitative PCR. Genotyping was performed on positive samples. A serological analysis by western blotting was performed to determine the seroprevalence and to detect seroconversion. Overall, T. whipplei was identified in 31.2% of the stool samples (139/446 and 3.5% of the saliva samples (13/370 obtained from healthy subjects. The carriage in the stool specimens was significantly (p<10(-3 higher in children who were between 0 and 4 years old (60/80, 75% compared to samples obtained from individuals who were between 5 to 10 years old (36/119, 30.2% or between 11 and 99 years old (43/247, 17.4%. The carriage in the stool was also significantly more common (p = 0.015 in subjects with diarrhea (25/51, 49%. We identified 22 genotypes, 16 of which were new. Only one genotype (#53 was common to both villages. Among the specific genotypes, one (#52 was epidemic in Dielmo (15/28, 53.4%, p<10(-3 and another (#49 in Ndiop (27.6%, p = 0.002. The overall seroprevalence was estimated at 72.8% (291/400. Seroconversion was detected in 66.7% (18/27 of children for whom PCR became positive in stools between 2008 and 2009. CONCLUSIONS/SIGNIFICANCE: T. whipplei is a common bacterium in the Sine-Saloum area of rural Senegal that is contracted early in childhood. Epidemic genotypes suggest a human transmission of the bacterium.

  20. Porphyrobacter algicida sp. nov., an algalytic bacterium isolated from seawater.

    Science.gov (United States)

    Kristyanto, Sylvia; Lee, Sang Don; Kim, Jaisoo

    2017-11-01

    A novel Gram-stain-negative, yellow-pigmented, catalase- and oxidase-positive, non-endospore-forming, flagellated bacterium, designated strain Yeonmyeong 2-22 T , was isolated from surface seawater of Geoje Island, Republic of Korea. Strain Yeonmyeong 2-22 T showed algalytic activity against the seven strains tested: Cochlodinium polykrikoides, Chattonella marina, Heterosigma akashiwo, Scrippsiella trochoidea, Heterocapsa triquetra, Prorocentrum minimum and Skeletonema costatum. A taxonomic study was carried out based on a polyphasic approach to characterize the exact taxonomic position of strain Yeonmyeong 2-22 T . The bacterium was able to grow at 10-40 °C, at salinities from 0 to 9 %, at pH from 4.0 to 9.0 and was not able to degrade gelatin or casein. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain Yeonmyeong 2-22 T was considered to represent a novel species of the genus Porphyrobacter, which belongs to the family Erythrobacteraceae, and was related most closely to Porphyrobacter dokdonensis DSW-74 T with 97.23 % 16S rRNA gene sequence similarity. The dominant cellular fatty acids of strain Yeonmyeong 2-22 T were C18 : 1ω7c (49.7 %), C16 : 0 (12.0 %) and 11-methyl C18 : 1ω7c (11.5 %), and ubiquinone-10 (Q-10) was the predominant respiratory lipoquinone. The genomic DNA G+C content of strain Yeonmyeong 2-22 T was calculated to be 63.0 mol%. Phenotypic characteristics of the novel strain also differed from other members of the genus Porphyrobacter. On the basis of polyphasic taxonomic data, strain Yeonmyeong 2-22 T represents as a novel species of the genus Porphyrobacter, for which the name of Porphyrobacter algicida sp. nov. is proposed. The type strain is Yeonmyeong 2-22 T (=KEMB 9005-328 T =JCM 31499 T ).

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

    Science.gov (United States)

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

    2016-09-01

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

  2. Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

    Science.gov (United States)

    Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

    1978-01-01

    Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

  3. Electromicrobiology of Dissimilatory Sulfur Reducing Bacterium Desulfuromonas acetexigens

    KAUST Repository

    Bin Bandar, Khaled

    2014-12-01

    Bioelectrochmical systems (BES) are engineered electrochemical devices that harness hidden chemical energy of the wastewater in to the form of electricity or hydrogen. Unique microbial communities enrich in these systems for oxidation of organic matter as well as transfer of resulted electron to anode, known them as “electricigens” communities. Exploring novel electricigenesis microbial communities in the nature and understanding their electromicrobiology is one the important aspect for BES systems scale up. Herein, we report first time the electricigenesis property of an anaerobic, fresh water sediment, sulfur reducing bacterium Desulfuromona acetexigens. The electrochemical behavior of D. acetexigens biofilms grown on graphite-rod electrodes in batch-fed mode under an applied potential was investigated with traditional electroanalytical tools, and correlate the electron transfer from biofilms to electrode with a model electricigen Geobacter sulfurreducens electrochemical behavior. Research findings suggest that D. acetexigens has the ability to use electrode as electron acceptor in BES systems through establishing the direct contact with anode by expressing the membrane bound redox proteins, but not due to the secretion of soluble redox mediators. Preliminary results revealed that D. acetexigens express three distinct redox proteins in their membranes for turnover of the electrons from biofilm to electrode, and the 4 whole electricigenesis process observed to be unique in the D. acetexigens compared to that of well-studied model organism G. sulfurreducens.

  4. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7.

    Science.gov (United States)

    Chen, Songcan; Li, Xiaomin; Sun, Guoxin; Zhang, Yingjiao; Su, Jianqiang; Ye, Jun

    2015-09-29

    Co-contamination of antibiotics and heavy metals prevails in the environment, and may play an important role in disseminating bacterial antibiotic resistance, but the selective effects of heavy metals on bacterial antibiotic resistance is largely unclear. To investigate this, the effects of heavy metals on antibiotic resistance were studied in a genome-sequenced bacterium, LSJC7. The results showed that the presence of arsenate, copper, and zinc were implicated in fortifying the resistance of LSJC7 towards tetracycline. The concentrations of heavy metals required to induce antibiotic resistance, i.e., the minimum heavy metal concentrations (MHCs), were far below (up to 64-fold) the minimum inhibition concentrations (MIC) of LSJC7. This finding indicates that the relatively low heavy metal levels in polluted environments and in treated humans and animals might be sufficient to induce bacterial antibiotic resistance. In addition, heavy metal induced antibiotic resistance was also observed for a combination of arsenate and chloramphenicol in LSJC7, and copper/zinc and tetracycline in antibiotic susceptible strain Escherichia coli DH5α. Overall, this study implies that heavy metal induced antibiotic resistance might be ubiquitous among various microbial species and suggests that it might play a role in the emergence and spread of antibiotic resistance in metal and antibiotic co-contaminated environments.

  5. Perchlorate reduction by a novel chemolithoautotrophic, hydrogen-oxidizing bacterium.

    Science.gov (United States)

    Zhang, Husen; Bruns, Mary Ann; Logan, Bruce E

    2002-10-01

    Water treatment technologies are needed that can remove perchlorate from drinking water without introducing organic chemicals that stimulate bacterial growth in water distribution systems. Hydrogen is an ideal energy source for bacterial degradation of perchlorate as it leaves no organic residue and is sparingly soluble. We describe here the isolation of a perchlorate-respiring, hydrogen-oxidizing bacterium (Dechloromonas sp. strain HZ) that grows with carbon dioxide as sole carbon source. Strain HZ is a Gram-negative, rod-shaped facultative anaerobe that was isolated from a gas-phase anaerobic packed-bed biofilm reactor treating perchlorate-contaminated groundwater. The ability of strain HZ to grow autotrophically with carbon dioxide as the sole carbon source was confirmed by demonstrating that biomass carbon (100.9%) was derived from CO2. Chemolithotrophic growth with hydrogen was coupled with complete reduction of perchlorate (10 mM) to chloride with a maximum doubling time of 8.9 h. Strain HZ also grew using acetate as the electron donor and chlorate, nitrate, or oxygen (but not sulphate) as an electron acceptor. Phylogenetic analysis of the 16S rRNA sequence placed strain HZ in the genus Dechloromonas within the beta subgroup of the Proteobacteria. The study of this and other novel perchlorate-reducing bacteria may lead to new, safe technologies for removing perchlorate and other chemical pollutants from drinking water.

  6. [Colonization of silicate bacterium strain NBT in wheat roots].

    Science.gov (United States)

    Sheng, Xiafang

    2003-11-01

    The strain NBT of silicate bacterium was labelled with streptomycin, and a stable streptomycin resistance strain NBT was obtained. Its colonization dynamics and affecting factors in wheat rhizosphere were studied in agar plates and greenhouse pots were studied by counting the method with selective medium. The results of pot culture experiment showed that strain NBT could successfully colonize in the rhizosphere of wheat. In pot cultures of sterile soil, the highest colonization level (3.4 x 10(7) cfu.g-1 root soil) was reached on 9th day after seeds sown; at 54th day, the population of strain NBT tended to stable, and decreased to 1.4 x 10(4) cfu.g-1 root soil. In pot cultures of unsterile soil, the highest colonization level (3.8 x 10(7) cfu.g-1 root soil) was reached at 9th day, and the population of strain NBT tended to a stationary state at 60th day, with the numbers being 1.4 x 10(4) cfu.g-1 root soil. Some biological and abiotic factors could greatly influence the colonization of the beneficial microorganism.

  7. Role of Individual Positive Charges in the Membrane Orientation and Activity of Transporters of the Small Multidrug Resistance Family

    NARCIS (Netherlands)

    Kolbusz, Magdalena A.; Slotboom, Dirk Jan; Lolkema, Juke S.

    2012-01-01

    The effect of individual positively charged residues on the orientation in the membrane was analyzed in three dual-topology transporters of the small. multidrug resistance (SMR) family: AAVE4701aave of Acidovorax avenae, EMREecol of Escherichia coli, and RRUA0272rrub of Rhodospirillum rubrum. It is

  8. Investigation of the effects of different carotenoids on the absorption and CD signals of light harvesting 1 complexes

    NARCIS (Netherlands)

    Georgakopoulou, S.; van der Zwan, G.; Olsen, J.D.; Hunter, C.N.; Niederman, R.A.; van Grondelle, R.

    2006-01-01

    Absorption and circular dichroism (CD) spectra of light-harvesting (LH)1 complexes from the purple bacteria Rhodobacter (Rba.) sphaeroides and Rhodospirillum (Rsp.) rubrum are presented. The complexes exhibit very low intensity, highly nonconservative, near-infrared (NIR) CD spectra. Absorption and

  9. Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium

    Czech Academy of Sciences Publication Activity Database

    Moon, C. D.; Pacheco, D. M.; Kelly, W. J.; Leahy, S. C.; Li, D.; Kopečný, Jan; Attwood, G. T.

    2008-01-01

    Roč. 58, - (2008), s. 2041-2045 ISSN 1466-5026 Institutional research plan: CEZ:AV0Z50450515 Keywords : Butyrivibrio * ruminal bacterium Subject RIV: EE - Microbiology, Virology Impact factor: 2.222, year: 2008

  10. Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences

    NARCIS (Netherlands)

    Vanfossen, A.L.; Verhaart, M.R.A.; Kengen, S.W.M.; Kelly, R.M.

    2009-01-01

    Co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on

  11. Molecular characterization of the glucose isomerase from the thermophilic bacterium Fervidobacterium gondwanense

    NARCIS (Netherlands)

    Kluskens, L.D.; Zeilstra, J.B.; Geerling, A.C.M.; Vos, de W.M.; Oost, van der J.

    2010-01-01

    The gene coding for xylose isomerase from the thermophilic bacterium Fervidobacterium gondwanense was cloned and overexpressed in Escherichia coli. The produced xylose isomerase (XylA), which closely resembles counterparts from Thermotoga maritima and T. neapolitana, was purified and characterized.

  12. High-level production of diacetyl in a metabolically engineered lactic acid bacterium

    DEFF Research Database (Denmark)

    2017-01-01

    The present invention provides a genetically modified lactic acid bacterium capable of producing diacetyl under aerobic conditions. Additionally the invention provides a method for producing diacetyl using the genetically modified lactic acid bacterium under aerobic conditions in the presence...... of a source of iron-containing porphyrin and a metal ion selected from Fe3+, Fe2+ and Cu2+. The lactic acid bacterium is genetically modified by deletion of those genes in its genome that encode polypeptides having lactate dehydrogenase (E.C 1.1.1.27/E.C.1.1.1.28); α-acetolactate decarboxylase (E.C 4.......C. 1.1.1.4/1.1.1.-) and alcohol dehydrogenase (E.C. 1.2.1.10) activity. The invention provides for use of the genetically modified lactic acid bacterium for the production of diacetyl and a food product....

  13. The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian

    2011-01-01

    A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows the bacter......A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...

  14. Effect of alginic acid decomposing bacterium on the growth of Laminaria japonica (Phaeophyceae).

    Science.gov (United States)

    Wang, You; Tang, Xue-Xi; Yang, Zhen; Yu, Zhi-Ming

    2006-01-01

    We collected the diseased blades of Laminaria japonica from Yantai Sea Farm from October to December 2002, and the alginic acid decomposing bacterium on the diseased blade was isolated and purified, and was identified as Alteromonas espejiana. This bacterium was applied as the causative pathogen to infect the blades of L. japonica under laboratory conditions. The aim of the present study was to identify the effects of the bacterium on the growth of L. japonica, and to find the possibly effective mechanism. Results showed that: (1) The blades of L. japonica exhibited symptoms of lesion, bleaching and deterioration when infected by the bacterium, and their growth and photosynthesis were dramatically suppressed. At the same time, the reactive oxygen species (ROS) generation enhanced obviously, and the relative membrane permeability increased significantly. The contents of malonaldehyde (MDA) and free fatty acid in the microsomol membrane greatly elevated, but the phospholipid content decreased. Result suggested an obvious peroxidation and deesterrification in the blades of L. japonica when infected by the bacterium. (2) The simultaneous assay on the antioxidant enzyme activities demonstrated that superoxide dismutase (SOD) and catalase (CAT) increased greatly when infected by the bacterium, but glutathione peroxidase (Gpx) and ascorbate peroxidase (APX) did not exhibit active responses to the bacterium throughout the experiment. (3) The histomorphological observations gave a distinctive evidence of the severity of the lesions as well as the relative abundance in the bacterial population on the blades after infection. The bacterium firstly invaded into the endodermis of L. japonica and gathered around there, and then resulted in the membrane damage, cells corruption and ultimately, the death of L. japonica.

  15. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin

    OpenAIRE

    Svitil, A. L.; Chadhain, S.; Moore, J. A.; Kirchman, D. L.

    1997-01-01

    Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), pro...

  16. Decomposition of Corn Seed Hemicellulose (CSH)by Bacterium No.101 during Accumulating Culture

    OpenAIRE

    今里, 祥子; 大宮, 満男

    1981-01-01

    The bacterium No.101 inducibly produced Corn seed hemicellulase when Corn seed hemicellulose was used as a sole carbon source in the culture medium. The decomposition of crude Corn seed hemicellulose by the bacterium No.101 during an accumulating culture was studied. Analysis of the culture medium indicated that the Corn seed hemicellulose (M. W. 730,000) was decomposed into polysaccharides with molecular weights of 2,000-3,000 during the cultivation of bacteria for one week.

  17. Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    Science.gov (United States)

    Oh, Young Joon; Jang, Ja-Young; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Kim, NamHee; Shin, Mi-Young; Park, Hyo Kyeong; Seo, Myung-Ji; Choi, Hak-Jong

    2017-12-01

    A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2 T , was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1-2 T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1 T (96.9%), V. sediminis YIM kkny3 T (96.8%), and V. salarius SA-Vb1 T (96.7%). The isolate grew at pH 6.5-10.0 (optimum, pH 8.5-9.0), 0.0-25.0% (w/v) NaCl (optimum, 10-15% NaCl), and 15-50°C (optimum, 37°C). The major menaquinone in the strain was menaquinone-7, and the main peptidoglycan of the strain was meso-diaminopimelic acid. The predominant fatty acids of the strain were iso-C 14:0 , anteisio-C 15:0 , iso- C 15:0 , and iso-C 16:0 (other components were < 10.0%). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G + C content of NKC1-2 T was 42.5 mol%. On the basis of these findings, strain NKC1-2 T is proposed as a novel species in the genus Virgibacillus, for which the name Virgibacillus kimchii sp. nov. is proposed (=KACC 19404 T =JCM 32284 T ). The type strain of Virgibacillus kimchii is NKC1-2T.

  18. Optimization protocol for the extraction of 6-gingerol and 6-shogaol from Zingiber officinale var. rubrum Theilade and improving antioxidant and anticancer activity using response surface methodology.

    Science.gov (United States)

    Ghasemzadeh, Ali; Jaafar, Hawa Z E; Rahmat, Asmah

    2015-07-30

    Analysis and extraction of plant matrices are important processes for the development, modernization, and quality control of herbal formulations. Response surface methodology is a collection of statistical and mathematical techniques that are used to optimize the range of variables in various experimental processes to reduce the number of experimental runs, cost , and time, compared to other methods. Response surface methodology was applied for optimizing reflux extraction conditions for achieving high 6-gingerol and 6-shogaol contents, and high antioxidant activity in Zingiber officinale var. rubrum Theilade . The two-factor central composite design was employed to determine the effects of two independent variables, namely extraction temperature (X1: 50-80 °C) and time (X2: 2-4 h), on the properties of the extracts. The 6-gingerol and 6-shogaol contents were measured using ultra-performance liquid chromatography. The antioxidant activity of the rhizome extracts was determined by means of the 1,1-diphenyl-2-picrylhydrazyl assay. Anticancer activity of optimized extracts against HeLa cancer cell lines was measured using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Increasing the extraction temperature and time induced significant response of the variables. The optimum extraction condition for all responses was at 76.9 °C for 3.4 h. Under the optimum condition, the corresponding predicted response values for 6-gingerol, 6-shogaol, and the antioxidant activity were 2.89 mg/g DW, 1.85 mg/g DW, and 84.3%, respectively. 6-gingerol and 6-shogaol were extracted under optimized condition to check the viability of the models. The values were 2.92 and 1.88 mg/g DW, and 84.0% for 6-gingerol, 6-shogaol, and the antioxidant activity respectively. The experimental values agreed with those predicted, thus indicating suitability of the models employed and the success of RSM in optimizing the extraction condition. With optimizing of reflux extraction

  19. Regulation of Polyhydroxybutyrate Synthesis in the Soil Bacterium Bradyrhizobium diazoefficiens.

    Science.gov (United States)

    Quelas, J I; Mesa, S; Mongiardini, E J; Jendrossek, D; Lodeiro, A R

    2016-07-15

    Polyhydroxybutyrate (PHB) is a carbon and energy reserve polymer in various prokaryotic species. We determined that, when grown with mannitol as the sole carbon source, Bradyrhizobium diazoefficiens produces a homopolymer composed only of 3-hydroxybutyrate units (PHB). Conditions of oxygen limitation (such as microoxia, oxic stationary phase, and bacteroids inside legume nodules) were permissive for the synthesis of PHB, which was observed as cytoplasmic granules. To study the regulation of PHB synthesis, we generated mutations in the regulator gene phaR and the phasin genes phaP1 and phaP4 Under permissive conditions, mutation of phaR impaired PHB accumulation, and a phaP1 phaP4 double mutant produced more PHB than the wild type, which was accumulated in a single, large cytoplasmic granule. Moreover, PhaR negatively regulated the expression of phaP1 and phaP4 as well as the expression of phaA1 and phaA2 (encoding a 3-ketoacyl coenzyme A [CoA] thiolases), phaC1 and phaC2 (encoding PHB synthases), and fixK2 (encoding a cyclic AMP receptor protein [CRP]/fumarate and nitrate reductase regulator [FNR]-type transcription factor of genes for microoxic lifestyle). In addition to the depressed PHB cycling, phaR mutants accumulated more extracellular polysaccharides and promoted higher plant shoot dry weight and competitiveness for nodulation than the wild type, in contrast to the phaC1 mutant strain, which is defective in PHB synthesis. These results suggest that phaR not only regulates PHB granule formation by controlling the expression of phasins and biosynthetic enzymes but also acts as a global regulator of excess carbon allocation and symbiosis by controlling fixK2 IMPORTANCE: In this work, we investigated the regulation of polyhydroxybutyrate synthesis in the soybean-nodulating bacterium Bradyrhizobium diazoefficiens and its influence in bacterial free-living and symbiotic lifestyles. We uncovered a new interplay between the synthesis of this carbon reserve polymer

  20. Vector transmission of a plant-pathogenic bacterium in the Arsenophonus clade sharing ecological traits with facultative insect endosymbionts.

    Science.gov (United States)

    Bressan, Alberto; Sémétey, Olivier; Arneodo, Joel; Lherminier, Jeannine; Boudon-Padieu, Elisabeth

    2009-11-01

    The planthopper Pentastiridius leporinus (Hemiptera: Cixiidae) is the major vector of a nonculturable plant-pathogenic gamma-3 proteobacterium associated with a disease of sugar beet called syndrome "basses richesses" (SBR). The bacterium, here called SBR bacterium, belongs to the Arsenophonous clade, which includes mostly insect-associated facultative symbionts. Assays using field-collected planthopper nymphs and adults were carried out to investigate the interaction of SBR bacterium with the insect vector and its transmission to sugar beet. Field-collected planthoppers showed a percentage of infection that averaged from 57% for early instar nymphs to near 100% for late instar nymphs and emerging adults. SBR bacterium was persistently transmitted by emerging adults. Root-feeding nymphs were able to inoculate SBR bacterium to sugar beet. The bacterium was transmitted vertically from infected parental females to their respective offspring with an average frequency of 30%. Real-time polymerase chain reaction assays on dissected planthopper internal organs revealed a high concentration of the bacterium within male and female reproductive organs and within female salivary glands. SBR-like bacteria were observed through transmission electron microscopy in the cytoplasm of different insect organs including ovaries, salivary glands, and guts with no evidence for cytological disorders. SBR bacterium seems to share common ecological traits of insect-transmitted plant pathogens and facultative insect endosymbionts suggesting it may have evolved primarily as an insect-associated bacterium.

  1. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  2. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  3. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Science.gov (United States)

    Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

  4. Proposal of a utilization of a luminous bacterium in the teaching and learning of radiation safety

    International Nuclear Information System (INIS)

    Hanafusa, Tadashi; Nagamatsu, Tomohiro; Kinno, Ikuo; Ono, Toshiro; Sakoda, Akihiro

    2011-01-01

    We isolated the luminous bacterium Vibrio phosphoreum H1 as a tool for education in radiation safety. It emits strong and steady luminescence. It is nonpathogenic, cannot be grown under normal low-salt conditions, and can be handled without any special equipment or reagents. We can cultivate it on a desk at room temperature, and can use a home-made broth containing a high salt concentration. Heat treatment at 37°C kills the bacterium, leading to its loss of luminescence. Although X-ray irradiation clearly kills it as the exposure dose increases, luminescence remains intact for some time, suggesting a delayed appearance of the biological effect of radiation exposure. We showed that the luminous bacterium Vibrio phosphoreum H1 can be used as a tool for teaching and learning about the effects of radiation. We proposed a practical plan that can be employed at high schools as well as universities. (author)

  5. [Isolation of endophytic antagonistic bacterium from Amorphophallus konjac and research on its antibacterial metabolite].

    Science.gov (United States)

    Zhou, Ying; Chen, Lin; Chai, Xin-Li; Yu, Zi-Niu; Sun, Ming

    2007-12-01

    An endophytic antagonistic bacterium was isolated from Amorphophallus konjac calli. In order to identify this bacterium, 16S rDNA was amplified and partially sequenced. Sequence comparison showed that this sequence has the highest similarity to that in Bacillus subtilis, with 99.0% identities. That demonstrated this bacterium belongs to Bacillus subtili , named BSn5. The extracted extracellular protein from strain BSn5 had antibacterial activity against Erwinia carotovora subp. carotovora, which was unstable after heated, sensitive to proteinase K and resistant to trypsin. There was only a 31.6kDa protein component as by SDS-PAGE detection. Nondenaturing polyacrylaminde gel was used to purify this protein. The purified 31.6kDa protein exhibited inhibitory activity against Erwinia carotovora subp. carotovora. This protein is different from all known metabolites from Bacillus subtilis, suggesting that it may be a novel antibacterial protein.

  6. Sensitivity of the bacterium Bacillus Thuringiensis as an insect disease agent to gamma-rays

    International Nuclear Information System (INIS)

    Merdam, A.I.; Abdu, R.M.

    1977-01-01

    The effect of gamma radiation on the viability of the entomopathogenic spore-forming bacterium, Bacillus thuringiensis, was tested. The different gamma doses varied much in their effect on such bacterium. All irradiated Bacillus suspensions with doses below 85 krad showed different degrees of inhibitory activity. However, bacterial suspensions irradiated at a dose of 90 krad. proved to promote spore germination. Changes in the physiological, and morphological characters of the irradiated Bacillus at these levels were detected. The new observed characters were induced at a particular dose level of 90 krad. These new characters are assumed to be due to genetic changes induced at this particular gamma dose

  7. Description of a bacterium associated with redmouth disease of rainbow trout (Salmo gairdneri)

    Science.gov (United States)

    Ross, A.J.; Rucker, R.R.; Ewing, W.H.

    1966-01-01

    A description was given of a gram-negative, peritrichously flagellated, fermentative bacterium that was isolated on numerous occasions from kidney tissues of rainbow trout (Salmo gairdneri) afflicted with redmouth disease. Although the bacteria apparently were members of the family Enterobacteriaceae, it was impossible to determine their taxonomic position within the family with certainty. Hence it was recommended that their taxonomic position remain sub judice for the present. As a temporary designation RM bacterium was used. Redmouth disease was transmitted from infected to normal fish through the medium of water.

  8. Draft genome sequence of a denitrifying bacterium Paracoccus marcusii PAMC 22219 isolated from Arctic marine sediment.

    Science.gov (United States)

    Cha, In-Tae; Song, Eun-Ji; Seok, Yoon Ji; Lee, Hyunjin; Park, Inhye; Lee, Yoo Kyung; Roh, Seong Woon; Choi, Hak-Jong; Nam, Young-Do; Seo, Myung-Ji

    2015-06-01

    A denitrifying bacterium, Paracoccus marcusii PAMC 22219, was isolated from Arctic marine sediment in Svalbard, Norway. The obtained contigs were 265 with genome size of 4.0Mb and G+C content of 66.1%. This bacterial genome revealed that it had nitrate and nitrite ammonification genes involved in the denitrification process, suggesting that P. marcusii PAMC 22219 is a denitrifying bacterium. This is the first genome that has been sequenced in the genus Paracoccus, isolated from an Arctic environment. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Isolation and characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium

    DEFF Research Database (Denmark)

    Mladenovska, Zuzana; Mathrani, Indra M.; Ahring, Birgitte Kiær

    1995-01-01

    and ethanol occurred as minor fermentation products. Only a restricted number of carbon sources (cellulose, xylan, starch, pectin, cellobiose, xylose, maltose and lactose) were used as substrates. During growth on Avicel, the bacterium produced free cellulases with carboxymethylcellulase and avicelase...... activity. The G + C content of the cellular DNA of strain 6A was 35.2 +/- 0.8 mol%. Complete 16S rDNA sequence analysis showed that strain 6A was phylogenetically related to Caldicellulosiruptor saccharolyticus. It is proposed that the isolated bacterium be named Caldicellulosiruptor lactoaceticus sp. nov....

  10. Draft Genome Sequence of Blood Disease Bacterium A2 HR-MARDI, a Pathogen Causing Banana Bacterial Wilt.

    Science.gov (United States)

    Badrun, Rafidah; Abu Bakar, Norliza; Laboh, Rozeita; Redzuan, Rohaiza; Bala Jaganath, Indu

    2017-06-01

    Blood disease bacterium A2 HR-MARDI was isolated from banana plants infected with banana blood disease and which were planted in Kuala Kangsar, Malaysia. Here, we report a draft genome sequence of blood disease bacterium A2 HR-MARDI, which could provide important information on the virulence mechanism of this pathogen. Copyright © 2017 Badrun et al.

  11. Draft Genome Sequence of Falsirhodobacter sp. Strain alg1, an Alginate-Degrading Bacterium Isolated from Fermented Brown Algae.

    Science.gov (United States)

    Mori, Tetsushi; Takahashi, Mami; Tanaka, Reiji; Shibata, Toshiyuki; Kuroda, Kouichi; Ueda, Mitsuyoshi; Takeyama, Haruko

    2014-08-21

    Falsirhodobacter sp. alg1 is an alginate-degrading bacterium, the second species from the nonphototrophic bacterial genus Falsirhodobacter. We report the first draft genome of a bacterium from this genus and point out possible important features related to alginate assimilation and its evolutionary aspects. Copyright © 2014 Mori et al.

  12. The Bacterium That Got Infected by a Cow!-Horizontal Gene ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 1. The Bacterium That Got Infected by a Cow! - Horizontal Gene Transfer and Evolution. Saurabh Dhawan Tomás John Ryan. General Article Volume 12 Issue 1 January 2007 pp 49-59 ...

  13. Two-dimensional gel-based alkaline proteome of the probiotic bacterium Lactobacillus acidophilus NCFM

    DEFF Research Database (Denmark)

    Majumder, Avishek; Cai, Liyang; Ejby, Morten

    2012-01-01

    Lactobacillus acidophilus NCFM (NCFM) is a well‐documented probiotic bacterium isolated from human gut. Detailed 2D gel‐based NCFM proteomics addressed the so‐called alkaline range, i.e., pH 6–11. Proteins were identified in 150 of the 202 spots picked from the Coomassie Brilliant Blue stained 2D...

  14. First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388

    Science.gov (United States)

    Poehlein, Anja; Alghaithi, Hamed S.; Chandran, Lenin; Chibani, Cynthia M.; Davydova, Elena; Dhamotharan, Karthikeyan; Ge, Wanwan; Gutierrez-Gutierrez, David A.; Jagirdar, Advait; Khonsari, Bahar; Nair, Kamal Prakash P. R.

    2014-01-01

    Clostridium litorale is a Gram-positive, rod-shaped, and spore-forming bacterium, which is able to use amino acids such as glycine, sarcosine, proline, and betaine as single carbon and energy sources via Stickland reactions. The genome consists of a circular chromosome (3.41 Mb) and a circular plasmid (27 kb). PMID:25081264

  15. Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

    Science.gov (United States)

    Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

    2011-05-01

    The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

  16. Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

    DEFF Research Database (Denmark)

    Tanaka, Reiji; Kawaichi, Satoshi; Nishimura, Hiroshi

    2006-01-01

    A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52-78°C (optimum, 70°C), pH 5-8 (optimum, pH 7...

  17. Identification and Characterization of Clostridium paraputrificum, a Chitinolytic Bacterium of Human Digestive Tract

    Czech Academy of Sciences Publication Activity Database

    Šimůnek, Jiří; Kopečný, Jan; Hodrová, Blanka; Bartoňová, Hana

    2002-01-01

    Roč. 47, č. 5 (2002), s. 559-564 ISSN 0015-5632 R&D Projects: GA AV ČR KSK5020115; GA ČR GA525/00/0984; GA AV ČR KSK5052113 Keywords : Clostridium paraputrificum * Chitinolytic bacterium * digestive tract Subject RIV: EE - Microbiology, Virology Impact factor: 0.979, year: 2002

  18. Isolation and Structure Elucidation of a Novel Yellow Pigment from the Marine Bacterium Pseudoalteromonas tunicata

    Directory of Open Access Journals (Sweden)

    N. Kumar

    2005-10-01

    Full Text Available The marine environment is a major source for many novel natural compounds. A new yellow pigment has been isolated from the marine bacterium P. tunicata and identified as a new member of the tambjamine class of compounds. The structural identification was achieved by a combination of 1D and 2D-NMR spectroscopy and high resolution mass spectrometry data.

  19. Intestinimonas butyriciproducens gen. nov., sp. nov., a novel butyrate-producing bacterium from the mouse intestine

    NARCIS (Netherlands)

    Kläring, K.; Hanske, L.; Bui, T.P.N.; Charrier, C.; Blaut, M.; Haller, D.; Plugge, C.M.; Clavel, T.

    2013-01-01

    Whilst creating a bacterial collection of strains from the mouse intestine, we isolated a Gram-negative, spore-forming, non-motile and strictly anaerobic rod-shaped bacterium from the caecal content of a TNFdeltaARE mouse. The isolate, referred to as strain SRB-521-5-IT, was originally cultured on a

  20. Purification and reconstitution of the glutamate carrier GltT of the thermophilic bacterium Bacillus stearothermophilus

    NARCIS (Netherlands)

    Gaillard, Isabelle; Slotboom, Dirk-Jan; Knol, Jan; Lolkema, Juke S.; Konings, Wil N.

    1996-01-01

    An affinity tag consisting of six adjacent histidine residues followed by an enterokinase cleavage site was genetically engineered at the N-terminus of the glutamate transport protein GltT of the thermophilic bacterium Bacillus stearothermophilus. The fusion protein was expressed in Escherichia coli

  1. Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery

    DEFF Research Database (Denmark)

    Martinez, Virginia; Herencias, Cristina; Jurkevitch, Edouard

    2016-01-01

    This work examines the potential of the predatory bacterium Bdellovibrio bacteriovorus HD100, an obligate predator of other Gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. The bio-product targets to be recovered...

  2. Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

    KAUST Repository

    Katuri, Krishna

    2017-03-03

    Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

  3. Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19

    Science.gov (United States)

    Papke, R. Thane; de la Haba, Rafael R.; Infante-Domínguez, Carmen; Pérez, Dolores; Sánchez-Porro, Cristina; Lapierre, Pascal

    2013-01-01

    Marinobacter lipolyticus strain SM19, isolated from saline soil in Spain, is a moderately halophilic bacterium belonging to the class Gammaproteobacteria. Here, we report the draft genome sequence of this strain, which consists of a 4.0-Mb chromosome and which is able to produce the halophilic enzyme lipase LipBL. PMID:23814106

  4. Draft Genome Sequence of the Moderately Halophilic Bacterium Pseudoalteromonas ruthenica Strain CP76.

    Science.gov (United States)

    de la Haba, Rafael R; Sánchez-Porro, Cristina; León, María José; Papke, R Thane; Ventosa, Antonio

    2013-05-23

    Pseudoalteromonas ruthenica strain CP76, isolated from a saltern in Spain, is a moderately halophilic bacterium belonging to the Gammaproteobacteria. Here we report the draft genome sequence, which consists of a 4.0-Mb chromosome, of this strain, which is able to produce the extracellular enzyme haloprotease CPI.

  5. Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis

    Directory of Open Access Journals (Sweden)

    Johan Larsbrink

    2017-04-01

    Full Text Available The secretion of carbohydrate-degrading enzymes by a bacterium sourced from a softwood forest environment has been investigated by mass spectrometry. The findings are discussed in full in the research article “Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis” in Journal of Proteomics by Larsbrink et al. ([1], doi: 10.1016/j.jprot.2017.01.003. The bacterium was grown on three carbon sources (glucose, glucomannan, and galactomannan which are likely to be nutrient sources or carbohydrate degradation products found in its natural habitat. The bacterium was grown on solid agarose plates to mimic the natural behaviour of growth on a solid surface. Secreted proteins were collected from the agarose following trypsin-mediated hydrolysis to peptides. The different carbon sources led to the secretion of different numbers and types of proteins. Most carbohydrate-degrading enzymes were found in the glucomannan-induced cultures. Several of these enzymes may have biotechnological potential in plant cell wall deconstruction for biofuel or biomaterial production, and several may have novel activities. A subset of carbohydrate-active enzymes (CAZymes with predicted activities not obviously related to the growth substrates were also found in samples grown on each of the three carbohydrates. The full dataset is accessible at the PRIDE partner repository (ProteomeXchange Consortium with the identifier PXD004305, and the full list of proteins detected is given in the supplementary material attached to this report.

  6. Active efflux systems in the solvent-tolerant bacterium Pseudomonas putida S12

    NARCIS (Netherlands)

    Kieboom, J.

    2002-01-01

    The aim of the research presented in this thesis was to study the molecular mechanisms of organic solvent tolerance in Pseudomonas putida S12. This bacterium is capable of growth at saturated solvent concentrations, which are lethal to normal bacteria. Organic

  7. Energy-Dependent Uptake of 4-Chlorobenzoate in the Coryneform Bacterium NTB-1

    NARCIS (Netherlands)

    Groenewegen, Peter E.J.; Driessen, Arnold J.M.; Konings, Wil N.; de Bont, J.A.M.

    The uptake of 4-chlorobenzoate (4-CBA) in intact cells of the coryneform bacterium NTB-1 was investigated. Uptake and metabolism of 4-CBA were observed in cells grown in 4-CBA but not in glucose-grown cells. Under aerobic conditions, uptake of 4-CBA occurred with a high apparent affinity (apparent

  8. Energy transduction in the thermophilic anaerobic bacterium Clostridium fervidus is exclusively coupled to sodium ions

    NARCIS (Netherlands)

    SPEELMANS, G; POOLMAN, B; ABEE, T; KONINGS, WN

    1993-01-01

    The thermophilic, peptidolytic, anaerobic bacterium Clostridium fervidus is unable to generate a pH gradient in the range of 5.5-8.0, which limits growth of the organism to a narrow pH range (6.3-7.7). A significant membrane potential (DELTApsi almost-equal-to -60 mV) and chemical gradient of Na+

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

    Science.gov (United States)

    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.

  10. Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

    Science.gov (United States)

    Jin, Decai; Zhou, Lisha; Wu, Liang; An, Wei; Zhao, Lin

    2014-01-01

    Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated marine sediments. Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment. PMID:24482505

  11. Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum subsp. nov., a thermophilic, syntrophic, propionate-oxidizing, spore-forming bacterium

    NARCIS (Netherlands)

    Plugge, C.M.; Balk, M.; Stams, A.J.M.

    2002-01-01

    From granular sludge from a laboratory-scale upflow anaerobic sludge bed reactor operated at 55 degrees C with a mixture of volatile fatty acids as feed, a novel anaerobic, moderately thermophilic, syntrophic, spore-forming bacterium, strain TPO, was enriched on propionate in co-culture with

  12. Novel Analysis of Bacterium-Substratum Bond Maturation Measured Using a Quartz Crystal Microbalance

    NARCIS (Netherlands)

    Olsson, Adam L. J.; van der Mei, Henny C.; Busscher, Henk J.; Sharma, Prashant K.

    2010-01-01

    Studies in now displacement systems have shown that the reversibility of bacterial adhesion decreases within seconds to minutes after initial contact of a bacterium with a substratum surface. Atomic force microscopy (A FM) has confirmed that the forces mediating bacterial adhesion increase over a

  13. The 2015 Nobel Prize in Physiology or Medicine: A Soil Bacterium ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 4. The 2015 Nobel Prize in Physiology or Medicine: A Soil Bacterium and a Chinese Herb Steal the Show. Pundi N Rangarajan. General Article Volume 21 Issue 4 April 2016 pp 315-326 ...

  14. Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater

    Science.gov (United States)

    A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50**T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rDNA sequences revealed that the novel isolate represented...

  15. New recombinant bacterium comprises a heterologous gene encoding glycerol dehydrogenase and/or an up-regulated native gene encoding glycerol dehydrogenase, useful for producing ethanol

    DEFF Research Database (Denmark)

    2010-01-01

    TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preparation (claimed): Producing recombinant bacterium having enhanced ethanol production characteristics when cultivated in growth medium comprising glycerol comprises: (a) transforming a parental bacterium by (i) the insertion of a heterologous gene encoding...

  16. Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

    KAUST Repository

    Narita, Yuko

    2017-08-18

    Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

  17. Isolation, identification, and biocontrol of antagonistic bacterium against Botrytis cinerea after tomato harvest

    Directory of Open Access Journals (Sweden)

    Jun-Feng Shi

    Full Text Available ABSTRACT Tomato is one of the most important vegetables in the world. Decay after harvest is a major issue in the development of tomato industry. Currently, the most effective method for controlling decay after harvest is storage of tomato at low temperature combined with usage of chemical bactericide; however, long-term usage of chemical bactericide not only causes pathogen resistance but also is harmful for human health and environment. Biocontrol method for the management of disease after tomato harvest has great practical significance. In this study, antagonistic bacterium B-6-1 strain was isolated from the surface of tomato and identified as Enterobacter cowanii based on morphological characteristics and physiological and biochemical features combined with sequence analysis of 16SrDNA and ropB gene and construction of dendrogram. Effects of different concentrations of antagonistic bacterium E. cowanii suspension on antifungal activity after tomato harvest were analyzed by mycelium growth rate method. Results revealed that antifungal activity was also enhanced with increasing concentrations of antagonistic bacterium; inhibitory rates of 1 × 105 colony-forming units (cfu/mL antagonistic bacterial solution on Fusarium verticillioides, Alternaria tenuissima, and Botrytis cinerea were 46.31%, 67.48%, and 75.67%, respectively. By using in vivo inoculation method, it was further confirmed that antagonistic bacterium could effectively inhibit the occurrence of B. cinerae after tomato harvest, biocontrol effect of 1 × 109 cfu/mL zymotic fluid reached up to 95.24%, and antagonistic bacterium E. cowanii has biocontrol potential against B. cinerea after harvest of fruits and vegetables.

  18. Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

    KAUST Repository

    Wang, Yong

    2016-07-01

    Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

  19. The influence of quorum sensing in compartment II of the MELiSSA loop

    Science.gov (United States)

    Condori, Sandra; Mastroleo, Felice; Wattiez, Ruddy; Leys, Natalie

    MELiSSA (Micro-Ecological Life Support System Alternative) has been conceived as a 5 compartments microorganisms and higher plants recycling system for long haul space flights. Rhodospirillum rubrum S1H colonizes compartment II. Previous work reported that continuous culture of the bacterium in a photobioreactor could lead to thick biofilm formation, leading to bioreactor arrest. Our aim is to investigate the unknown quorum sensing (QS) system of R. rubrum S1H, specifically under MELiSSA relevant culture conditions meaning light anaerobic (LAN) and using acetate as carbon source. In that purpose an autoinducer synthase gene (Rru_A3396) knockout mutant was constructed by allelic exchange generating strain M68. In addition phenotypic comparison between wild type (WT) and M68 was performed. Results of thin layer chromatography assay where Agrobacterium tumefaciens NT1 have been used as reporter strain showed that WT produces acyl-homoserine lactones (AHLs) from C4 to C12 acyl carbon chain length; however, in M68 no AHLs were detected confirming that gene Rru_A3396 (named rruI) encodes an autoinducer synthase. Interestingly under a low shear or static environment M68 showed cell aggregation similar as reported in a closely related bacterium Rhodobacter sphaeroides (cerI mutant). In contrast to WT, M68 did not form biofilm and exhibited a decreased motility and pigment content. M68 vs wild type transcriptomics results showed that 326 genes were statistically significant differentially expressed. Downregulation of genes related to photosynthesis e.g., reaction center subunits, light harvesting complex and photosynthetic assembly proteins was observed. Similar results were obtained for preliminary proteomic analysis. Results obtained showed that in R. rubrum S1H the AHL-based QS system regulates almost 8% of the genome which is linked to biofilm formation among other biological processes described above. Since strain M68 could not be used in compartment II due to its less

  20. Bioconversion of Waste Gases into Biofuel via Fermentation in a Continuous Stirred Tank Bioreactor

    Directory of Open Access Journals (Sweden)

    Najafpour, G.

    2005-01-01

    Full Text Available Biological hydrogen production was carried out in a continuous stirred tank bioreactor. A photosynthetic bacterium, Rhodospirillum rubrum, was used as biocatalyst to oxidize carbon monoxides in the waste gas generated from biomass in a gasification process. The fresh liquid media was supplied for microbial growth which contained sodium acetate as carbon source at initial concentration of 4 gL-1. The optimum media space velocity or the suitable ratio of liquid flow rate to the reactor volume (F/VL was 0.02 h-1. At the steady state condition, the concentration of acetate was independent of the dilution rate and it was approximately 1.5 gL-1. The average cell dry weight in the fermentation broth was at satisfactory concentration, approximately 3.4 gL-1 with dilution rate at 0.55 mL min-1. The maximum value of KLa and CO conversion were about 58 h-1 and 80%, respectively, with agitation speed at 500 rpm and gas flow rate at 14 mL min-1. At this condition, the maximum yield of hydrogen production was 0.82 mmol H2•mmol-1 CO.

  1. Quenching Capabilities of Long-Chain Carotenoids in Light-Harvesting-2 Complexes from Rhodobacter sphaeroides with an Engineered Carotenoid Synthesis Pathway.

    Science.gov (United States)

    Dilbeck, Preston L; Tang, Qun; Mothersole, David J; Martin, Elizabeth C; Hunter, C Neil; Bocian, David F; Holten, Dewey; Niedzwiedzki, Dariusz M

    2016-06-23

    Six light-harvesting-2 complexes (LH2) from genetically modified strains of the purple photosynthetic bacterium Rhodobacter (Rb.) sphaeroides were studied using static and ultrafast optical methods and resonance Raman spectroscopy. These strains were engineered to incorporate carotenoids for which the number of conjugated groups (N = NC═C + NC═O) varies from 9 to 15. The Rb. sphaeroides strains incorporate their native carotenoids spheroidene (N = 10) and spheroidenone (N = 11), as well as longer-chain analogues including spirilloxanthin (N = 13) and diketospirilloxantion (N = 15) normally found in Rhodospirillum rubrum. Measurements of the properties of the carotenoid first singlet excited state (S1) in antennas from the Rb. sphaeroides set show that carotenoid-bacteriochlorophyll a (BChl a) interactions are similar to those in LH2 complexes from various other bacterial species and thus are not significantly impacted by differences in polypeptide composition. Instead, variations in carotenoid-to-BChl a energy transfer are primarily regulated by the N-determined energy of the carotenoid S1 excited state, which for long-chain (N ≥ 13) carotenoids is not involved in energy transfer. Furthermore, the role of the long-chain carotenoids switches from a light-harvesting supporter (via energy transfer to BChl a) to a quencher of the BChl a S1 excited state B850*. This quenching is manifested as a substantial (∼2-fold) reduction of the B850* lifetime and the B850* fluorescence quantum yield for LH2 housing the longest carotenoids.

  2. Strategies to enhance the excitation energy-transfer efficiency in a light-harvesting system using the intra-molecular charge transfer character of carotenoids

    Energy Technology Data Exchange (ETDEWEB)

    Yukihira, Nao [Department of Applied Chemistry for Environment; School of Science and Technology; Kwansei Gakuin University; Sanda; Japan; Sugai, Yuko [Department of Applied Chemistry for Environment; School of Science and Technology; Kwansei Gakuin University; Sanda; Japan; Fujiwara, Masazumi [Department of Applied Chemistry for Environment; School of Science and Technology; Kwansei Gakuin University; Sanda; Japan; Kosumi, Daisuke [Institute of Pulsed Power Science; Kumamoto University; Kumamoto; Japan; Iha, Masahiko [South Product Co. Ltd.; Uruma-shi; Japan; Sakaguchi, Kazuhiko [Department of Chemistry; Graduate School of Science; Osaka City University; Osaka 558-8585; Japan; Katsumura, Shigeo [Department of Chemistry; Graduate School of Science; Osaka City University; Osaka 558-8585; Japan; Gardiner, Alastair T. [Glasgow Biomedical Research Centre; University of Glasgow; 126 University Place; Glasgow, G12 8QQ; UK; Cogdell, Richard J. [Glasgow Biomedical Research Centre; University of Glasgow; 126 University Place; Glasgow, G12 8QQ; UK; Hashimoto, Hideki [Department of Applied Chemistry for Environment; School of Science and Technology; Kwansei Gakuin University; Sanda; Japan

    2017-01-01

    Fucoxanthin is a carotenoid that is mainly found in light-harvesting complexes from brown algae and diatoms. Due to the presence of a carbonyl group attached to polyene chains in polar environments, excitation produces an excited intra-molecular charge transfer. This intra-molecular charge transfer state plays a key role in the highly efficient (~95%) energy-transfer from fucoxanthin to chlorophyllain the light-harvesting complexes from brown algae. In purple bacterial light-harvesting systems the efficiency of excitation energy-transfer from carotenoids to bacteriochlorophylls depends on the extent of conjugation of the carotenoids. In this study we were successful, for the first time, in incorporating fucoxanthin into a light-harvesting complex 1 from the purple photosynthetic bacterium,Rhodospirillum rubrumG9+ (a carotenoidless strain). Femtosecond pump-probe spectroscopy was applied to this reconstituted light-harvesting complex in order to determine the efficiency of excitation energy-transfer from fucoxanthin to bacteriochlorophyllawhen they are bound to the light-harvesting 1 apo-proteins.

  3. Mitigation of membrane biofouling by a quorum quenching bacterium for membrane bioreactors.

    Science.gov (United States)

    Ham, So-Young; Kim, Han-Shin; Cha, Eunji; Park, Jeong-Hoon; Park, Hee-Deung

    2018-06-01

    In this study, a quorum-quenching (QQ) bacterium named HEMM-1 was isolated at a membrane bioreactor (MBR) plant. HEMM-1 has diplococcal morphology and 99% sequence identity to Enterococcus species. The HEMM-1 cell-free supernatant (CFS) showed higher QQ activities than the CFS of other QQ bacteria, mostly by degrading N-acyl homoserine lactones (AHLs) with short acyl chains. Instrumental analyses revealed that HEMM-1 CFS degraded AHLs via lactonase activity. Under static, flow, and shear conditions, the HEMM-1 CFS was effective in reducing bacterial and activated-sludge biofilms formed on membrane surfaces. In conclusion, the HEMM-1 isolate is a QQ bacterium applicable to the control of biofouling in MBRs via inhibition of biofilm formation on membrane surfaces. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Experimental study of the quasi 1d motion of a ``robot bacterium'' within a tube

    Science.gov (United States)

    Liu, Kai; Jiao, Yusheng; Li, Shutong; Ding, Yang; Xu, Xinliang; Complex Fluids Team

    2017-11-01

    Understanding how solid boundary influences the motion of a micro-swimmer can be quite important. Here we experimentally study the problem with a system of centi-meter size ``robot bacterium'' immersed in the solvent silicon oil. Equipped with build-in battery and motor, the robot mimics a free swimmer and the overall Reynolds number of the system is kept very small as we use silicon oil with very high viscosity. The motion of centi-meter size ``robot bacterium'' within cylindrical tube is experimentally studied in detail. Our results show that robot bacteria with different shapes respond very different to the solid boundary. For certain shapes the swimmers actually swim much faster within a tube, when compared to their motions without any confinement, in good agreement with our numerical evaluations of the hydrodynamics of the system.

  5. Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

    Science.gov (United States)

    Tago, Damian; Meyer, Damien F

    2016-01-01

    Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria.

  6. Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

    International Nuclear Information System (INIS)

    Aguayo, S; Bozec, L; Donos, N; Spratt, D

    2015-01-01

    The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine. (topical review)

  7. Exo- and surface proteomes of the probiotic bacterium Lactobacillus acidophilus NCFM

    DEFF Research Database (Denmark)

    Celebioglu, Hasan Ufuk; Svensson, Birte

    2017-01-01

    Lactobacillus acidophilus NCFM is a well-known probiotic bacterium extensively studied for its beneficial health effects. Exoproteome (proteins exported into culture medium) and surface proteome (proteins attached to S-layer) of this probiotic were identified by using 2DE followed by MALDI TOF MS......-classically secreted proteins. Identification of exo- and surface proteomes contributes describing potential protein-mediated probiotic-host interactions....

  8. Fourier transform infrared spectroscopic study of intact cells of the nitrogen-fixing bacterium Azospirillum brasilense

    Science.gov (United States)

    Kamnev, A. A.; Ristić, M.; Antonyuk, L. P.; Chernyshev, A. V.; Ignatov, V. V.

    1997-06-01

    The data of Fourier transform infrared (FTIR) spectroscopic measurements performed on intact cells of the soil nitrogen-fixing bacterium Azospirillum brasilense grown in a standard medium and under the conditions of an increased metal uptake are compared and discussed. The structural FTIR information obtained is considered together with atomic absorption spectrometry (AAS) data on the content of metal cations in the bacterial cells. Some methodological aspects concerning preparation of bacterial cell samples for FTIR measurements are also discussed.

  9. Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3

    OpenAIRE

    Manzoor, Shahid; M?ller, Bettina; Niazi, Adnan; Schn?rer, Anna; Bongcam-Rudloff, Erik

    2015-01-01

    Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mesophilic methanogenic digester. It has been shown to oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming methane. The draft genome shows a total size of 3,196,921?bp, encoding 3,688 open reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA genes. Here, we are...

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

    Science.gov (United States)

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

    2016-12-01

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

  11. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

    OpenAIRE

    Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; Klenk, Hans-Peter; Spring, Stefan; G?ker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.

    2017-01-01

    © 2017 Kublanov, Sigalova, Gavrilov, Lebedinsky, Rinke, Kovaleva, Chernyh, Ivanova, Daum, Reddy, Klenk, Spring, Göker, Reva, Miroshnichenko, Kyrpides, Woyke, Gelfand, Bonch-Osmolovskaya. The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to impl...

  12. Bacterium induces cryptic meroterpenoid pathway in the pathogenic fungus Aspergillus fumigatus.

    Science.gov (United States)

    König, Claudia C; Scherlach, Kirstin; Schroeckh, Volker; Horn, Fabian; Nietzsche, Sandor; Brakhage, Axel A; Hertweck, Christian

    2013-05-27

    Stimulating encounter: The intimate, physical interaction between the soil-derived bacterium Streptomyces rapamycinicus and the human pathogenic fungus Aspergillus fumigatus led to the activation of an otherwise silent polyketide synthase (PKS) gene cluster coding for an unusual prenylated polyphenol (fumicycline A). The meroterpenoid pathway is regulated by a pathway-specific activator gene as well as by epigenetic factors. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

    KAUST Repository

    Li, Yongxin

    2012-02-03

    Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

  14. Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

    KAUST Repository

    Harjes, Janno

    2014-03-06

    The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

  15. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

    KAUST Repository

    Haroon, Mohamed

    2016-02-11

    A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

  16. Alteration of the Canine Small-Intestinal Lactic Acid Bacterium Microbiota by Feeding of Potential Probiotics

    OpenAIRE

    Manninen, Titta J. K.; Rinkinen, Minna L.; Beasley, Shea S.; Saris, Per E. J.

    2006-01-01

    Five potentially probiotic canine fecal lactic acid bacterium (LAB) strains, Lactobacillus fermentum LAB8, Lactobacillus salivarius LAB9, Weissella confusa LAB10, Lactobacillus rhamnosus LAB11, and Lactobacillus mucosae LAB12, were fed to five permanently fistulated beagles for 7 days. The survival of the strains and their potential effects on the indigenous intestinal LAB microbiota were monitored for 17 days. Denaturing gradient gel electrophoresis (DGGE) demonstrated that the five fed LAB ...

  17. Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

    Science.gov (United States)

    Liu, Yang; Wang, Runping; Zeng, Runying

    2014-12-01

    Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    OpenAIRE

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

    1996-01-01

    A novel sulfate-reducing bacterium isolated from fuel-contaminated subsurface soil, strain PRTOL1, mineralizes toluene as the sole electron donor and carbon source under strictly anaerobic conditions. The mineralization of 80% of toluene carbon to CO2 was demonstrated in experiments with [ring-U-14C]toluene; 15% of toluene carbon was converted to biomass and nonvolatile metabolic by-products, primarily the former. The observed stoichiometric ratio of moles of sulfate consumed per mole of tolu...

  19. DNA damage response in a radiation resistant bacterium Deinococcus radiodurans: a paradigm shift

    International Nuclear Information System (INIS)

    Misra, H.S.

    2015-01-01

    Deinococcusradiodurans is best known for its extraordinary resistance to gamma radiation with its D 10 12kGy, and several other DNA damaging agents including desiccation to less than 5% humidity and chemical xenotoxicants. An efficient DNA double strand break (DSB) repair and its ability to protect biomolecules from oxidative damage are a few mechanisms attributed to these phenotypes in this bacterium. Although it regulates its proteome and transcriptome in response to DNA damage for its growth and survival, it lacks LexA mediated classical SOS response mechanism. Since LexA mediated damages response mechanism is highly and perhaps only, characterized DNA damage response processes in prokaryotes, this bacterium keeps us guessing how it responds to extreme doses of DNA damage. Interestingly, this bacterium encodes a large number of eukaryotic type serine threonine/tyrosine protein kinases (eST/YPK), phosphatases and response regulators and roles of eST/YPKs in cellular response to DNA damage and cell cycle regulations are well established in eukaryotes. Here, we characterized an antioxidant and DNA damage inducible eST/YPK (RqkA) and established its role in extraordinary radioresistance and DSB repair in this bacterium. We identified native phosphoprotein substrates for this kinase and demonstrated the involvement of some of these proteins phosphorylation in the regulation of DSB repair and growth under radiation stress. Findings suggesting the possible existence of eST/YPK mediated DNA damage response mechanism as an alternate to classical SOS response in this prokaryote would be discussed. (author)

  20. Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)".

    Science.gov (United States)

    Yang, Yu; Yang, Jun; Jiang, Lei

    2016-08-19

    Yoshida et al (Report, 11 March 2016, p. 1196) reported that the bacterium Ideonella sakaiensis 201-F6 can degrade and assimilate poly(ethylene terephthalate) (PET). However, the authors exaggerated degradation efficiency using a low-crystallinity PET and presented no straightforward experiments to verify depolymerization and assimilation of PET. Thus, the authors' conclusions are rather misleading. Copyright © 2016, American Association for the Advancement of Science.

  1. IDENTIFICATION AND PATHOGENICITY OF ISOLATE OF BACTERIUM CAUSED LEAF BLIGHT DISEASE ON Maranta arundinacea

    Directory of Open Access Journals (Sweden)

    Supriadi Supriadi

    2018-01-01

    Full Text Available Arrowroot (Maranta arundinacea L is a multi-functional plant used as a source of medicinal, carbohydrate (especially the green leaf type and also as ornamental plant (the streaked white leaf type. A leaf blight disease is recently found on the streaked white type in Bogor. Preliminary observation indicated that the disease was associated with bacterial infection. The cause of the disease has not been studied. This study was aimed to identify the cause of bacterial leaf blight disease. Experiments were conducted in the laboratory of Research Institute for Spice and Medicinal Crops in Bogor. Suspected bacteria were isolated from diseased leaves. The results showed that the bacterium produced white to brownish colonies on rich agar media containing peptone or cassamino acid. 3-5 mm in diameter, circular, and did not yield fluorescent pigment on King’s B medium. The bacterium formed rod cells, Gram negative, accumulated poly β hydroxybutyrate, utilized glucose under aerobic condition, not hydrolyse arginine and starch, positive catalase, insensitive to tetrazolium salt (0.1%, and grew at 35oC. The bacterium neither producted xanthomonadin pigment nor reduced nitrate to nitrite. The pathogen was tolerant to penicillin and oxolinic acid, but sensitive to streptomycin and oxytetracycline at high concentration (1.000 ppm. These characteristics met to those of Pseudomonas cepacia. Pathogenicity test on detached leaves showed that the typical symptom of blight was similar to that of natural infection on arrowroot. This is the first report on occurrence of P cepacia on arrowroot plant.

  2. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides.

    Science.gov (United States)

    Devendran, Saravanan; Abdel-Hamid, Ahmed M; Evans, Anton F; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I; Cann, Isaac

    2016-10-17

    Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.

  3. Searching for the Bacterial Effector: The Example of the Multi-Skilled Commensal Bacterium Faecalibacterium prausnitzii

    Directory of Open Access Journals (Sweden)

    Rebeca Martín

    2018-03-01

    Full Text Available Faecalibacterium prausnitzii represents approximately 5% of the total fecal microbiota in healthy adults being one of the most abundant bacterium in the human intestinal microbiota of healthy adults. Furthermore, this bacterium has been proposed to be a sensor and a major actor of the human intestinal health because of its importance in the gut ecosystem. In this context, F. prausnitzii population levels have been found to be reduced in patients suffering from several syndromes and diseases such as inflammatory bowel diseases. These diseases are characterized by a breakage of the intestinal homeostasis called dysbiosis and the use of F. prausnitzii as a next generation probiotic (also called live biotherapeutics has been proposed as a natural tool to restore such dysbiosis within the gut. Nevertheless, despite the potential importance of this bacterium in human health, little is known about its main effectors underlying its beneficial effects. In this perspective note, we aim to present the actual state in the research about F. prausnitzii effectors and the future milestones in this field.

  4. FtsZ from radiation resistant bacterium Deinococcus radiodurans is different from its characterized homologues

    International Nuclear Information System (INIS)

    Mehta, Kruti P.; Misra, H.S.

    2012-01-01

    Polymerization/depolymerization dynamics of FtsZ and its GTPase activity are interdependent and the regulation of these processes determines the growth rate in a bacterium. Deinococcus radiodurans R1 that is best known for its extraordinary radiation resistance and efficient DNA double strand break repair is a comparatively slow growing bacterium and its growth gets arrested in response to gamma radiation. Mechanisms of cell division and its regulation under gamma stressed growth condition would be worth investigating. Genome of this bacterium encodes at least all the known components of divisome. Recombinant FtsZ of D. radiodurans (drFtsZ) preferred Mg 2+ for its GTPase activity. Relatively a very low GTPase activity was observed in presence of Mn 2+ , Co 2+ and Ni 2+ while release of inorganic phosphate could not be detected in presence of other divalent ions including Ca 2+ . GTPase activity of drFtsZ was lower than E. coli but higher than Mycobacterium and it required both Mg 2+ and GTP for its polymerization. Its GTPase activity did not increase with increasing concentration of Mg 2+ and correlates with the bundling of protofilaments. Results obtained from transmission electron microscopy and sedimentation analysis supported the reciprocal correlation of polymerization/depolymerization with the levels of GTPase activity. Dynamic light scattering in presence of 5mM or higher concentration of Mg 2+ and Mn 2 showed a characteristic cyclic change in light scattering without addition of extra metal ion or GTP

  5. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin.

    Science.gov (United States)

    Svitil, A L; Chadhain, S; Moore, J A; Kirchman, D L

    1997-02-01

    Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products.

  6. [Identification and antagonistic activities of an endophytic bacterium MGP3 isolated from papaya fruit].

    Science.gov (United States)

    Shi, Jingying; Liu, Aiyuan; Li, Xueping; Chen, Weixin

    2011-09-01

    Postharvest decay resulted from anthracnose caused by pathogens Colletotrichum gloeosporioides and blight diseases caused by Phytophthora nicotianae leads to significant loss of papaya fruits. In order to reduce such loss, we isolated endophytic bacteria that may possess powerful antagonistic activities toward these pathogens for effective biological control of anthracnose and blight diseases. The methods of dilution and inhibition circle were used for isolating and screening endophytic bacteria from papaya fruit. Based on morphological, physiological and biochemical characteristics, and homology analysis of the partial sequence of 16S rDNA, an endophytic bacterium was identified. The colonization of the antagonistic endophyte in papaya was detected by inoculating suspension of strains in caudices of papaya plant after Rifampicin-resistant mutants (rif(r)) induction. The effects on diseases caused by Colletotrichum gloeosporioides and Phytophthora nicotianae were tested by preharvest and postharvest experiments. One of the endophytic bacteria named MGP3 was selected from the papaya pericarp and identified as Pseudomonas aeruginosa (Accession No. JF708186). This bacterium was able to colonize in the laminae, leafstalk or pericarp of papaya, and strongly inhibit 10 phytopathogens. In the postharvest experiment, MGP3 inhibited 50% anthracnose and 71% blight of harvested papaya fruits. The application of MGP3 at five preharvest stages of papaya significantly reduced latent infection rate of Colletotrichum gloeosporioides and disease index of anthracnose. Antagonistic endophytic bacterium MGP3 isolated from papaya fruit had potential application value as a biological control agent.

  7. A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.

    Science.gov (United States)

    Lavy, Adi; Keren, Ray; Yu, Ke; Thomas, Brian C; Alvarez-Cohen, Lisa; Banfield, Jillian F; Ilan, Micha

    2018-02-01

    Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides

    Science.gov (United States)

    Devendran, Saravanan; Abdel-Hamid, Ahmed M.; Evans, Anton F.; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I.; Cann, Isaac

    2016-10-01

    Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.

  9. Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

    Directory of Open Access Journals (Sweden)

    Bhagwan N. Rekadwad

    2016-01-01

    Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

  10. In search of an uncultured human-associated TM7 bacterium in the environment.

    Science.gov (United States)

    Dinis, Jorge M; Barton, David E; Ghadiri, Jamsheed; Surendar, Deepa; Reddy, Kavitha; Velasquez, Fernando; Chaffee, Carol L; Lee, Mei-Chong Wendy; Gavrilova, Helen; Ozuna, Hazel; Smits, Samuel A; Ouverney, Cleber C

    2011-01-01

    We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA gene homology to a group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as TM7a-like) was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites. We speculate that upon further characterization of the physiology and genetics of the TM7a-like bacterium from environmental sources and confirmation of its genomic identity to human-associated counterparts it will serve as model organisms to better understand its role in human health. The approach proposed circumvents difficulties imposed by sampling humans, provides an alternative strategy to characterizing some diseases of unknown etiology, and renders a much needed understanding of the ecophysiological role hundreds of unique Bacteria and Archaea strains play in mixed microbial communities.

  11. In search of an uncultured human-associated TM7 bacterium in the environment.

    Directory of Open Access Journals (Sweden)

    Jorge M Dinis

    Full Text Available We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA gene homology to a group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as TM7a-like was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites. We speculate that upon further characterization of the physiology and genetics of the TM7a-like bacterium from environmental sources and confirmation of its genomic identity to human-associated counterparts it will serve as model organisms to better understand its role in human health. The approach proposed circumvents difficulties imposed by sampling humans, provides an alternative strategy to characterizing some diseases of unknown etiology, and renders a much needed understanding of the ecophysiological role hundreds of unique Bacteria and Archaea strains play in mixed microbial communities.

  12. Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes. Final Report

    International Nuclear Information System (INIS)

    Lidstrom, Mary E.

    2003-01-01

    Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions

  13. Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes--Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Mary E. Lidstrom

    2003-12-26

    Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions.

  14. Comparative proteomics and activity of a green sulfur bacterium across the water column of Lake Cadagno, Switzerland

    DEFF Research Database (Denmark)

    Habicht, Kirsten S.; Miller, Mette; Cox, Raymond P.

    2011-01-01

    Primary production in the meromictic Lake Cadagno, Switzerland, is dominated by anoxygenic photosynthesis. The green sulfur bacterium Chlorobium clathratiforme is the dominant phototrophic organism in the lake, comprising more than half of the bacterial population, and its biomass increases 3...

  15. Thermophilic Anaerobic Degradation of Butyrate by a Butyrate-Utilizing Bacterium in Coculture and Triculture with Methanogenic Bacteria

    OpenAIRE

    Ahring, Birgitte K.; Westermann, Peter

    1987-01-01

    We studied syntrophic butyrate degradation in thermophilic mixed cultures containing a butyrate-degrading bacterium isolated in coculture with Methanobacterium thermoautotrophicum or in triculture with M. thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic bacterium. Butyrate was β-oxidized to acetate with protons as the electron acceptors. Acetate was used concurrently with its production in the triculture. We found a higher butyrate degradation rate in th...

  16. Alcanivorax dieselolei, an alkane-degrading bacterium associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa)

    OpenAIRE

    Campos,FF.; Garcia,JE.; Luna-Finkler,CL.; Davolos,CC.; Lemos,MVF.; Pérez,CD.

    2015-01-01

    Analyses of 16S rDNA genes were used to identify the microbiota isolated from the mucus of the zoanthid Palythoa caribaeorum at Porto de Galinhas on the coast of Pernambuco State, Brazil. This study is important as the first report of this association, because of the potential biotechnological applications of the bacterium Alcanivorax dieselolei, and as evidence for the presence of a hydrocarbon degrading bacterium in a reef ecosystem such as Porto de Galinhas.

  17. Alcanivorax dieselolei, an alkane-degrading bacterium associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa).

    Science.gov (United States)

    Campos, F F; Garcia, J E; Luna-Finkler, C L; Davolos, C C; Lemos, M V F; Pérez, C D

    2015-05-01

    Analyses of 16S rDNA genes were used to identify the microbiota isolated from the mucus of the zoanthid Palythoa caribaeorum at Porto de Galinhas on the coast of Pernambuco State, Brazil. This study is important as the first report of this association, because of the potential biotechnological applications of the bacterium Alcanivorax dieselolei, and as evidence for the presence of a hydrocarbon degrading bacterium in a reef ecosystem such as Porto de Galinhas.

  18. Alcanivorax dieselolei, an alkane-degrading bacterium associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa

    Directory of Open Access Journals (Sweden)

    FF. Campos

    Full Text Available Analyses of 16S rDNA genes were used to identify the microbiota isolated from the mucus of the zoanthid Palythoa caribaeorum at Porto de Galinhas on the coast of Pernambuco State, Brazil. This study is important as the first report of this association, because of the potential biotechnological applications of the bacterium Alcanivorax dieselolei, and as evidence for the presence of a hydrocarbon degrading bacterium in a reef ecosystem such as Porto de Galinhas.

  19. Role of Chitin-Binding Proteins in the Specific Attachment of the Marine Bacterium Vibrio harveyi to Chitin

    OpenAIRE

    Montgomery, Michael T.; Kirchman, David L.

    1993-01-01

    We examined the mechanism of attachment of the marine bacterium Vibrio harveyi to chitin. Wheat germ agglutinin and chitinase bind to chitin and competitively inhibited the attachment of V. harveyi to chitin, but not to cellulose. Bovine serum albumin and cellulase do not bind to chitin and had no effect on bacterial attachment to chitin. These data suggest that this bacterium recognizes specific attachment sites on the chitin particle. The level of attachment of a chitinase-overproducing mut...

  20. Understanding the interaction between an obligate hyperparasitic bacterium, Pasteuria penetrans and its obligate plant-parasitic nematode host, Meloidogyne spp.

    Science.gov (United States)

    Davies, Keith G

    2009-01-01

    Pasteuria penetrans is an endospore-forming bacterium, which is a hyperparasite of root-knot nematodes Meloidogyne spp. that are economically important pests of a wide range of crops. The life cycle of the bacterium and nematode are described with emphasis on the bacterium's potential as a biocontrol agent. Two aspects that currently prohibit the commercial development of the bacterium as a biocontrol agent are the inability to culture it outside its host and its host specificity. Vegetative growth of the bacterium is possible in vitro; however, getting the vegetative stages of the bacterium to enter sporogenesis has been problematic. Insights from genomic survey sequences regarding the role of cation concentration and the phosphorylation of Spo0F have proved useful in inducing vegetative bacteria to sporulate. Similarly, genomic data have also proved useful in understanding the attachment of endospores to the cuticle of infective nematode juveniles, and a Velcro-like model of spore attachment is proposed that involves collagen-like fibres on the surface of the endospore interacting with mucins on the nematode cuticle. Ecological studies of the interactions between Daphnia and Pasteuria ramosa are examined and similarities are drawn between the co-evolution of virulence in the Daphnia system and that of plant-parasitic nematodes.

  1. Cloning and characterization of nif structural and regulatory genes in the purple sulfur bacterium, Halorhodospira halophila.

    Science.gov (United States)

    Tsuihiji, Hisayoshi; Yamazaki, Yoichi; Kamikubo, Hironari; Imamoto, Yasushi; Kataoka, Mikio

    2006-03-01

    Halorhodospira halophila is a halophilic photosynthetic bacterium classified as a purple sulfur bacterium. We found that H. halophila generates hydrogen gas during photoautotrophic growth as a byproduct of a nitrogenase reaction. In order to consider the applied possibilities of this photobiological hydrogen generation, we cloned and characterized the structural and regulatory genes encoding the nitrogenase, nifH, nifD and nifA, from H. halophila. This is the first description of the nif genes for a purple sulfur bacterium. The amino-acid sequences of NifH and NifD indicated that these proteins are an Fe protein and a part of a MoFe protein, respectively. The important residues are conserved completely. The sequence upstream from the nifH region and sequence similarities of nifH and nifD with those of the other organisms suggest that the regulatory system might be a NifL-NifA system; however, H. halophila lacks nifL. The amino-acid sequence of H. halophila NifA is closer to that of the NifA of the NifL-NifA system than to that of NifA without NifL. H. halophila NifA does not conserve either the residue that interacts with NifL or the important residues involved in NifL-independent regulation. These results suggest the existence of yet another regulatory system, and that the development of functional systems and their molecular counterparts are not necessarily correlated throughout evolution. All of these Nif proteins of H. halophila possess an excess of acidic residues, which acts as a salt-resistant mechanism.

  2. High Prevalence of Antibodies against the Bacterium Treponema pallidum in Senegalese Guinea Baboons (Papio papio).

    Science.gov (United States)

    Knauf, Sascha; Barnett, Ulrike; Maciej, Peter; Klapproth, Matthias; Ndao, Ibrahima; Frischmann, Sieghard; Fischer, Julia; Zinner, Dietmar; Liu, Hsi

    2015-01-01

    The bacterium Treponema pallidum is known to cause syphilis (ssp. pallidum), yaws (ssp. pertenue), and endemic syphilis (ssp. endemicum) in humans. Nonhuman primates have also been reported to be infected with the bacterium with equally versatile clinical manifestations, from severe skin ulcerations to asymptomatic. At present all simian strains are closely related to human yaws-causing strains, an important consideration for yaws eradication. We tested clinically healthy Guinea baboons (Papio papio) at Parc National Niokolo Koba in south eastern Senegal for the presence of anti-T. pallidum antibodies. Since T. pallidum infection in this species was identified 50 years ago, and there has been no attempt to treat non-human primates for infection, it was hypothesized that a large number of West African baboons are still infected with simian strains of the yaws-bacterium. All animals were without clinical signs of treponematoses, but 18 of 20 (90%) baboons tested positive for antibodies against T. pallidum based on treponemal tests. Yet, Guinea baboons seem to develop no clinical symptoms, though it must be assumed that infection is chronic or comparable to the latent stage in human yaws infection. The non-active character is supported by the low anti-T. pallidum serum titers in Guinea baboons (median = 1:2,560) versus serum titers that are found in genital-ulcerated olive baboons with active infection in Tanzania (range of medians among the groups of initial, moderate, and severe infected animals = 1:15,360 to 1:2.097e+7). Our findings provide evidence for simian infection with T. pallidum in wild Senegalese baboons. Potentially, Guinea baboons in West Africa serve as a natural reservoir for human infection, as the West African simian strain has been shown to cause sustainable yaws infection when inoculated into humans. The present study pinpoints an area where further research is needed to support the currently on-going second WHO led yaws eradication campaign with

  3. Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

    International Nuclear Information System (INIS)

    Imam, S.H.; Greene, R.V.; Griffin, H.L.

    1990-01-01

    Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. 35 S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA [ethylene hlycol-bis(β-aminoethyl ether)-N,N,N'N'-tetraacetic acid] had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction

  4. Antimicrobial polyketide furanoterpenoids from seaweed-associated heterotrophic bacterium Bacillus subtilis MTCC 10403.

    Science.gov (United States)

    Chakraborty, Kajal; Thilakan, Bini; Raola, Vamshi Krishna

    2017-10-01

    Brown seaweed Anthophycus longifolius (Turner) Kützing (family Sargassaceae) associated heterotrophic bacterium Bacillus subtilis MTCC 10403 was found to be a potent isolate with broad range of antibacterial activity against important perceptive food pathogens Vibrio parahaemolyticus, V. vulnificus, and Aeromonas hydrophila. This bacterium was positive for polyketide synthetase gene (KC589397), and therefore, was selected to bioprospect specialized metabolites bearing polyketide backbone. Bioactivity-guided chromatographic fractionation of the ethyl acetate extract of the seaweed-associated bacterium segregated four homologous polyketide furanoterpenoids with potential antibacterial activities against clinically important pathogens. The minimum inhibitory concentration (MIC) assay showed that the referral antibiotics tetracycline and ampicillin were active at 25 μg/mL against the test pathogens, whereas the previously undescribed (4E)-methyl 13-((16-(furan-2-yl) ethyl)-octahydro-7-hydroxy-4-((E)-23-methylbut-21-enyl)-2H-chromen-6-yl)-4-methylpent-4-enoate (compound 1) and methyl 3-(hexahydro-9-((E)-3-methylpent-1-enyl)-4H-furo[3,2-g]isochromen-6-yl) propanoate (compound 3) displayed antibacterial activities against the test pathogens at a lesser concentration (MIC Polyketide synthase catalyzed putative biosynthetic mechanism additionally corroborated the structural ascriptions of the hitherto undescribed furanoterpenoids from seaweed-associated bacterial symbiont. The electronic and hydrophobic parameters appeared to hold a conspicuous part in directing the antibacterial properties of the compounds. Seaweed-associated B. subtilis MTCC 10403 demonstrated to represent a potential source of antimicrobial polyketides for pharmaceutical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium.

    Science.gov (United States)

    Watts, Mathew P; Khijniak, Tatiana V; Boothman, Christopher; Lloyd, Jonathan R

    2015-08-15

    Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments. Copyright © 2015, Watts et al.

  6. Novel insights into the algicidal bacterium DH77-1 killing the toxic dinoflagellate Alexandrium tamarense.

    Science.gov (United States)

    Yang, Xiaoru; Li, Xinyi; Zhou, Yanyan; Zheng, Wei; Yu, Changping; Zheng, Tianling

    2014-06-01

    Algicidal bacteria may play a major role in controlling harmful algal blooms (HABs) dynamics. Bacterium DH77-1 was isolated with high algicidal activity against the toxic dinoflagellate Alexandrium tamarense and identified as Joostella sp. DH77-1. The results showed that DH77-1 exhibited algicidal activity through indirect attack, which excreted active substance into the filtrate. It had a relatively wide host range and the active substance of DH77-1 was relatively stable since temperature, pH and storage condition had no obvious effect on the algicidal activity. The algicidal compound from bacterium DH77-1 was isolated based on activity-guided bioassay and the molecular weight was determined to be 125.88 by MALDI-TOF mass spectrometer, however further identification via nuclear magnetic resonance (NMR) spectra is ongoing. The physiological responses of algal cells after exposure to the DH77-1 algicidal substances were as follows: the antioxidant system of A. tamarense responded positively in self-defense; total protein content decreased significantly as did the photosynthetic pigment content; superoxide dismutase, peroxidase enzyme and malondialdehyde content increased extraordinarily and algal cell nucleic acid leaked seriously ultimately inducing cell death. Furthermore, DH77-1 is the first record of a Joostella sp. bacterium being algicidal to the harmful dinoflagellate A. tamarense, and the bacterial culture and the active compounds might be potentially used as a bio-agent for controlling harmful algal blooms. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics.

    Science.gov (United States)

    Cerisy, Tristan; Souterre, Tiffany; Torres-Romero, Ismael; Boutard, Magali; Dubois, Ivan; Patrouix, Julien; Labadie, Karine; Berrabah, Wahiba; Salanoubat, Marcel; Doring, Volker; Tolonen, Andrew C

    2017-06-01

    Increasing the resistance of plant-fermenting bacteria to lignocellulosic inhibitors is useful to understand microbial adaptation and to develop candidate strains for consolidated bioprocessing. Here, we study and improve inhibitor resistance in Clostridium phytofermentans (also called Lachnoclostridium phytofermentans ), a model anaerobe that ferments lignocellulosic biomass. We survey the resistance of this bacterium to a panel of biomass inhibitors and then evolve strains that grow in increasing concentrations of the lignin phenolic, ferulic acid, by automated, long-term growth selection in an anaerobic GM3 automat. Ultimately, strains resist multiple inhibitors and grow robustly at the solubility limit of ferulate while retaining the ability to ferment cellulose. We analyze genome-wide transcription patterns during ferulate stress and genomic variants that arose along the ferulate growth selection, revealing how cells adapt to inhibitors through changes in gene dosage and regulation, membrane fatty acid structure, and the surface layer. Collectively, this study demonstrates an automated framework for in vivo directed evolution of anaerobes and gives insight into the genetic mechanisms by which bacteria survive exposure to chemical inhibitors. IMPORTANCE Fermentation of plant biomass is a key part of carbon cycling in diverse ecosystems. Further, industrial biomass fermentation may provide a renewable alternative to fossil fuels. Plants are primarily composed of lignocellulose, a matrix of polysaccharides and polyphenolic lignin. Thus, when microorganisms degrade lignocellulose to access sugars, they also release phenolic and acidic inhibitors. Here, we study how the plant-fermenting bacterium Clostridium phytofermentans resists plant inhibitors using the lignin phenolic, ferulic acid. We examine how the cell responds to abrupt ferulate stress by measuring changes in gene expression. We evolve increasingly resistant strains by automated, long-term cultivation at

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

    Science.gov (United States)

    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

  9. Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

    Science.gov (United States)

    Abdoun, Hamid; McMillan, Mary; Pereg, Lily

    2016-04-01

    Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

  10. A bacterium that can grow by using arsenic instead of phosphorus

    Energy Technology Data Exchange (ETDEWEB)

    Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

    2010-11-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

  11. Response to Comments on "A Bacterium That Can Grow Using Arsenic Instead of Phosphorus"

    Energy Technology Data Exchange (ETDEWEB)

    Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

    2011-03-07

    Concerns have been raised about our recent study describing a bacterium that can grow using arsenic (As) instead of phosphorus (P). Our data suggested that As could act as a substitute for P in major biomolecules in this organism. Although the issues raised are of investigative interest, we contend that they do not invalidate our conclusions. We argue that while no single line of evidence we presented was sufficient to support our interpretation of the data, taken as an entire dataset we find no plausible alternative to our conclusions. Here we reply to the critiques and provide additional arguments supporting the assessment of the data we reported.

  12. Complete genome sequence of Pseudomonas azotoformans S4, a potential biocontrol bacterium

    Science.gov (United States)

    Fang, Yang; Wu, Lijuan; Chen, Guoqing; Feng, Guozhong

    2016-01-01

    Pseudomonas azotoformans is a Gram-negative bacterium and infects cereal grains, especially rice. P. azotoformans S4 from soil sample derived from Lijiang, Yunnan Province, China, appeared to be strong inhibitory activity against Fusarium fujikurio, a serious rice fungal pathogen. Here, we present the complete genome of P. azotoformans S4, which consists of 6,859,618 bp with a circle chromosome, 5991 coding DNA sequences, 70 tRNA and 19 rRNA. The genomic analysis revealed that 9 candidate gene clusters are involved in the biosynthesis of secondary metabolites. PMID:27080451

  13. A bacterium that can grow by using arsenic instead of phosphorus.

    Science.gov (United States)

    Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

    2011-06-03

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

  14. Cadmium-nickel toxicity interactions towards a bacterium, filamentous fungi, and a cultured mammalian cell line

    Energy Technology Data Exchange (ETDEWEB)

    Babich, H.; Shopsis, C.; Borenfreund, E.

    1986-10-01

    The response of the biota to exposure to individual metals may differ from its response to multiple metals, as mixtures of metals may interact antagonistically or synergistically in their resultant toxicity. The present study evaluated the effects of a combination of Cd and Ni on the freshwater bacterium, Aeromonas hydrophila, the terrestrial fungi, Trichodema viride and Aspergillus niger, and the mammalian cell line, BALB/c mouse 3T3 fibroblasts. This particular spectrum of target cells was selected because studies in the literature show a wide variety of possible interactions between Cd and Ni in their combined toxicities towards bacteria cyanobacteria, slime molds, isolated rat hepatocytes, and rats.

  15. Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium.

    Science.gov (United States)

    Zhang, Shumei; Jiang, Wei; Li, Jing; Meng, Liqiang; Cao, Xu; Hu, Jihua; Liu, Yushuai; Chen, Jingyu; Sha, Changqing

    2016-01-01

    Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of inhibition of a broad range of plant pathogenic fungi. The strain has the potential to be developed into a biocontrol agent for use in agriculture. Here we report the whole-genome shotgun sequence of the strain. The genome size of B. amyloliquefaciens TF28 is 3,987,635 bp which consists of 3754 protein-coding genes, 65 tandem repeat sequences, 47 minisatellite DNA, 2 microsatellite DNA, 63 tRNA, 7rRNA, 6 sRNA, 3 prophage and CRISPR domains.

  16. Illuminating the landscape of host–pathogen interactions with the bacterium Listeria monocytogenes

    Science.gov (United States)

    Cossart, Pascale

    2011-01-01

    Listeria monocytogenes has, in 25 y, become a model in infection biology. Through the analysis of both its saprophytic life and infectious process, new concepts in microbiology, cell biology, and pathogenesis have been discovered. This review will update our knowledge on this intracellular pathogen and highlight the most recent breakthroughs. Promising areas of investigation such as the increasingly recognized relevance for the infectious process, of RNA-mediated regulations in the bacterium, and the role of bacterially controlled posttranslational and epigenetic modifications in the host will also be discussed. PMID:22114192

  17. Mutagenesis and reparation processes in the methylotrophic bacterium Pseudomonas methanolica after UV irradiation

    International Nuclear Information System (INIS)

    Naumov, G.N.; Bokhan, I.K.; Multykh, I.G.

    1986-01-01

    High resistance of cells of methylotrophic bacterium Pseudomonas methanolica to bactericidal and mutagenous effects of ultraviolet irradiation is shown as well as activity of reparation processes after UV irradiation. The presence of low photoreactivating activity in P. methanolica is shown as well. Observed recovery in innutritious medium and decrease of irradiated cells survival rates under effect of reparation inhibitors (coffeine and acriflavine) testify to activity of excision reparation and, perhaps, recombination branch of postreplicative reparation. No manifestation of inducible reparation system is discovered. It is concluded that increased resistance of P. methanolica cells to bactericidal and mutagenous effects of short-wave ultraviolet radiation is related to activity of exact reparation systems

  18. Dissolution of Fe(III)(hydr)oxides by an Aerobic Bacterium

    International Nuclear Information System (INIS)

    Maurice, P.

    2004-01-01

    This project investigated the effects of an aerobic Pseudomonas mendocina bacterium on the dissolution of Fe(III)(hydr)oxides. The research is important because metals and radionuclides that adsorb to Fe(III)(hydr)oxides could potentially be remobilized by dissolving bacteria. We showed that P. mendocina is capable of dissolving Fe-bearing minerals by a variety of mechanisms, including production of siderophores, pH changes, and formation of reductants. The production of siderophores by P. mendocina was quantified under a variety of growth conditions. Finally, we demonstrated that microbial siderophores may adsorb to and enhance dissolution of clay minerals

  19. Molecular characterization of the glucose isomerase from the thermophilic bacterium Fervidobacterium gondwanense.

    Science.gov (United States)

    Kluskens, L D; Zeilstra, J; Geerling, A C M; de Vos, W M; van der Oost, J

    2010-09-01

    The gene coding for xylose isomerase from the thermophilic bacterium Fervidobacterium gondwanense was cloned and overexpressed in Escherichia coli. The produced xylose isomerase (XylA), which closely resembles counterparts from Thermotoga maritima and T. neapolitana, was purified and characterized. It is optimally active at 70 degrees C, pH 7.3, with a specific activity of 15.0 U/mg for the interconversion of glucose to fructose. When compared with T. maritima XylA at 85 degrees C, a higher catalytic efficiency was observed. Divalent metal ions Co2+ and Mg2+ were found to enhance the thermostability.

  20. A bacterium that can grow by using arsenic instead of phosphorus

    Science.gov (United States)

    Wolfe-Simon, Felisa; Blum, J.S.; Kulp, T.R.; Gordon, G.W.; Hoeft, S.E.; Pett-Ridge, J.; Stolz, J.F.; Webb, S.M.; Weber, P.K.; Davies, P.C.W.; Anbar, A.D.; Oremland, R.S.

    2011-01-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

  1. Effect of lead, mercury and cadmium on a sulphate-reducing bacterium

    Digital Repository Service at National Institute of Oceanography (India)

    LokaBharathi, P.A.; Sathe, V.; Chandramohan, D.

    Hg and 125·1 Jlg ml- 1 Pb (Hg being 137·1 % and Pb 2320/0 of the weight of the Cd used). Thormann and Weyland (1980), in a study of the effect of Cd and Pb, state that Cd causes a stronger growth inhibition than Pb. Also, the relative importance... Pollution 67 (1990) 361-374 Effect of Lead, Mercury and Cadmium on a Sulphate-Reducing Bacterium P. A. Loka Bharathi, V. Sathe & D. Chandramohan National Institute of Oceanography, Dona Paula, Goa-403004, India (Received 9 March 1990; revised version...

  2. Intestinal bacterium-derived cyp27a1 prevents colon cancer cell apoptosis

    OpenAIRE

    Ji, Yan-Chao; Liu, Chang; Zhang, Xia; Zhang, Cheng-Sen; Wang, Dong; Zhang, Yan

    2016-01-01

    The pathogenesis of metastasis of colon cancer (Cca) is to be further investigated. The dysfunction of apoptotic mechanism plays a role in the cancer cell over growth. This study tests a hypothesis by which intestinal bacterium-derived cyp27a1 prevents apoptosis in colon cancer cells. In this study, the levels of cyp27a1 in human stool samples were assessed by enzyme-linked immunosorbent assay. The apoptosis of Cca cells was observed by flow cytometry. The expression of cyp27a1 was assessed b...

  3. Acoustic sensing of the bacterium-substratum interface using QCM-D and the influence of extracellular polymeric substances.

    Science.gov (United States)

    Olsson, Adam L J; van der Mei, Henny C; Busscher, Henk J; Sharma, Prashant K

    2011-05-01

    It is commonly assumed that bacterial presence on a QCM sensor-surface is associated with a negative frequency shift according to conventional mass-loading theory. Here, we demonstrate that bacteria adhering to QCM sensor-surface may yield positive frequency shifts up to 1.9×10(-6) Hz per bacterium according to a coupled-oscillator theory. Furthermore, it is demonstrated that the excretion of extracellular polymeric substances (EPS) by adhering bacteria can change the frequency shift in the negative direction by 1.7×10(-6) Hz per bacterium, according to conventional mass-loading theory. The difference in frequency shifts between an EPS-producing and a non-EPS producing staphylococcal strain correlated with the excretion of 3×10(-14) g EPS per bacterium, representing only a few percent of the weight of a bacterium. Thus an adsorbed molecular mass as low as a few percent of the mass of an adhering bacterium significantly alters the QCM-signal. Since adhesion of many different bacterial strains is accompanied by molecular adsorption of EPS, with potentially opposite effects on the QCM-signal, a combination of the coupled-oscillator and normal mass-loading theory has to be applied for proper interpretation of QCM-frequency shifts in bacterial detection. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Expression and surface display of Cellulomonas endoglucanase in the ethanologenic bacterium Zymobacter palmae.

    Science.gov (United States)

    Kojima, Motoki; Akahoshi, Tomohiro; Okamoto, Kenji; Yanase, Hideshi

    2012-11-01

    In order to reduce the cost of bioethanol production from lignocellulosic biomass, we developed a tool for cell surface display of cellulolytic enzymes on the ethanologenic bacterium Zymobacter palmae. Z. palmae is a novel ethanol-fermenting bacterium capable of utilizing a broad range of sugar substrates, but not cellulose. Therefore, to express and display heterologous cellulolytic enzymes on the Z. palmae cell surface, we utilized the cell-surface display motif of the Pseudomonas ice nucleation protein Ina. The gene encoding Ina from Pseudomonas syringae IFO3310 was cloned, and its product was comprised of three functional domains: an N-terminal domain, a central domain with repeated amino acid residues, and a C-terminal domain. The N-terminal domain of Ina was shown to function as the anchoring motif for a green fluorescence protein fusion protein in Escherichia coli. To express a heterologous cellulolytic enzyme extracellularly in Z. palmae, we fused the N-terminal coding sequence of Ina to the coding sequence of an N-terminal-truncated Cellulomonas endoglucanase. Z. palmae cells carrying the fusion endoglucanase gene were shown to degrade carboxymethyl cellulose. Although a portion of the expressed fusion endoglucanase was released from Z. palmae cells into the culture broth, we confirmed the display of the protein on the cell surface by immunofluorescence microscopy. The results indicate that the N-terminal anchoring motif of Ina from P. syringae enabled the translocation and display of the heterologous cellulase on the cell surface of Z. palmae.

  5. Keratinolytic activity of Bacillus megaterium F7-1, a feather-degrading mesophilic bacterium.

    Science.gov (United States)

    Park, Geun-Tae; Son, Hong-Joo

    2009-01-01

    The aim of this study was to investigate environmental conditions affecting chicken feather degradation and keratinolytic enzyme production by Bacillus megaterium F7-1, a feather-degrading mesophilic bacterium. B. megaterium F7-1 degraded whole chicken feather completely within 7 days. The bacterium grew with an optimum at pH 7.0-11.0 and 25-40 degrees C, where maximum keratinolytic activity was also observed. The production of keratinolytic enzyme by B. megaterium F7-1 was inducible with feather. Keratinolytic enzyme production by B. megaterium F7-1 at 0.6% (w/v) skim milk was 468U/ml, which was about 9.4-fold higher than that without skim milk. The amount of keratinolytic enzyme production depended on feather concentrations. The degradation rate of autoclaved chicken feathers by cell-free culture supernatant was 26% after 24h of incubation, but the degradation of untreated chicken feathers was unsuccessful. B. megaterium F7-1 effectively degraded feather meal, duck feather and human nail, whereas human hair and sheep wool showed relatively low degradation rates. B. megaterium F7-1 presented high keratinolytic activity and was very effective in feather degradation, providing potential use for biotechnological processes of keratin hydrolysis.

  6. Detection of a novel bacterium associated with spores of the arbuscular mycorrhizal fungus Gigaspora margarita.

    Science.gov (United States)

    Long, Liangkun; Yao, Qing; Ai, Yuncan; Deng, Mingrong; Zhu, Honghui

    2009-06-01

    With PCR-denaturing gradient gel electrophoresis analysis, two bacterial 16S rRNA gene V3 region sequences, 7A and 7B, were detected in association with the crushed spores of the arbuscular mycorrhizal fungus Gigaspora margarita W.N. Becker & I.R. Hall 1976 MAFF520054. DNA sequencing and phylogenetic analysis revealed that 7B was mostly related to the documented cytoplasm endosymbiotic bacterium Candidatus Glomeribacter gigasporarum of G. margarita, but 7A could not be confidently assigned to a known taxon. Further characterization of 7A was conducted by obtaining its almost complete 16S rRNA gene sequence via PCR amplification and sequencing. BLAST search indicates that the 16S rRNA gene sequence did not match any identified species sequences in the GenBank database. Further detection revealed that 7A was also associated with the clean G. margarita MAFF520054 spores that were obtained by the surface-sterilized method or dual culture with Ri T-DNA transformed carrot roots. Many ellipse-shaped or egg-shaped bacterium-like organisms were clustered in layer 3 of the fungal spore wall by transmission electron microscopy observation. Our results indicate that 7A represents a novel bacterial population associated with G. margarita MAFF520054 spores, and its doubtless location (wall or cytoplasm) remains unclear based on the present data.

  7. Melanin from the nitrogen-fixing bacterium Azotobacter chroococcum: a spectroscopic characterization.

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    Aulie Banerjee

    Full Text Available Melanins, the ubiquitous hetero-polymer pigments found widely dispersed among various life forms, are usually dark brown/black in colour. Although melanins have variety of biological functions, including protection against ultraviolet radiation of sunlight and are used in medicine, cosmetics, extraction of melanin from the animal and plant kingdoms is not an easy task. Using complementary physicochemical techniques (i.e. MALDI-TOF, FTIR absorption and cross-polarization magic angle spinning solid-state (13C NMR, we report here the characterization of melanins extracted from the nitrogen-fixing non-virulent bacterium Azotobacter chroococcum, a safe viable source. Moreover, considering dihydroxyindole moiety as the main constituent, an effort is made to propose the putative molecular structure of the melanin hetero-polymer extracted from the bacterium. Characterization of the melanin obtained from Azotobacter chroococcum would provide an inspiration in extending research activities on these hetero-polymers and their use as protective agent against UV radiation.

  8. Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae.

    Science.gov (United States)

    Greenberg, David E; Porcella, Stephen F; Stock, Frida; Wong, Alexandra; Conville, Patricia S; Murray, Patrick R; Holland, Steven M; Zelazny, Adrian M

    2006-11-01

    A Gram-negative, aerobic, coccobacillus to rod-shaped bacterium was isolated from three patients with chronic granulomatous disease. The organism was subjected to a polyphasic taxonomic study. A multilocus phylogenetic analysis based on the 16S rRNA gene, the internal transcribed spacer (ITS) region and the RecA protein demonstrated that the organism belongs to a new sublineage within the acetic acid bacteria in the family Acetobacteraceae. Phenotypic features are summarized as follows: the organism grew at an optimum temperature of 35-37 degrees C and optimum pH of 5.0-6.5. It produced a yellow pigment, oxidized lactate and acetate, the latter weakly, produced little acetic acid from ethanol and could use methanol as a sole carbon source. The two major fatty acids were a straight-chain unsaturated acid (C18:1omega7c) and C16:0. The DNA base composition was 59.1 mol% G+C. The very weak production of acetic acid from ethanol, the ability to use methanol, the yellow pigmentation and high optimum temperature for growth distinguished this organism from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the bacterium should be classified within a separate genus, for which the name Granulibacter bethesdensis gen. nov., sp. nov. is proposed. The type strain is CGDNIH1T (=ATCC BAA-1260T=DSM 17861T).

  9. Biofilm and capsule formation of the diatom Achnanthidium minutissimum are affected by a bacterium.

    Science.gov (United States)

    Windler, Miriam; Leinweber, Katrin; Bartulos, Carolina Rio; Philipp, Bodo; Kroth, Peter G

    2015-04-01

    Photoautotrophic biofilms play an important role in various aquatic habitats and are composed of prokaryotic and/or eukaryotic organisms embedded in extracellular polymeric substances (EPS). We have isolated diatoms as well as bacteria from freshwater biofilms to study organismal interactions between representative isolates. We found that bacteria have a strong impact on the biofilm formation of the pennate diatom Achnanthidium minutissimum. This alga produces extracellular capsules of insoluble EPS, mostly carbohydrates (CHO), only in the presence of bacteria (xenic culture). The EPS themselves also have a strong impact on the aggregation and attachment of the algae. In the absence of bacteria (axenic culture), A. minutissimum did not form capsules and the cells grew completely suspended. Fractionation and quantification of CHO revealed that the diatom in axenic culture produces large amounts of soluble CHO, whereas in the xenic culture mainly insoluble CHO were detected. For investigation of biofilm formation by A. minutissimum, a bioassay was established using a diatom satellite Bacteroidetes bacterium that had been shown to induce capsule formation of A. minutissimum. Interestingly, capsule and biofilm induction can be achieved by addition of bacterial spent medium, indicating that soluble hydrophobic molecules produced by the bacterium may mediate the diatom/bacteria interaction. With the designed bioassay, a reliable tool is now available to study the chemical interactions between diatoms and bacteria with consequences for biofilm formation. © 2015 Phycological Society of America.

  10. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.

    Science.gov (United States)

    Han, Yejun; Agarwal, Vinayak; Dodd, Dylan; Kim, Jason; Bae, Brian; Mackie, Roderick I; Nair, Satish K; Cann, Isaac K O

    2012-10-12

    Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

  11. Data supporting functional diversity of the marine bacterium Cobetia amphilecti KMM 296

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    Larissa Balabanova

    2016-09-01

    Full Text Available Data is presented in support of functionality of hyper-diverse protein families encoded by the Cobetia amphilecti KMM 296 (formerly Cobetia marina KMM 296 genome (“The genome of the marine bacterium Cobetia marina KMM 296 isolated from the mussel Crenomytilus grayanus (Dunker, 1853” [1] providing its nutritional versatility, adaptability and biocontrol that could be the basis of the marine bacterium evolutionary and application potential. Presented data include the information of growth and biofilm-forming properties of the food-associated isolates of Pseudomonas, Bacillus, Listeria, Salmonella and Staphylococcus under the conditions of their co-culturing with C. amphilecti KMM 296 to confirm its high inter-species communication and anti-microbial activity. Also included are the experiments on the crude petroleum consumption by C. amphilecti KMM 296 as the sole source of carbon in the presence of sulfate or nitrate to ensure its bioremediation capacity. The multifunctional C. amphilecti KMM 296 genome is a promising source for the beneficial psychrophilic enzymes and essential secondary metabolites.

  12. Identification and Characterization of a High Efficiency Aniline Resistance and Degrading Bacterium MC-01.

    Science.gov (United States)

    Yang, Liu; Ying, Chen; Fang, Ni; Zhong, Yao; Zhao-Xiang, Zhong; Yun, Sun

    2017-05-01

    Biodegradation is one of the important methods for the treatment of industrial wastewater containing aniline. In this paper, a degrading bacterium named MC-01, which could survive in high concentration aniline wastewater, was screened from industrial wastewater containing aniline and sludge. MC-01 was preliminarily identified as Ochrobactrum sp. based on the amplified 16S rDNA gene sequence and Biolog system identification. MC-01 was highly resistant to aniline. After 24-h culture under aniline concentration of 6500 mg/L, the amount of bacterium survived still remained 0.05 × 10 6  CFU/mL. Experiments showed that there was no coupling expression between the growth of MC-01 and aniline degradation. The optimum growth conditions in LB culture were pH 6.0, 30 °C of temperature, and 4% of incubation amount, respectively. And the optimum conditions of aniline degradation of MC-01 were pH 7.0, 45 °C of temperature, and 3.0% of salt concentration, respectively. The degradation rate of MC-01 (48 h) in different aniline concentrations (200~1600 mg/L) was stable under the optimum conditions, which could reach more than 75%.

  13. Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.

    Science.gov (United States)

    Boutard, Magali; Cerisy, Tristan; Nogue, Pierre-Yves; Alberti, Adriana; Weissenbach, Jean; Salanoubat, Marcel; Tolonen, Andrew C

    2014-11-01

    Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.

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

    Science.gov (United States)

    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).

  15. Enhanced Cadmium (Cd Phytoextraction from Contaminated Soil using Cd-Resistant Bacterium

    Directory of Open Access Journals (Sweden)

    Kunchaya Setkit

    2014-01-01

    Full Text Available A cadmium (Cd-resistant bacterium, Micrococcus sp. MU1, is able to produce indole-3-acetic acid and promotes root elongation and plant growth. The potential of this bacterium on enhancement of Cd uptake and bioaccumulation of Cd in Helianthus annuus L. planted in Cd-contaminated soil was evaluated in greenhouse condition. The results showed that Micrococcus sp. MU1promoted the growth of H. annuus L. by increasing the root length, stem height, dry biomass, root to shoot ratio and also significantly increased Cd accumulation in the root and above-ground tissues of H. annuus L. compared to uninoculated control. Re-inoculation with Micrococcus sp. MU1in contaminated soil helped in promoting plant growth and Cd phytoextraction throughout the cultivation period. In addition, phytoextraction coefficient and translocation factor (TF of H. annuus L. inoculated with Micrococcus sp. MU1were higher than that of uninoculated control and TF continuously increased with time. Our results suggested that Micrococcus sp. MU1 has an ability to enhance plant growth and Cd uptake in H. annuus L. Synergistic interaction between Micrococcus sp. MU1 and H. annuus L. could be further applied for Cd phytoextraction in polluted areas.

  16. The fate of a nitrobenzene-degrading bacterium in pharmaceutical wastewater treatment sludge.

    Science.gov (United States)

    Ren, Yuan; Yang, Juan; Chen, Shaoyi

    2015-12-01

    This paper describes the fate of a nitrobenzene-degrading bacterium, Klebsiella oxytoca NBA-1, which was isolated from a pharmaceutical wastewater treatment facility. The 90-day survivability of strain NBA-1 after exposure to sludge under anaerobic and aerobic conditions was investigated. The bacterium was inoculated into sludge amended with glucose and p-chloronitrobenzene (p-CNB) to compare the bacterial community variations between the modified sludge and nitrobenzene amendment. The results showed that glucose had no obvious effect on nitrobenzene biodegradation in the co-metabolism process, regardless of the presence/absence of oxygen. When p-CNB was added under anaerobic conditions, the biodegradation rate of nitrobenzene remained unchanged although p-CNB inhibited the production of aniline. The diversity of the microbial community increased and NBA-1 continued to be one of the dominant strains. Under aerobic conditions, the degradation rate of both nitrobenzene and p-CNB was only 20% of that under anaerobic conditions. p-CNB had a toxic effect on the microorganisms in the sludge so that most of the DGGE (denaturing gradient gel electrophoresis) bands, including that of NBA-1, began to disappear under aerobic conditions after 90days of exposure. These data show that the bacterial community was stable under anaerobic conditions and the microorganisms, including NBA-1, were more resistant to the adverse environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Non-specific immune response of bullfrog Rana catesbeiana to intraperitoneal injection of bacterium Aeromonas hydrophila

    Science.gov (United States)

    Zhang, Junjie; Zou, Wenzheng; Yan, Qingpi

    2008-08-01

    Non-specific immune response of bullfrog Rana catesbeiana to pathogenic Aeromonas hydrophila was studied to 60 individuals in two groups. Each bullfrog in bacterium-injected group was injected intraperitoneally (i.p.) with 0.2 ml bacterial suspension at a density of 5.2 × 106 CFU/ml, while each one in control group injected i.p. with 0.2 ml sterile saline solution (0.85%, w/v). Three bullfrogs in both groups were sampled at 0, 1, 3, 7, 11, 15 and 20 days post-injection (dpi) for the evaluation of non-specific immune parameters. It was observed that intraperitoneal injection of A. hydrophila significantly increased the number of leucocytes and that of NBT-positive cells in peripheral blood. Significant increases in serum bactericidal activity and serum acid phosphatase activity were also observed in the bacterium-injected frogs when compared with those in the control group. However, a significant reduction was detected in vitro in phagocytosis activity of peripheral blood phagocytes. No significant difference in changes in the number of peripheral erythrocytes, serum superoxide dismutase (SOD) activity, and lysozyme activity was detected between the two groups. It is suggested that bullfrogs may produce a series of non-specific immune reactions in response to the A. hydrophila infection.

  18. Isolation of a soil bacterium capable of biodegradation and detoxification of endosulfan and endosulfan sulfate.

    Science.gov (United States)

    Lee, Jung-Bok; Sohn, Ho-Yong; Shin, Kee-Sun; Jo, Min-Sub; Kim, Jang-Eok; Lee, Se-Won; Shin, Ji-Won; Kum, Eun-Joo; Kwon, Gi-Seok

    2006-11-15

    Endosulfan, an endocrine disrupting chemical, is a widely used cyclodiene organochlorine pesticide worldwide, and it blocks neuronal GABA(A)-gated chloride channels in mammals and aquatic organisms. Endosulfan and its metabolites, such as endosulfan sulfate, are persistent in environments and are considered as toxic chemicals. For bioremediation of endosulfan, in this study, an attempt was made to isolate an endosulfan and endosulfan sulfate degrading bacterium from endosulfan-polluted agricultural soil. Through repetitive enrichment and successive subculture using endosulfan or endosulfan sulfate as the sole carbon source, a bacterium KS-2P was isolated. The KS-2P was identified as Pseudomonas sp. on the basis of the results of a 16S rDNA sequencing analysis and MIDI test. The degradation ratios for endosulfan or endosulfan sulfate in minimal medium containing endosulfan (23.5 microg mL(-1)) or endosulfan sulfate (21 microg mL(-1)) were 52% and 71%, respectively. Our results suggest that Pseudomonas sp. KS-2P has potential as a biocatalyst for endosulfan bioremediation.

  19. Expression and surface display of Cellulomonas endoglucanase in the ethanologenic bacterium Zymobacter palmae

    Energy Technology Data Exchange (ETDEWEB)

    Kojima, Motoki; Akahoshi, Tomohiro; Okamoto, Kenji; Yanase, Hideshi [Tottori Univ. (Japan). Dept. of Chemistry and Biotechnology

    2012-11-15

    In order to reduce the cost of bioethanol production from lignocellulosic biomass, we developed a tool for cell surface display of cellulolytic enzymes on the ethanologenic bacterium Zymobacter palmae. Z. palmae is a novel ethanol-fermenting bacterium capable of utilizing a broad range of sugar substrates, but not cellulose. Therefore, to express and display heterologous cellulolytic enzymes on the Z. palmae cell surface, we utilized the cell-surface display motif of the Pseudomonas ice nucleation protein Ina. The gene encoding Ina from Pseudomonas syringae IFO3310 was cloned, and its product was comprised of three functional domains: an N-terminal domain, a central domain with repeated amino acid residues, and a C-terminal domain. The N-terminal domain of Ina was shown to function as the anchoring motif for a green fluorescence protein fusion protein in Escherichia coli. To express a heterologous cellulolytic enzyme extracellularly in Z. palmae, we fused the N-terminal coding sequence of Ina to the coding sequence of an N-terminal-truncated Cellulomonas endoglucanase. Z. palmae cells carrying the fusion endoglucanase gene were shown to degrade carboxymethyl cellulose. Although a portion of the expressed fusion endoglucanase was released from Z. palmae cells into the culture broth, we confirmed the display of the protein on the cell surface by immunofluorescence microscopy. The results indicate that the N-terminal anchoring motif of Ina from P. syringae enabled the translocation and display of the heterologous cellulase on the cell surface of Z. palmae. (orig.)

  20. Heterologous expression and functional characterization of a novel chitinase from the chitinolytic bacterium Chitiniphilus shinanonensis.

    Science.gov (United States)

    Huang, Lanxiang; Shizume, Arisa; Nogawa, Masahiro; Taguchi, Goro; Shimosaka, Makoto

    2012-01-01

    Chitiniphilus shinanonensis strain SAY3(T) is a chitinolytic bacterium isolated from moat water of Ueda Castle in Nagano Prefecture, Japan. Fifteen genes encoding putative chitinolytic enzymes (chiA-chiO) have been isolated from this bacterium. Five of these constitute a single operon (chiCDEFG). The open reading frames of chiC, chiD, chiE, and chiG show sequence similarity to family 18 chitinases, while chiF encodes a polypeptide with two chitin-binding domains but no catalytic domain. Each of the five genes was successfully expressed in Escherichia coli, and the resulting recombinant proteins were characterized. Four of the recombinant proteins (ChiC, ChiD, ChiE, and ChiG) exhibited endo-type chitinase activity toward chitinous substrates, while ChiF showed no chitinolytic activity. In contrast to most endo-type chitinases, which mainly produce a dimer of N-acetyl-D-glucosamine (GlcNAc) as final product, ChiG completely split the GlcNAc dimer into GlcNAc monomers, indicating that it is a novel chitinase.

  1. Optimization of liquid media and biosafety assessment for algae-lysing bacterium NP23.

    Science.gov (United States)

    Liao, Chunli; Liu, Xiaobo; Shan, Linna

    2014-09-01

    To control algal bloom caused by nutrient pollution, a wild-type algae-lysing bacterium was isolated from the Baiguishan reservoir in Henan province of China and identified as Enterobacter sp. strain NP23. Algal culture medium was optimized by applying a Placket-Burman design to obtain a high cell concentration of NP23. Three minerals (i.e., 0.6% KNO3, 0.001% MnSO4·H2O, and 0.3% K2HPO4) were found to be independent factors critical for obtaining the highest cell concentration of 10(13) CFU/mL, which was 10(4) times that of the control. In the algae-lysing experiment, the strain exhibited a high lysis rate for the 4 algae test species, namely, Chlorella vulgari, Scenedesmus, Microcystis wesenbergii, and Chlorella pyrenoidosa. Acute toxicity and mutagenicity tests showed that the bacterium NP23 had no toxic and mutagenic effects on fish, even in large doses such as 10(7) or 10(9) CFU/mL. Thus, Enterobacter sp. strain NP23 has strong potential application in the microbial algae-lysing project.

  2. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

    Science.gov (United States)

    Caccavo, F.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

    1996-01-01

    A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

  3. Isolation, identification and characteristics of an endophytic quinclorac degrading bacterium Bacillus megaterium Q3.

    Directory of Open Access Journals (Sweden)

    Min Liu

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

  4. Application of agglomerative clustering for analyzing phylogenetically on bacterium of saliva

    Science.gov (United States)

    Bustamam, A.; Fitria, I.; Umam, K.

    2017-07-01

    Analyzing population of Streptococcus bacteria is important since these species can cause dental caries, periodontal, halitosis (bad breath) and more problems. This paper will discuss the phylogenetically relation between the bacterium Streptococcus in saliva using a phylogenetic tree of agglomerative clustering methods. Starting with the bacterium Streptococcus DNA sequence obtained from the GenBank, then performed characteristic extraction of DNA sequences. The characteristic extraction result is matrix form, then performed normalization using min-max normalization and calculate genetic distance using Manhattan distance. Agglomerative clustering technique consisting of single linkage, complete linkage and average linkage. In this agglomerative algorithm number of group is started with the number of individual species. The most similar species is grouped until the similarity decreases and then formed a single group. Results of grouping is a phylogenetic tree and branches that join an established level of distance, that the smaller the distance the more the similarity of the larger species implementation is using R, an open source program.

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

    KAUST Repository

    Balk, Melike

    2010-08-03

    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.

  6. Interface-mediated synthesis of monodisperse ZnS nanoparticles with sulfate-reducing bacterium culture.

    Science.gov (United States)

    Liang, Zhanguo; Mu, Jun; Mu, Ying; Shi, Jiaming; Hao, Wenjing; Dong, Xuewei; Yu, Hongquan

    2013-12-01

    We have created a new method of ZnS nanospheres synthesis. By interface-mediated precipitation method (IMPM), monodisperse ZnS nanoparticles was synthesized on the particle surface of sulfate-reducing bacterium nutritious agar culture. Sulfate-reducing bacterium (SRB) was used as a sulfide producer because of its dissimilatory sulfate reduction capability, meanwhile produced a variety of amino acids acting as templates for nanomaterials synthesis. Then zinc acetate was dispersed into nutritious agar plate. Subsequently agar plate was broken into particles bearing much external surface, which successfully mediated the synthesis of monodisperse ZnS nanoparticles. The morphology of monodisperse ZnS nanospheres and SRB were examined by scanning electron microscopy (SEM), and the microstructure was investigated by X-ray diffraction (XRD). The thermostability of ZnS nanoparticles was determined by thermo gravimetric-differential thermo gravimetric (TG-DTG). The maximum absorption wavelengh was analysed with an ultraviolet-visible spectrophotometer within a range of 199-700 nm. As a result, monodisperse ZnS nanoparticles were successfully synthesized, with an average diameter of 80 nm. Maximum absorption wavelengh was 228 nm, and heat decomposed temperature of monodisperse ZnS nanoparticles was 596°C. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

  7. Production and characterization of bioemulsifier from a marine bacterium, Acinetobacter calcoaceticus subsp. anitratus SM7

    Directory of Open Access Journals (Sweden)

    Kulnaree Phetrong

    2008-05-01

    Full Text Available Marine bacterium strain SM7 was isolated as a bioemulsifier-producing bacterium from oil-spilled seawater in Songkhla lagoon, Thailand. It was identified as Acinetobacter calcoaceticus subsp. anitratus based on morphology, biochemicalcharacteristics and 16S rRNA sequence. A. calcoaceticus subsp. anitratus SM7 produced an extracellular emulsifying agent when grown in a minimal salt medium (pH 7.0 containing 0.3% (v/v n-heptadecane and 0.1% (w/v ammoniumhydrogen carbonate as carbon source and nitrogen source, respectively, at 30oC with agitation rate of 200 rpm. Crude bioemulsifier was recovered from the culture supernatant by ethanol precipitation with a yield of 2.94 g/l and had a criticalemulsifier concentration of 0.04 g/ml. The crude bioemulsifier was capable of emulsifying n-hexadecane in a broad pH range (6-12, temperatures (30-121oC and in the presence of NaCl up to 12% (w/v. The bioemulsifier was stable in saltsolution ranging from 0 to 0.1% (w/v of MgCl2 and CaCl2. The broad range of pH stability, thermostability and salt tolerance suggested that the bioemulsifier from A. calcoaceticus subsp. anitratus SM7 could be useful in environmentalapplication, especially bioremediation of oil-polluted seawater.

  8. Involvement of a novel fermentative bacterium in acidification in a thermophilic anaerobic digester.

    Science.gov (United States)

    Hori, Tomoyuki; Akuzawa, Masateru; Haruta, Shin; Ueno, Yoshiyuki; Ogata, Atsushi; Ishii, Masaharu; Igarashi, Yasuo

    2014-12-01

    Acidification results from the excessive accumulation of volatile fatty acids and the breakthrough of buffering capacity in anaerobic digesters. However, little is known about the identity of the acidogenic bacteria involved. Here, we identified an active fermentative bacterium during acidification in a thermophilic anaerobic digester by sequencing and phylogenetic analysis of isotopically labeled rRNA. The digestion sludge retrieved from the beginning of pH drop in the laboratory-scale anaerobic digester was incubated anaerobically at 55 °C for 4 h during which 13 C-labeled glucose was supplemented repeatedly. 13 CH 4 and 13 CO 2 were produced after substrate addition. RNA extracts from the incubated sludge was density-separated by ultracentrifugation, and then bacterial communities in the density fractions were screened by terminal restriction fragment length polymorphism and clone library analyses based on 16S rRNA transcripts. Remarkably, a novel lineage within the genus Thermoanaerobacterium became abundant with increasing the buoyant density and predominated in the heaviest fraction of RNA. The results in this study indicate that a thermoacidophilic bacterium exclusively fermented the simple carbohydrate glucose, thereby playing key roles in acidification in the thermophilic anaerobic digester. © 2014 Federation of European Microbiological Societies.

  9. [Identification and function test of an alkali-tolerant denitrifying bacterium].

    Science.gov (United States)

    Wang, Ru; Zheng, Ping; Li, Wei; Chen, Hui; Chen, Tingting; Ghulam, Abbas

    2013-04-04

    We obtained an alkali-tolerant denitrifying bacterium, and determined its denitrifying activity and alkali-tolerance. An alkali-tolerant denitrifying bacterial strain was obtained by isolation and purification. We identified the bacterial strain by morphological observation, physiological test and 16S rRNA analysis. We determined the denitrifying activity and alkali-tolerance by effects of initial nitrate concentration and initial pH on denitrification. An alkali-tolerant denitrifier strain R9 was isolated from the lab-scale high-rate denitrifying reactor, and it was identified as Diaphorobater nitroreducens. The strain R9 grew heterotrophically with methanol as the electron donor and nitrate as the electron acceptor. The nitrate conversion was 93.25% when strain R9 was cultivated for 288 h with initial nitrate concentration 50 mg/L and initial pH 9.0. The denitrification activity could be inhibited at high nitrate concentration with a half inhibition constant of 202.73 mg N/L. Strain R9 showed a good alkali tolerance with the nitrate removal rate at pH 11.0 remained 86% of that at pH 9.0. Strain R9 was identified as Diaphorobater nitroreducens, and it was an alkali-tolerant denitrifying bacterium with optimum pH value of 9.0.

  10. Biological control of postharvest pear diseases using a bacterium, Pantoea agglomerans CPA-2.

    Science.gov (United States)

    Nunes, C; Usall, J; Teixidó, N; Viñas, I

    2001-10-22

    Epiphytic microorganisms isolated from the fruits and leaf surfaces of apples and pears were screened for antagonistic activity against Penicillium expansum on pears. From 247 microorganisms tested for antagonistic properties against P. expansum, a bacterium strain identified as Pantoea agglomerans (CPA-2) was selected. This bacterium was very effective against Botrytis cinerea, P. expansum and Rhizopus stolonifer. Complete control at the three tested concentrations (2 x 10(7), 8 x 10(7) and 1 x 10(8) CFU ml(-1)) was obtained on wounded pears inoculated with 10(3), 10(4) and 10(5) conidia ml(-1) of P. expansum and R. stolonifer. At 8 x 10(7) CFU ml(-1), Pan. agglomerans reduced B. cinerea decay by more than 80% at the three concentrations of the pathogen. In over 3 years of experiments in semicommercial trials, Pan. agglomerans provided excellent control against B. cinerea and P. expansum under cold storage, either in air or in low oxygen atmospheres. Equal control was obtained with Pan. agglomerans at 8 x 10(7) CFU ml(-1), as with the fungicide imazalil at commercial doses, against both pathogens. Pan. agglomerans grew well inside wounds on pears at both room and cold temperatures and under modified atmospheres. In contrast, it grew poorly on the surface of intact fruit.

  11. Intestinal bacterium-derived cyp27a1 prevents colon cancer cell apoptosis.

    Science.gov (United States)

    Ji, Yan-Chao; Liu, Chang; Zhang, Xia; Zhang, Cheng-Sen; Wang, Dong; Zhang, Yan

    2016-01-01

    The pathogenesis of metastasis of colon cancer (Cca) is to be further investigated. The dysfunction of apoptotic mechanism plays a role in the cancer cell over growth. This study tests a hypothesis by which intestinal bacterium-derived cyp27a1 prevents apoptosis in colon cancer cells. In this study, the levels of cyp27a1 in human stool samples were assessed by enzyme-linked immunosorbent assay. The apoptosis of Cca cells was observed by flow cytometry. The expression of cyp27a1 was assessed by real time RT-PCR and Western blotting. We observed higher levels of cyp27a1 in the stool samples of Cca patients than that from healthy subjects. Cca colon epithelial biopsy contained high levels of cyp27a1 protein, but not the cyp27a1 mRNA. Cyp27a1 prevented Cca cell apoptosis induced by vitamin D3. In conclusion, intestinal bacterium-derived cyp27a1 facilitates Cca survival by inhibiting Cca cell apoptosis.

  12. Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study

    Directory of Open Access Journals (Sweden)

    OCKY KARNA RADJASA

    2005-06-01

    Full Text Available A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity, a multifunctional peptide synthetase from Nostoc sp. GSV224, and NdaB (44% identity, a peptide synthetase module of Nodularia spumigena

  13. Effects of an equol-producing bacterium isolated from human faeces on isoflavone and lignan metabolism in mice.

    Science.gov (United States)

    Tamura, Motoi; Hori, Sachiko; Nakagawa, Hiroyuki; Yamauchi, Satoshi; Sugahara, Takuya

    2016-07-01

    Equol is a metabolite of daidzein that is produced by intestinal microbiota. The oestrogenic activity of equol is stronger than daidzein. Equol-producing bacteria are believed to play an important role in the gut. The rod-shaped and Gram-positive anaerobic equol-producing intestinal bacterium Slackia TM-30 was isolated from healthy human faeces and its effects on urinary phyto-oestrogen, plasma and faecal lipids were assessed in adult mice. The urinary amounts of equol in urine were significantly higher in mice receiving the equol-producing bacterium TM-30 (BAC) group than in the control (CO) group (P mice. The equol-producing bacterium TM-30 likely influences the metabolism of phyto-oestrogen via changes in the gastrointestinal environment. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  14. Bacterium-like Particles for efficient immune stimulation of existing vaccines and new subunit vaccines in mucosal applications

    Directory of Open Access Journals (Sweden)

    Natalija eVan Braeckel-Budimir

    2013-09-01

    Full Text Available The successful development of a mucosal vaccine critically depends on the use of a safe and effective immunostimulant and/or carrier system. This review describes the effectiveness and mode of action of an immunostimulating particle derived from bacteria in mucosal subunit vaccines. The non-living particles, designated Bacterium-like Particles (BLPs are based on the food-grade bacterium Lactococcus lactis. The focus of the overview is on the development of intranasal BLP-based vaccines to prevent diseases caused by influenza and respiratory syncytial virus, and includes a selection of Phase I clinical data for the intranasal FluGEM vaccine.

  15. Joseph Lister: first use of a bacterium as a 'model organism' to illustrate the cause of infectious disease of humans.

    Science.gov (United States)

    Santer, Melvin

    2010-03-20

    Joseph Lister's goal was to show that a pure culture of Bacterium lactis, normally present in milk, uniquely caused the lactic acid fermentation of milk. To demonstrate this fact he devised a procedure to obtain a pure clonal population of B. lactis, a result that had not previously been achieved for any microorganism. Lister equated the process of fermentation with infectious disease and used this bacterium as a model organism, demonstrating its role in fermentation; from this result he made the inductive inference that infectious diseases of humans are the result of the growth of specific, microscopic, living organisms in the human host.

  16. The impact of a pathogenic bacterium on a social carnivore population.

    Science.gov (United States)

    Höner, Oliver P; Wachter, Bettina; Goller, Katja V; Hofer, Heribert; Runyoro, Victor; Thierer, Dagmar; Fyumagwa, Robert D; Müller, Thomas; East, Marion L

    2012-01-01

    1. The long-term ecological impact of pathogens on group-living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium, Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyena Crocuta crocuta population in the Ngorongoro Crater, Tanzania. 2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent ('outbreak') and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rate R(0) of the bacterium. 3. During the five pre-outbreak years, the mean annual hyena mortality rate was 0.088, and annual population growth was relatively high (13.6%). During the outbreak, mortality increased by 78% to a rate of 0.156, resulting in an annual population decline of 4.3%. After the outbreak, population size increased moderately (5.1%) during the first three post-outbreak years before resuming a growth similar to pre-outbreak levels (13.9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors. 4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females - the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimated R(0) for the bacterium to be 2.7, indicating relatively fast transmission. 5. Our results suggest that the short-term 'top-down' impact of S. equi ruminatorum during the outbreak was driven by 'bottom-up' effects on nutritionally disadvantaged age-sex classes, whereas the longer-term post-outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent

  17. Metabolism of 4-chloro-2-nitrophenol in a Gram-positive bacterium, Exiguobacterium sp. PMA

    Directory of Open Access Journals (Sweden)

    Arora Pankaj

    2012-11-01

    Full Text Available Abstract Background Chloronitrophenols (CNPs are widely used in the synthesis of dyes, drugs and pesticides, and constitute a major group of environmental pollutants. 4-Chloro-2-nitrophenol (4C2NP is an isomer of CNPs that has been detected in various industrial effluents. A number of physicochemical methods have been used for treatment of wastewater containing 4C2NP. These methods are not as effective as microbial degradation, however. Results A 4C2NP-degrading bacterium, Exiguobacterium sp. PMA, which uses 4C2NP as the sole carbon and energy source was isolated from a chemically-contaminated site in India. Exiguobacterium sp. PMA degraded 4C2NP with the release of stoichiometeric amounts of chloride and ammonium ions. The effects of different substrate concentrations and various inoculum sizes on degradation of 4C2NP were investigated. Exiguobacterium sp. PMA degraded 4C2NP up to a concentration of 0.6 mM. High performance liquid chromatography and gas chromatography–mass spectrometry identified 4-chloro-2-aminophenol (4C2AP and 2-aminophenol (2AP as possible metabolites of the 4C2NP degradation pathway. The crude extract of 4C2NP-induced PMA cells contained enzymatic activity for 4C2NP reductase and 4C2AP dehalogenase, suggesting the involvement of these enzymes in the degradation of 4C2NP. Microcosm studies using sterile and non-sterile soils spiked with 4C2NP were carried out to monitor the bioremediation potential of Exiguobacterium sp. PMA. The bioremediation of 4C2NP by Exiguobacterium sp. PMA was faster in non-sterilized soil than sterilized soil. Conclusions Our studies indicate that Exiguobacterium sp. PMA may be useful for the bioremediation of 4C2NP-contaminated sites. This is the first report of (i the formation of 2AP in the 4C2NP degradation pathway by any bacterium and (iii the bioremediation of 4C2NP by any bacterium.

  18. A pathway closely related to the (D)-tagatose pathway of gram-negative enterobacteria identified in the gram-positive bacterium Bacillus licheniformis.

    Science.gov (United States)

    Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M; Galleni, Moreno; Joris, Bernard

    2013-06-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

  19. A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

    Science.gov (United States)

    Van der Heiden, Edwige; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

    2013-01-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. PMID:23524682

  20. A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

    OpenAIRE

    Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

    2013-01-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

  1. Biochemical Characterization and Relative Expression Levels of Multiple Carbohydrate Esterases of the Xylanolytic Rumen Bacterium Prevotella ruminicola 23 Grown on an Ester-Enriched Substrate

    NARCIS (Netherlands)

    Kabel, M.A.; Yeoman, C.J.; Han, Y.; Dodd, D.; Abbas, C.A.; Bont, de J.A.M.; Morrison, M.; Cann, I.K.O.; Mackie, R.I.

    2011-01-01

    We measured expression and used biochemical characterization of multiple carbohydrate esterases by the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate to gain insight into the carbohydrate esterase activities of this hemicellulolytic rumen bacterium. The P.

  2. Proteomic Profiling of the Dioxin-Degrading Bacterium Sphingomonas wittichii RW1

    Directory of Open Access Journals (Sweden)

    David R. Colquhoun

    2012-01-01

    Full Text Available Sphingomonas wittichii RW1 is a bacterium of interest due to its ability to degrade polychlorinated dioxins, which represent priority pollutants in the USA and worldwide. Although its genome has been fully sequenced, many questions exist regarding changes in protein expression of S. wittichii RW1 in response to dioxin metabolism. We used difference gel electrophoresis (DIGE and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS to identify proteomic changes induced by growth on dibenzofuran, a surrogate for dioxin, as compared to acetate. Approximately 10% of the entire putative proteome of RW1 could be observed. Several components of the dioxin and dibenzofuran degradation pathway were shown to be upregulated, thereby highlighting the utility of using proteomic analyses for studying bioremediation agents. This is the first global protein analysis of a microorganism capable of utilizing the carbon backbone of both polychlorinated dioxins and dibenzofurans as the sole source for carbon and energy.

  3. Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16.

    Science.gov (United States)

    Pohlmann, Anne; Fricke, Wolfgang Florian; Reinecke, Frank; Kusian, Bernhard; Liesegang, Heiko; Cramm, Rainer; Eitinger, Thomas; Ewering, Christian; Pötter, Markus; Schwartz, Edward; Strittmatter, Axel; Voss, Ingo; Gottschalk, Gerhard; Steinbüchel, Alexander; Friedrich, Bärbel; Bowien, Botho

    2006-10-01

    The H(2)-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically versatile organism capable of subsisting, in the absence of organic growth substrates, on H(2) and CO(2) as its sole sources of energy and carbon. R. eutropha H16 first attracted biotechnological interest nearly 50 years ago with the realization that the organism's ability to produce and store large amounts of poly[R-(-)-3-hydroxybutyrate] and other polyesters could be harnessed to make biodegradable plastics. Here we report the complete genome sequence of the two chromosomes of R. eutropha H16. Together, chromosome 1 (4,052,032 base pairs (bp)) and chromosome 2 (2,912,490 bp) encode 6,116 putative genes. Analysis of the genome sequence offers the genetic basis for exploiting the biotechnological potential of this organism and provides insights into its remarkable metabolic versatility.

  4. Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree.

    Science.gov (United States)

    Rivas, Raúl; Trujillo, Martha E; Mateos, P F; Martínez-Molina, E; Velázquez, Encarna

    2004-03-01

    A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99.0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11(T) in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA-DNA hybridization with C. humilata ATCC 25174(T), in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11(T) should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11(T) (=LMG 21723(T)=CECT 5729(T)) as the type strain.

  5. Plague bacterium as a transformer species in prairie dogs and the grasslands of western North America

    Science.gov (United States)

    Eads, David A.; Biggins, Dean E.

    2015-01-01

    Invasive transformer species change the character, condition, form, or nature of ecosystems and deserve considerable attention from conservation scientists. We applied the transformer species concept to the plague bacterium Yersinia pestis in western North America, where the pathogen was introduced around 1900. Y. pestis transforms grassland ecosystems by severely depleting the abundance of prairie dogs (Cynomys spp.) and thereby causing declines in native species abundance and diversity, including threatened and endangered species; altering food web connections; altering the import and export of nutrients; causing a loss of ecosystem resilience to encroaching invasive plants; and modifying prairie dog burrows. Y. pestis poses an important challenge to conservation biologists because it causes trophic-level perturbations that affect the stability of ecosystems. Unfortunately, understanding of the effects of Y. pestis on ecosystems is rudimentary, highlighting an acute need for continued research.

  6. Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense.

    Science.gov (United States)

    Sant'Anna, Fernando H; Almeida, Luiz G P; Cecagno, Ricardo; Reolon, Luciano A; Siqueira, Franciele M; Machado, Maicon R S; Vasconcelos, Ana T R; Schrank, Irene S

    2011-08-12

    The species Azospirillum amazonense belongs to a well-known genus of plant growth-promoting bacteria. This bacterium is found in association with several crops of economic importance; however, there is a lack of information on its physiology. In this work, we present a comprehensive analysis of the genomic features of this species. Genes of A. amazonense related to nitrogen/carbon metabolism, energy production, phytohormone production, transport, quorum sensing, antibiotic resistance, chemotaxis/motility and bacteriophytochrome biosynthesis were identified. Noteworthy genes were the nitrogen fixation genes and the nitrilase gene, which could be directly implicated in plant growth promotion, and the carbon fixation genes, which had previously been poorly investigated in this genus. One important finding was that some A. amazonense genes, like the nitrogenase genes and RubisCO genes, were closer phylogenetically to Rhizobiales members than to species of its own order. The species A. amazonense presents a versatile repertoire of genes crucial for its plant-associated lifestyle.

  7. Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118.

    Science.gov (United States)

    Lobley, Carina M C; Aller, Pierre; Douangamath, Alice; Reddivari, Yamini; Bumann, Mario; Bird, Louise E; Nettleship, Joanne E; Brandao-Neto, Jose; Owens, Raymond J; O'Toole, Paul W; Walsh, Martin A

    2012-12-01

    The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.

  8. Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118

    International Nuclear Information System (INIS)

    Lobley, Carina M. C.; Aller, Pierre; Douangamath, Alice; Reddivari, Yamini; Bumann, Mario; Bird, Louise E.; Nettleship, Joanne E.; Brandao-Neto, Jose; Owens, Raymond J.; O’Toole, Paul W.; Walsh, Martin A.

    2012-01-01

    The crystal structure of ribose 5-phosphate isomerase has been determined to 1.72 Å resolution and is presented with a brief comparison to other known ribose 5-phosphate isomerase A structures. The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β d-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography

  9. Separation and characterization of a radioresistant bacterium strain BR501 from radiation polluted soil

    International Nuclear Information System (INIS)

    Chen Ming; Liu Xiumin; Zhang Wei; Lin Min

    2007-01-01

    Strain BR501, an extremely radioresistant bacterium isolated from the radioactive experimental soil. The optimal temperature for the growth of strain BR501 was 30 degree C. The UV radiation and γ-radiation survival curves showed the strain BR501 had highly radio-resistance. The strain was sensitive to Amp, Km, Rif, Cm and Tc. The 16S rDNA of the BR501 shared highly similarity to those of species in genus Deinococcus, especially to that of D.radiodurans r1(99%). Based on the 16S rDNA sequence analysis and the phenotype characteristics, the BR501 belongs to the evolution branch of Deinococcus and was designated Deinococcus sp. BR501. (authors)

  10. Inhibition of a sulfate reducing bacterium, Desulfovibrio marinisediminis GSR3, by biosynthesized copper oxide nanoparticles.

    Science.gov (United States)

    Alasvand Zarasvand, Kiana; Rai, V Ravishankar

    2016-06-01

    To control the severe problem of microbiologically influenced corrosion, industries require highly potent antibacterial agent which can inhibit the growth of bacteria on man-made surfaces. This need drove the research towards the synthesis of nanoscale antimicrobial compounds. We, therefore, screened several bacteria for the biosynthesis of copper/copper compound nanoparticles which could inhibit the growth of Desulfovibrio marinisediminis, a sulfate reducing bacterium. Supernatant of thirty bacteria isolated from the biofilm formed on ship hull was mixed with 1 mM CuCl 2 solution at room temperature. Eight bacterial strains, whose mixtures exhibited colour change, were selected for antimicrobial test. One nanoparticle which has been biosynthesized by Shewanella indica inhibited the growth of D. marinisediminis. Characterization of this particle by UV-visible spectrophotometer, XRD, TEM, DLS and FTIR showed that the particle is polydisperse CuO nanoparticle with average size of 400 nm.

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

    Science.gov (United States)

    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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Isolation and characterization of transducing bacteriophage BP1 for Bacterium anitratum (Achromobacter sp.).

    Science.gov (United States)

    Twarog, R; Blouse, L E

    1968-07-01

    A small transducing phage has been isolated against a strain of Bacterium anitratum. The particle has a head dimension of 450 A and a tail approximately 200 A long. The latent period is 16 min and the average burst size is 98. The intact particle has an absorption maximum and minimum at 260 and 237 mmu, respectively. The sedimentation coefficient (S(20)) is 460. The phage contains double-stranded DNA with an S degrees (20,w) of 32.8. Molecular weight estimates of the deoxyribonucleic acid ranged from 2.33 x 10(7) to 2.66 x 10(7) based on sedimentation velocity studies. The percentage guanine plus cytosine compositions of the deoxyribonucleic acid, determined by melting temperature and cesium chloride equilibrium centrifugation, were 40.7 and 42.0, respectively.

  13. Novel Poly[(R-3-Hydroxybutyrate]-Producing Bacterium Isolated from a Bolivian Hypersaline Lake

    Directory of Open Access Journals (Sweden)

    María Soledad Marqués-Calvo

    2013-01-01

    Full Text Available Poly[(R-3-hydroxybutyrate] (PHB constitutes a biopolymer synthesized from renewable resources by various microorganisms. This work focuses on finding a new PHB-producing bacterium capable of growing in conventional media used for industrial biopolymer production, its taxonomical identification, and characterization of its biopolymer. Thus, a bacterial isolation process was carried out from environmental samples of water and mud. Among the isolates, strain S29 was selected and used in a fed-batch fermentation to generate a biopolymer. This biopolymer was recovered and identified as PHB homopolymer. Surprisingly, it featured several fractions of different molecular masses, and thermal properties unusual for PHB. Hence, the microorganism S29, genetically identified as a new strain of Bacillus megaterium, proved to be interesting not only due to its growth and PHB accumulation kinetics under the investigated cultivation conditions, but also due to the thermal properties of the produced PHB.

  14. Chitinolytic enzymes from bacterium inhabiting human gastrointestinal tract -- critical parameters of protein isolation from anaerobic culture.

    Science.gov (United States)

    Dušková, Jarmila; Tishchenko, Galina; Ponomareva, Evgenia; Šimůnek, Jiří; Koppová, Ingrid; Skálová, Tereza; Štěpánková, Andrea; Hašek, Jindřich; Dohnálek, Jan

    2011-01-01

    The object of this study are chitinolytic enzymes produced by bacterium Clostridium paraputrificum J4 isolated from the gastrointestinal tract of a healthy human. In particular, we focus on the development of purification protocols, determination of properties of the enzymes and their activity profiles. The process of bacteria cultivation and isolation of chitinolytic complex of enzymes showing specific activities of endo-, exo-chitinase and N-acetyl-β-glucosaminidase was optimized. A range of various purification procedures were used such as ultrafiltration, precipitation, chromatographic separations (ion-exchange, size exclusion, chromatofocusing) in altered combinations. The optimal purification protocol comprises two or three steps. Individual samples were analyzed by SDS/PAGE electrophoresis and after renaturation their activity could be detected using zymograms. Mass spectroscopy peptide fragment analysis and MALDI analysis of the purest samples indicate presence of endochitinase B (molecular mass about 85 kDa) and of 60-kDa endo- and exochitinases.

  15. Plague bacterium as a transformer species in prairie dogs and the grasslands of western North America.

    Science.gov (United States)

    Eads, David A; Biggins, Dean E

    2015-08-01

    Invasive transformer species change the character, condition, form, or nature of ecosystems and deserve considerable attention from conservation scientists. We applied the transformer species concept to the plague bacterium Yersinia pestis in western North America, where the pathogen was introduced around 1900. Y. pestis transforms grassland ecosystems by severely depleting the abundance of prairie dogs (Cynomys spp.) and thereby causing declines in native species abundance and diversity, including threatened and endangered species; altering food web connections; altering the import and export of nutrients; causing a loss of ecosystem resilience to encroaching invasive plants; and modifying prairie dog burrows. Y. pestis poses an important challenge to conservation biologists because it causes trophic-level perturbations that affect the stability of ecosystems. Unfortunately, understanding of the effects of Y. pestis on ecosystems is rudimentary, highlighting an acute need for continued research. © 2015 Society for Conservation Biology.

  16. Microbially influenced corrosion of stainless steel by marine bacterium Vibrio natriegens: (I) Corrosion behavior

    International Nuclear Information System (INIS)

    Cheng Sha; Tian Jintao; Chen Shougang; Lei Yanhua; Chang Xueting; Liu Tao; Yin Yansheng

    2009-01-01

    The microbially influenced corrosion of stainless steel (SS) by marine bacterium Vibrio natriegens (V. natriegens) was investigated using surface analysis (atomic force microscopy (AFM), scanning electron microscopy (SEM), and energy dispersive X-ray analysis (EDXA)) and electrochemical techniques (the open circuit potential, electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization curves ). AFM images corroborated the results from the EIS models which show biofilm attachment and subsequent detachment over time. The SEM images revealed the occurrence of micro-pitting corrosion underneath the biofilms on the metal surface after the biofilm removal. The presence of carbon, oxygen, phosphor and sulfur obtained from EDXA proved the formation of biofilm. The electrochemical results showed that the corrosion of SS was accelerated in the presence of V. natriegens based on the decrease in the resistance of the charge transfer resistance (R ct ) obtained from EIS and the increase in corrosion current densities obtained from potentiodynamic polarization curves.

  17. Tyrosine binding and promiscuity in the arginine repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis.

    Science.gov (United States)

    Mariutti, Ricardo Barros; Ullah, Anwar; Araujo, Gabriela Campos; Murakami, Mario Tyago; Arni, Raghuvir Krishnaswamy

    2016-07-08

    The arginine repressor (ArgR) regulates arginine biosynthesis in a number of microorganisms and consists of two domains interlinked by a short peptide; the N-terminal domain is involved in DNA binding and the C-terminal domain binds arginine and forms a hexamer made-up of a dimer of trimers. The crystal structure of the C-terminal domain of ArgR from the pathogenic Corynebacterium pseudotuberculosis determined at 1.9 Å resolution contains a tightly bound tyrosine at the arginine-binding site indicating hitherto unobserved promiscuity. Structural analysis of the binding pocket displays clear molecular adaptations to accommodate tyrosine binding suggesting the possible existence of an alternative regulatory process in this pathogenic bacterium. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. A Marine Sulfate-Reducing Bacterium Producing Multiple Antibiotics: Biological and Chemical Investigation

    Directory of Open Access Journals (Sweden)

    Xiaoliang Wang

    2009-07-01

    Full Text Available A marine sulfate-reducing bacterium SRB-22 was isolated by means of the agar shake dilution method and identified as Desulfovibrio desulfuricans by morphological, physiological and biochemical characteristics and 16S rDNA analysis. In the bioassay, its extract showed broad-spectrum antimicrobial activity using the paper disc agar diffusion method. This isolate showed a different antimicrobial profile than either ampicillin or nystatin and was found to produce at least eight antimicrobial components by bioautography. Suitable fermentation conditions for production of the active constituents were determined to be 28 day cultivation at 25 °C to 30 °C with a 10% inoculation ratio. Under these conditions, the SRB-22 was fermented, extracted and chemically investigated. So far an antimicrobial compound, mono-n-butyl phthalate, and an inactive compound, thymine, have been isolated and characterized.

  19. Thermotoga subterranea sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir.

    Science.gov (United States)

    Jeanthon, C; Reysenbach, A L; L'Haridon, S; Gambacorta, A; Pace, N R; Glénat, P; Prieur, D

    1995-08-01

    A thermophilic, strictly anaerobic bacterium, designated strain SL1, was isolated from a deep, continental oil reservoir in the East Paris Basin (France). This organism grew between 50 and 75 degrees C, with an optimum at 70 degrees C. It was inhibited by elemental sulfur and was able to reduce cystine and thiosulfate to hydrogen sulfide. The G+C content (40 mol%), the presence of a lipid structure unique to the genus Thermotoga, and the 16S rRNA sequence of strain SL1 indicated that the isolate belongs to the genus Thermotoga. Based on DNA-DNA hybridization, isolate SL1 does not show species-level similarity with the recognized species T. maritima, T. neapolitana, and T. thermarum. Based on this description of strain SL1, we propose the recognition of a new species: Thermotoga subterranea.

  20. Identification of ceramide phosphorylethanolamine and ceramide phosphorylglycerol in the lipids of an anaerobic bacterium.

    Science.gov (United States)

    LaBach, J P; White, D C

    1969-09-01

    Nearly half the phospholipids isolated from the anerobic bacterium Bacteroides melaninogenicus are phosphosphingolipids. The two major phosphosphingolipids have been characterized as ceramide phosphorylethanolamine and ceramide phosphorylglycerol. The long-chain bases of these phosphosphingolipids appear to have branched and normal saturated carbon chains of 17, 18, and 19 atoms; the phosphate is at the 1-position of the long-chain base. The composition of the amide-linked fatty acids of the phosphosphingolipids differs from that of the ester-linked fatty acids of the diacylphosphoglycerides in having a higher percentage of 14:0, 17:0, and 18:0 acids as well as containing nearly all the monoenoic fatty acids found in the bacterial lipids. The finding of phosphosphingolipids in bacteria is exceedingly rare and to our knowledge ceramide phosphorylglycerol has not been previously found in nature.

  1. Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum

    DEFF Research Database (Denmark)

    Frigaard, Niels-Ulrik; Maresca, Julia A; Yunker, Colleen E

    2004-01-01

    The green sulfur bacterium Chlorobium tepidum is a strict anaerobe and an obligate photoautotroph. On the basis of sequence similarity with known enzymes or sequence motifs, nine open reading frames encoding putative enzymes of carotenoid biosynthesis were identified in the genome sequence of C....... tepidum, and all nine genes were inactivated. Analysis of the carotenoid composition in the resulting mutants allowed the genes encoding the following six enzymes to be identified: phytoene synthase (crtB/CT1386), phytoene desaturase (crtP/CT0807), zeta-carotene desaturase (crtQ/CT1414), gamma......-carotene desaturase (crtU/CT0323), carotenoid 1',2'-hydratase (crtC/CT0301), and carotenoid cis-trans isomerase (crtH/CT0649). Three mutants (CT0180, CT1357, and CT1416 mutants) did not exhibit a discernible phenotype. The carotenoid biosynthetic pathway in C. tepidum is similar to that in cyanobacteria and plants...

  2. Degradation of pyrene by an enteric bacterium, Leclercia adecarboxylata PS4040.

    Science.gov (United States)

    Sarma, Priyangshu Manab; Duraja, Prem; Deshpande, Shilpanjali; Lal, Banwari

    2010-02-01

    A newly discovered enteric bacterium Leclercia adecarboxylata PS4040, isolated from oily sludge contaminated soil sample was reported for degradation of polycyclic aromatic hydrocarbons (Appl Environ Microbiol 70:3163-3166, 2004a). This strain could degrade 61.5% of pyrene within 20 days when used as sole source of carbon and energy. The time course degradation experiment detected several intermediate products and the metabolites were identified by gas chromatography mass spectrometry analysis. Metabolite I was the detected on the 5th day and was identified as 1-hydroxypyrene and was detected till 10th day. Metabolite II which was detected on 10th day was identified as 1,2-phenanthrenedicarboxylic acid. Metabolite III and Metabolite IV were identified as 2-carboxy benzaldehyde and ortho-phthalic acid, respectively and were detected in the culture broth on 10th and 15th day. 1,2-benzene diol (catechol) was the fifth metabolite detected in the culture extracts on the 15th day and was subsequently reduced on day 20. Identification of Metabolite I as 1-hydroxypyrene was further investigated as this intermediate was not previously reported as a ring oxidation product for degradation of pyrene by bacterial strains. Purification by preparative high performance liquid chromatography and nuclear magnetic resonance spectroscopy, confirmed the identification of Metabolite I as 1-hydroxypyrene. L. adecarboxylata PS4040 could also use 1-hydroxypyrene as a sole source of carbon and energy. Thus a probable pathway for degradation of pyrene by enteric bacterium is proposed in this study, with 1-hydroxypyrene as initial ring oxidation product.

  3. Isolation and characterization of a radiation resistant thermophilic bacterium from radon hot spring

    International Nuclear Information System (INIS)

    Liang Xinle; Yang Long; Zhang Hong; Zhang Lei

    2011-01-01

    A radiation resistant and thermophilic bacterium strain R4-33 was isolated from radon hot spring water samples, pretreated with 60 Co γ-rays and UV irradiation. Tests on morphological, physiological and biochemical characters, fatty acid compositions, (G + C) mol% contents, and 16S rDNA sequencing were conducted. The results showed that strain R4-33 was of rod-shape, Gram-negative, atrichous, and endospore-forming. The optimum growth temperature and pH were 60 ℃ and 7.5, respectively. The strain utilized glucose, maltose and trehalose as carbon sources, and hydrolyzed casein and starch. Its catalase positive. The strain was sensitive to penicillin, neomycin, erythromycin, vancomycin, streptomycin, gentamycin, amikacin and ampicillin. The major cellular fatty acids were C 14:1 (48.8%) and C 15:1 (15.2%). The (G + C) mol% content of DNA was 58.2%. Phylogenetic tree based on 16S rDNA sequence showed R4-33 shared highly similarity to those of species in genus Anoxybacillus, especially to that of Anoxybacillus gonensis (99.5%). Based on the above, the strain R4-33 was proposed to the evolution branch of Anoxybacillus and designated as Anoxybacillu sp. R4-33. The UV and γ-radiation tests showed that the strain R4-33 had an ability of resistance to UV of 396 J/m 2 and 60 Co γ-rays irradiation of 14.0 kGy, indicating that the strain was a radiation resistant and thermophilic bacterium. (authors)

  4. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress.

    Science.gov (United States)

    Chen, Yanmei; Chao, Yuanqing; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong; Qiu, Rongliang

    2016-01-04

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  5. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    Science.gov (United States)

    Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

    2010-01-01

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

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

    Directory of Open Access Journals (Sweden)

    Guangli Wang

    2010-06-01

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

  7. Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales.

    Science.gov (United States)

    Bao, Zhihua; Sato, Yoshinori; Fujimura, Reiko; Ohta, Hiroyuki

    2014-03-01

    A thallium-tolerant, aerobic bacterium, designated strain SK200a-9(T), isolated from a garden soil sample was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain SK200a-9(T) was affiliated with an uncultivated lineage within the Alphaproteobacteria and the nearest cultivated neighbours were bacteria in genera in the family Methylocystaceae (93.3-94.4% 16S rRNA gene sequence similarity) and the family Beijerinckiaceae (92.3-93.1%) in the order Rhizobiales. Cells of strain SK200a-9(T) were Gram-stain-negative, non-motile, non-spore-forming, poly-β-hydroxybutyrate-accumulating rods. The strain was a chemo-organotrophic bacterium, which was incapable of growth on C1 substrates. Catalase and oxidase were positive. Atmospheric nitrogen fixation and nitrate reduction were negative. The strain contained ubiquinone Q-10 and cellular fatty acids C18 : 1ω7c, C18 : 0, C16 : 1ω7c and C16 : 0 as predominant components. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 64.8 mol%. On the basis of the information described above, strain SK200a-9(T) is considered to represent a novel species of a new genus in the order Rhizobiales, for which the name Alsobacter metallidurans gen. nov., sp. nov. is proposed. The type strain of Alsobacter metallidurans is SK200a-9(T) ( = NBRC 107718(T) = CGMCC 1.12214(T)).

  8. Regulation of dissimilatory sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum

    Directory of Open Access Journals (Sweden)

    Frauke eGrimm

    2011-03-01

    Full Text Available In the purple sulfur bacterium Allochromatium vinosum, thiosulfate oxidation is strictly dependent on the presence of three periplasmic Sox proteins encoded by the soxBXAK and soxYZ genes. It is also well documented that proteins encoded in the dsr (dissimilatory sulfite reductase operon, dsrABEFHCMKLJOPNRS, are essential for the oxidation of sulfur that is stored intracellularly as an obligatory intermediate during the oxidation of thiosulfate and sulfide. Until recently, detailed knowledge about the regulation of the sox genes was not available. We started to fill this gap and show that these genes are expressed on a low constitutive level in A. vinosum in the absence of reduced sulfur compounds. Thiosulfate and possibly sulfide lead to an induction of sox gene transcription. Additional translational regulation was not apparent. Regulation of soxXAK is probably performed by a two-component system consisting of a multisensor histidine kinase and a regulator with proposed di-guanylate cyclase activity. Previous work already provided some information about regulation of the dsr genes encoding the second important sulfur-oxidizing enzyme system in the purple sulfur bacterium. The expression of most dsr genes was found to be at a low basal level in the absence of reduced sulfur compounds and enhanced in the presence of sulfide. In the present work, we focused on the role of DsrS, a protein encoded by the last gene of the dsr locus in A. vinosum. Transcriptional and translational gene fusion experiments suggest a participation of DsrS in the post-transcriptional control of the dsr operon. Characterization of an A. vinosum ΔdsrS mutant showed that the monomeric cytoplasmic 41.1 kDa protein DsrS is important though not essential for the oxidation of sulfur stored in the intracellular sulfur globules.

  9. Extracellular polymer substance synthesized by a halophilic bacterium Chromohalobacter canadensis 28.

    Science.gov (United States)

    Radchenkova, Nadja; Boyadzhieva, Ivanka; Atanasova, Nikolina; Poli, Annarita; Finore, Ilaria; Di Donato, Paola; Nicolaus, Barbara; Panchev, Ivan; Kuncheva, Margarita; Kambourova, Margarita

    2018-04-03

    Halophilic microorganisms are producers of a lot of new compounds whose properties suggest promising perspectives for their biotechnological exploration. Moderate halophilic bacterium Chromohalobacter canadensis 28 was isolated from Pomorie salterns as an extracellular polymer substance (EP) producer. The best carbon source for extracellular polymer production was found to be lactose, a sugar received as a by-product from the dairy industry. After optimization of the culture medium and physicochemical conditions for cultivation, polymer biosynthesis increased more than 2-fold. The highest level of extracellular polymer synthesis by C. canadensis 28 was observed in an unusually high NaCl concentration (15% w/v). Chemical analysis of the purified polymer revealed the presence of an exopolysaccharide (EPS) fraction (14.3% w/w) and protein fraction (72% w/w). HPLC analysis of the protein fraction showed the main presence of polyglutamic acid (PGA) (75.7% w/w). EPS fraction analysis revealed the following sugar composition (% w/w): glucosamine 36.7, glucose 32.3, rhamnose 25.4, xylose 1.7, and not identified sugar 3.9. The hydrogel formed by PGA and EPS fractions showed high swelling behavior, very good emulsifying and stabilizing properties, and good foaming ability. This is the first report for halophilic bacterium able to synthesize a polymer containing PGA fraction. The synthesized biopolymer shows an extremely high hydrophilicity, due to the simultaneous presence of PGA and EPS. The analysis of its functional properties and the presence of glucosamine in the highest proportion in EPS fraction clearly determine the potential of EP synthesized by C. canadensis 28 for application in the cosmetics industry.

  10. Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium

    Directory of Open Access Journals (Sweden)

    Leong-Keat eChan

    2012-05-01

    Full Text Available Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC, a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ~50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium Ruegeria pomeroyi (a member of the Roseobacter clade under four element limitation regimes (C, N, P, and S. Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S-limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to 6-fold were measured in R. pomeroyi biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometery in R. pomeroyi may have implications for global carbon cycling. Strong homeostatic responses to N limitation by heterotrophic marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean.

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

    Science.gov (United States)

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

    1996-01-01

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

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

    Science.gov (United States)

    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.

  13. Reduction of chalcogen oxyanions and generation of nanoprecipitates by the photosynthetic bacterium Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Baccolini, Chiara; Francia, Francesco [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Sabatino, Piera [Department of Chemistry G. Ciamician, University of Bologna (Italy); Turner, Raymond J. [Department of Biological Sciences, University of Calgary, Calgary, Alberta (Canada); Zannoni, Davide, E-mail: davide.zannoni@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy)

    2014-03-01

    Graphical abstract: - Highlights: • R. capsulatus cells produce extracellular chalcogens nanoprecipitates when lawsone is present. • Lawsone acts as a redox mediator from reducing equivalents to tellurite and selenite. • Nanoprecipitates production depends on carbon source and requires metabolically active cells. • Te{sup 0} and Se{sup 0} nanoprecipitates are identified by X-ray diffraction (XRD) spectroscopy. - Abstract: The facultative photosynthetic bacterium Rhodobacter capsulatus is characterized in its interaction with the toxic oxyanions tellurite (Te{sup IV}) and selenite (Se{sup IV}) by a highly variable level of resistance that is dependent on the growth mode making this bacterium an ideal organism for the study of the microbial interaction with chalcogens. As we have reported in the past, while the oxyanion tellurite is taken up by R. capsulatus cells via acetate permease and it is reduced to Te{sup 0} in the cytoplasm in the form of splinter-like black intracellular deposits no clear mechanism was described for Se{sup 0} precipitation. Here, we present the first report on the biotransformation of tellurium and selenium oxyanions into extracellular Te{sup 0} and Se{sup 0}nanoprecipitates (NPs) by anaerobic photosynthetically growing cultures of R. capsulatus as a function of exogenously added redox-mediator lawsone, i.e. 2-hydroxy-1,4-naphthoquinone. The NPs formation was dependent on the carbon source used for the bacterial growth and the rate of chalcogen reduction was constant at different lawsone concentrations, in line with a catalytic role for the redox mediator. X-ray diffraction (XRD) analysis demonstrated the Te{sup 0} and Se{sup 0} nature of the nanoparticles.

  14. Growth-arresting Activity of Acmella Essential Oil and its Isolated Component D-Limonene (1, 8 P-Mentha Diene) againstTrichophyton rubrum(Microbial Type Culture Collection 296).

    Science.gov (United States)

    Padhan, Diptikanta; Pattnaik, Smaranika; Behera, Ajaya Kumar

    2017-10-01

    Spilanthes acmella is used as a remedy in toothache complaints by the tribal people of Western part of Odisha, India. The objective of this study was to study the growth-arresting activity of an indigenous Acmella essential oil (EO) ( S. acmella Murr, Asteraceae ) and its isolated component, d-limonene against Trichophyton rubrum (microbial type culture collection 296). The EO was extracted from flowers of indigenous S. acmella using Clevenger's apparatus and analyzed by gas chromatography-mass spectrometry (GC-MS). High pressure liquid chromatography (HPLC) was carried out to isolate the major constituent. The isolated fraction was subjected to fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR). The antidermatophytic activity was screened for using "disc diffusion" and "slant dilution" method followed by optical, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) studies. The molecular dockings were made between d-limonene with cell wall synthesis-related key enzymes (14 methyl deaminase and monooxygenase). The GC-MS analysis EO had inferred the presence of 7 number of major (≥2%) components. The component with highest peak area (%) was found to be 41.02. The HPLC-isolated fraction was identified as d-limonene (1,8 p-Mentha-diene) by FTIR and NMR. Qualitative and quantitative assays had suggested the growth inhibitory activity of Acmella EO and its component. Shrinkage, evacuation, cell wall puncture, and leakage of cellular constituents by the activity of Acmella oil and d-limonene were evidenced from optical, SEM, and TEM studies. The computer simulation had predicted the binding strengths of d-limonene and fluconazole with dermatophyte cell wall enzymes. There could have been synergistic action of all or some of compounds present in indigenous Acmella EO. There was presence of seven number of (d-limonene, ocimene, β-myrcene, cyclohexene, 3-(1, 5-dimethyl-4-hexenyl)-6-methylene,

  15. Effect of the aqueous, acidic and alcoholic extract of dried leaves of Erythroxylum coca var. coca (coca in Trichophyton rubrum, Trichophyton mentagrophytes, Microsporum canis and Candida albicans in vitro

    Directory of Open Access Journals (Sweden)

    Medalit Luna-Vílchez

    2017-06-01

    Full Text Available Objective: To evaluate the effect of the aqueous, acidic and alcoholic extract of dried leaves of Erythroxylum coca var. coca (coca in Trichophyton rubrum (TR, Trichophyton mentagrophytes (TM, Microsporum canis (MC and Candida albicans (CA in vitro. Materials and methods: An experimental study which evaluated the presence or absence of fungal growth, and fungal growth rate from the seeding point, compared to fungal growth in Sabouraud Agar (SA using Siegel-Tukey and KruskalWallis tests (p<0.05. Results: The CA group showed a statistical difference (p<0.05 between the following groups: 99.9% ethanol vs. aqueous, 99.9% ethanol vs. 0.01M HCl, 99.9% ethanol vs. control, control vs. aqueous, 0.01M HCl vs. control. The TR group showed a statistical difference (p<0.05 between the following groups: 99.9% ethanol vs. 0.01M HCl, 99.9% ethanol vs. aqueous, 99.9% ethanol vs. control, 0.01M HCl vs. control. The TM group showed a statistical difference (p<0.05 between the following groups: 99.9% ethanol vs. 0.01M HCl, 99.9% ethanol vs. control, aqueous vs. acid, aqueous vs. control. The MC group showed a statistical difference (p<0.05 between the following groups: 99.9% ethanol vs. 0.01M HCl, 99.9% ethanol vs. control, aqueous vs. acid, aqueous vs. control. In all the cases, the results of the 0.01M HCl vs. aqueous group were not significant. Conclusions: The aqueous, acidic and alcoholic extracts have no effect on the growth of CA and TM, but the alcoholic extract has effects on the growth of TR and MC. In addition, there were differences in the growth rate of CA, TR and TM in the aqueous, acidic and alcoholic extracts compared to that in SA. However only TR, TM and MC showed differences in their growth rate in the alcoholic extract.

  16. Concentration and Transport of Nitrate by the Mat-Forming Sulfur Bacterium Thioploca Rid E-1821-2011

    DEFF Research Database (Denmark)

    FOSSING, H.; GALLARDO, VA; JØRGENSEN, BB

    1995-01-01

    , at between 40 and 280 m water depth. The metabolism of this marine bacterium(5,6) remained a mystery until long after its discovery(1,7). We report here that Thioploca cells are able to concentrate nitrate to up to 500 mM in a liquid vacuole that occupies >80% of the cell volume. Gliding filaments transport...

  17. Note: Physiological aspects of the growth of the lactic acid bacterium Tetragenococcus halophila during Indonesian soy sauce

    NARCIS (Netherlands)

    Roling, W.F.M.; Prasetyo, A.B.; Stouthamer, A.H.; van Verseveld, H.W.

    1999-01-01

    The lactic acid bacterium Tetragenococcus halophila is the dominant species in Indonesian soy mash. Tetragenococcus halophila growing in continuous and retention cultures under defined glucose-limited conditions showed a switch from homolactic (only lactate produced) to mixed acid fermentation (two

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

    Science.gov (United States)

    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.

  19. Draft genome sequence of Enterobacter sp. Sa187, an endophytic bacterium isolated from the desert plant Indigofera argentea

    NARCIS (Netherlands)

    Lafi, Feras F.; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged M.

    2017-01-01

    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

  20. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

    OpenAIRE

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Fran?oise; Loux, Valentin; Vidal, Marie; Passot, St?phanie; B?al, Catherine; Layec, S?verine; Fonseca, Fernanda

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes.

  1. First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974, a Butyrate-Producing Bacterium Isolated from Palm Wine.

    Science.gov (United States)

    Poehlein, Anja; Hettwer, Eva; Mohnike, Lennart; Daniel, Rolf

    2018-04-26

    Clostridium thermopalmarium is a moderate thermophilic, rod-shaped, and endospore-forming bacterium, which was isolated from palm wine in Senegal. Butyrate is produced from a broad variety of sugar substrates. Here, we present the draft genome sequence of C. thermopalmarium DSM 5974 (2.822 Mb) containing 2,665 predicted protein-encoding genes. Copyright © 2018 Poehlein et al.

  2. Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis

    NARCIS (Netherlands)

    van der Horst, M.A.; Stalcup, T.P.; Kaledhonkar, S.; Kumauchi, M.; Hara, M.; Xie, A.; Hellingwerf, K.J.; Hoff, W.D.

    2009-01-01

    Idiomarina loihiensis is a heterotrophic deep sea bacterium with no known photobiology. We show that light suppresses biofilm formation in this organism. The genome of I. loihiensis encodes a single photoreceptor protein: a homologue of photoactive yellow protein (PYP), a blue light receptor with

  3. Microbacter margulisiae gen. nov., sp. nov., a novel propionigenic bacterium isolated from sediments of an acid rock drainage pond

    NARCIS (Netherlands)

    Sanchez Andrea, I.; Luis Sanz, J.; Stams, A.J.M.

    2014-01-01

    A novel anaerobic propionigenic bacterium, strain ADRIT, was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6 x 1-1.7 µm), non-motile and non-spore forming rods. Cells possessed a Gram-negative cell wall structure and were vancomycin

  4. Draft Genome Sequence of Chryseobacterium sp. Strain GSE06, a Biocontrol Endophytic Bacterium Isolated from Cucumber (Cucumis sativus)

    Science.gov (United States)

    Jeong, Jin-Ju; Park, Byeong Hyeok; Park, Hongjae

    2016-01-01

    Chryseobacterium sp. strain GSE06 is a biocontrol endophytic bacterium against the destructive soilborne oomycete Phytophthora capsici, which causes Phytophthora blight of pepper. Here, we present its draft genome sequence, which contains genes related to biocontrol traits, such as colonization, antimicrobial activity, plant growth promotion, and abiotic or biotic stress adaptation. PMID:27313310

  5. Adhesion forces of the sea-water bacterium Paracoccus seriniphilus on titanium: Influence of microstructures and environmental conditions.

    Science.gov (United States)

    Davoudi, Neda; Huttenlochner, Katharina; Chodorski, Jonas; Schlegel, Christin; Bohley, Martin; Müller-Renno, Christine; Aurich, Jan C; Ulber, Roland; Ziegler, Christiane

    2017-11-06

    The bacterial attachment to surfaces is the first step of biofilm formation. This attachment is governed by adhesion forces which act between the bacterium and the substrate. Such forces can be measured by single cell force spectroscopy, where a single bacterium is attached to a cantilever of a scanning force microscope, and force-distance curves are measured. For the productive sea-water bacterium Paracoccus seriniphilus, pH dependent measurements reveal the highest adhesion forces at pH 4. Adhesion forces measured at salinities between 0% and 4.5% NaCl are in general higher for higher salinity. However, there is an exception for 0.9% where a higher adhesion force was measured than expected. These results are in line with zeta potential measurements of the bacterium, which also show an exceptionally low zeta potential at 0.9% NaCl. In the absence of macromolecular interactions, the adhesion forces are thus governed by (unspecific) electrostatic interactions, which can be adjusted by pH and ionic strength. It is further shown that microstructures on the titanium surface increase the adhesion force. Growth medium reduces the interaction forces dramatically, most probably through macromolecular bridging.

  6. Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air

    NARCIS (Netherlands)

    Khan, M. Tanweer; van Dijl, Jan Maarten; Harmsen, Hermie J M

    2014-01-01

    The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Thermotoga lettingae sp. nov. : a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor

    NARCIS (Netherlands)

    Balk, M.; Weijma, J.; Stams, A.J.M.

    2002-01-01

    A novel, anaerobic, non-spore-forming, mobile, Gram-negative, thermophilic bacterium, strain TMO(T), was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 degrees C with methanol as the sole substrate. The G C content of the DNA of strain TMO(T) was 39.2 molÐThe optimum pH,

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

    KAUST Repository

    Lafi, Feras Fawzi

    2017-02-17

    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.

  10. Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacterium Dinoroseobacter shibae

    Czech Academy of Sciences Publication Activity Database

    Piwosz, Kasia; Kaftan, David; Dean, Jason; Šetlík, Jiří; Koblížek, Michal

    2018-01-01

    Roč. 20, č. 2 (2018), s. 724-733 ISSN 1758-2229 R&D Projects: GA MŠk(CZ) LO1416 Institutional support: RVO:61388971 Keywords : PHOTOSYNTHETIC BACTERIUM * LEUCINE INCORPORATION * SOLAR-RADIATION Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.363, year: 2016

  11. Draft genome sequence of Enterobacter cloacae subsp. cloacae strain 08XA1, a fecal bacterium of giant pandas.

    Science.gov (United States)

    Yan, Yue; Zhao, Chuan-Wu; Zhang, Yi-Zheng; Zhang, Zhi-He; Pan, Guang-Lin; Liu, Wen-Wang; Ma, Qing-Yi; Hou, Rong; Tan, Xue-Mei

    2012-12-01

    Enterobacter cloacae, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed the draft genome of Enterobacter cloacae subsp. cloacae strain 08XA1 from the feces of a giant panda in China. Genes encoding a β-lactamase and efflux pumps, as well as other factors, have been found in the genome.

  12. Successful split thickness skin grafting in the presence of heavy colonisation with rare bacterium Aeromonas hydrophila: A case report

    Directory of Open Access Journals (Sweden)

    S. Koschel

    2017-09-01

    Discussion: Contemporary literature is yet to make the distinction between colonisation and infection of this bacterium, with clinicians relying solely on the presence of infective stigmata and serum analysis. However, this is a critically important distinction when ascertaining the likelihood of success of wound healing.

  13. Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

    Directory of Open Access Journals (Sweden)

    Zhiping Wang

    Full Text Available Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

  14. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    Energy Technology Data Exchange (ETDEWEB)

    Taghavi, S.; van der Lelie, D.; Hoffman, A.; Zhang, Y.-B.; Walla, M. D.; Vangronsveld, J.; Newman, L.; Monchy, S.

    2010-05-13

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa x deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  15. A Novel Treatment Protects Chlorella at Commercial Scale from the Predatory Bacterium Vampirovibrio chlorellavorus

    Science.gov (United States)

    Ganuza, Eneko; Sellers, Charles E.; Bennett, Braden W.; Lyons, Eric M.; Carney, Laura T.

    2016-01-01

    The predatory bacterium, Vampirovibrio chlorellavorus, can destroy a Chlorella culture in just a few days, rendering an otherwise robust algal crop into a discolored suspension of empty cell walls. Chlorella is used as a benchmark for open pond cultivation due to its fast growth. In nature, V. chlorellavorus plays an ecological role by controlling this widespread terrestrial and freshwater microalga, but it can have a devastating effect when it attacks large commercial ponds. We discovered that V. chlorellavorus was associated with the collapse of four pilot commercial-scale (130,000 L volume) open-pond reactors. Routine microscopy revealed the distinctive pattern of V. chlorellavorus attachment to the algal cells, followed by algal cell clumping, culture discoloration and ultimately, growth decline. The “crash” of the algal culture coincided with increasing proportions of 16s rRNA sequencing reads assigned to V. chlorellavorus. We designed a qPCR assay to predict an impending culture crash and developed a novel treatment to control the bacterium. We found that (1) Chlorella growth was not affected by a 15 min exposure to pH 3.5 in the presence of 0.5 g/L acetate, when titrated with hydrochloric acid and (2) this treatment had a bactericidal effect on the culture (2-log decrease in aerobic counts). Therefore, when qPCR results indicated a rise in V. chlorellavorus amplicons, we found that the pH-shock treatment prevented the culture crash and doubled the productive longevity of the culture. Furthermore, the treatment could be repeatedly applied to the same culture, at the beginning of at least two sequential batch cycles. In this case, the treatment was applied preventively, further increasing the longevity of the open pond culture. In summary, the treatment reversed the infection of V. chlorellavorus as confirmed by observations of bacterial attachment to Chlorella cells and by detection of V. chlorellavorus by 16s rRNA sequencing and qPCR assay. The p

  16. Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi

    Directory of Open Access Journals (Sweden)

    Carlow Clotilde KS

    2009-11-01

    Full Text Available Abstract Background Wolbachia (wBm is an obligate endosymbiotic bacterium of Brugia malayi, a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such as B. malayi. As wBm is required for B. malayi development and fertility, targeting wBm is a promising approach. However, the lifecycle of neither B. malayi nor wBm can be maintained in vitro. To facilitate selection of potential drug targets we computationally ranked the wBm genome based on confidence that a particular gene is essential for the survival of the bacterium. Results wBm protein sequences were aligned using BLAST to the Database of Essential Genes (DEG version 5.2, a collection of 5,260 experimentally identified essential genes in 15 bacterial strains. A confidence score, the Multiple Hit Score (MHS, was developed to predict each wBm gene's essentiality based on the top alignments to essential genes in each bacterial strain. This method was validated using a jackknife methodology to test the ability to recover known essential genes in a control genome. A second estimation of essentiality, the Gene Conservation Score (GCS, was calculated on the basis of phyletic conservation of genes across Wolbachia's parent order Rickettsiales. Clusters of orthologous genes were predicted within the 27 currently available complete genomes. Druggability of wBm proteins was predicted by alignment to a database of protein targets of known compounds. Conclusion Ranking wBm genes by either MHS or GCS predicts and prioritizes potentially essential genes. Comparison of the MHS to GCS produces quadrants representing four types of predictions: those with high confidence of essentiality by both methods (245 genes, those highly conserved across Rickettsiales (299 genes, those similar to distant essential genes (8 genes, and those with low confidence of essentiality (253 genes. These data facilitate

  17. Evaluation of dna extraction methods of the Salmonella sp. bacterium in artificially infected chickens eggs

    Directory of Open Access Journals (Sweden)

    Ana Cristina dos Reis Ferreira

    2015-06-01

    Full Text Available ABSTRACT. Ferreira A.C.dosR. & dos Santos B.M. [Evaluation of dna extraction methods of the Salmonella sp. bacterium in artificially infected chickens eggs.] Avaliação de três métodos de extração de DNA de Salmonella sp. em ovos de galinhas contaminados artificialmente. Revista Brasileira de Medicina Veterinária, 37(2:115-119, 2015. Departamento de Veterinária, Universidade Federal de Viçosa, Campus Universitário, Av. Peter Henry Rolfs, s/n, Viçosa, MG 36571-000, Brasil. E-mail: bmsantos@ufv.br The present study evaluated the efficiency of different protocols for the genomic DNA extraction of Salmonella bacteria in chicken eggs free of specific pathogens – SPF. Seventy-five eggs were used and divided into five groups with fifteen eggs each. Three of the five groups of eggs were inoculated with enteric Salmonella cultures. One of the five groups was inoculated with Escherichia coli bacterium culture. And another group of eggs was the negative control that received saline solution 0.85% infertile. The eggs were incubated on a temperature that varied from 20 to 25°C during 24, 48 and 72 hours. Five yolks of each group were collected every 24 hours. These yolks were homogenized and centrifuged during 10 minutes. The supernatant was rejected. After the discard, PBS ph 7.2 was added and centrifuged again. The sediment obtained of each group was used for the extraction of bacterial genomic DNA. Silica particles and a commercial kit were utilized as the extraction methods. The extracted DNA was kept on a temperature of 20°C until the evaluation through PCR. The primers utilized were related with the invA gene and they were the following: 5’ GTA AAA TTA TCG CCA CGT TCG GGC AA 3’ and 5’ TCA TCG CAC CGT CAA AGG AAC C 3’. The amplification products were visualized in transilluminator with ultraviolet light. The obtained results through the bacterial DNA extractions demonstrated that the extraction method utilizing silica particles was

  18. Sphaerotilus natans, a neutrophilic iron-related filamentous bacterium : mechanisms of uranium scavenging

    International Nuclear Information System (INIS)

    Seder-Colomina, Marina

    2014-01-01

    Heavy metals and radionuclides are present in some ecosystems worldwide due to natural contaminations or anthropogenic activities. The use of microorganisms to restore those polluted ecosystems, a process known as bioremediation, is of increasing interest, especially under near-neutral pH conditions. Iron minerals encrusting neutrophilic iron-related bacteria, especially Bacterio-genic Iron Oxides (BIOS), have a poorly crystalline structure, which in addition to their large surface area and reactivity make them excellent scavengers for inorganic pollutants. In this PhD work we studied the different mechanisms of uranium scavenging by the neutrophilic bacterium Sphaerotilus natans, chosen as a model bacterium for iron-related sheath-forming filamentous microorganisms. S. natans can grow as single cells and filaments. The latter were used to investigate U(VI) bio-sorption and U(VI) sorption onto BIOS. In addition, uranium sorption onto the abiotic analogues of such iron minerals was assessed. In order to use S. natans filaments for U(VI) scavenging, it was necessary to identify factors inducing S. natans filamentation. The influence of oxygen was ascertained by using molecular biology techniques and our results revealed that while saturated oxygen conditions resulted in single cell growth, a moderate oxygen depletion to ∼ 3 mg O 2 .L -1 led to the desired filamentous growth of S. natans. BIOS attached to S. natans filaments as well as the abiotic analogues were analysed by XAS at Fe K-edge. Both materials were identified as amorphous iron(III) phosphates with a small component of Fe(II), with a high reactivity towards scavenging of inorganic pollutants. In addition, EXAFS at the U LIII-edge revealed a common structure for the O shells, while those for P, Fe and C were different for each sorbent. An integrated approach combining experimental techniques and speciation calculations made it possible to describe U(VI) adsorption isotherms by using a surface complexation

  19. Homologues of insecticidal toxin complex genes within a genomic island in the marine bacterium Vibrio parahaemolyticus.

    Science.gov (United States)

    Tang, Kathy F J; Lightner, Donald V

    2014-12-01

    Three insecticidal toxin complex (tc)-like genes were identified in Vibrio parahaemolyticus 13-028/A3, which can cause acute hepatopancreatic necrosis disease in penaeid shrimp. The three genes are a tcdA-like gene (7710 bp), predicted to code for a 284-kDa protein; a tcdB-like gene (4272 bp), predicted to code for a 158-kDa protein; and a tccC3-like gene (2916 bp), predicted to encode a 107-kDa protein. All three predicted proteins contain conserved domains that are characteristic of their respective Tc proteins. By RT-PCR, all three tc-like genes were found to be expressed in this bacterium. Through genome walking and the use of PCR to join contigs surrounding these three genes, a genomic island (87 712 bp, named tc-GIvp) was found on chromosome II localized next to the tRNA Gly. The GC content of this island, which is not found in other Vibrio species, is 40%. The tc-GIvp is characterized to have 60 ORFs encoding regulatory or virulence factors. These include a type 6 secretion protein VgrG, EAL domain-containing proteins, fimbriae subunits and assembly proteins, invasin-like proteins, peptidoglycan-binding proteins, and Tc proteins. The tc-GIvp also contains 21 transposase genes, suggesting that it was acquired through horizontal transfer from other organisms. © 2014 Federation of European Microbiological Societies.

  20. Proteomic comparison of the probiotic bacterium Lactobacillus casei Zhang cultivated in milk and soy milk.

    Science.gov (United States)

    Wang, Jicheng; Wu, Rina; Zhang, Wenyi; Sun, Zhihong; Zhao, Wenjing; Zhang, Heping

    2013-09-01

    Soy milk is regarded as a substitute for milk and has become popular in varied diets throughout the world. It has been shown that a newly characterized probiotic bacterium (Lactobacillus casei Zhang) actually grows faster in soy milk than in bovine milk. To elucidate the mechanism involved, we carried out a proteomic analysis to characterize bacterial proteins that varied upon growth in soy milk and bovine milk at 3 different growth phases, and compare their expression under these conditions. A total of 104 differentially expressed spots were identified from different phases using a peptide mass fingerprinting assay. Functional analysis revealed that a major part of these identified proteins is associated with transport and metabolism of carbohydrates, nucleotides, and amino acids as well. The results from our proteomic analysis were clarified by real-time quantitative PCR assay, which showed that Lb. casei Zhang loci involved in purine and pyrimidine biosynthesis were transcriptionally enhanced during growth in soy milk at lag phase (pH 6.4), whereas the loci involved in carbohydrate metabolism were upregulated in bovine milk. Particularly, our results showed that l-glutamine might play an important role in the growth of Lb. casei Zhang in soy milk and bovine milk, perhaps by contributing to purine, pyrimidine, and amino sugar metabolism. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  1. Assessment of mixture toxicity of copper, cadmium, and phenanthrenequinone to the marine bacterium Vibrio fischeri.

    Science.gov (United States)

    Wang, Wenxi; Lampi, Mark A; Huang, Xiao-Dong; Gerhardt, Karen; Dixon, D George; Greenberg, Bruce M

    2009-04-01

    Transition metals and polycyclic aromatic hydrocarbons (PAHs) are cocontaminants at many sites. Contaminants in mixtures are known to interact with biological systems in ways that can greatly alter the toxicity of individual compounds. The toxicities (individually and as mixtures) of copper (Cu), a redox-active metal; cadmium (Cd), a nonredox active metal; and phenanthrenequinone (PHQ), a redox-active oxygenated PAH, were examined using the bioluminescent bacterium Vibrio fischeri. We found that the cotoxicity of Cu/PHQ was dependent on the ratio of concentrations of each chemical in the mixture. Different interaction types (synergism, antagonism, and additivity) were observed with different combinations of these toxicants. The interaction types changed from antagonism at a low Cu to PHQ ratio (1:4), to additive at an intermediate Cu to PHQ ratio (2:3), to synergistic at higher Cu to PHQ ratios (3:2 and 4:1). In contrast to Cu/PHQ mixtures, the cotoxicity of Cd/PHQ did not change at different mixture ratios and was found for the most part to be additive. For the individual chemicals and their mixtures, reactive oxygen species (ROS) production was observed in V. fischeri, suggesting that individual and mixture toxicity of Cu, Cd, and PHQ to V. fischeri involves ROS-related mechanisms. This study shows that mixture ratios can alter individual chemical toxicity, and should be taken into account in risk assessment. Copyright 2008 Wiley Periodicals, Inc.

  2. Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda.

    Science.gov (United States)

    Xu, Zhen-Xing; Yu, Pei; Mu, Da-Shuai; Liu, Yan; Du, Zong-Jun

    2017-12-01

    A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1 T , was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1 T in the genus Tenacibaculum, and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1 T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1 T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculumagarivorans sp. nov. is proposed. The type strain is HZ1 T (=MCCC 1H00174 T =KCTC 52476 T ).

  3. The plant growth-promoting bacterium Kosakonia radicincitans improves fruit yield and quality of Solanum lycopersicum.

    Science.gov (United States)

    Berger, Beatrice; Baldermann, Susanne; Ruppel, Silke

    2017-11-01

    Production and the quality of tomato fruits have a strong economic relevance. Microorganisms such as the plant growth-promoting bacterium (PGPB) Kosakonia radicincitans (DSM 16656) have been demonstrated to improve shoot and root growth of young tomato plants, but data on yield increase and fruit quality by K. radicincitans are lacking. This study investigated how K. radicincitans affects tomato fruits. After inoculation of tomato seeds with K. radicincitans or a sodium chloride buffer control solution, stalk length, first flowering and the amount of ripened fruits produced by inoculated and non-inoculated plants were monitored over a period of 21 weeks. Inoculation of tomato seeds with K. radicincitans accelerated flowering and ripening of tomato fruits. Sugars, acidity, amino acids, volatile organic compounds and carotenoids in the fruits were also analyzed. It was found that the PGPB K. radicincitans affected the amino acid, sugar and volatile composition of ripened fruits, contributing to a more pleasant-tasting fruit without forfeiting selected quality indicators. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

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

    Science.gov (United States)

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

    2007-06-01

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

  5. Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

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    Alvaro Banderas

    2013-08-01

    Full Text Available The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS, we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process.

  6. Infections Caused by Actinomyces neuii: A Case Series and Review of an Unusual Bacterium

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    Nathan Zelyas

    2016-01-01

    Full Text Available Background. Actinomyces neuii is a Gram-positive bacillus rarely implicated in human infections. However, its occurrence is being increasingly recognized with the use of improved identification systems. Objective. To analyse A. neuii infections in Alberta, Canada, and review the literature regarding this unusual pathogen. Methods. Cases of A. neuii were identified in 2013-2014 in Alberta. Samples were cultured aerobically and anaerobically. A predominant catalase positive Gram-positive coryneform bacillus with no branching was isolated in each case. Testing was initially done with API-CORYNE® (bioMérieux and isolates were sent to the Provincial Laboratory for Public Health for further testing. Isolates’ identities were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry microbial identification system (MALDI-TOF MS MIS; bioMérieux and/or DNA sequencing. Results. Six cases of A. neuii infection were identified. All patients had soft tissue infections; typically, incision and drainage were done followed by a course of antibiotics. Agents used included cephalexin, ertapenem, ciprofloxacin, and clindamycin. All had favourable outcomes. Conclusions. While A. neuii is infrequently recognized, it can cause a diverse array of infections. Increased use of MALDI-TOF MS MIS is leading to increased detection; thus, understanding the pathogenicity of this bacterium and its typical susceptibility profile will aid clinical decision-making.

  7. The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4.

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    Jin Duan

    Full Text Available The plant growth-promoting bacterium (PGPB Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated "housekeeping" genes (16S rRNA, gyrB, rpoB and rpoD of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

  8. A lactic acid bacterium isolated from kimchi ameliorates intestinal inflammation in DSS-induced colitis.

    Science.gov (United States)

    Park, Jin-Soo; Joe, Inseong; Rhee, Paul Dong; Jeong, Choon-Soo; Jeong, Gajin

    2017-04-01

    Some species of lactic acid bacteria have been shown to be beneficial in inflammatory bowel disease (IBD). In the present study, a strain of lactic acid bacterium (Lactobacillus paracasei LS2) was isolated from the Korean food, kimchi, and was shown to inhibit the development of experimental colitis induced by dextran sulfate sodium (DSS). To investigate the role of LS2 in IBD, mice were fed DSS in drinking water for seven days along with LS2 bacteria which were administered intragastrically to some of the mice, while phosphate-buffered saline (PBS) was administered to others (the controls). The administration of LS2 reduced body weight loss and increased survival, and disease activity indexes (DAI) and histological scores indicated that the severity of colitis was significantly reduced. The production of inflammatory cytokines and myeloperoxidase (MPO) activity also decreased. Flow cytometry analysis showed that the number of Th1 (IFN-γ) population cells was significantly reduced in the LS2-administered mice compared with the controls. The administration of LS2 induced the increase of CD4 + FOXP3 + Treg cells, which are responsible for IL-10. Numbers of macrophages (CD11b + F4/80 + ), and neutrophils (CD11b + Gr-1 + ) among lamina propria lymphocytes (LPL) were also reduced. These results indicate that LS2 has an anti-inflammatory effect and ameliorates DSS-induced colitis.

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

    Science.gov (United States)

    Khan, Sana; Malik, Abdul

    2016-03-01

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

  10. Tools for genetic manipulation of the plant growth-promoting bacterium Azospirillum amazonense.

    Science.gov (United States)

    Sant'anna, Fernando H; Andrade, Dieime S; Trentini, Débora B; Weber, Shana S; Schrank, Irene S

    2011-05-16

    Azospirillum amazonense has potential to be used as agricultural inoculant since it promotes plant growth without causing pollution, unlike industrial fertilizers. Owing to this fact, the study of this species has gained interest. However, a detailed understanding of its genetics and physiology is limited by the absence of appropriate genetic tools for the study of this species. Conjugation and electrotransformation methods were established utilizing vectors with broad host-replication origins (pVS1 and pBBR1). Two genes of interest--glnK and glnB, encoding PII regulatory proteins--were isolated. Furthermore, glnK-specific A. amazonense mutants were generated utilizing the pK19MOBSACB vector system. Finally, a promoter analysis protocol based on fluorescent protein expression was optimized to aid genetic regulation studies on this bacterium. In this work, genetic tools that can support the study of A. amazonense were described. These methods could provide a better understanding of the genetic mechanisms of this species that underlie its plant growth promotion.

  11. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions.

    Science.gov (United States)

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Salekdeh, Ghasem Hosseini; Karimi, Keikhosro

    2016-01-04

    The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated.

  12. Novel Acetone Metabolism in a Propane-Utilizing Bacterium, Gordonia sp. Strain TY-5▿

    Science.gov (United States)

    Kotani, Tetsuya; Yurimoto, Hiroya; Kato, Nobuo; Sakai, Yasuyoshi

    2007-01-01

    In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane → 2-propanol → acetone → methyl acetate → acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism. PMID:17071761

  13. [Isolation, identification and characterization of a microcystin-degrading bacterium Paucibacter sp. strain CH].

    Science.gov (United States)

    You, Di-Jie; Chen, Xiao-Guo; Xiang, Hui-Yi; Ouyang, Liao; Yang, Bing

    2014-01-01

    A bacterium capable of degrading microcystin (MC), strain CH, was isolated from the sediment of Lake Chaohu, China. Strain CH was tentatively identified as Paucibacter sp. based on the analysis of 16S rRNA gene sequences. Paucibacter sp. strain CH can use microcystin LR (MCLR) as the sole carbon and energy sources, and 11.6 microg x mL(-1) of MCLR was degraded to below the detection limit within 10 hours with the first-order reaction rate constant of 0.242 h(-1). The optimum temperature and initial pH for MC degradation were 25-30 degrees C and pH 6-9, respectively. A novel intermediate product containing the Adda residue was detected during the degradation of MCLR, which is different from those produced by strain ACM-3962, and Adda was recognized as the final product of the degradation process. Furthermore, no homologue to any of the four genes, mlrA, mlrB, mlrC and mlrD previously associated with the degradation of MCLR by strain ACM-3962 was found in strain CH. These findings suggest that Paucibacter sp. strain CH mighe degrade MC through a different pathway from that of strain ACM-3962.

  14. Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense

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    Sant'Anna Fernando H

    2011-08-01

    Full Text Available Abstract Background The species Azospirillum amazonense belongs to a well-known genus of plant growth-promoting bacteria. This bacterium is found in association with several crops of economic importance; however, there is a lack of information on its physiology. In this work, we present a comprehensive analysis of the genomic features of this species. Results Genes of A. amazonense related to nitrogen/carbon metabolism, energy production, phytohormone production, transport, quorum sensing, antibiotic resistance, chemotaxis/motility and bacteriophytochrome biosynthesis were identified. Noteworthy genes were the nitrogen fixation genes and the nitrilase gene, which could be directly implicated in plant growth promotion, and the carbon fixation genes, which had previously been poorly investigated in this genus. One important finding was that some A. amazonense genes, like the nitrogenase genes and RubisCO genes, were closer phylogenetically to Rhizobiales members than to species of its own order. Conclusion The species A. amazonense presents a versatile repertoire of genes crucial for its plant-associated lifestyle.

  15. Antioxidant and DNA Damage Protecting Activity of Exopolysaccharides from the Endophytic Bacterium Bacillus cereus SZ1

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    Li Ping Zheng

    2016-02-01

    Full Text Available An endophytic bacterium was isolated from the Chinese medicinal plant Artemisia annua L. The phylogenetic and physiological characterization indicated that the isolate, strain SZ-1, was Bacillus cereus. The endophyte could produce an exopolysaccharide (EPS at 46 mg/L. The 1,1-diphenyl-2-picrylhydracyl (DPPH radical scavenging activity of the EPS reached more than 50% at 3–5 mg/mL. The EPS was also effective in scavenging superoxide radical in a concentration dependent fashion with an EC50 value of 2.6 mg/mL. The corresponding EC50 for scavenging hydroxyl radical was 3.1 mg/mL. Moreover, phenanthroline-copper complex-mediated chemiluminescent emission of DNA damage was both inhibited and delayed by EPS. The EPS at 0.7–1.7 mg/mL also protected supercoiled DNA strands in plasmid pBR322 against scission induced by Fenton-mediated hydroxyl radical. The preincubation of PC12 cells with the EPS prior to H2O2 exposure increased the cell survival and glutathione (GSH level and catalase (CAT activities, and decreased the level of malondialdehyde (MDA and lactate dehydrogenase (LDH activity in a dose-dependent manner, suggesting a pronounced protective effect against H2O2-induced cytotoxicity. Our study indicated that the EPS could be useful for preventing oxidative DNA damage and cellular oxidation in pharmaceutical and food industries.

  16. Enterobacter cloacae, an Emerging Plant-Pathogenic Bacterium Affecting Chili Pepper Seedlings

    Science.gov (United States)

    García-González, Tanahiri; Sáenz-Hidalgo, Hilda Karina; Silva-Rojas, Hilda Victoria; Morales-Nieto, Carlos; Vancheva, Taca; Koebnik, Ralf; Ávila-Quezada, Graciela Dolores

    2018-01-01

    A previously unreported bacterial disease on chili pepper (Capsicum annuum L.) seedlings affecting as many as 4% of seedlings was observed in greenhouses in Chihuahua, Mexico (Delicias and Meoqui counties). Initial lesions appeared as irregular small spots on leaves and brown necrosis at margins tips were observed. Later, the spots became necrotic with a chlorotic halo. Advanced disease was associated with defoliation. A Gram negative, rod-shaped bacterium was isolated from diseased chili pepper seedlings. Three inoculation methods revealed that isolated strains produce foliage symptoms, similar to those observed in naturally infected seedlings. Pathogenic strains that caused symptoms in inoculated seedlings were re-isolated and identified to fulfill koch’s postulate. Polyphasic approaches for identification including biochemical assays (API 20E and 50CH), carbon source utilization profiling (Biolog) and 16S rDNA, hsp60 and rpoB sequence analysis were done. Enterobacter cloacae was identified as the causal agent of this outbreak on chili pepper seedlings. PMID:29422783

  17. Vibrio parahaemolyticus a causative bacterium for tail rot disease in ornamental fish, Amphiprion sebae

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    Thangapandi Marudhupandi

    2017-11-01

    Full Text Available The present study was performed to identify the tail rot disease causing bacterium in marine ornamental fish, Amphiprion sebae. Bacteria were isolated from the infected immune organs and tail region of A. sebae. Five different bacterial isolates (S1-S5 with different shape, size and colour were chosen for the infection study. The isolated strains were individually challenged with A. sebae at a constant dose of 1 × 107 CFU/fish. The virulent strain was found to be S-3, which showed maximum reproducing ability in A. sebae by causing typical tail rot disease and mortality. Furthermore, S-3 strain was identified as Vibrio parahaemolyticus by 16S rRNA gene sequencing (KF738005, biochemical analysis and amplification of tox R gene. Subsequently, extracellular products (ECPs of V. parahaemolyticus were prepared by cellophane overlay method. The LD50 value of V. parahaemolyticus and its ECPS were found to be 1 × 105 CFU and 5 μg/fish. The histology results revealed that V. parahaemolyticus and its ECPS are the major cause of tail rot disease in A. sebae.

  18. Helicobacter Catalase Devoid of Catalytic Activity Protects the Bacterium against Oxidative Stress*♦

    Science.gov (United States)

    Benoit, Stéphane L.; Maier, Robert J.

    2016-01-01

    Catalase, a conserved and abundant enzyme found in all domains of life, dissipates the oxidant hydrogen peroxide (H2O2). The gastric pathogen Helicobacter pylori undergoes host-mediated oxidant stress exposure, and its catalase contains oxidizable methionine (Met) residues. We hypothesized catalase may play a large stress-combating role independent of its classical catalytic one, namely quenching harmful oxidants through its recyclable Met residues, resulting in oxidant protection to the bacterium. Two Helicobacter mutant strains (katAH56A and katAY339A) containing catalase without enzyme activity but that retain all Met residues were created. These strains were much more resistant to oxidants than a catalase-deletion mutant strain. The quenching ability of the altered versions was shown, whereby oxidant-stressed (HOCl-exposed) Helicobacter retained viability even upon extracellular addition of the inactive versions of catalase, in contrast to cells receiving HOCl alone. The importance of the methionine-mediated quenching to the pathogen residing in the oxidant-rich gastric mucus was studied. In contrast to a catalase-null strain, both site-change mutants proficiently colonized the murine gastric mucosa, suggesting that the amino acid composition-dependent oxidant-quenching role of catalase is more important than the well described H2O2-dissipating catalytic role. Over 100 years after the discovery of catalase, these findings reveal a new non-enzymatic protective mechanism of action for the ubiquitous enzyme. PMID:27605666

  19. The endosymbiotic bacterium Wolbachia induces resistance to dengue virus in Aedes aegypti.

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    Guowu Bian

    2010-04-01

    Full Text Available Genetic strategies that reduce or block pathogen transmission by mosquitoes have been proposed as a means of augmenting current control measures to reduce the growing burden of vector-borne diseases. The endosymbiotic bacterium Wolbachia has long been promoted as a potential vehicle for introducing disease-resistance genes into mosquitoes, thereby making them refractory to the human pathogens they transmit. Given the large overlap in tissue distribution and intracellular localization between Wolbachia and dengue virus in mosquitoes, we conducted experiments to characterize their interactions. Our results show that Wolbachia inhibits viral replication and dissemination in the main dengue vector, Aedes aegypti. Moreover, the virus transmission potential of Wolbachia-infected Ae. aegypti was significantly diminished when compared to wild-type mosquitoes that did not harbor Wolbachia. At 14 days post-infection, Wolbachia completely blocked dengue transmission in at least 37.5% of Ae. aegypti mosquitoes. We also observed that this Wolbachia-mediated viral interference was associated with an elevated basal immunity and increased longevity in the mosquitoes. These results underscore the potential usefulness of Wolbachia-based control strategies for population replacement.

  20. Functional analyses of multiple lichenin-degrading enzymes from the rumen bacterium Ruminococcus albus 8.

    Science.gov (United States)

    Iakiviak, Michael; Mackie, Roderick I; Cann, Isaac K O

    2011-11-01

    Ruminococcus albus 8 is a fibrolytic ruminal bacterium capable of utilization of various plant cell wall polysaccharides. A bioinformatic analysis of a partial genome sequence of R. albus revealed several putative enzymes likely to hydrolyze glucans, including lichenin, a mixed-linkage polysaccharide of glucose linked together in β-1,3 and β-1,4 glycosidic bonds. In the present study, we demonstrate the capacity of four glycoside hydrolases (GHs), derived from R. albus, to hydrolyze lichenin. Two of the genes encoded GH family 5 enzymes (Ra0453 and Ra2830), one gene encoded a GH family 16 enzyme (Ra0505), and the last gene encoded a GH family 3 enzyme (Ra1595). Each gene was expressed in Escherichia coli, and the recombinant protein was purified to near homogeneity. Upon screening on a wide range of substrates, Ra0453, Ra2830, and Ra0505 displayed different hydrolytic properties, as they released unique product profiles. The Ra1595 protein, predicted to function as a β-glucosidase, preferred cleavage of a nonreducing end glucose when linked by a β-1,3 glycosidic bond to the next glucose residue. The major product of Ra0505 hydrolysis of lichenin was predicted to be a glucotriose that was degraded only by Ra0453 to glucose and cellobiose. Most importantly, the four enzymes functioned synergistically to hydrolyze lichenin to glucose, cellobiose, and cellotriose. This lichenin-degrading enzyme mix should be of utility as an additive to feeds administered to monogastric animals, especially those high in fiber.

  1. Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.

    Science.gov (United States)

    Hong, Pei-Ying; Iakiviak, Michael; Dodd, Dylan; Zhang, Meiling; Mackie, Roderick I; Cann, Isaac

    2014-04-01

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

  2. Morphological characterization of several strains of the rice-pathogenic bacterium Burkholderia glumae in North Sumatra

    Science.gov (United States)

    Hasibuan, M.; Safni, I.; Lisnawita; Lubis, K.

    2018-02-01

    Burkholderia glumae is a quarantine seed-borne bacterial pathogen causing panicle blight disease on rice. This pathogen has been detected in some locations in Java, and recently, farmers in North Sumatra have reported rice yield loss with symptoms similar with those on rice infeced by the rice-pathogenic bacterium B. glumae. This research was aimed to isolate several bacterial strains from several rice varieties in various locations in North Sumatra and characterize the morphology of the strains to detect and identify the unknown bacterial strains presumably B. glumae. Several rice seed varieties were collected from Medan and Deli Serdang Districts. The seed samples were extracted, isolated and purified, then grown in semi-selective media PPGA. The morphological characteristics of the bacterial strains were determined including Gram staining, bacterial colony’s and bacterial cell’s morphology. The results showed that of eleven strains isolated, two strains were Gram negative and nine strains were Gram positive. On the basis of colony morphology, all strains had circular form, flat elevation and cream colour while the colony margin varied, i.e. entire and undulate. Most strains had bacillus/rod shape (8 strains) and only 3 strains were coccus.

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

    Science.gov (United States)

    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)).

  4. Salinity fluctuation influencing biological adaptation: growth dynamics and Na+ /K+ -ATPase activity in a euryhaline bacterium.

    Science.gov (United States)

    Yang, Hao; Meng, Yang; Song, Youxin; Tan, Yalin; Warren, Alan; Li, Jiqiu; Lin, Xiaofeng

    2017-07-01

    Although salinity fluctuation is a prominent characteristic of many coastal ecosystems, its effects on biological adaptation have not yet been fully recognized. To test the salinity fluctuations on biological adaptation, population growth dynamics and Na + /K + -ATPase activity were investigated in the euryhaline bacterium Idiomarina sp. DYB, which was acclimated at different salinity exposure levels, exposure times, and shifts in direction of salinity. Results showed: (1) bacterial population growth dynamics and Na + /K + -ATPase activity changed significantly in response to salinity fluctuation; (2) patterns of variation in bacterial growth dynamics were related to exposure times, levels of salinity, and shifts in direction of salinity change; (3) significant tradeoffs were detected between growth rate (r) and carrying capacity (K) on the one hand, and Na + /K + -ATPase activity on the other; and (4) beneficial acclimation was confirmed in Idiomarina sp. DYB. In brief, this study demonstrated that salinity fluctuation can change the population growth dynamics, Na + /K + -ATPase activity, and tradeoffs between r, K, and Na + /K + -ATPase activity, thus facilitating bacterial adaption in a changing environment. These findings provide constructive information for determining biological response patterns to environmental change. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  6. Pseudomonas glareae sp. nov., a marine sediment-derived bacterium with antagonistic activity.

    Science.gov (United States)

    Romanenko, Lyudmila A; Tanaka, Naoto; Svetashev, Vassilii I; Mikhailov, Valery V

    2015-06-01

    An aerobic, Gram-negative, motile, rod-shaped bacterium designated KMM 9500(T) was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis affiliated strain KMM 9500(T) to the genus Pseudomonas as a distinct subline clustered with Pseudomonas marincola KMM 3042(T) and Pseudomonas segetis KCTC 12331(T) sharing the highest similarities of 98 and 97.9 %, respectively. Strain KMM 9500(T) was characterized by mainly possessing ubiquinone Q-9, and by the predominance of C18:1 ω7c, C16:1 ω7c, and C16:0 followed by C12:0 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, and unknown phospholipids. Strain KMM 9500(T) was found to inhibit growth of Gram-negative and Gram-positive indicatory microorganisms. Based on the phylogenetic analysis and distinctive phenotypic characteristics, strain 9500(T) is concluded to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas glareae sp. nov. is proposed. The type strain of the species is strain KMM 9500(T) (=NRIC 0939(T)).

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

    Science.gov (United States)

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

    2014-11-01

    Microbiological and histological analysis of a sample from a swollen testicle of a 2-year-old Border Collie dog revealed a mixed infection of the fungus Blastomyces dermatitidis and the Gram-negative bacterium Aureimonas altamirensis. When subjected to an automated microbial identification system, the latter isolate was provisionally identified as Psychrobacter phenylpyruvicus, but the organism shared several biochemical features with Brucella canis and exhibited agglutination, albeit weakly, with anti-B. canis antiserum. Unequivocal identification of the organism was only achieved by 16S ribosomal RNA gene sequencing, ultimately establishing the identity as A. altamirensis. Since its first description in 2006, this organism has been isolated infrequently from human clinical samples, but, to the authors' knowledge, has not been reported from a veterinary clinical sample. While of unknown clinical significance with respect to the pathology observed for the polymicrobial infection described herein, it highlights the critical importance to unambiguously identify the microbe for diagnostic, epidemiological, infection control, and public health purposes. © 2014 The Author(s).

  8. Identification and characterization of a core fucosidase from the bacteriumElizabethkingia meningoseptica.

    Science.gov (United States)

    Li, Tiansheng; Li, Mengjie; Hou, Linlin; Guo, Yameng; Wang, Lei; Sun, Guiqin; Chen, Li

    2018-01-26

    All reported α-l-fucosidases catalyze the removal of nonreducing terminal l-fucoses from oligosaccharides or their conjugates, while having no capacity to hydrolyze core fucoses in glycoproteins directly. Here, we identified an α-fucosidase from the bacterium Elizabethkingia meningoseptica with catalytic activity against core α-1,3-fucosylated substrates, and we named it core fucosidase I (cFase I). Using site-specific mutational analysis, we found that three acidic residues (Asp-242, Glu-302, and Glu-315) in the predicted active pocket are critical for cFase I activity, with Asp-242 and Glu-315 acting as a pair of classic nucleophile and acid/base residues and Glu-302 acting in an as yet undefined role. These findings suggest a catalytic mechanism for cFase I that is different from known α-fucosidase catalytic models. In summary, cFase I exhibits glycosidase activity that removes core α-1,3-fucoses from substrates, suggesting cFase I as a new tool for glycobiology, especially for studies of proteins with core fucosylation. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Toxicity of herbicides used in the sugarcane crop to diazotrophic bacterium Herbaspirillum seropedicae

    Directory of Open Access Journals (Sweden)

    Sergio de Oliveira Procópio

    2014-10-01

    Full Text Available The objective of this work was to identify herbicides used in the sugarcane crop that affects neither the growth, the development, of nor the process of biological nitrogen fixation (BNF by the diazotrophic bacterium Herbaspirillum seropedicae. Eighteen herbicides (paraquat, ametryne, tebuthiuron, amicarbazone, diuron, metribuzin, [hexazinone + diuron], [hexazinone + clomazone], clomazone, isoxaflutole, sulfentrazone, oxyfluorfen, imazapic, imazapyr, [trifloxysulfuron sodium + ametryne], glyphosate, MSMA e 2,4-D were tested in their respective commercial doses regarding their impact on the growth of the bacteria in liquid medium DIGs. For this, we determined the duration of lag phase, generation time and maximum cell density of H. seropedicae, calculated from optical density data obtained at regular intervals during the incubation of cultures for 33 h at 32oC. We also evaluated the impact of herbicides on nitrogenase activity of H. seropedicae grown in semi-solid N-free JNFb medium. The effects of herbicides on the growth variables and the ARA were compared with the untreated control by Dunnett test. A completely randomized design was used. The herbicides paraquat, imazapyr, ametryne, glyphosate and oxyfluorfen inhibited the growth of H. seropedicae in vitro. Ametryne, oxyfluorfen and glyphosate caused a small reduction in the duration of the lag phase of diazotrophic bacteria H. seropedicae. Oxyfluorfen, ametryne and imazapyr resulted in increased the generation time by H. seropedicae. Glyphosate promoted drastic reduction in biological nitrogen fixation in vitro by H. seropedicae. The other tested herbicides did not affect the growth or the same BNF by H. seropedicae.

  10. Metabolism of nitrodiphenyl ether herbicides by dioxin-degrading bacterium Sphingomonas wittichii RW1.

    Science.gov (United States)

    Keum, Young Soo; Lee, Young Ju; Kim, Jeong-Han

    2008-10-08

    Nitrodiphenyl ether herbicides, including chlomethoxyfen, nitrofen, and oxyfluorfen are potent herbicides. Some metabolites and parent compounds are considered as possible mutagens and endocrine disruptors. Both properties pose serious hygienic and environmental risks. Sphingomonas wittichii RW1 is a well-known degrader of polychlorinated dibenzo- p-dioxins, dibenzofurans, and diphenyl ethers. However, no detailed research of its metabolic activity has been performed against pesticides with a diphenyl ether scaffold. In this study, we report S. wittichii RW1 as a very potent diphenyl ether herbicide-metabolizing bacterium with broad substrate specificity. The structures of metabolites were determined by instrumental analysis and synthetic standards. Most pesticides were rapidly removed from the culture medium in the order of nitrofen > oxyfluorfen > chlomethoxyfen. In general, herbicides were degraded through the initial reduction and N-acetylation of nitro groups, followed by ether bond cleavage. Relatively low concentrations of phenolic and catecholic metabolites throughout the study suggested that these metabolites were rapidly metabolized and incorporated into primary metabolism. These results indicate that strain RW1 has very versatile metabolic activities over a wide range of environmental contaminants.

  11. Application of antioxidant indicators to select nicotine-degrading bacterium for bioaugmented treatment of tobacco wastewater

    International Nuclear Information System (INIS)

    Hongzhen, H.; Zheng, X.

    2013-01-01

    To select nicotine-degrading bacterium for bioaugmented treatment of tobacco wastewater, the activities of antioxidant indicators such as superoxide dismutase (SOD), catalase (CAT) and glutathione (GSH), and the ability to treat pollutants including nicotine degradation and chemical oxygen demand (COD) removal, were compared between Acinetobacter sp. TW and Sphingomonas sp. TY. When complicated toxins were present, the activities of SOD induced in strain TY were significantly higher than those in strain TW. However, the activities of CAT were inhibited in strain TY (CAT/CATLB 1). Additionally, the levels of GSH induced in strain TW were significantly higher than those in strain TY. These findings suggest that the antioxidant ability of strain TW was higher than that of strain TY, especially in tobacco wastewater. Moreover, when applied to the treatment of tobacco wastewater, the rate of nicotine degradation at 24 h was 99.50% for TW and 28.76% for TY, while the rate of COD removal at 48 h was 62.69% for TW and 45.80% for TY. Taken together, these findings indicate that the pollution treatment ability of strain TW was stronger than that of TY, and that the stronger the ability of the antioxidant, the higher the potential for treatment of tobacco wastewater. (author)

  12. Sorption of ferrous iron by EPS from the acidophilic bacterium Acidiphilium Sp.: A mechanism proposal

    International Nuclear Information System (INIS)

    Tapia, J.M.; MuNoz, J.; Gonzlez, F.; Blazquez, M.L.; Ballester, A.

    2016-01-01

    The aim of this work was to assess the uptake of Fe(II) by extracellular polymeric substances (EPS) from the acidophilic bacterium Acidiphillium 3.2Sup(5). These EPS were extracted using EDTA. EPS of A. 3.2Sup(5) loaded in sorption tests with Fe(II), were characterized using the following experimental techniques: scanning electron microscopy (SEM) with energy dispersive X-ray microanalysis (EDX), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The experimental results indicate that EPS adsorb ferrous iron according to Freundlich model with a metal sorption uptake of K = 1.14 mg1−1/n L1/n g−1 and a sorption intensity of 1/n = 1.26. In addition, ferrous iron sorption by EPS took place by preferential interaction with the carboxyl group which promotes the formation of ferrous iron oxalates (FeC2O4). Since the interaction reaction was reversible (Log K = 0.77 ± 0.33), that means that the cation sorption can be reversed at convenience. (Author)

  13. Sorption of ferrous iron by EPS from the acidophilic bacterium Acidiphilium Sp.: A mechanism proposal

    Energy Technology Data Exchange (ETDEWEB)

    Tapia, J.M.; MuNoz, J.; Gonzlez, F.; Blazquez, M.L.; Ballester, A.

    2016-07-01

    The aim of this work was to assess the uptake of Fe(II) by extracellular polymeric substances (EPS) from the acidophilic bacterium Acidiphillium 3.2Sup(5). These EPS were extracted using EDTA. EPS of A. 3.2Sup(5) loaded in sorption tests with Fe(II), were characterized using the following experimental techniques: scanning electron microscopy (SEM) with energy dispersive X-ray microanalysis (EDX), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The experimental results indicate that EPS adsorb ferrous iron according to Freundlich model with a metal sorption uptake of K = 1.14 mg1−1/n L1/n g−1 and a sorption intensity of 1/n = 1.26. In addition, ferrous iron sorption by EPS took place by preferential interaction with the carboxyl group which promotes the formation of ferrous iron oxalates (FeC2O4). Since the interaction reaction was reversible (Log K = 0.77 ± 0.33), that means that the cation sorption can be reversed at convenience. (Author)

  14. Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori

    International Nuclear Information System (INIS)

    Han Cong; Wang Qi; Dong Lei; Sun Haifang; Peng Shuying; Chen Jing; Yang Yiming; Yue Jianmin; Shen Xu; Jiang Hualiang

    2004-01-01

    Helicobacter pylori is a gram-negative pathogenic bacterium, which is associated with peptic ulcer disease and gastric cancer. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. In bacteria, peptide deformylase (PDF) catalyzes the removal of a formyl group from the N-termini of nascent polypeptides. Due to its essentiality and absence in mammalian cells, PDF has been considered as an attractive target for the discovery of novel antibiotics. In this work, a new PDF gene (def) from H. pylori strain SS1 was cloned, expressed, and purified in Escherichia coli system. Sequence alignment shows that H. pylori PDF (HpPDF) shares about 40% identity to E. coli PDF (EcPDF). The enzymatic properties of HpPDF demonstrate its relatively high activity toward formyl-Met-Ala-Ser, with K cat of 3.4 s -1 , K m of 1.7 mM, and K cat /K m of 2000 M -1 s -1 . HpPDF enzyme appears to be fully active at pH between 8.0 and 9.0, and temperature 50 deg. C. The enzyme activity of Co 2+ -containing HpPDF is apparently higher than that of Zn 2+ -containing HpPDF. This present work thereby supplies a potential platform that facilitates the discovery of novel HpPDF inhibitors and further of possible antimicrobial agents against H. pylori

  15. Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori.

    Science.gov (United States)

    Han, Cong; Wang, Qi; Dong, Lei; Sun, Haifang; Peng, Shuying; Chen, Jing; Yang, Yiming; Yue, Jianmin; Shen, Xu; Jiang, Hualiang

    2004-07-09

    Helicobacter pylori is a gram-negative pathogenic bacterium, which is associated with peptic ulcer disease and gastric cancer. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. In bacteria, peptide deformylase (PDF) catalyzes the removal of a formyl group from the N-termini of nascent polypeptides. Due to its essentiality and absence in mammalian cells, PDF has been considered as an attractive target for the discovery of novel antibiotics. In this work, a new PDF gene (def) from H. pylori strain SS1 was cloned, expressed, and purified in Escherichia coli system. Sequence alignment shows that H. pylori PDF (HpPDF) shares about 40% identity to E. coli PDF (EcPDF). The enzymatic properties of HpPDF demonstrate its relatively high activity toward formyl-Met-Ala-Ser, with K(cat) of 3.4s(-1), K(m) of 1.7 mM, and K(cat) / K(m) of 2000M(-1)s(-1). HpPDF enzyme appears to be fully active at pH between 8.0 and 9.0, and temperature 50 degrees C. The enzyme activity of Co(2+)-containing HpPDF is apparently higher than that of Zn(2+)-containing HpPDF. This present work thereby supplies a potential platform that facilitates the discovery of novel HpPDF inhibitors and further of possible antimicrobial agents against H. pylori.

  16. Bacillus notoginsengisoli sp. nov., a novel bacterium isolated from the rhizosphere of Panax notoginseng.

    Science.gov (United States)

    Zhang, Meng-Yue; Cheng, Juan; Cai, Ying; Zhang, Tian-Yuan; Wu, Ying-Ying; Manikprabhu, Deene; Li, Wen-Jun; Zhang, Yi-Xuan

    2017-08-01

    A Gram-stain-positive, rod-shaped, motile bacterium designated as SYP-B691T was isolated from rhizospheric soil of Panax notoginseng. Phylogenetic analysis indicated that SYP-B691T clearly represented a member of the genus Bacillus and showed 16S rRNA gene similarity lower than 97.0 % with the type strains of species of the genus Bacillus, which indicates that it should be considered as a candidate novel species within this genus. The optimum growth of the strain was found to occur at 37 °C and pH 7.0-9.0. The genomic DNA G+C content was determined to be 45.2 mol%. It contained meso-2,6-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. MK-7 was the only menaquinone identified. The major cellular fatty acids of SYP-B691T were identified as iso-C15 : 0 and anteiso-C15 : 0. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, SYP-B691T merits recognition as a representative of a novel species of the genus Bacillus, for which the name Bacillus notoginsengisoli sp. nov. is proposed, with SYP-B691T(=DSM 29196T=JCM 30743T) as the type strain.

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

    Science.gov (United States)

    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. Copyright © 2013 Elsevier GmbH. All rights reserved.

  18. Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil.

    Science.gov (United States)

    Cunha, Sofia; Tiago, Igor; Paiva, Gabriel; Nobre, Fernanda; da Costa, Milton S; Veríssimo, António

    2012-03-01

    A Gram-staining-positive, motile, rod-shaped, spore-forming bacterium, designated P9(T), was isolated from soil in Portugal. This organism was aerobic and catalase- and oxidase-positive. It had an optimum growth temperature of about 35 °C and an optimum growth pH of about 8.0-8.5, and grew in medium with 0-9% (w/v) NaCl. The cell-wall peptidoglycan was of the A1α type, with L-lysine as the diagnostic diamino acid. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C(15:0) (45.4%), iso-C(15:0) (22.0%) and anteiso-C(17:0) (11.2%). The genomic DNA G+C content was about 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P9(T) was most closely related to Jeotgalibacillus campisalis DSM 18983(T) (96.8%) and Jeotgalibacillus marinus DSM 1297(T) (96.5%). These two recognized species formed a coherent cluster with strain P9(T) that was supported by a bootstrap value of 99%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, strain P9(T) (=DSM 23228(T)=LMG 25523(T)) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus soli sp. nov. is proposed.

  19. Cloning, expression, purification and application of a novel chitinase from a thermophilic marine bacterium Paenibacillus barengoltzii.

    Science.gov (United States)

    Yang, Shaoqing; Fu, Xing; Yan, Qiaojuan; Guo, Yu; Liu, Zhuqing; Jiang, Zhengqiang

    2016-02-01

    A novel chitinase gene (PbChi70) from a marine bacterium Paenicibacillus barengoltzii was cloned and functionally expressed in Escherichia coli. The recombinant enzyme (PbChi70) was purified to homogeneity with a recovery yield of 51.9%. The molecular mass of purified enzyme was estimated to be 70.0 kDa by SDS-PAGE. PbChi70 displayed maximal activity at pH 5.5 and 55 °C, respectively. It exhibited strict substrate specificity for colloidal chitin, glycol chitin, powdery chitin, and N-acetyl chitooligosaccharides with degrees of polymerization above three. The enzyme exhibited an endo-type cleavage pattern and hydrolyzed colloidal chitin to yield mainly (GlcNAc)2. Furthermore, colloidal chitin was hydrolyzed by PbChi70 to produce 21.6 mg mL(-1) (GlcNAc)2 with the highest conversion yield of 89.5% (w/w). (GlcNAc)2 was further separated by an active charcoal column with a purity of 99% and a final yield of 61%. The unique enzymatic properties of the chitinase may make it a good candidate for (GlcNAc)2 production. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Architecture of a flagellar apparatus in the fast-swimming magnetotactic bacterium MO-1.

    Science.gov (United States)

    Ruan, Juanfang; Kato, Takayuki; Santini, Claire-Lise; Miyata, Tomoko; Kawamoto, Akihiro; Zhang, Wei-Jia; Bernadac, Alain; Wu, Long-Fei; Namba, Keiichi

    2012-12-11

    The bacterial flagellum is a motility organelle that consists of a rotary motor and a helical propeller. The flagella usually work individually or by forming a loose bundle to produce thrust. However, the flagellar apparatus of marine bacterium MO-1 is a tight bundle of seven flagellar filaments enveloped in a sheath, and it has been a mystery as to how the flagella rotate smoothly in coordination. Here we have used electron cryotomography to visualize the 3D architecture of the sheathed flagella. The seven filaments are enveloped with 24 fibrils in the sheath, and their basal bodies are arranged in an intertwined hexagonal array similar to the thick and thin filaments of vertebrate skeletal muscles. This complex and exquisite architecture strongly suggests that the fibrils counter-rotate between flagella in direct contact to minimize the friction of high-speed rotation of individual flagella in the tight bundle within the sheath to enable MO-1 cells to swim at about 300 µm/s.

  1. Partial characterization of an extracellular polysaccharide produced by the moderately halophilic bacterium Halomonas xianhensis SUR308.

    Science.gov (United States)

    Biswas, Jhuma; Ganguly, J; Paul, A K

    2015-01-01

    A moderately halophilic bacterium, Halomonas xianhensis SUR308 (Genbank Accession No. KJ933394) was isolated from a multi-pond solar saltern at Surala, Ganjam district, Odisha, India. The isolate produced a significant amount (7.87 g l(-1)) of extracellular polysaccharides (EPS) when grown in malt extract-yeast extract medium supplemented with 2.5% NaCl, 0.5% casein hydrolysate and 3% glucose. The EPS was isolated and purified following the conventional method of precipitation and dialysis. Chromatographic analysis (paper, GC and GC-MS) of the hydrolyzed EPS confirmed its heteropolymeric nature and showed that it is composed mainly of glucose (45.74 mol%), galactose (33.67 mol %) and mannose (17.83 mol%). Fourier-transform infrared spectroscopy indicated the presence of methylene and carboxyl groups as characteristic functional groups. In addition, its proton nuclear magnetic resonance spectrum revealed functional groups specific for extracellular polysaccharides. X-ray diffraction analysis revealed the amorphous nature (CIxrd, 0.56) of the EPS. It was thermostable up to 250 °C and displayed pseudoplastic rheology and remarkable stability against pH and salts. These unique properties of the EPS produced by H. xianhensis indicate its potential to act as an agent for detoxification, emulsification and diverse biological activities.

  2. Extracellular proteases of Halobacillus blutaparonensis strain M9, a new moderately halophilic bacterium.

    Science.gov (United States)

    Santos, Anderson F; Valle, Roberta S; Pacheco, Clarissa A; Alvarez, Vanessa M; Seldin, Lucy; Santos, André L S

    2013-12-01

    Halophilic microorganisms are source of potential hydrolytic enzymes to be used in industrial and/or biotechnological processes. In the present study, we have investigated the ability of the moderately halophilic bacterium Halobacillus blutaparonensis (strain M9), a novel species described by our group, to release proteolytic enzymes. This bacterial strain abundantly proliferated in Luria-Bertani broth supplemented with 2.5% NaCl as well as secreted proteases to the extracellular environment. The production of proteases occurred in bacterial cells grown under different concentration of salt, ranging from 0.5% to 10% NaCl, in a similar way. The proteases secreted by H. blutaparonensis presented the following properties: (i) molecular masses ranging from 30 to 80 kDa, (ii) better hydrolytic activities under neutral-alkaline pH range, (iii) expression modulated according to the culture age, (iv) susceptibility to phenylmethylsulphonyl fluoride, classifying them as serine-type proteases, (v) specific cleavage over the chymotrypsin substrate, and (vi) enzymatic stability in the presence of salt (up to 20% NaCl) and organic solvents (e.g., ether, isooctane and cyclohexane). The proteases described herein are promising for industrial practices due to its haloalkaline properties.

  3. Structural and biochemical characterization of a nitrilase from the thermophilic bacterium, Geobacillus pallidus RAPc8.

    Science.gov (United States)

    Williamson, Dael S; Dent, Kyle C; Weber, Brandon W; Varsani, Arvind; Frederick, Joni; Thuku, Robert N; Cameron, Rory A; van Heerden, Johan H; Cowan, Donald A; Sewell, B Trevor

    2010-09-01

    Geobacillus pallidus RAPc8 (NRRL: B-59396) is a moderately thermophilic gram-positive bacterium, originally isolated from Australian lake sediment. The G. pallidus RAPc8 gene encoding an inducible nitrilase was located and cloned using degenerate primers coding for well-conserved nitrilase sequences, coupled with inverse PCR. The nitrilase open reading frame was cloned into an expression plasmid and the expressed recombinant enzyme purified and characterized. The protein had a monomer molecular weight of 35,790 Da, and the purified functional enzyme had an apparent molecular weight of approximately 600 kDa by size exclusion chromatography. Similar to several plant nitrilases and some bacterial nitrilases, the recombinant G. pallidus RAPc8 enzyme produced both acid and amide products from nitrile substrates. The ratios of acid to amide produced from the substrates we tested are significantly different to those reported for other enzymes, and this has implications for our understanding of the mechanism of the nitrilases which may assist with rational design of these enzymes. Electron microscopy and image classification showed complexes having crescent-like, "c-shaped", circular and "figure-8" shapes. Protein models suggested that the various complexes were composed of 6, 8, 10 and 20 subunits, respectively.

  4. Expression and Characterization of a Novel Nitrilase from Hyperthermophilic Bacterium Thermotoga maritima MSB8.

    Science.gov (United States)

    Chen, Zhi; Chen, Huayou; Ni, Zhong; Tian, Rui; Zhang, Tianxi; Jia, Jinru; Yang, Shengli

    2015-10-01

    The present study describes the gene cloning, overexpression and characterization of a novel nitrilase from hyperthermophilic bacterium Thermotoga maritima MSB8. The nitrilase gene consisted of 804 base pairs, encoding a protein of 268 amino acid residues with a molecular mass of 30.07 kDa after SDS-PAGE analysis. The optimal temperature and pH of the purified enzyme were 45°C and 7.5, respectively. The enzyme demonstrated good temperature tolerance, with 40% residual activity after 60 min of heat treatment at 75°C. The kinetic constants Vmax and Km of this nitrilase toward 3-cyanopyridine were 3.12 μmol/min/mg and 7.63 mM, respectively. Furthermore, this novel nitrilase exhibited a broad spectrum toward the hydrolysis of the aliphatic nitriles among the tested substrates, and particularly was specific to aliphatic dinitriles like succinonitrile, which was distinguished from most nitrilases ever reported. The catalytic efficiency kcat/Km was 0.44 /mM/s toward succinonitrile. This distinct characteristic might enable this nitrilase to be a potential candidate for industrial applications for biosynthesis of carboxylic acid.

  5. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

    KAUST Repository

    Tian, Renmao

    2014-08-29

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. A bacterium targets maternally inherited centrosomes to kill males in Nasonia.

    Science.gov (United States)

    Ferree, Patrick M; Avery, Amanda; Azpurua, Jorge; Wilkes, Timothy; Werren, John H

    2008-09-23

    Male killing is caused by diverse microbial taxa in a wide range of arthropods. This phenomenon poses important challenges to understanding the dynamics of sex ratios and host-pathogen interactions. However, the mechanisms of male killing are largely unknown. Evidence from one case in Drosophila suggests that bacteria can target components of the male-specific sex-determination pathway. Here, we investigated male killing by the bacterium Arsenophonus nasoniae in the haplo-diploid wasp Nasonia vitripennis, in which females develop as diploids from fertilized eggs and males develop parthenogenetically as haploids from unfertilized eggs. We found that Arsenophonus inhibits the formation of maternal centrosomes, organelles required specifically for early male embryonic development, resulting in unorganized mitotic spindles and developmental arrest well before the establishment of somatic sexual identity. Consistent with these results, rescue of Arsenophonus-induced male lethality was achieved by fertilization with sperm bearing the supernumerary chromosome paternal sex ratio (PSR), which destroys the paternal genome but bypasses the need for maternal centrosomes by allowing transmission of the sperm-derived centrosome into the egg. These findings reveal a novel mechanism of male killing in Nasonia, demonstrating that bacteria have evolved different mechanisms for inducing male killing in the Arthropods.

  7. Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393

    KAUST Repository

    Hong, Pei-Ying

    2014-01-24

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

  8. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

    Science.gov (United States)

    Behrendt, Undine; Kämpfer, Peter; Glaeser, Stefanie P; Augustin, Jürgen; Ulrich, Andreas

    2016-06-01

    In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed.

  9. Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis.

    Science.gov (United States)

    Mandelli, F; Couger, M B; Paixão, D A A; Machado, C B; Carnielli, C M; Aricetti, J A; Polikarpov, I; Prade, R; Caldana, C; Paes Leme, A F; Mercadante, A Z; Riaño-Pachón, D M; Squina, Fabio Marcio

    2017-07-01

    Thermus filiformis is an aerobic thermophilic bacterium isolated from a hot spring in New Zealand. The experimental study of the mechanisms of thermal adaptation is important to unveil response strategies of the microorganism to stress. In this study, the main pathways involved on T. filiformis thermoadaptation, as well as, thermozymes with potential biotechnological applications were revealed based on omics approaches. The strategy adopted in this study disclosed that pathways related to the carbohydrate metabolism were affected in response to thermoadaptation. High temperatures triggered oxidative stress, leading to repression of genes involved in glycolysis and the tricarboxylic acid cycle. During heat stress, the glucose metabolism occurred predominantly via the pentose phosphate pathway instead of the glycolysis pathway. Other processes, such as protein degradation, stringent response, and duplication of aminoacyl-tRNA synthetases, were also related to T. filiformis thermoadaptation. The heat-shock response influenced the carotenoid profile of T. filiformis, favoring the synthesis of thermozeaxanthins and thermobiszeaxanthins, which are related to membrane stabilization at high temperatures. Furthermore, antioxidant enzymes correlated with free radical scavenging, including superoxide dismutase, catalase and peroxidase, and metabolites, such as oxaloacetate and α-ketoglutarate, were accumulated at 77 °C.

  10. Study on bioremediation of Lead by exopolysaccharide producing metallophilic bacterium isolated from extreme habitat

    Directory of Open Access Journals (Sweden)

    Debajit Kalita

    2017-12-01

    Full Text Available Lead released from manufacturing factories, recycling plants, automobile company and landfill leachate is abundantly found in wastewater. An efficient bioremediating agent for lead removal from wastewater is expected to ease the ever increasing problem. The present study reports Pseudomonas sp. W6 isolated from extreme habitat of hot water spring of North–East India evaluated for its Lead biosorption property. The bacterium showed capacity to resist 1.0 mM lead in both solid and liquid minimal media. Epifluorescence microscopy reveal the viability of bacterial cells under metal stress condition. ICP-MS analysis revealed 65% and 61.2% removal of lead from the Synthetic Bangladesh Ground Water medium in batch culture and column study respectively which was higher when compared to biosorption capacity of P. aeruginosa MTCC2474, P. alcaligenes MJ7 from forest soil and P. ficuserectae PKRS11 from uranium rich soil. Exopolysaccharide released by the isolate which influenced biosorption revealed the presence of ligands assayed using microbial hydrophobicity and FTIR. The extremophilic isolate is proposed as a choice for efficient bioremediation of lead contaminated wastewater. Keywords: Extremophile, Pseudomonas, Lead bioremediation, Epifluorescence microscopy, ICP-MS, FTIR

  11. Study on bioremediation of Lead by exopolysaccharide producing metallophilic bacterium isolated from extreme habitat.

    Science.gov (United States)

    Kalita, Debajit; Joshi, S R

    2017-12-01

    Lead released from manufacturing factories, recycling plants, automobile company and landfill leachate is abundantly found in wastewater. An efficient bioremediating agent for lead removal from wastewater is expected to ease the ever increasing problem. The present study reports Pseudomonas sp. W6 isolated from extreme habitat of hot water spring of North-East India evaluated for its Lead biosorption property. The bacterium showed capacity to resist 1.0 mM lead in both solid and liquid minimal media. Epifluorescence microscopy reveal the viability of bacterial cells under metal stress condition. ICP-MS analysis revealed 65% and 61.2% removal of lead from the Synthetic Bangladesh Ground Water medium in batch culture and column study respectively which was higher when compared to biosorption capacity of P. aeruginosa MTCC 2474, P. alcaligenes MJ7 from forest soil and P. ficuserectae PKRS11 from uranium rich soil. Exopolysaccharide released by the isolate which influenced biosorption revealed the presence of ligands assayed using microbial hydrophobicity and FTIR. The extremophilic isolate is proposed as a choice for efficient bioremediation of lead contaminated wastewater.

  12. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus

    Energy Technology Data Exchange (ETDEWEB)

    Saw, Jimmy H [Los Alamos National Laboratory; Mountain, Bruce W [NEW ZEALAND; Feng, Lu [NANKAI UNIV; Omelchenko, Marina V [NCBI/NLM/NIH; Hou, Shaobin [UNIV OF HAWAII; Saito, Jennifer A [UNIV OF HAWAII; Stott, Matthew B [NEW ZEALAND; Li, Dan [NANKAI UNIV; Zhao, Guang [NANKAI UNIV; Wu, Junli [NANKAI UNIV; Galperin, Michael Y [NCBI/NLM/NIH; Koonin, Eugene V [NCBI/NLM/NIH; Makarova, Kira S [NCBI/NLM/NIH; Wolf, Yuri I [NCBI/NLM/NIH; Rigden, Daniel J [UNIV OF LIVERPOOL; Dunfield, Peter F [UNIV OF CALGARY; Wang, Lei [NANKAI UNIV; Alam, Maqsudul [UNIV OF HAWAII

    2008-01-01

    Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.

  13. Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium.

    Science.gov (United States)

    Singh, Rahul; Grigg, Jason C; Qin, Wei; Kadla, John F; Murphy, Michael E P; Eltis, Lindsay D

    2013-04-19

    DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn(2+)), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine increased the enzyme's apparent k(cat) and k(cat)/K(m) values for Mn(2+) by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn(2+) to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different from that of another bacterial Mn(2+)-oxidizing peroxidase. The first coordination sphere was entirely composed of solvent, consistent with the variant's high K(m) for Mn(2+) (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin.

  14. Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

    Directory of Open Access Journals (Sweden)

    Alexander B. Chase

    2017-11-01

    Full Text Available Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. The response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment.

  15. Remediation of contaminated subsurface materials by a metal-reducing bacterium

    International Nuclear Information System (INIS)

    Gorby, Y.A.; Amonette, J.E.; Fruchter, J.S.

    1994-11-01

    A biotic approach for remediating subsurface sediments and groundwater contaminated with carbon tetrachloride (CT) and chromium was evaluated. Cells of the Fe(iii)-reducing bacterium strain BrY were added to sealed, anoxic flasks containing Hanford groundwater, natural subsurface sediments, and either carbon tetrachloride, CT, or oxidized chromium, Cr(VI). With lactate as the electron donor, BrY transformed CT to chloroform (CF), which accumulated to about 1 0 % of the initial concentration of CT. The remainder of the CT was transformed to unidentified, nonvolatile compounds. Transformation of CT by BrY was an indirect process Cells reduced solid phase Fe(ill) to chemically reactive FE(II) that chemically transformed the chlorinated contaminant. Cr(VI), in contrast, was reduced by a direct enzymatic reaction in the presence or absence of Fe(III)-bearing sediments. These results demonstrate that Fe(ill)-reducing bacteria provide potential for transforming CT and for reducing CR(VI) to less toxic Cr(III). Technologies for stimulating indigenous populations of metal-reducing bacteria or for introducing specific metal-reducing bacteria to the subsurface are being investigated

  16. Atomic-resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti.

    Science.gov (United States)

    Starks, Courtney M; Francois, Julie A; MacArthur, Kelly M; Heard, Brittney Z; Kappock, T Joseph

    2007-01-01

    The crystal structure of thioredoxin (AaTrx) from the acetic acid bacterium Acetobacter aceti was determined at 1 A resolution. This is currently the highest resolution crystal structure available for any thioredoxin. Thioredoxins facilitate thiol-disulfide exchange, a process that is expected to be slow at the low pH values encountered in the A. aceti cytoplasm. Despite the apparent need to function at low pH, neither the active site nor the surface charge distribution of AaTrx is notably different from that of Escherichia coli thioredoxin. Apparently the ancestral thioredoxin was sufficiently stable for use in A. aceti or the need to interact with multiple targets constrained the variation of surface residues. The AaTrx structure presented here provides a clear view of all ionizable protein moieties and waters, a first step in understanding how thiol-disulfide exchange might occur in a low pH cytoplasm, and is a basis for biophysical studies of the mechanism of acid-mediated unfolding. The high resolution of this structure should be useful for computational studies of thioredoxin function, protein structure and dynamics, and side-chain ionization.

  17. Iridescence of a Marine Bacterium and Classification of Prokaryotic Structural Colors

    Science.gov (United States)

    Vukusic, Peter; Luke, Stephen

    2012-01-01

    Iridescence is a property of structural color that is occasionally encountered in higher eukaryotes but that has been poorly documented in the prokaryotic kingdom. In the present work, we describe a marine bacterium, identified as Cellulophaga lytica, isolated from the surface of an anemone, that exhibits bright green iridescent colonies under direct epi-illumination. This phenomenon has not previously been investigated in detail. In this study, color changes of C. lytica colonies were observed at various angles of direct illumination or observation. Its iridescent green appearance was dominant on various growth media. Red and violet colors were also discerned on colony edges. Remarkable C. lytica bacterial iridescence was revealed and characterized using high-resolution optical spectrometry. In addition to this, by culturing other bacterial strains to which various forms of faintly iridescent traits have previously been attributed, we identify four principal appearance characteristics of structural color in prokaryotes. A new general classification of bacterial iridescence is therefore proposed in this study. Furthermore, a specific separate class is described for iridescent C. lytica strains because they exhibit what is so far a unique intense glitter-like iridescence in reflection. C. lytica is the first prokaryote discovered to produce the same sort of intense iridescence under direct illumination as that associated with higher eukaryotes, like some insects and birds. Due to the nature of bacterial biology, cultivation, and ubiquity, this discovery may be of significant interest for both ecological and nanoscience endeavors. PMID:22267664

  18. Genome sequence of Enterobacter sp. ST3, a quorum sensing bacterium associated with marine dinoflagellate

    Directory of Open Access Journals (Sweden)

    Jin Zhou

    2016-03-01

    Full Text Available Phycosphere environment is a typical marine niche, harbor diverse populations of microorganisms, which are thought to play a critical role in algae host and influence mutualistic and competitive interactions. Understanding quorum sensing-based acyl-homoserine lactone (AHL language may shed light on the interaction between algal-associated microbial communities in the native environment. In this work, we isolated an epidermal bacterium (was tentatively named Enterobacter sp. ST3, and deposited in SOA China, the number is MCCC1K02277-ST3 from the marine dinoflagellate Scrippsiella trochoidea, and found it has the ability to produce short-chain AHL signal. In order to better understand its communication information at molecular level, the genomic map was investigated. The genome size was determined to be 4.81 Mb with a G + C content of 55.59%, comprising 6 scaffolds of 75 contigs containing 4647 protein-coding genes. The functional proteins were predicted, and 3534 proteins were assigned to COG functional categories. An AHL-relating gene, LuxR, was found in upstream position at contig 1. This genome data may provide clues to increase understanding of the chemical characterization and ecological behavior of strain ST3 in the phycosphere microenvironment.

  19. Enterobacter cloacae, an Emerging Plant-Pathogenic Bacterium Affecting Chili Pepper Seedlings

    Directory of Open Access Journals (Sweden)

    Tanahiri García-González

    2018-02-01

    Full Text Available A previously unreported bacterial disease on chili pepper (Capsicum annuum L. seedlings affecting as many as 4% of seedlings was observed in greenhouses in Chihuahua, Mexico (Delicias and Meoqui counties. Initial lesions appeared as irregular small spots on leaves and brown necrosis at margins tips were observed. Later, the spots became necrotic with a chlorotic halo. Advanced disease was associated with defoliation. A Gram negative, rod-shaped bacterium was isolated from diseased chili pepper seedlings. Three inoculation methods revealed that isolated strains produce foliage symptoms, similar to those observed in naturally infected seedlings. Pathogenic strains that caused symptoms in inoculated seedlings were re-isolated and identified to fulfill koch’s postulate. Polyphasic approaches for identification including biochemical assays (API 20E and 50CH, carbon source utilization profiling (Biolog and 16S rDNA, hsp60 and rpoB sequence analysis were done. Enterobacter cloacae was identified as the causal agent of this outbreak on chili pepper seedlings.

  20. Direct bioconversion of brown algae into ethanol by thermophilic bacterium Defluviitalea phaphyphila.

    Science.gov (United States)

    Ji, Shi-Qi; Wang, Bing; Lu, Ming; Li, Fu-Li

    2016-01-01

    Brown algae are promising feedstocks for biofuel production with inherent advantages of no structural lignin, high growth rate, and no competition for land and fresh water. However, it is difficult for one microorganism to convert all components of brown algae with different oxidoreduction potentials to ethanol. Defluviitalea phaphyphila Alg1 is the first characterized thermophilic bacterium capable of direct utilization of brown algae. Defluviitalea phaphyphila Alg1 can simultaneously utilize mannitol, glucose, and alginate to produce ethanol, and high ethanol yields of 0.47 g/g-mannitol, 0.44 g/g-glucose, and 0.3 g/g-alginate were obtained. A rational redox balance system under obligate anaerobic condition in fermenting brown algae was revealed in D. phaphyphila Alg1 through genome and redox analysis. The excess reducing equivalents produced from mannitol metabolism were equilibrated by oxidizing forces from alginate assimilation. Furthermore, D. phaphyphila Alg1 can directly utilize unpretreated kelp powder, and 10 g/L of ethanol was accumulated within 72 h with an ethanol yield of 0.25 g/g-kelp. Microscopic observation further demonstrated the deconstruction process of brown algae cell by D. phaphyphila Alg1. The integrated biomass deconstruction system of D. phaphyphila Alg1, as well as its high ethanol yield, provided us an excellent alternative for brown algae bioconversion at elevated temperature.

  1. Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137

    Science.gov (United States)

    Powell, Ryan J.

    2013-01-01

    Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

  2. Interactions between the pathogenic bacterium Vibrio parahaemolyticus and red-tide dinoflagellates

    Science.gov (United States)

    Seong, Kyeong Ah; Jeong, Hae Jin

    2011-06-01

    Vibrio parahaemolyticus is a common pathogenic bacterium in marine and estuarine waters. To investigate interactions between V. parahaemolyticus and co-occurring redtide dinoflagellates, we monitored the daily abundance of 5 common red tide dinoflagellates in laboratory culture; Amphidinium carterae, Cochlodinium ploykrikoides, Gymnodinium impudicum, Prorocentrum micans, and P. minimum. Additionally, we measured the ingestion rate of each dinoflagellate on V. parahaemolyticus as a function of prey concentration. Each of the dinoflagellates responded differently to the abundance of V. parahaemolyticus. The abundances of A. carterae and P. micans were not lowered by V. parahaemolyticus, whereas that of C. polykrikodes was lowered considerably. The harmful effect depended on bacterial concentration and incubation time. Most C. polykrikoides cells died after 1 hour incubation when the V. parahaemolyticus concentration was 1.4×107 cells ml-1, while cells died within 2 days of incubation when the bacterial concentration was 1.5×106 cells ml-1. With increasing V. parahaemolyticus concentration, ingestion rates of P. micans, P. minimum, and A. carterae on the prey increased, whereas that on C. polykrikoides decreased. The maximum or highest ingestion rates of P. micans, P. minimum, and A. carterae on V. parahaemolyticus were 55, 5, and 2 cells alga-1 h-1, respectively. The results of the present study suggest that V. parahaemolyticus can be both the killer and prey for some red tide dinoflagellates.

  3. Deciphering a unique biotin scavenging pathway with redundant genes in the probiotic bacterium Lactococcus lactis.

    Science.gov (United States)

    Zhang, Huimin; Wang, Qingjing; Fisher, Derek J; Cai, Mingzhu; Chakravartty, Vandana; Ye, Huiyan; Li, Ping; Solbiati, Jose O; Feng, Youjun

    2016-05-10

    Biotin protein ligase (BPL) is widespread in the three domains of the life. The paradigm BPL is the Escherichia coli BirA protein, which also functions as a repressor for the biotin biosynthesis pathway. Here we report that Lactococcus lactis possesses two different orthologues of birA (birA1_LL and birA2_LL). Unlike the scenario in E. coli, L. lactis appears to be auxotrophic for biotin in that it lacks a full biotin biosynthesis pathway. In contrast, it retains two biotin transporter-encoding genes (bioY1_LL and bioY2_LL), suggesting the use of a scavenging strategy to obtain biotin from the environment. The in vivo function of the two L. lactis birA genes was judged by their abilities to complement the conditional lethal E. coli birA mutant. Thin-layer chromatography and mass spectroscopy assays demonstrated that these two recombinant BirA proteins catalyze the biotinylation reaction of the acceptor biotin carboxyl carrier protein (BCCP), through the expected biotinoyl-AMP intermediate. Gel shift assays were used to characterize bioY1_LL and BirA1_LL. We also determined the ability to uptake (3)H-biotin by L. lactis. Taken together, our results deciphered a unique biotin scavenging pathway with redundant genes present in the probiotic bacterium L. lactis.

  4. A cold-adapted, solvent and salt tolerant esterase from marine bacterium Psychrobacter pacificensis.

    Science.gov (United States)

    Wu, Gaobing; Zhang, Xiangnan; Wei, Lu; Wu, Guojie; Kumar, Ashok; Mao, Tao; Liu, Ziduo

    2015-11-01

    Lipolytic enzymes with unique physico-chemical characteristics are gaining more attention for their immense industrial importance. In this study, a novel lipolytic enzyme (Est11) was cloned from the genomic library of a marine bacterium Psychrobacter pacificensis. The enzyme was expressed in Escherichia coli and purified to homogeneity with molecular mass of 32.9kDa. The recombinant Est11 was able to hydrolyze short chain esters (C2-C8) and displayed an optimum activity against butyrate ester (C4). The optimal temperature and pH were 25°C and 7.5, respectively. Est11 retained more than 70% of its original activity at 10°C, suggesting that it was a cold-active esterase. The enzyme was highly active and stable at high concentration of NaCl (5M). Further, incubation with ethanol, isopropanol, propanediol, DMSO, acetonitrile, and glycerol rendered remarkable positive effects on Est11 activity. Typically, even at the concentration of 30% (v/v), ethanol, DMSO, and propanediol increased Est11 activity by 1.3, 2.0, and 2.4-folds, respectively. This new robust enzyme with remarkable properties like cold-adaptability, exceptional tolerance to salt and organic solvents provides us a promising candidate to meet the needs of some harsh industrial processes. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. A polysaccharide-degrading marine bacterium Flammeovirga sp. MY04 and its extracellular agarase system

    Science.gov (United States)

    Han, Wenjun; Gu, Jingyan; Yan, Qiujie; Li, Jungang; Wu, Zhihong; Gu, Qianqun; Li, Yuezhong

    2012-09-01

    Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported regarding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L-1 ± 18.2 mg L-1 liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These proteins have an activity of 310 U mg-1 ± 9.6 U mg-1 proteins. The extracellular agarase system (EAS) in the crude extracellular enzymes contains at least four agarose depolymerases, which are with molecular masses of approximately 30-70 kDa. The EAS is stable at a wide range of pH values (6.0-11.0), temperatures (0-50°C), and sodium chloride (NaCl) concentrations (0-0.9 mol L-1). Two major degradation products generated from agarose by the EAS are identified to be neoagarotetraose and neoagarohexaose, suggesting that β-agarases are the major constituents of the MY04 EAS. These results suggest that the Flammeovirga strain MY04 and its polysaccharide-degradation system hold great promise in industrial applications.

  6. A thermostable serralysin inhibitor from marine bacterium Flavobacterium sp. YS-80-122

    Science.gov (United States)

    Liang, Pengjuan; Li, Shangyong; Wang, Kun; Wang, Fang; Xing, Mengxin; Hao, Jianhua; Sun, Mi

    2017-06-01

    Serralysin inhibitors have been proposed as potent drugs against many diseases and may help to prevent further development of antibiotic-resistant pathogenic bacteria. In this study, a novel serralysin inhibitor gene, lupI, was cloned from the marine bacterium Flavobacterium sp. YS-80-122 and expressed in Escherichia coli. The deduced serralysin inhibitor, LupI, shows <40% amino acid identity to other reported serralysin inhibitors. Multiple sequence alignment and phylogenetic analysis of LupI with other serralysin inhibitors indicated that LupI was a novel type of serralysin inhibitor. The inhibitory constant for LupI towards its target metalloprotease was 0.64 μmol/L. LupI was thermostable at high temperature, in which 35.6%-90.7% of its inhibitory activity was recovered after treatment at 100°C for 1-60 min followed by incubation at 0°C. This novel inhibitor may represent a candidate drug for the treatment of serralysin-related infections.

  7. Bidirectional gene sequences with similar homology to functional proteins of alkane degrading bacterium pseudomonas fredriksbergensis DNA

    International Nuclear Information System (INIS)

    Megeed, A.A.

    2011-01-01

    The potential for two overlapping fragments of DNA from a clone of newly isolated alkanes degrading bacterium Pseudomonas frederiksbergensis encoding sequences with similar homology to two parts of functional proteins is described. One strand contains a sequence with high homology to alkanes monooxygenase (alkB), a member of the alkanes hydroxylase family, and the other strand contains a sequence with some homology to alcohol dehydrogenase gene (alkJ). Overlapping of the genes on opposite strands has been reported in eukaryotic species, and is now reported in a bacterial species. The sequence comparisons and ORFS results revealed that the regulation and the genes organization involved in alkane oxidation represented in Pseudomonas frederiksberghensis varies among the different known alkane degrading bacteria. The alk gene cluster containing homologues to the known alkane monooxygenase (alkB), and rubredoxin (alkG) are oriented in the same direction, whereas alcohol dehydrogenase (alkJ) is oriented in the opposite direction. Such genomes encode messages on both strands of the DNA, or in an overlapping but different reading frames, of the same strand of DNA. The possibility of creating novel genes from pre-existing sequences, known as overprinting, which is a widespread phenomenon in small viruses. Here, the origin and evolution of the gene overlap to bacteriophages belonging to the family Microviridae have been investigated. Such a phenomenon is most widely described in extremely small genomes such as those of viruses or small plasmids, yet here is a unique phenomenon. (author)

  8. The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

    Science.gov (United States)

    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R.

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup. PMID:23516524

  9. Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments.

    Science.gov (United States)

    Vasconcellos, Rafael L F; Santos, Suikinai Nobre; Zucchi, Tiago Domingues; Silva, Fábio Sérgio Paulino; Souza, Danilo Tosta; Melo, Itamar Soares

    2017-10-01

    Strain CMAA 1215 T , a Gram-reaction-negative, aerobic, catalase positive, polarly flagellated, motile, rod-shaped (0.5-0.8 × 1.3-1.9 µm) bacterium, was isolated from mangrove sediments, Cananéia Island, Brazil. Analysis of the 16S rRNA gene sequences showed that strain CMAA 1215 T forms a distinct phyletic line within the Pseudomonas putida subclade, being closely related to P. plecoglossicida ATCC 700383 T , P. monteilii NBRC 103158 T , and P. taiwanensis BCRC 17751 T of sequence similarity of 98.86, 98.73, and 98.71%, respectively. Genomic comparisons of the strain CMAA 1215 T with its closest phylogenetic type strains using average nucleotide index (ANI) and DNA:DNA relatedness approaches revealed 84.3-85.3% and 56.0-63.0%, respectively. A multilocus sequence analysis (MLSA) performed concatenating 16S rRNA, gyrB and rpoB gene sequences from the novel species was related with Pseudomonas putida subcluster and formed a new phylogenetic lineage. The phenotypic, physiological, biochemical, and genetic characteristics support the assignment of CMAA 1215 T to the genus Pseudomonas, representing a novel species. The name Pseudomonas aestus sp.nov. is proposed, with CMAA 1215 T (=NRRL B-653100 T  = CBMAI 1962 T ) as the type strain.

  10. Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola DG893.

    Science.gov (United States)

    Romano, Ariel; Trimble, Lyndsay; Hobusch, Ashtian R; Schroeder, Kristine J; Amin, Shady A; Hartnett, Andrej D; Barker, Ryan A; Crumbliss, Alvin L; Carrano, Carl J

    2013-08-01

    While there has been extensive interest in the use of boron isotope ratios as a surrogate of pH in paleoclimate studies in the context of climate change-related questions, the high (0.4 mM) concentration and the depth-independent (conservative or non-nutrient-like) concentration profile of this element have led to boron being neglected as a potentially biologically relevant element in the modern ocean. Here we report that boron affects the expression of a number of protein and genes in the "algal-associated" Gram-negative marine bacterium Marinobacter algicola DG893. Most intriguingly, a number of these proteins and genes are related to iron uptake. In a recent separate publication we have shown that boron regulates one such iron transport related protein, i.e. the periplasmic iron binding protein FbpA via a direct interaction of the metalloid with this protein. Here we show that a number of other iron uptake related genes are also affected by boron but in the opposite way i.e. they are up-regulated. We propose that the differential effect of boron on FbpA expression relative to other iron transport related genes is a result of an interaction between boron and the global iron regulatory protein Fur.

  11. Pseudomonas kunmingensis sp. nov., an exopolysaccharide-producing bacterium isolated from a phosphate mine.

    Science.gov (United States)

    Xie, Fuhong; Ma, Huan; Quan, Shujing; Liu, Dehai; Chen, Guocan; Chao, Yapeng; Qian, Shijun

    2014-02-01

    A Gram-stain-negative, rod-shaped, exopolysaccharide-producing, strictly aerobic bacterium with a single polar flagellum, designated strain HL22-2(T), was isolated from a phosphate mine situated in a suburb of Kunmming in Yunnan province in south-western China. The taxonomic status of this strain was evaluated by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HL22-2(T) was related to members of the genus Pseudomonas. 16S rRNA gene sequence similarities between strain HL22-2(T) and Pseudomonas xanthomarina KMM 1447(T), Pseudomonas alcaliphila AL15-21(T) and Pseudomonas stutzeri ATCC 17588(T) were 98.9, 98.10% and 98.06%, respectively. The major cellular fatty acids were C(18 : 1)ω7c, C(16 : 0) and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c). The DNA G+C content was 60.3 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness values, strain HL22-2(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas kunmingensis sp. nov. is proposed. The type strain is HL22-2(T) ( = CGMCC 1.12273(T) = DSM 25974(T)).

  12. Colwellia polaris sp. nov., a psychrotolerant bacterium isolated from Arctic sea ice.

    Science.gov (United States)

    Zhang, De-Chao; Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Zhou, Pei-Jin; Zhou, Yu-Guang

    2008-08-01

    A novel psychrotolerant, Gram-negative, aerobic bacterium, designated strain 537T, was isolated from sea-ice samples from the Arctic. Strain 537T was able to grow at 4-26 degrees C, with optimum growth occurring at 20-21 degrees C. Strain 537T had Q-8 as the major respiratory quinone and contained iso-C15:0 2-OH and/or C16:1 omega7c (22.95 %), C15:1 (17.64 %) and C17:1 omega8c (13.74 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 38.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 537T formed a coherent cluster within the genus Colwellia. The highest level of 16S rRNA gene sequence similarity (97.5 %) exhibited by strain 537T was obtained with respect to the type strain of Colwellia aestuarii. On the basis of phenotypic, chemotaxonomic and phylogenetic properties and DNA-DNA relatedness data, strain 537T represents a novel species of the genus Colwellia, for which the name Colwellia polaris sp. nov. is proposed. The type strain is 537T (=CGMCC 1.6132T =JCM 13952T).

  13. Role of extracellular compounds in Cd-sequestration relative to Cd uptake by bacterium Sinorhizobium meliloti

    Energy Technology Data Exchange (ETDEWEB)

    Slaveykova, Vera I., E-mail: vera.slaveykova@epfl.c [Environmental Biophysical Chemistry, IIE-ENAC, Ecole Polytechnique Federale de Lausanne (EPFL), Station 2, CH-1015 Lausanne (Switzerland); Parthasarathy, Nalini [Department of Inorganic, Analytic and Applied Chemistry, University of Geneva, Sciences II, 30 Quai Ernest Ansermet, 1211 Geneva 4 (Switzerland); Dedieu, Karine; Toescher, Denis [Environmental Biophysical Chemistry, IIE-ENAC, Ecole Polytechnique Federale de Lausanne (EPFL), Station 2, CH-1015 Lausanne (Switzerland)

    2010-08-15

    The role of bacterially derived compounds in Cd(II) complexation and uptake by bacterium Sinorhizobium meliloti wild type (WT) and genetically modified ExoY-mutant, deficient in exopolysaccharide production, was explored combining chemical speciation measurements and assays with living bacteria. Obtained results demonstrated that WT- and ExoY-strains excreted siderophores in comparable amounts, while WT-strain produced much higher amount of exopolysaccharides and less exoproteins. An evaluation of Cd(II) distribution in bacterial suspensions under short term exposure conditions, showed that most of the Cd is bound to bacterial surface envelope, including Cd bound to the cell wall and to the attached extracellular polymeric substances. However, the amount of Cd bound to the dissolved extracellular compounds increases at high Cd(II) concentrations. The implications of these findings to more general understanding of the Cd(II) fate and cycling in the environment is discussed. - Bacterial excreted extracellular compounds play minor role in Cd(II) sequestration relative to bacteria.

  14. Degradation of γ-irradiated cellulose by the accumulating culture of a cellulose bacterium

    International Nuclear Information System (INIS)

    Namsaraev, B.B.; Kuznetsova, E.A.; Termkhitarova, N.G.

    1987-01-01

    Possibility of degradation of γ-irradiated cellulose by the accumulating culture of an anaerobic cellulose bacterium has been investigated. Cellulose irradiation by γ-quanta (Co 60 ) has been carried out using the RKh-30 device with 35.9 Gy/min dose rate. Radiation monitoring has been carried out by the standard ferrosulfate method. Samples have been irradiated in dry state or when water presenting with MGy. It is detected that the accumulating culture with the growth on the irradiated cellulose has a lag-phase, which duration reduces when the cellulose cleaning by flushing with distillation water. The culture has higher growth and substrate consumption rate when growing by cellulose irradiated in comparison with non-irradiated one. The economical coefficient is the same in using both the irradiated and non-irradiated cellulose. The quantity of forming reducing saccharides, organic acids, methane and carbon dioxide is the same both when cultivating by irradiated cellulose and by non-irradiated. pH of the culture liquid is shifted to the acid nature in the process of growth

  15. Three Alginate Lyases from Marine Bacterium Pseudomonas fluorescens HZJ216: Purification and Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Liyan, Li [Ocean University of China, Qingdao, PRC; Jiang, Xiaolu [Ocean University of China, Qingdao, PRC; Wang, Peng [Ocean University of China, Qingdao, PRC; Guan, Huashi [Ocean University of China, Qingdao, PRC; Guo, Hong [ORNL

    2010-01-01

    Three alginate lyases (A, B, and C) from an alginate-degrading marine bacterium strain HZJ216 isolated from brown seaweed in the Yellow Sea of China and identified preliminarily as Pseudomonas fluorescens are purified, and their biochemical properties are described. Molecular masses of the three enzymes are determined by SDS-PAGE to be 60.25, 36, and 23 kDa with isoelectric points of 4, 4.36, and 4.59, respectively. Investigations of these enzymes at different pH and temperatures show that they are most active at pH 7.0 and 35 C. Alginate lyases A and B are stable in the pH range of 5.0 9.0, while alginate lyase C is stable in the pH range of 5.0 7.0. Among the metal ions tested, additions of Na+, K+, and Mg2+ ions can enhance the enzyme activities while Fe2+, Fe3+, Ba2+, and Zn2+ ions show inhibitory effects. The substrate specificity results demonstrate that alginate lyase C has the specificity for G block while alginate lyases A and B have the activities for both M and G blocks. It is the first report about extracellular alginate lyases with high alginate-degrading activity from P. fluorescens.

  16. Purification and Characterization of Catalase from Marine Bacterium Acinetobacter sp. YS0810

    Directory of Open Access Journals (Sweden)

    Xinhua Fu

    2014-01-01

    Full Text Available The catalase from marine bacterium Acinetobacter sp. YS0810 (YS0810CAT was purified and characterized. Consecutive steps were used to achieve the purified enzyme as follows: ethanol precipitation, DEAE Sepharose ion exchange, Superdex 200 gel filtration, and Resource Q ion exchange. The active enzyme consisted of four identical subunits of 57.256 kDa. It showed a Soret peak at 405 nm, indicating the presence of iron protoporphyrin IX. The catalase was not apparently reduced by sodium dithionite but was inhibited by 3-amino-1,2,4-triazole, hydroxylamine hydrochloride, and sodium azide. Peroxidase-like activity was not found with the substrate o-phenylenediamine. So the catalase was determined to be a monofunctional catalase. N-terminal amino acid of the catalase analysis gave the sequence SQDPKKCPVTHLTTE, which showed high degree of homology with those of known catalases from bacteria. The analysis of amino acid sequence of the purified catalase by matrix-assisted laser desorption ionization time-of-flight mass spectrometry showed that it was a new catalase, in spite of its high homology with those of known catalases from other bacteria. The catalase showed high alkali stability and thermostability.

  17. FTIR and Raman spectroscopic studies of selenium nanoparticles synthesised by the bacterium Azospirillum thiophilum

    Science.gov (United States)

    Tugarova, Anna V.; Mamchenkova, Polina V.; Dyatlova, Yulia A.; Kamnev, Alexander A.

    2018-03-01

    Vibrational (Fourier transform infrared (FTIR) and Raman) spectroscopic techniques can provide unique molecular-level information on the structural and compositional characteristics of complicated biological objects. Thus, their applications in microbiology and related fields are steadily increasing. In this communication, biogenic selenium nanoparticles (Se NPs) were obtained via selenite (SeO32-) reduction by the bacterium Azospirillum thiophilum (strain VKM B-2513) for the first time, using an original methodology for obtaining extracellular NPs. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) showed the Se NPs to have average diameters within 160-250 nm; their zeta potential was measured to be minus 18.5 mV. Transmission FTIR spectra of the Se NPs separated from bacterial cells showed typical proteinacious, polysaccharide and lipid-related bands, in line with TEM data showing a thin layer covering the Se NPs surface. Raman spectra of dried Se NPs layer in the low-frequency region (under 500 cm-1 down to 150 cm-1) showed a single very strong band with a maximum at 250 cm-1 which, in line with its increased width (ca. 30 cm-1 at half intensity), can be attributed to amorphous elementary Se. Thus, a combination of FTIR and Raman spectroscopic approaches is highly informative in non-destructive analysis of structural and compositional properties of biogenic Se NPs.

  18. Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Wada, M.; Fukunaga, N.; Sasaki, S. (Hokkaido Univ., Sapporo (Japan))

    1989-08-01

    Biosynthesis of palmitic, palmitoleic, and cis-vaccenic acids in Pseudomonas sp. strain E-3 was investigated with in vitro and in vivo systems. (1-{sup 14}C)palmitic acid was aerobically converted to palmitoleate and cis-vaccenate, and the radioactivities on their carboxyl carbons were 100 and 43%, respectively, of the total radioactivity in the fatty acids. Palmitoyl coenzyme A desaturase activity was found in the membrane fraction. (1-{sup 14}C)stearic acid was converted to octadecenoate and C16 fatty acids. The octadecenoate contained oleate and cis-vaccenate, but only oleate was produced in the presence of cerulenin. (1-{sup 14}C)lauric acid was aerobically converted to palmitate, palmitoleate, and cis-vaccenate. Under anaerobic conditions, palmitate (62%), palmitoleate (4%), and cis-vaccenate (34%) were produced from (1-{sup 14}C)acetic acid, while they amounted to 48, 39, and 14%, respectively, under aerobic conditions. In these incorporation experiments, 3 to 19% of the added radioactivity was detected in released {sup 14}CO{sub 2}, indicating that part of the added fatty acids were oxidatively decomposed. Partially purified fatty acid synthetase produced saturated and unsaturated fatty acids with chain lengths of C10 to C18. These results indicated that both aerobic and anaerobic mechanisms for the synthesis of unsaturated fatty acid are operating in this bacterium.

  19. Microbial deposition of gold nanoparticles by the metal-reducing bacterium Shewanella algae

    International Nuclear Information System (INIS)

    Konishi, Y.; Tsukiyama, T.; Tachimi, T.; Saitoh, N.; Nomura, T.; Nagamine, S.

    2007-01-01

    Microbial reduction and deposition of gold nanoparticles was achieved at 25 deg. C over the pH range 2.0-7.0 using the mesophilic bacterium Shewanella algae in the presence of H 2 as the electron donor. The reductive deposition of gold by the resting cells of S. algae was a fast process: 1 mM AuCl 4 - ions were completely reduced to elemental gold within 30 min. At a solution pH of 7, gold nanoparticles 10-20 nm in size were deposited in the periplasmic space of S. algae cells. At pH 2.8, gold nanoparticles 15-200 nm in size were deposited on the bacterial cells, and the biogenic nanoparticles exhibited a variety of shapes that included nanotriangles: in particular, single crystalline gold nanotriangles 100-200 nm in size were microbially deposited. At a solution pH of 2.0, gold nanoparticles about 20 nm in size were deposited intracellularly, and larger gold particles approximately 350 nm in size were deposited extracellularly. The solution pH was an important factor in controlling the morphology of the biogenic gold particles and the location of gold deposition. Microbial deposition of gold nanoparticles is potentially attractive as an environmentally friendly alternative to conventional methods

  20. Biomimetic Synthesis of Silver Nanoparticles Using Endosymbiotic Bacterium Inhabiting Euphorbia hirta L. and Their Bactericidal Potential

    Directory of Open Access Journals (Sweden)

    Baker Syed

    2016-01-01

    Full Text Available The present investigation aims to evaluate biomimetic synthesis of silver nanoparticles using endophytic bacterium EH 419 inhabiting Euphorbia hirta L. The synthesized nanoparticles were initially confirmed with change in color from the reaction mixture to brown indicating the synthesis of nanoparticles. Further confirmation was achieved with the characteristic absorption peak at 440 nm using UV-Visible spectroscopy. The synthesized silver nanoparticles were subjected to biophysical characterization using hyphenated techniques. The possible role of biomolecules in mediating the synthesis was depicted with FTIR analysis. Further crystalline nature of synthesized nanoparticles was confirmed using X-ray diffraction (XRD with prominent diffraction peaks at 2θ which can be indexed to the (111, (200, (220, and (311 reflections of face centered cubic structure (fcc of metallic silver. Transmission electron microscopy (TEM revealed morphological characteristics of synthesized silver nanoparticles to be polydisperse in nature with size ranging from 10 to 60 nm and different morphological characteristics such as spherical, oval, hexagonal, and cubic shapes. Further silver nanoparticles exhibited bactericidal activity against panel of significant pathogenic bacteria among which Pseudomonas aeruginosa was most sensitive compared to other pathogens. To the best of our knowledge, present study forms first report of bacterial endophyte inhabiting Euphorbia hirta L. in mediating synthesizing silver nanoparticles.

  1. Biomimetic Synthesis of Silver Nanoparticles Using Endosymbiotic Bacterium Inhabiting Euphorbia hirta L. and Their Bactericidal Potential.

    Science.gov (United States)

    Syed, Baker; Yashavantha Rao, Hoovinakola Chinnappa; Nagendra-Prasad, Mysore Nagalingaswamy; Prasad, Ashwini; Harini, Ballagere Puttaraju; Azmath, Pasha; Rakshith, Devaraju; Satish, Sreedharamurthy

    2016-01-01

    The present investigation aims to evaluate biomimetic synthesis of silver nanoparticles using endophytic bacterium EH 419 inhabiting Euphorbia hirta L. The synthesized nanoparticles were initially confirmed with change in color from the reaction mixture to brown indicating the synthesis of nanoparticles. Further confirmation was achieved with the characteristic absorption peak at 440 nm using UV-Visible spectroscopy. The synthesized silver nanoparticles were subjected to biophysical characterization using hyphenated techniques. The possible role of biomolecules in mediating the synthesis was depicted with FTIR analysis. Further crystalline nature of synthesized nanoparticles was confirmed using X-ray diffraction (XRD) with prominent diffraction peaks at 2θ which can be indexed to the (111), (200), (220), and (311) reflections of face centered cubic structure (fcc) of metallic silver. Transmission electron microscopy (TEM) revealed morphological characteristics of synthesized silver nanoparticles to be polydisperse in nature with size ranging from 10 to 60 nm and different morphological characteristics such as spherical, oval, hexagonal, and cubic shapes. Further silver nanoparticles exhibited bactericidal activity against panel of significant pathogenic bacteria among which Pseudomonas aeruginosa was most sensitive compared to other pathogens. To the best of our knowledge, present study forms first report of bacterial endophyte inhabiting Euphorbia hirta L. in mediating synthesizing silver nanoparticles.

  2. Extracellular proteases of Halobacillus blutaparonensis strain M9, a new moderately halophilic bacterium

    Directory of Open Access Journals (Sweden)

    Anderson F. Santos

    2013-12-01

    Full Text Available Halophilic microorganisms are source of potential hydrolytic enzymes to be used in industrial and/or biotechnological processes. In the present study, we have investigated the ability of the moderately halophilic bacterium Halobacillus blutaparonensis (strain M9, a novel species described by our group, to release proteolytic enzymes. This bacterial strain abundantly proliferated in Luria-Bertani broth supplemented with 2.5% NaCl as well as secreted proteases to the extracellular environment. The production of proteases occurred in bacterial cells grown under different concentration of salt, ranging from 0.5% to 10% NaCl, in a similar way. The proteases secreted by H. blutaparonensis presented the following properties: (i molecular masses ranging from 30 to 80 kDa, (ii better hydrolytic activities under neutral-alkaline pH range, (iii expression modulated according to the culture age, (iv susceptibility to phenylmethylsulphonyl fluoride, classifying them as serine-type proteases, (v specific cleavage over the chymotrypsin substrate, and (vi enzymatic stability in the presence of salt (up to 20% NaCl and organic solvents (e.g., ether, isooctane and cyclohexane. The proteases described herein are promising for industrial practices due to its haloalkaline properties.

  3. Metabolism of cyclohexane carboxylic acid by the photosynthetic bacterium Rhodopseudomonas palustris.

    Science.gov (United States)

    Küver, J; Xu, Y; Gibson, J

    1995-11-01

    Cyclohexane carboxylate supported relatively rapid growth (doubling times 7-8 h) of Rhodopseudomonas palustris under oxic or photosynthetic conditions, but did not serve as a substrate for either of the known aromatic CoA ligases. A CoA ligase that thioesterifies cyclohexane carboxylate was partially purified and did not cross react immunologically with the two CoA ligases purified previously from this bacterium. Crude extracts of R. palustris cells grown with a range of aromatic or alicyclic acids contained a dehydrogenase that reacted with cyclohexane carboxyl-CoA or cyclohex-1-ene carboxyl-CoA, using 2,6-dichlorophenolindophenol or ferricenium ion as electron carrier. This activity was not detected in extracts of adipate-, glutamate-, or succinate-grown cells. No oxidation or reduction of nonesterified cyclohexane carboxylate or cyclohexene carbocylate was detected in extracts of cells grown with aromatic or aliphatic substrates, neither aerobically nor anaerobically. A constitutively expressed thioesterase that hydrolyzed cyclohexane carboxyl-CoA and also some alicyclic and aliphatic CoA derivatives was purified and characterized. The enzyme had little or no activity on benzoyl-CoA or 4-hydroxybenzoyl-CoA. The presence of a thioesterase that effectively hydrolyzes cyclohexane carboxyl-CoA suggests that transient production of cyclohexane carboxylate is a physiological response to temporary excess of reductant during metabolism of aromatic compounds.

  4. What drives the occurrence of the melioidosis bacterium Burkholderia pseudomallei in domestic gardens?

    Directory of Open Access Journals (Sweden)

    Mirjam Kaestli

    2015-03-01

    Full Text Available Melioidosis is an often fatal infectious disease affecting humans and animals in tropical regions and is caused by the saprophytic environmental bacterium Burkholderia pseudomallei. Domestic gardens are not only a common source of exposure to soil and thus to B. pseudomallei, but they also have been found to contain more B. pseudomallei than other environments. In this study we addressed whether anthropogenic manipulations common to gardens such as irrigation or fertilizers change the occurrence of B. pseudomallei. We conducted a soil microcosm experiment with a range of fertilizers and soil types as well as a longitudinal interventional study over three years on an experimental fertilized field site in an area naturally positive for B. pseudomallei. Irrigation was the only consistent treatment to increase B. pseudomallei occurrence over time. The effects of fertilizers upon these bacteria depended on soil texture, physicochemical soil properties and biotic factors. Nitrates and urea increased B. pseudomallei load in sand while phosphates had a positive effect in clay. The high buffering and cation exchange capacities of organic material found in a commercial potting mix led to a marked increase in soil salinity with no survival of B. pseudomallei after four weeks in the potting mix sampled. Imported grasses were also associated with B. pseudomallei occurrence in a multivariate model. With increasing population density in endemic areas these findings inform the identification of areas in the anthropogenic environment with increased risk of exposure to B. pseudomallei.

  5. A novel glycan modifies the flagellar filament proteins of the oral bacterium Treponema denticola.

    Science.gov (United States)

    Kurniyati, Kurni; Kelly, John F; Vinogradov, Evgeny; Robotham, Anna; Tu, Youbing; Wang, Juyu; Liu, Jun; Logan, Susan M; Li, Chunhao

    2017-01-01

    While protein glycosylation has been reported in several spirochetes including the syphilis bacterium Treponema pallidum and Lyme disease pathogen Borrelia burgdorferi, the pertinent glycan structures and their roles remain uncharacterized. Herein, a novel glycan with an unusual chemical composition and structure in the oral spirochete Treponema denticola, a keystone pathogen of periodontitis was reported. The identified glycan of mass 450.2 Da is composed of a monoacetylated nonulosonic acid (Non) with a novel extended N7 acyl modification, a 2-methoxy-4,5,6-trihydroxy-hexanoyl residue in which the Non has a pseudaminic acid configuration (L-glycero-L-manno) and is β-linked to serine or threonine residues. This novel glycan modifies the flagellin proteins (FlaBs) of T. denticola by O-linkage at multiple sites near the D1 domain, a highly conserved region of bacterial flagellins that interact with Toll-like receptor 5. Furthermore, mutagenesis studies demonstrate that the glycosylation plays an essential role in the flagellar assembly and motility of T. denticola. To our knowledge, this novel glycan and its unique modification sites have not been reported previously in any bacteria. © 2016 John Wiley & Sons Ltd.

  6. [Isolation and identification of Mn oxidizing bacterium Aminobacter sp. H1 and its oxidation mechanism].

    Science.gov (United States)

    Yan, Ping; Jiang, Li-Ying; Chen, Jian-Meng; He, Zhi-Min; Xiao, Shao-Dan; Jiang, Yi-Feng

    2014-04-01

    A bacterium with high manganese oxidizing activity was isolated from a biological manganese removal filter and named as H1. Based on its characteristics and the analysis of 16S rDNA sequence, the strain H1 belonged to the genus Aminobacter sp. and its manganese oxidizing ability had never been reported. In this paper, the microbiologic properties of the strain H1, the manganese oxidation mechanisms and characteristics of biogenic manganese oxides were investigated. The results showed that the maximal tolerant Mn concentration of strain H1 was 50 mmol x L(-1), and Mn(II) could be completely removed by strain H1 when the concentration was lower than 10 mmol x L(-1). Strain H1 could oxidize Mn2+ by both the production of manganese oxidizing activity factor and alkaline metabolites during growth, which were synthesized in the cell and then secreted into extracellular culture medium. During the oxidation process, the intermediate of soluble Mn(III) was detected. SEM showed that the biogenic manganese oxides were amorphous and poorly-crystalline, and it closely combined with bacteria. The components of the biogenic manganese oxides produced by strain H1 were identified as MnCO3, MnOOH, Mn3O4 and MnO2 by XRD, XPS and SEM-EDX.

  7. The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals.

    Science.gov (United States)

    Sneed, Jennifer M; Sharp, Koty H; Ritchie, Kimberly B; Paul, Valerie J

    2014-07-07

    Microbial biofilms induce larval settlement for some invertebrates, including corals; however, the chemical cues involved have rarely been identified. Here, we demonstrate the role of microbial biofilms in inducing larval settlement with the Caribbean coral Porites astreoides and report the first instance of a chemical cue isolated from a marine biofilm bacterium that induces complete settlement (attachment and metamorphosis) of Caribbean coral larvae. Larvae settled in response to natural biofilms, and the response was eliminated when biofilms were treated with antibiotics. A similar settlement response was elicited by monospecific biofilms of a single bacterial strain, Pseudoalteromonas sp. PS5, isolated from the surface biofilm of a crustose coralline alga. The activity of Pseudoalteromonas sp. PS5 was attributed to the production of a single compound, tetrabromopyrrole (TBP), which has been shown previously to induce metamorphosis without attachment in Pacific acroporid corals. In addition to inducing settlement of brooded larvae (P. astreoides), TBP also induced larval settlement for two broadcast-spawning species, Orbicella (formerly Montastraea) franksi and Acropora palmata, indicating that this compound may have widespread importance among Caribbean coral species. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  8. Exopolysaccharides play a role in the swarming of the benthic bacterium Pseudoalteromonas sp. SM9913

    Directory of Open Access Journals (Sweden)

    Ang eLiu

    2016-04-01

    Full Text Available Most marine bacteria secrete exopolysaccharide (EPS, which is important for bacterial survival in the marine environment. However, it is still unclear whether the self-secreted EPS is involved in marine bacterial motility. Here we studied the role of EPS in the lateral flagella-driven swarming motility of benthic bacterium Pseudoalteromonas sp. SM9913 (SM9913 by a comparison of wild SM9913 and ΔepsT, an EPS synthesis defective mutant. Reduction of EPS production in ΔepsT did not affect the growth rate or the swimming motility, but significantly decreased the swarming motility on a swarming plate, suggesting that the EPS may play a role in SM9913 swarming. However, the expression and assembly of lateral flagella in ΔepsT were not affected. Instead, ΔepsT had a different swarming behavior from wild SM9913. The swarming of ΔepsT did not have an obvious rapid swarming period, and its rate became much lower than that of wild SM9913 after 35 h incubation. An addition of surfactin or SM9913 EPS on the surface of the swarming plate could rescue the swarming level. These results indicate that the self-secreted EPS is required for the swarming of SM9913. This study widens our understanding of the function of the EPS of benthic bacteria.

  9. Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27.

    Science.gov (United States)

    Schwarzenlander, Cornelia; Averhoff, Beate

    2006-09-01

    Horizontal gene transfer has been a major force for genome plasticity over evolutionary history, and is largely responsible for fitness-enhancing traits, including antibiotic resistance and virulence factors. In particular, for adaptation of prokaryotes to extreme environments, lateral gene transfer seems to have played a crucial role. Recently, by performing a genome-wide mutagenesis approach with Thermus thermophilus HB27, we identified the first genes in a thermophilic bacterium for the uptake of free DNA, a process called natural transformation. Here, we present the first data on the biochemistry and bioenergetics of the DNA transport process in this thermophile. We report that linear and circular plasmid DNA are equally well taken up with a high maximal velocity of 1.5 microg DNA.(mg protein)(-1).min(-1), demonstrating an extremely efficient binding and uptake rate of 40 kb.s(-1).cell(-1). Uncouplers and ATPase inhibitors immediately inhibited DNA uptake, providing clear evidence that DNA translocation in HB27 is an energy-dependent process. DNA uptake studies with genomic DNA of Bacteria, Archaea and Eukarya revealed that Thermus thermophilus HB27 takes up DNA from members of all three domains of life. We propose that the extraordinary broad substrate specificity of the highly efficient Thermus thermophilus HB27 DNA uptake system may contribute significantly to thermoadaptation of Thermus thermophilus HB27 and to interdomain DNA transfer in hot environments.

  10. A putative twin-arginine translocation system in the phytopathogenic bacterium Xylella fastidiosa.

    Science.gov (United States)

    Ciapina, Luciane Prioli; Picchi, Simone Cristina; Lacroix, Jean-Marie; Lemos, Eliana Gertrudes de Macedo; Ödberg-Ferragut, Carmen

    2011-02-01

    The twin-arginine translocation (Tat) pathway of the xylem-limited phytopathogenic bacterium Xylella fastidiosa strain 9a5c, responsible for citrus variegated chlorosis, was explored. The presence of tatA, tatB, and tatC in the X. fastidiosa genome together with a list of proteins harboring 2 consecutive arginines in their signal peptides suggested the presence of a Tat pathway. The functional Tat dependence of X. fastidiosa OpgD was examined. Native or mutated signal peptides were fused to the β-lactamase. Expression of fusion with intact signal peptides mediated high resistance to ampicillin in Escherichia coli tat+ but not in the E. coli tat null mutant. The replacement of the 2 arginines by 2 lysines prevented the export of β-lactamase in E. coli tat+, demonstrating that X. fastidiosa OpgD carries a signal peptide capable of engaging the E. coli Tat machinery. RT-PCR analysis revealed that the tat genes are transcribed as a single operon. tatA, tatB, and tatC genes were cloned. Complementation assays in E. coli devoid of all Tat or TatC components were unsuccessful, whereas X. fastidiosa Tat components led to a functional Tat translocase in E. coli TatB-deficient strain. Additional experiments implicated that X. fastidiosa TatB component could form a functional heterologous complex with the E. coli TatC component.

  11. Discovery of a Marine Bacterium Producing 4-Hydroxybenzoate and Its Alkyl Esters, Parabens

    Science.gov (United States)

    Peng, Xue; Adachi, Kyoko; Chen, Choryu; Kasai, Hiroaki; Kanoh, Kaneo; Shizuri, Yoshikazu; Misawa, Norihiko

    2006-01-01

    Chemically synthesized 4-hydroxybenzoate (4HBA) is widely used in the chemical and electrical industries as a material for producing polymers such as those of the liquid crystal type. Its alkyl esters, called parabens, have been the most widely used preservatives by the food and cosmetic industries. We report here for the first time a microorganism, a marine bacterium, which biosynthesizes these petrochemical products. The marine bacterial strain, A4B-17, which was found to belong to the genus Microbulbifer on the basis of its rRNA and gyrB sequences, was isolated from an ascidian in the coastal waters of Palau. Strain A4B-17 was, surprisingly, found to produce 10 mg/liter of 4HBA, together with its butyl (24 mg/liter), heptyl (0.4 mg/liter), and nonyl (6 mg/liter) esters. We therefore characterized 23 other marine bacteria belonging to the genus Microbulbifer, which our institute had previously isolated from various marine environments, and found that these bacteria also produced 4HBA, although with low production levels (less than one-fifth of that produced by A4B-17). We also show that the alkyl esters of 4HBA produced by strain A4B-17 were effective in preventing the growth of yeasts, molds, and gram-positive bacteria. PMID:16885309

  12. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262 T forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na + ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na + ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Electricity Generation in Microbial Fuel Cell (MFC) by Bacterium Isolated from Rice Paddy Field Soil

    Science.gov (United States)

    Fakhirruddin, Fakhriah; Amid, Azura; Salim, Wan Wardatul Amani Wan; Suhaida Azmi, Azlin

    2018-03-01

    Microbial fuel cell (MFC) is an alternative approach in generating renewable energy by utilising bacteria that will oxidize organic or inorganic substrates, producing electrons yielded as electrical energy. Different species of exoelectrogenic bacteria capable of generating significant amount of electricity in MFC has been identified, using various organic compounds for fuel. Soil sample taken from rice paddy field is proven to contain exoelectrogenic bacteria, thus electricity generation using mixed culture originally found in the soil, and pure culture isolated from the soil is studied. This research will isolate the exoelectrogenic bacterial species in the rice paddy field soil responsible for energy generation. Growth of bacteria isolated from the MFC is observed by measuring the optical density (OD), cell density weight (CDW) and viable cell count. Mixed bacterial species found in paddy field soil generates maximum power of 77.62 μW and 0.70 mA of current. In addition, the research also shows that the pure bacterium in rice paddy field soil can produce maximum power and current at 51.32 μW and 0.28 mA respectively.

  14. Characterization of bornite (Cu5FeS4 electrodes in the presence of the bacterium Acidithiobacillus ferrooxidans

    Directory of Open Access Journals (Sweden)

    Bevilaqua Denise

    2003-01-01

    Full Text Available Bornite electrodes were characterized in the absence or in the presence of Acidithiobacillus ferrooxidans, which is an important microorganism involved in metal bioleaching processes. The presence of the bacterium modified the mineral/electrolyte interface, increasing the corrosion rate, as revealed by interferometric, AEM, ICP and EIS analyses. As a consequence of bacterial activity the electrode became porous, increasing its surface heterogeneity. This behavior was correlated with the evolution of impedance diagrams obtained during the time course of experiments. The main difference in these diagrams was the presence of an inductive feature (up to 44 h, which was related to bacterial action on the mineral dissolution, better than to its adhesion on the bornite. The total real impedance measured in presence of the bacterium was about 10 times lower than in its absence, due to the acceleration of the mineral dissolution, because an oxidant environment was maintained.

  15. Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan

    Directory of Open Access Journals (Sweden)

    Pilla Sankara Krishna

    2015-12-01

    Full Text Available We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

  16. Stereochemical course of hydrolytic reaction catalyzed by alpha-galactosidase from cold adaptable marine bacterium of genus Pseudoalteromonas

    Directory of Open Access Journals (Sweden)

    Irina Yu Bakunina

    2014-10-01

    Full Text Available The recombinant α-galactosidase of the marine bacterium (α-PsGal was synthesized with the use of the plasmid 40Gal, consisting of plasmid pET-40b (+ (Novagen and the gene corresponding to the open reading frame of the mature α-galactosidase of marine bacterium Pseudoalteromonas sp. KMM 701, transformed into the E. coli Rosetta(DE3 cells. In order to understand the mechanism of action, the stereochemistry of hydrolysis of 4-nitrophenyl α-D-galactopyranoside (4-NPGP by α-PsGal was measured by 1H NMR spectroscopy. The kinetics of formation of α- and β-anomer of galactose showed that α-anomer initially formed and accumulated, and then an appreciable amount of β-anomer appeared as a result of mutarotation. The data clearly show that the enzymatic hydrolysis of 4-NPGP proceeds with the retention of anomeric configuration, probably, due to a double displacement mechanism of reaction.

  17. Roles of dental pulp fibroblasts in the recognition of bacterium-related factors and subsequent development of pulpitis

    Directory of Open Access Journals (Sweden)

    Tadashi Nakanishi

    2011-08-01

    Full Text Available As caries-related bacteria invade deeply into dentin and come into close proximity to the pulp, inflammatory cells (such as lymphocytes, macrophages and neutrophils infiltrate into the bacterium-invaded area and consequently pulpitis develops. Many types of cytokines and adhesion molecules are responsible for the initiation and progression of pulpitis. Dental pulp fibroblasts, a major cell type in the dental pulp, also have capacity to produce pro-inflammatory cytokines and express adhesion molecules in response to pathogen-associated molecular patterns (PAMPs, including lipopolysaccharide. The innate immune system senses microbial infection using pattern recognition receptors, such as Toll-like receptors (TLRs and nucleotide-binding oligomerization domain (NOD, for PAMPs. In this review, we summarize the roles of dental pulp fibroblasts in the recognition of invaded bacterium-related factors via TLR and NOD pathways, and the subsequent pulpal immune responses, leading to progressive pulpitis.

  18. Stereochemical course of hydrolytic reaction catalyzed by alpha-galactosidase from cold adaptable marine bacterium of genus Pseudoalteromonas

    Science.gov (United States)

    Bakunina, Irina; Balabanova, Larissa; Golotin, Vasiliy; Slepchenko, Lyubov; Isakov, Vladimir; Rasskazov, Valeriy

    2014-10-01

    The recombinant α-galactosidase of the marine bacterium (α-PsGal) was synthesized with the use of the plasmid 40Gal, consisting of plasmid pET-40b (+) (Novagen) and the gene corresponding to the open reading frame of the mature α-galactosidase of marine bacterium Pseudoalteromonas sp. KMM 701, transformed into the E. coli Rosetta(DE3) cells. In order to understand the mechanism of action, the stereochemistry of hydrolysis of 4-nitrophenyl α-D-galactopyranoside (4-NPGP) by α-PsGal was measured by 1H NMR spectroscopy. The kinetics of formation of α- and β-anomer of galactose showed that α-anomer initially formed and accumulated, and then an appreciable amount of β-anomer appeared as a result of mutarotation. The data clearly show that the enzymatic hydrolysis of 4-NPGP proceeds with the retention of anomeric configuration, probably, due to a double displacement mechanism of reaction.

  19. Differential proteome and cellular adhesion analyses of the probiotic bacterium Lactobacillus acidophilus NCFM grown on raffinose - an emerging prebiotic

    DEFF Research Database (Denmark)

    Celebioglu, Hasan Ufuk; Hansen, Morten Ejby; Majumder, Avishek

    2016-01-01

    Whole cell and surface proteomes were analyzed together with adhesive properties of the probiotic bacterium Lactobacillus acidophilus NCFM (NCFM) grown on the emerging prebiotic raffinose, exemplifying a synbiotic. Adhesion of NCFM to mucin and intestinal HT-29 cells increased three-fold after......); galactose (+2.9/+3.1 fold) and fructose (+2.8 fold) kinases. The insights at the molecular and cellular levels contributed to the understanding of the interplay of a synbiotic composed of NCFM and raffinose with the host....

  20. Oxygen uncouples light absorption by the chlorosome antenna and photosynthetic electron transfer in the green sulfur bacterium Chlorobium tepidum

    DEFF Research Database (Denmark)

    Frigaard, N-U; Matsuura, K

    1999-01-01

    center as a consequence of the quenching mechanism which is activated by O2. This reversible uncoupling of the chlorosome antenna might prevent formation of toxic reactive oxygen species from photosynthetically produced reductants under aerobic conditions. The green filamentous bacterium Chloroflexus...... aurantiacus also contains chlorosomes but energy transfer from the BChl c and BChl a antennas to the reaction center in this species was not affected by O2....

  1. Characterization of bornite (Cu5FeS4) electrodes in the presence of the bacterium Acidithiobacillus ferrooxidans

    OpenAIRE

    Bevilaqua,Denise; Diéz-Perez,Ismael; Fugivara,Cecílio S.; Sanz,Fausto; Garcia Jr.,Oswaldo; Benedetti,Assis V.

    2003-01-01

    Bornite electrodes were characterized in the absence or in the presence of Acidithiobacillus ferrooxidans, which is an important microorganism involved in metal bioleaching processes. The presence of the bacterium modified the mineral/electrolyte interface, increasing the corrosion rate, as revealed by interferometric, AEM, ICP and EIS analyses. As a consequence of bacterial activity the electrode became porous, increasing its surface heterogeneity. This behavior was correlated with the evolu...

  2. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    OpenAIRE

    Bollmann, A.; Sedlacek, C.J.; Norton, J.; Laanbroek, H.J.; Suwa, Y.; Stein, L.Y.; Klotz, M.G.; Arp, D.; Sayavedra-Soto, L.; Lu, M.; Bruce, D.; Detter, C.; Tapia, R.; Han, J.; Woyke, T.

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromos...

  3. Pumilacidin-Like Lipopeptides Derived from Marine Bacterium Bacillus sp. Strain 176 Suppress the Motility of Vibrio alginolyticus.

    Science.gov (United States)

    Xiu, Pengyuan; Liu, Rui; Zhang, Dechao; Sun, Chaomin

    2017-06-15

    Bacterial motility is a crucial factor during the invasion and colonization processes of pathogens, which makes it an attractive therapeutic drug target. Here, we isolated a marine bacterium ( Vibrio alginolyticus strain 178) from a seamount in the tropical West Pacific that exhibits vigorous motility on agar plates and severe pathogenicity to zebrafish. We found that V. alginolyticus 178 motility was significantly suppressed by another marine bacterium, Bacillus sp. strain 176, isolated from the same niche. We isolated, purified, and characterized two different cyclic lipopeptides (CLPs) from Bacillus sp. 176 using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The two related CLPs have a pumilacidin-like structure and were both effective inhibitors of V. alginolyticus 178 motility. The CLPs differ by only one methylene group in their fatty acid chains. In addition to motility suppression, the CLPs also induced cell aggregation in the medium and reduced adherence of V. alginolyticus 178 to glass substrates. Notably, upon CLP treatment, the expression levels of two V. alginolyticus flagellar assembly genes ( flgA and flgP ) dropped dramatically. Moreover, the CLPs inhibited biofilm formation in several other strains of pathogenic bacteria without inducing cell death. This study indicates that CLPs from Bacillus sp. 176 show promise as antimicrobial lead compounds targeting bacterial motility and biofilm formation with a low potential for eliciting antibiotic resistance. IMPORTANCE Pathogenic bacteria often require motility to establish infections and subsequently spread within host organisms. Thus, motility is an attractive therapeutic target for the development of novel antibiotics. We found that cyclic lipopeptides (CLPs) produced by marine bacterium Bacillus sp. strain 176 dramatically suppress the motility of the pathogenic bacterium Vibrio alginolyticus strain 178, reduce biofilm formation, and promote

  4. The bacterium Wolbachia exploits host innate immunity to establish a symbiotic relationship with the dengue vector mosquito Aedes aegypti

    OpenAIRE

    Pan, Xiaoling; Pike, Andrew; Joshi, Deepak; Bian, Guowu; McFadden, Michael J; Lu, Peng; Liang, Xiao; Zhang, Fengrui; Raikhel, Alexander S; Xi, Zhiyong

    2017-01-01

    A host’s immune system plays a central role in shaping the composition of the microbiota and, in return, resident microbes influence immune responses. Symbiotic associations of the maternally transmitted bacterium Wolbachia occur with a wide range of arthropods. It is, however, absent from the dengue and Zika vector mosquito Aedes aegypti in nature. When Wolbachia is artificially forced to form symbiosis with this new mosquito host, it boosts the basal immune response and enhances the mosquit...

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

    Science.gov (United States)

    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.

  6. Refractory Chronic Pleurisy Caused by Helicobacter equorum-Like Bacterium in a Patient with X-Linked Agammaglobulinemia ▿

    Science.gov (United States)

    Funato, Michinori; Kaneko, Hideo; Ohkusu, Kiyofumi; Sasai, Hideo; Kubota, Kazuo; Ohnishi, Hidenori; Kato, Zenichiro; Fukao, Toshiyuki; Kondo, Naomi

    2011-01-01

    We describe a 35-year-old man with X-linked agammaglobulinemia who had refractory chronic pleurisy caused by a Helicobacter equorum-like bacterium. Broad-range bacterial PCR targeting the 16S and 23S rRNA genes and in situ hybridization targeting the 16S rRNA gene of H. equorum confirmed the presence of this pathogen in a human for the first time. PMID:21677071

  7. Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity

    Digital Repository Service at National Institute of Oceanography (India)

    Srinivas, T.N.R.; Aditya, S.; Bhumika, V.; AnilKumar, P.

    parsimony methods using the MEGA5 package [32] and the resultant tree topologies were evaluated based on 1000 resamplings. The bacterium was subjected to Matrix-assisted laser-desorption/ionization time- of flight (MALDI-TOF) assay (Bruker Daltonics.... Acknowledgements We thank Council of Scientific and Industrial Research (CSIR), Directors of IMTECH, Chandigarh and NIO, Goa and Department of Biotechnology, Government of India for financial assistance and encouragement. We would like to thank Mr. Deepak...

  8. Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage.

    Science.gov (United States)

    Balakrishna Pillai, Aneesh; Jaya Kumar, Arjun; Thulasi, Kavitha; Reghunathan, Dinesh; Prasannakumar, Manoj; Kumarapillai, Harikrishnan

    2017-10-12

    Bacillus aryabhattai PHB10 is a poly(3-hydroxybutyrate) (PHB)-accumulating bacterium isolated from domestic sewerage. Here, we report the 4.19-Mb draft genome sequence, with 4,050 protein-coding genes and a G+C content of 37.5%. This sequence will be helpful in the study of the high-level PHB accumulation mechanism of the strain. Copyright © 2017 Balakrishna Pillai et al.

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Shedding light on microbial dark matter: a TM6 bacterium as natural endosymbiont of a free-living amoeba.

    Science.gov (United States)

    Delafont, Vincent; Samba-Louaka, Ascel; Bouchon, Didier; Moulin, Laurent; Héchard, Yann

    2015-12-01

    The TM6 phylum belongs to the so-called microbial dark matter that gathers uncultivated bacteria detected only via DNA sequencing. Recently, the genome sequence of a TM6 bacterium (TM6SC1) has led to suggest that this bacterium would adopt an endosymbiotic life. In the present paper, free-living amoebae bearing a TM6 strain were isolated from a water network. The amoebae were identified as Vermamoeba vermiformis and the presence of a TM6 strain was detected by polymerase chain reaction and microscopy. The partial sequence of its 16S rRNA gene showed this strain to be closely related to the sequenced TM6SC1 strain. These bacteria displayed a pyriform shape and were found within V. vermiformis. Therefore, these bacteria were named Vermiphilus pyriformis. Interactions studies showed that V. pyriformis was highly infectious and that its relation with V. vermiformis was specific and highly stable. Finally, it was found that V. pyriformis inhibited the encystment of V. vermiformis. Overall, this study describes for the first time an endosymbiotic relationship between a TM6 bacterium and a free-living amoeba in the environment. It suggests that other bacteria of the TM6 phylum might also be endosymbiotic bacteria and may be found in other free-living amoebae or other organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air.

    Directory of Open Access Journals (Sweden)

    M Tanweer Khan

    Full Text Available The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far precluded its clinical application in the treatment of patients with inflammatory bowel diseases. The present studies were therefore aimed at developing a strategy to keep F. prausnitzii alive at ambient air. Our previous research showed that F. prausnitzii can survive in moderately oxygenized environments like the gut mucosa by transfer of electrons to oxygen. For this purpose, the bacterium exploits extracellular antioxidants, such as riboflavin and cysteine, that are abundantly present in the gut. We therefore tested to what extent these antioxidants can sustain the viability of F. prausnitzii at ambient air. The present results show that cysteine can facilitate the survival of F. prausnitzii upon exposure to air, and that this effect is significantly enhanced the by addition of riboflavin and the cryoprotectant inulin. The highly oxygen-sensitive gut bacterium F. prausnitzii can be kept alive at ambient air for 24 h when formulated with the antioxidants cysteine and riboflavin plus the cryoprotectant inulin. Improved formulations were obtained by addition of the bulking agents corn starch and wheat bran. Our present findings pave the way towards the biomedical exploitation of F. prausnitzii in redox-based therapeutics for treatment of dysbiosis-related inflammatory disorders of the human gut.

  12. Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group.

    Directory of Open Access Journals (Sweden)

    Vitaly V Kadnikov

    Full Text Available Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2(T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.

  13. Natural Competence of Xylella fastidiosa Occurs at a High Frequency Inside Microfluidic Chambers Mimicking the Bacterium's Natural Habitats.

    Science.gov (United States)

    Kandel, Prem P; Lopez, Samantha M; Almeida, Rodrigo P P; De La Fuente, Leonardo

    2016-09-01

    Xylella fastidiosa is a xylem-limited bacterium that is the causal agent of emerging diseases in a number of economically important crops. Genetic diversity studies have demonstrated homologous recombination occurring among X. fastidiosa strains, which has been proposed to contribute to host plant shifts. Moreover, experimental evidence confirmed that X. fastidiosa is naturally competent for recombination in vitro Here, as an approximation of natural habitats (plant xylem vessels and insect mouthparts), recombination was studied in microfluidic chambers (MCs) filled with media amended with grapevine xylem sap. First, different media were screened for recombination in solid agar plates using a pair of X. fastidiosa strains that were previously reported to recombine in coculture. The highest frequency of recombination was obtained with PD3 medium, compared to those with the other two media (X. fastidiosa medium [XFM] and periwinkle wilt [PW] medium) used in previous studies. Dissection of the media components led to the identification of bovine serum albumin as an inhibitor of recombination that was correlated to its previously known effect on inhibition of twitching motility. When recombination was performed in liquid culture, the frequencies were significantly higher under flow conditions (MCs) than under batch conditions (test tubes). The recombination frequencies in MCs and agar plates were not significantly different from each other. Grapevine xylem sap from both susceptible and tolerant varieties allowed high recombination frequency in MCs when mixed with PD3. These results suggest that X. fastidiosa has the ability to be naturally competent in the natural growth environment of liquid flow, and this phenomenon could have implications in X. fastidiosa environmental adaptation. Xylella fastidiosa is a plant pathogen that lives inside xylem vessels (where water and nutrients are transported inside the plant) and the mouthparts of insect vectors. This bacterium

  14. Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus.

    Science.gov (United States)

    Wefers, Daniel; Dong, Jia; Abdel-Hamid, Ahmed M; Paul, Hans Müller; Pereira, Gabriel V; Han, Yejun; Dodd, Dylan; Baskaran, Ramiya; Mayer, Beth; Mackie, Roderick I; Cann, Isaac

    2017-09-15

    The plant cell wall polysaccharide arabinan provides an important supply of arabinose, and unraveling arabinan-degrading strategies by microbes is important for understanding its use as a source of energy. Here, we explored the arabinan-degrading enzymes in the thermophilic bacterium Caldanaerobius polysaccharolyticus and identified a gene cluster encoding two glycoside hydrolase (GH) family 51 α-l-arabinofuranosidases (CpAbf51A, CpAbf51B), a GH43 endoarabinanase (CpAbn43A), a GH27 β-l-arabinopyranosidase (CpAbp27A), and two GH127 β-l-arabinofuranosidases (CpAbf127A, CpAbf127B). The genes were expressed as recombinant proteins, and the functions of the purified proteins were determined with para -nitrophenyl ( p NP)-linked sugars and naturally occurring pectin structural elements as the substrates. The results demonstrated that CpAbn43A is an endoarabinanase while CpAbf51A and CpAbf51B are α-l-arabinofuranosidases that exhibit diverse substrate specificities, cleaving α-1,2, α-1,3, and α-1,5 linkages of purified arabinan-oligosaccharides. Furthermore, both CpAbf127A and CpAbf127B cleaved β-arabinofuranose residues in complex arabinan side chains, thus providing evidence of the function of this family of enzymes on such polysaccharides. The optimal temperatures of the enzymes ranged between 60°C and 75°C, and CpAbf43A and CpAbf51A worked synergistically to release arabinose from branched and debranched arabinan. Furthermore, the hydrolytic activity on branched arabinan oligosaccharides and degradation of pectic substrates by the endoarabinanase and l-arabinofuranosidases suggested a microbe equipped with diverse activities to degrade complex arabinan in the environment. Based on our functional analyses of the genes in the arabinan degradation cluster and the substrate-binding studies on a component of the cognate transporter system, we propose a model for arabinan degradation and transport by C. polysaccharolyticus IMPORTANCE Genomic DNA sequencing and

  15. Cold adaptation of the mononuclear molybdoenzyme periplasmic nitrate reductase from the Antarctic bacterium Shewanella gelidimarina

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Philippa J.L. [School of Chemistry, University of Sydney, New South Wales 2006 (Australia); Codd, Rachel, E-mail: rachel.codd@sydney.edu.au [School of Chemistry, University of Sydney, New South Wales 2006 (Australia); School of Medical Sciences (Pharmacology) and Bosch Institute, University of New South Wales, New South Wales 2006 (Australia)

    2011-11-04

    Highlights: Black-Right-Pointing-Pointer Cold-adapted phenotype of NapA from the Antarctic bacterium Shewanella gelidimarina. Black-Right-Pointing-Pointer Protein homology model of NapA from S. gelidimarina and mesophilic homologue. Black-Right-Pointing-Pointer Six amino acid residues identified as lead candidates governing NapA cold adaptation. Black-Right-Pointing-Pointer Molecular-level understanding of designing cool-temperature in situ oxyanion sensors. -- Abstract: The reduction of nitrate to nitrite is catalysed in bacteria by periplasmic nitrate reductase (Nap) which describes a system of variable protein subunits encoded by the nap operon. Nitrate reduction occurs in the NapA subunit, which contains a bis-molybdopterin guanine dinucleotide (Mo-MGD) cofactor and one [4Fe-4S] iron-sulfur cluster. The activity of periplasmic nitrate reductase (Nap) isolated as native protein from the cold-adapted (psychrophilic) Antarctic bacterium Shewanella gelidimarina (Nap{sub Sgel}) and middle-temperature adapted (mesophilic) Shewanella putrefaciens (Nap{sub Sput}) was examined at varied temperature. Irreversible deactivation of Nap{sub Sgel} and Nap{sub Sput} occurred at 54.5 and 65 Degree-Sign C, respectively. When Nap{sub Sgel} was preincubated at 21-70 Degree-Sign C for 30 min, the room-temperature nitrate reductase activity was maximal and invariant between 21 and 54 Degree-Sign C, which suggested that Nap{sub Sgel} was poised for optimal catalysis at modest temperatures and, unlike Nap{sub Sput}, did not benefit from thermally-induced refolding. At 20 Degree-Sign C, Nap{sub Sgel} reduced selenate at 16% of the rate of nitrate reduction. Nap{sub Sput} did not reduce selenate. Sequence alignment showed 46 amino acid residue substitutions in Nap{sub Sgel} that were conserved in NapA from mesophilic Shewanella, Rhodobacter and Escherichia species and could be associated with the Nap{sub Sgel} cold-adapted phenotype. Protein homology modeling of Nap{sub Sgel} using a

  16. Pantoea agglomerans: a mysterious bacterium of evil and good. Part IV. Beneficial effects.

    Science.gov (United States)

    Dutkiewicz, Jacek; Mackiewicz, Barbara; Lemieszek, Marta Kinga; Golec, Marcin; Milanowski, Janusz

    2016-06-02

    a biocontrol agent permits the decrease of pesticide doses, being a healthy and environmental-friendly procedure. The application of the preparations of this bacterium efficiently protects the stored pome, stone and citrus fruits against invasion of moulds. P. agglomerans strains associated with both rhizosphere and plant tissues (as endophytes) efficiently promote the growth of many plants, including rice and wheat, which are the staple food for the majority of mankind. The promotion mechanisms are diverse and include fixation of atmospheric nitrogen, production of phytohormones, as well as degradation of phytate and phosphate solubilizing which makes the soil phosphorus available for plants. Accordingly, P. agglomerans is regarded as an ideal candidate for an environmental-friendly bioinoculant replacing chemical fertilizers. It has been documented that the Pantoea strains show biodegradation activity on various chemical pollutants of soil and water, including petroleum hydrocarbons and toxic metals. P. agglomerans prevents the penetration of harmful industrial contaminants into deeper parts of soil by biofilm formation, and has an ability to produce hydrogen from waste. Thus, this bacterium appears as a valuable bioremediator which, in some cases, may be acquired as a cheap form of energy. In conclusion, in spite of the proven pathologic role of P. agglomerans in causing occupational diseases of allergic and/or immunotoxic background and accidental infections, the beneficial traits of this species, and of related species of Pantoea genus, are of great value for potential use in many areas of biotechnology. Hence, any restrictions on the use of these organisms and their products should be declined, providing safety precautions at work with the Pantoea biopreparations are maintained.

  17. Pantoea agglomerans: a mysterious bacterium of evil and good. Part IV. Beneficial effects

    Directory of Open Access Journals (Sweden)

    Jacek Dutkiewicz

    2016-06-01

    production, competition mechanisms or induction of plant resistance. Its use as a biocontrol agent permits the decrease of pesticide doses, being a healthy and environmental-friendly procedure. The application of the preparations of this bacterium efficiently protects the stored pome, stone and citrus fruits against invasion of moulds. [i]P. agglomerans[/i] strains associated with both rhizosphere and plant tissues (as endophytes efficiently promote the growth of many plants, including rice and wheat, which are the staple food for the majority of mankind. The promotion mechanisms are diverse and include fixation of atmospheric nitrogen, production of phytohormones, as well as degradation of phytate and phosphate solubilizing which makes the soil phosphorus available for plants. Accordingly, [i]P. agglomerans[/i] is regarded as an ideal candidate for an environmental-friendly bioinoculant replacing chemical fertilizers. It has been documented that the [i]Pantoea[/i] strains show biodegradation activity on various chemical pollutants of soil and water, including petroleum hydrocarbons and toxic metals. [i]P. agglomerans[/i] prevents the penetration of harmful industrial contaminants into deeper parts of soil by biofilm formation, and has an ability to produce hydrogen from waste. Thus, this bacterium appears as a valuable bioremediator which, in some cases, may be acquired as a cheap form of energy. In conclusion, in spite of the proven pathologic role of [i]P. agglomerans[/i] in causing occupational diseases of allergic and/or immunotoxic background and accidental infections, the beneficial traits of this species, and of related species of [i]Pantoea [/i]genus, are of great value for potential use in many areas of biotechnology. Hence, any restrictions on the use of these organisms and their products should be declined, providing safety precautions at work with the [i]Pantoea[/i] biopreparations are maintained.

  18. Pantoea agglomerans : a mysterious bacterium of evil and good. Part IV. Beneficial effects

    Directory of Open Access Journals (Sweden)

    Jacek Dutkiewicz

    2016-06-01

    plant resistance. Its use as a biocontrol agent permits the decrease of pesticide doses, being a healthy and environmental-friendly procedure. The application of the preparations of this bacterium efficiently protects the stored pome, stone and citrus fruits against invasion of moulds. P. agglomerans strains associated with both rhizosphere and plant tissues (as endophytes efficiently promote the growth of many plants, including rice and wheat, which are the staple food for the majority of mankind. The promotion mechanisms are diverse and include fixation of atmospheric nitrogen, production of phytohormones, as well as degradation of phytate and phosphate solubilizing which makes the soil phosphorus available for plants. Accordingly, P. agglomerans is regarded as an ideal candidate for an environmental-friendly bioinoculant replacing chemical fertilizers. It has been documented that the Pantoea strains show biodegradation activity on various chemical pollutants of soil and water, including petroleum hydrocarbons and toxic metals. P. agglomerans prevents the penetration of harmful industrial contaminants into deeper parts of soil by biofilm formation, and has an ability to produce hydrogen from waste. Thus, this bacterium appears as a valuable bioremediator which, in some cases, may be acquired as a cheap form of energy. In conclusion, in spite of the proven pathologic role of P. agglomerans in causing occupational diseases of allergic and/or immunotoxic background and accidental infections, the beneficial traits of this species, and of related species of Pantoea genus, are of great value for potential use in many areas of biotechnology. Hence, any restrictions on the use of these organisms and their products should be declined, providing safety precautions at work with the Pantoea biopreparations are maintained.

  19. Eubacterium rangiferina, a novel usnic acid-resistant bacterium from the reindeer rumen

    Science.gov (United States)

    Sundset, Monica A.; Kohn, Alexandra; Mathiesen, Svein D.; Præsteng, Kirsti E.

    2008-08-01

    Reindeer are able to eat and utilize lichens as an important source of energy and nutrients. In the current study, the activities of antibiotic secondary metabolites including usnic, antranoric, fumarprotocetraric, and lobaric acid commonly found in lichens were tested against a collection of 26 anaerobic rumen bacterial isolates from reindeer ( Rangifer tarandus tarandus) using the agar diffusion method. The isolates were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequences. Usnic acid had a potent antimicrobial effect against 25 of the isolates, belonging to Clostridiales, Enterococci, and Streptococci. Isolates of Clostridia and Streptococci were also susceptible to atranoric and lobaric acid. However, one isolate (R3_91_1) was found to be resistant to usnic, antranoric, fumarprotocetraric, and lobaric acid. R3_91_1 was also seen invading and adhering to lichen particles when grown in a liquid anaerobic culture as demonstrated by transmission electron microscopy. This was a Gram-negative, nonmotile rod (0.2-0.7 × 2.0-3.5 μm) with a deoxyribonucleic acid G + C content of 47.0 mol% and main cellular fatty acids including 15:0 anteiso-dimethyl acetal (DMA), 16:0 iso-fatty acid methyl ester (FAME), 13:0 iso-3OH FAME, and 17:0 anteiso-FAME, not matching any of the presently known profiles in the MIDI database. Combined, the phenotypic and genotypic traits including the 16S rRNA gene sequence show that R3_91_1 is a novel species inside the order Clostridiales within the family Lachnospiraceae, for which we propose the name Eubacterium rangiferina. This is the first record of a rumen bacterium able to tolerate and grow in the presence of usnic acid, indicating that the rumen microorganisms in these animals have adapted mechanisms to deal with lichen secondary metabolites, well known for their antimicrobial and toxic effects.

  20. Toxicity of Phenol and Salt on the Phenol-Degrading Pseudomonas aeruginosa Bacterium

    Directory of Open Access Journals (Sweden)

    Samaei

    2016-08-01

    Full Text Available Background Phenolic compounds, phenol and phenol derivatives are environmental contaminants in some industrial effluents. Entrance of such substances into the environment causes severe environmental pollution, especially pollution of water resources. Biological treatment is a method that uses the potential of microorganisms to clean up contaminated environments. Among microorganisms, bacteria play an important role in treating wastewater contaminated with phenol. Objectives This study aimed to examine the effects of Pseudomonas aeruginosa on degradation of phenol in wastewater contaminated with this pollutant. Methods In this method, the growth rate of P. aeruginosa bacteria was investigated using different concentrations of salt and phenol. This is an experimental study conducted as a pilot in a batch reactor with different concentrations of phenol (25, 50, 100, 150, 300 and 600 mg L-1 and salt (0%, 0.5%, 1%, 2.5% and 5% during 9, 12 and 15 hours. During three days, from 5 experimental and 3 control samples, 18 samples were taken a day forming a sample size of 54 samples for each phenol concentration. Given the number of phenol concentrations (n = 6, a total of 324 samples were analyzed using a spectrophotometer at a wavelength of 600 nm. Results The phenol concentration of 600 mg L-1 was toxic for P. aeruginosa. However, at a certain concentration, it acts as a carbon source for P. aeruginosa. During investigations, it was found that increasing the concentration of phenol increases the rate of bacteria growth. The highest bacteria growth rate occurred was at the salt concentration of zero and phenol concentration of 600 mg L-1. Conclusions The findings of the current study indicate that at high concentrations of salt, the growth of bacteria reduces so that it stops at a concentration of 50 mg L-1 (5%. Thus, the bacterium is halotolerant or halophilic. With an increase in phenol concentration, the growth rate increased. Phenol toxicity appears