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Sample records for acidophilic chemolithoautotrophic bacterium

  1. Astrobiological Significance of Chemolithoautotrophic Acidophiles

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.

    2003-01-01

    For more than a century (since Winogradsky discovered lithoautotrophic bacteria) a dilemma in microbiology has concerned life that first inhabited the Earth. Which types of life forms first appeared in the primordial oceans during the earliest geological period on Earth as the primary ancestors of modem biological diversity? How did a metabolism of ancestors evolve: from lithoautotrophic to lithohetherotrophic and organoheterotrophic or from organoheterotrophic to organoautotrophic and lithomixotrophic types? At the present time, it is known that chemolithoheterotrophic and chemolithoautotrophic metabolizing bacteria are wide spread in different ecosystems. On Earth the acidic ecosystems are associated with geysers, volcanic fumaroles, hot springs, deep sea hydrothermal vents, caves, acid mine drainage and other technogenic ecosystems. Bioleaching played a significant role on a global geological scale during the Earth's formation. This important feature of bacteria has been successfully applied in industry. The lithoautotrophs include Bacteria and Archaea belonging to diverse genera containing thermophilic and mesophilic species. In this paper we discuss the lithotrophic microbial acidophiles and present some data with a description of new acidophilic iron- and sulfur- oxidizing bacterium isolated from the Chena Hot Springs in Alaska. We also consider the possible relevance of microbial acidophiles to Venus, Io, and acidic inclusions in glaciers and icy moons.

  2. Iron Meteorites Can Support the Growth of Acidophilic Chemolithoautotrophic Microorganisms

    NASA Astrophysics Data System (ADS)

    González-Toril, Elena; Martínez-Frías, Jesús; Gómez, José María; Rull, Fernando; Amils, Ricardo

    2005-06-01

    Chemolithoautotrophy based on reduced inorganic minerals is considered a primitive energy transduction system. Evidence that a high number of meteorites crashed into the planet during the early period of Earth history led us to test the ability of iron-oxidizing bacteria to grow using iron meteorites as their source of energy. Here we report the growth of two acidophilic iron-oxidizing bacteria, Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans, on a piece of the Toluca meteorite as the only source of energy. The alteration of the surface of the exposed piece of meteorite, the solubilization of its oxidized metal constituents, mainly ferric iron, and the formation of goethite precipitates all clearly indicate that iron-meteoritebased chemolithotrophic metabolism is viable.

  3. Iron meteorites can support the growth of acidophilic chemolithoautotrophic microorganisms.

    PubMed

    González-Toril, Elena; Martínez-Frías, Jesús; Gómez Gómez, José María; Rull, Fernando; Amils, Ricardo

    2005-06-01

    Chemolithoautotrophy based on reduced inorganic minerals is considered a primitive energy transduction system. Evidence that a high number of meteorites crashed into the planet during the early period of Earth history led us to test the ability of iron-oxidizing bacteria to grow using iron meteorites as their source of energy. Here we report the growth of two acidophilic iron-oxidizing bacteria, Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans, on a piece of the Toluca meteorite as the only source of energy. The alteration of the surface of the exposed piece of meteorite, the solubilization of its oxidized metal constituents, mainly ferric iron, and the formation of goethite precipitates all clearly indicate that iron-meteorite-based chemolithotrophic metabolism is viable.

  4. High cell density cultivation of the chemolithoautotrophic bacterium Nitrosomonas europaea.

    PubMed

    Papp, Benedek; Török, Tibor; Sándor, Erzsébet; Fekete, Erzsébet; Flipphi, Michel; Karaffa, Levente

    2016-05-01

    Nitrosomonas europaea is a chemolithoautotrophic nitrifier, a gram-negative bacterium that can obtain all energy required for growth from the oxidation of ammonia to nitrite, and this may be beneficial for various biotechnological and environmental applications. However, compared to other bacteria, growth of ammonia oxidizing bacteria is very slow. A prerequisite to produce high cell density N. europaea cultures is to minimize the concentrations of inhibitory metabolic by-products. During growth on ammonia nitrite accumulates, as a consequence, N. europaea cannot grow to high cell concentrations under conventional batch conditions. Here, we show that single-vessel dialysis membrane bioreactors can be used to obtain substantially increased N. europaea biomasses and substantially reduced nitrite levels in media initially containing high amounts of the substrate. Dialysis membrane bioreactor fermentations were run in batch as well as in continuous mode. Growth was monitored with cell concentration determinations, by assessing dry cell mass and by monitoring ammonium consumption as well as nitrite formation. In addition, metabolic activity was probed with in vivo acridine orange staining. Under continuous substrate feed, the maximal cell concentration (2.79 × 10(12)/L) and maximal dry cell mass (0.895 g/L) achieved more than doubled the highest values reported for N. europaea cultivations to date.

  5. Growth of the acidophilic iron-sulfur bacterium Acidithiobacillus ferrooxidans under Mars-like geochemical conditions

    NASA Astrophysics Data System (ADS)

    Bauermeister, Anja; Rettberg, Petra; Flemming, Hans-Curt

    2014-08-01

    The question of life on Mars has been in focus of astrobiological research for several decades, and recent missions in orbit or on the surface of the planet are constantly expanding our knowledge on Martian geochemistry. For example, massive stratified deposits have been identified on Mars containing sulfate minerals and iron oxides, which suggest the existence of acidic aqueous conditions in the past, similar to acidic iron- and sulfur-rich environments on Earth. Acidophilic organisms thriving in such habitats could have been an integral part of a possibly widely extinct Martian ecosystem, but remains might possibly even exist today in protected subsurface niches. The chemolithoautotrophic strain Acidithiobacillus ferrooxidans was selected as a model organism to study the metabolic capacities of acidophilic iron-sulfur bacteria, especially regarding their ability to grow with in situ resources that could be expected on Mars. The experiments were not designed to accurately simulate Martian physical conditions (except when certain single parameters such as oxygen partial pressure were considered), but rather the geochemical environment that can be found on Mars. A. ferrooxidans could grow solely on the minerals contained in synthetic Mars regolith mixtures with no added nutrients, using either O2 as an external electron acceptor for iron oxidation, or H2 as an external electron donor for iron reduction, and thus might play important roles in the redox cycling of iron on Mars. Though the oxygen partial pressure of the Martian atmosphere at the surface was not sufficient for detectable iron oxidation and growth of A. ferrooxidans during short-term incubation (7 days), alternative chemical O2-generating processes in the subsurface might yield microhabitats enriched in oxygen, which principally are possible under such conditions. The bacteria might also contribute to the reductive dissolution of Fe3+-containing minerals like goethite and hematite, which are

  6. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

    SciTech Connect

    Beller, H.R.; Legler, T.C.; Kane, S.R.

    2011-07-15

    Chemolithoautotrophic bacteria can be of industrial and environmental importance, but they present a challenge for systems biology studies, as their central metabolism deviates from that of model organisms and there is a much less extensive experimental basis for their gene annotation than for typical organoheterotrophs. For microbes with sequenced genomes but unconventional metabolism, the ability to create knockout mutations can be a powerful tool for functional genomics and thereby render an organism more amenable to systems biology approaches. In this chapter, we describe a genetic system for Thiobacillus denitrificans, with which insertion mutations can be introduced by homologous recombination and complemented in trans. Insertion mutations are generated by in vitro transposition, the mutated genes are amplified by the PCR, and the amplicons are introduced into T. denitrificans by electroporation. Use of a complementation vector, pTL2, based on the IncP plasmid pRR10 is also addressed.

  7. Anaerobic, Nitrate-Dependent Oxidation of U(IV) Oxide Minerals by the Chemolithoautotrophic Bacterium Thiobacillus denitrificans

    PubMed Central

    Beller, Harry R.

    2005-01-01

    Under anaerobic conditions and at circumneutral pH, cells of the widely distributed, obligate chemolithoautotrophic bacterium Thiobacillus denitrificans oxidatively dissolved synthetic and biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: U(IV) oxidation required the presence of nitrate and was strongly correlated with nitrate consumption. This is the first report of anaerobic U(IV) oxidation by an autotrophic bacterium. PMID:15812053

  8. Anaerobic, Nitrate-Dependent Oxidation of U(IV) Oxide Minerals by the Chemolithoautotrophic Bacterium Thiobacillus denitrificans

    SciTech Connect

    Beller, H R

    2004-06-25

    Under anaerobic conditions and at circumneutral pH, cells of the widely-distributed, obligate chemolithoautotrophic bacterium Thiobacillus denitrificans oxidatively dissolved synthetic and biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: U(IV) oxidation required the presence of nitrate and was strongly correlated to nitrate consumption. This is the first report of anaerobic U(IV) oxidation by an autotrophic bacterium.

  9. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitfificans.

    SciTech Connect

    Beller, H R; Larimer, Frank W

    2006-02-01

    The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, {beta}-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by {beta}-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.

  10. Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707

    SciTech Connect

    Klots, Martin G.; Arp, D J; Chain, Patrick S; El-Sheikh, Amal F.; Hauser, Loren John; Hommes, Norman G.; Larimer, Frank W; Malfatti, Stephanie; Norton, Jeanette M.; Poret-Peterson, Amisha T.; Vergez, Lisa; Ward, Bess B.

    2006-01-01

    The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type).

  11. Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707†

    PubMed Central

    Klotz, Martin G.; Arp, Daniel J.; Chain, Patrick S. G.; El-Sheikh, Amal F.; Hauser, Loren J.; Hommes, Norman G.; Larimer, Frank W.; Malfatti, Stephanie A.; Norton, Jeanette M.; Poret-Peterson, Amisha T.; Vergez, Lisa M.; Ward, Bess B.

    2006-01-01

    The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type). PMID:16957257

  12. The Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC19707

    SciTech Connect

    Klotz, M G; Arp, D J; Chain, P S; El-Sheikh, A F; Hauser, L J; Hommes, N G; Larimer, F W; Malfatti, S A; Norton, J M; Poret-Peterson, A T; Vergez, L M; Ward, B B

    2006-08-03

    The Gammaproteobacterium, Nitrosococcus oceani (ATCC 19707), is a Gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; 50.4% G+C) and a plasmid (40,420 bp) that contain 3052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. In contrast to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance and the ability to assimilate carbon via gluconeogenesis. One set of genes for type I RuBisCO was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H{sup +}-dependent F{sub 0}F{sub 1}-type, one Na{sup +}-dependent V-type).

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

    PubMed

    Simbahan, Jessica; Drijber, Rhae; Blum, Paul

    2004-09-01

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

  14. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea.

    PubMed

    Chain, Patrick; Lamerdin, Jane; Larimer, Frank; Regala, Warren; Lao, Victoria; Land, Miriam; Hauser, Loren; Hooper, Alan; Klotz, Martin; Norton, Jeanette; Sayavedra-Soto, Luis; Arciero, Dave; Hommes, Norman; Whittaker, Mark; Arp, Daniel

    2003-05-01

    Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with approximately 47% transcribed from one strand and approximately 53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO(2) and NH(3) assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.

  15. Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea†

    PubMed Central

    Chain, Patrick; Lamerdin, Jane; Larimer, Frank; Regala, Warren; Lao, Victoria; Land, Miriam; Hauser, Loren; Hooper, Alan; Klotz, Martin; Norton, Jeanette; Sayavedra-Soto, Luis; Arciero, Dave; Hommes, Norman; Whittaker, Mark; Arp, Daniel

    2003-01-01

    Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with ∼47% transcribed from one strand and ∼53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO2 and NH3 assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria. PMID:12700255

  16. Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255

    SciTech Connect

    Hauser, Loren John; Land, Miriam L; Larimer, Frank W; Arp, D J; Hickey, W J

    2006-03-01

    The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.

  17. Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255

    PubMed Central

    Starkenburg, Shawn R.; Chain, Patrick S. G.; Sayavedra-Soto, Luis A.; Hauser, Loren; Land, Miriam L.; Larimer, Frank W.; Malfatti, Stephanie A.; Klotz, Martin G.; Bottomley, Peter J.; Arp, Daniel J.; Hickey, William J.

    2006-01-01

    The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes. PMID:16517654

  18. Effect of external pH perturbations on in vivo protein synthesis by the acidophilic bacterium Thiobacillus ferrooxidans.

    PubMed Central

    Amaro, A M; Chamorro, D; Seeger, M; Arredondo, R; Peirano, I; Jerez, C A

    1991-01-01

    The response of the obligate acidophilic bacterium Thiobacillus ferrooxidans to external pH changes is reported. When T. ferrooxidans cells grown at pH 1.5 were shifted to pH 3.5, there were several changes in the general protein synthesis pattern, including a large stimulation of the synthesis of a 36-kDa protein (p36). The apparent low isoelectric point of p36, its location in the membrane fraction, and its cross-reaction with anti-OmpC from Salmonella typhi suggested that it may be a porin whose expression is regulated by extracellular pH. Images PMID:1987171

  19. Thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent.

    PubMed

    Alain, Karine; Postec, Anne; Grinsard, Elodie; Lesongeur, Françoise; Prieur, Daniel; Godfroy, Anne

    2010-01-01

    A novel, strictly anaerobic, thermophilic, sulfate-reducing bacterium, designated strain AT1325(T), was isolated from a deep-sea hydrothermal vent at the Rainbow site on the Mid-Atlantic Ridge. This strain was subjected to a polyphasic taxonomic analysis. Cells were Gram-negative motile rods (approximately 2.4 x 0.6 microm) with a single polar flagellum. Strain AT1325(T) grew at 55-75 degrees C (optimum, 65-70 degrees C), at pH 5.5-8.0 (optimum, 6.5-7.5) and in the presence of 1.5-4.5 % (w/v) NaCl (optimum, 2.5 %). Cells grew chemolithoautotrophically with H2 as an energy source and SO4(2-) as an electron acceptor. Alternatively, the novel isolate was able to use methylamine, peptone or yeast extract as carbon sources. The dominant fatty acids (>5 % of the total) were C(16 : 0), C(18 : 1)omega7c, C(18 : 0) and C(19 : 0) cyclo omega8c. The G+C content of the genomic DNA of strain AT1325(T) was 45.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain AT1325(T) within the family Thermodesulfobacteriaceae, in the bacterial domain. Comparative 16S rRNA gene sequence analysis indicated that strain AT1325(T) belonged to the genus Thermodesulfatator, sharing 97.8 % similarity with the type strain of Thermodesulfatator indicus, the unique representative species of this genus. On the basis of the data presented, it is suggested that strain AT1325(T) represents a novel species of the genus Thermodesulfatator, for which the name Thermodesulfatator atlanticus sp. nov. is proposed. The type strain is AT1325(T) (=DSM 21156(T)=JCM 15391(T)).

  20. Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

    PubMed Central

    Beller, Harry R.; Zhou, Peng; Legler, Tina C.; Chakicherla, Anu; Kane, Staci; Letain, Tracy E.; A. O’Day, Peggy

    2013-01-01

    Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV) oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II) oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II)-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II) oxidation, namely (a) whole-genome transcriptional studies [using FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions], (b) Fe(II) oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c) random transposon-mutagenesis studies with screening for Fe(II) oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II) oxidation. The non-defective mutants included the c1-cytochrome subunit of the cytochrome bc1 complex (complex III), which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II) oxidation and to current concepts of reverse electron transfer. A transposon mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I) was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II) oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV) oxidation, nor have other c-type cytochromes yet been implicated in the process. PMID:24065960

  1. Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent.

    PubMed

    Alain, Karine; Callac, Nolwenn; Guégan, Marianne; Lesongeur, Françoise; Crassous, Philippe; Cambon-Bonavita, Marie-Anne; Querellou, Joël; Prieur, Daniel

    2009-06-01

    A novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (1 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60 x 0.40 microm) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H(2) as an energy source, S(0) as an electron acceptor and CO(2) as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209(T) fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209(T) belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209(T) (=DSM 21157(T)=JCM 15390(T)).

  2. Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake

    DOE PAGES

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; ...

    2015-11-19

    Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. Moreover, this organism was sequenced as part of the community science program at the DOE Joint Genome Institute.

  3. Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

    DOE PAGES

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; ...

    2015-10-26

    Thioalkalivibrio thiocyanodenitrificans strain ARhD 1T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete denitrification under anaerobic conditions. In addition, the draft genome sequence consists of 3,746,647 bp in 3 scaffolds, containing 3558 protein-coding and 121 RNA genes. T. thiocyanodenitrificans ARhD 1T was sequenced as part of the DOE Joint Genome Institute Community Science Program.

  4. Genome-Enabled Studies of Anaerobic, Nitrate-Dependent Iron Oxidation in the Chemolithoautotrophic Bacterium Thiobacillus denitrificans

    NASA Astrophysics Data System (ADS)

    Beller, H. R.; Zhou, P.; Legler, T. C.; Chakicherla, A.; O'Day, P. A.

    2013-12-01

    Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV) oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II) oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II)-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II) oxidation, namely (a) whole-genome transcriptional studies [using FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions], (b) Fe(II) oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c) random transposon-mutagenesis studies with screening for Fe(II) oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II) oxidation. The non-defective mutants included the c1-cytochrome subunit of the cytochrome bc1 complex (complex III), which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II) oxidation and to current concepts of reverse electron transfer. Of the transposon mutants defective in Fe(II) oxidation, one mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I) was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II) oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV) oxidation, nor have other c-type cytochromes yet been implicated in the process.

  5. Complete genome sequence of Thermovibrio ammonificans HB-1T, a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent

    SciTech Connect

    Giovannelli, Donato; Ricci, Jessica; Perez-Rodriguez, Ileana; Hugler, Michael; O'Brien, Charles; Keddis, Ramaydalis; Grosche, Ashley; Goodwin, Lynne A.; Bruce, David; Davenport, Karen W.; Detter, J. Chris; Han, James; Han, Cliff; Ivanova, N; Land, Miriam L; Mikhailova, Natalia; Nolan, Matt; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Vetriani, Costantino

    2012-01-01

    Thermovibrio ammonificans type strain HB-1T is a thermophilic (Topt: 75 C), strictly anaero- bic, chemolithoautotrophic bacterium that was isolated from an active, high temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism grows on mineral salts medium in the presence of CO2/H2, using NO3- or S0 as electron acceptors, which are re- duced to ammonium or hydrogen sulfide, respectively. T. ammonificans is one of only three species within the genus Thermovibrio, a member of the family Desulfurobacteriaceae, and it forms a deep branch within the phylum Aquificae. Here we report the main features of the genome of T. ammonificans strain HB-1T (DSM 15698T).

  6. Sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity.

    PubMed

    Kodama, Yumiko; Watanabe, Kazuya

    2004-11-01

    A facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium, strain YK-1(T), was isolated from an underground crude-oil storage cavity at Kuji in Iwate, Japan. The cells were motile, curved rods and had a single polar flagellum. Optimum growth occurred in a low-strength salt medium at pH 7.0 and 25 degrees C. It utilized sulfide, elemental sulfur, thiosulfate and hydrogen as the electron donors and nitrate as the electron acceptor under anaerobic conditions, but it did not use nitrite. Oxygen also served as the electron acceptor under the microaerobic condition (O(2) in the head space 1 %). It did not grow on sugars, organic acids or hydrocarbons as carbon and energy sources. The DNA G+C content of strain YK-1(T) was 45 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that its closest relative was Thiomicrospira denitrificans in the 'Epsilonproteobacteria', albeit with low homology (90 %). On the basis of physiological and phylogenetic data, strain YK-1(T) should be classified into a novel genus and species, for which the name Sulfuricurvum kujiense gen. nov., sp. nov. is proposed. The type strain is YK-1(T) (=JCM 11577(T)=MBIC 06352(T)=ATCC BAA-921(T)).

  7. Genome sequence of Desulfosporosinus sp. OT, an acidophilic sulfate-reducing bacterium from copper mining waste in Norilsk, Northern Siberia.

    PubMed

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

    2011-11-01

    We have sequenced the genome of Desulfosporosinus sp. OT, a Gram-positive, acidophilic sulfate-reducing Firmicute isolated from copper tailing sediment in the Norilsk mining-smelting area in Northern Siberia, Russia. This represents the first sequenced genome of a Desulfosporosinus species. The genome has a size of 5.7 Mb and encodes 6,222 putative proteins.

  8. Uncovering a Microbial Enigma: Isolation and Characterization of the Streamer-Generating, Iron-Oxidizing, Acidophilic Bacterium “Ferrovum myxofaciens”

    PubMed Central

    Hallberg, Kevin B.; Hedrich, Sabrina

    2014-01-01

    A betaproteobacterium, shown by molecular techniques to have widespread global distribution in extremely acidic (pH 2 to 4) ferruginous mine waters and also to be a major component of “acid streamer” growths in mine-impacted water bodies, has proven to be recalcitrant to enrichment and isolation. A modified “overlay” solid medium was devised and used to isolate this bacterium from a number of mine water samples. The physiological and phylogenetic characteristics of a pure culture of an isolate from an abandoned copper mine (“Ferrovum myxofaciens” strain P3G) have been elucidated. “F. myxofaciens” is an extremely acidophilic, psychrotolerant obligate autotroph that appears to use only ferrous iron as an electron donor and oxygen as an electron acceptor. It appears to use the Calvin-Benson-Bassham pathway to fix CO2 and is diazotrophic. It also produces copious amounts of extracellular polymeric materials that cause cells to attach to each other (and to form small streamer-like growth in vitro) and to different solid surfaces. “F. myxofaciens” can catalyze the oxidative dissolution of pyrite and, like many other acidophiles, is tolerant of many (cationic) transition metals. “F. myxofaciens” and related clone sequences form a monophyletic group within the Betaproteobacteria distantly related to classified orders, with genera of the family Nitrosomonadaceae (lithoautotrophic, ammonium-oxidizing neutrophiles) as the closest relatives. On the basis of the phylogenetic and phenotypic differences of “F. myxofaciens” and other Betaproteobacteria, a new family, “Ferrovaceae,” and order, “Ferrovales,” within the class Betaproteobacteria are proposed. “F. myxofaciens” is the first extreme acidophile to be described in the class Betaproteobacteria. PMID:24242243

  9. Purification and characterization of 2-oxoglutarate:ferredoxin oxidoreductase from a thermophilic, obligately chemolithoautotrophic bacterium, Hydrogenobacter thermophilus TK-6.

    PubMed Central

    Yoon, K S; Ishii, M; Igarashi, Y; Kodama, T

    1996-01-01

    2-Oxoglutarate:ferredoxin oxidoreductase from a thermophilic, obligately autotrophic, hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6, was purified to homogeneity by precipitation with ammonium sulfate and by fractionation by DEAE-Sepharose CL-6B, polyacrylate-quaternary amine, hydroxyapatite, and Superdex-200 chromatography. The purified enzyme had a molecular mass of about 105 kDa and comprised two subunits (70 kDa and 35 kDa). The activity of the 2-oxoglutarate:ferredoxin oxidoreductase was detected by the use of 2-oxoglutarate, coenzyme A, and one of several electron acceptors in substrate amounts (ferredoxin isolated from H. thermophilus, flavin adenine dinucleotide, flavin mononucleotide, or methyl viologen). NAD, NADP, and ferredoxins from Chlorella spp. and Clostridium pasteurianum were ineffective. The enzyme was extremely thermostable; the temperature optimum for 2-oxoglutarate oxidation was above 80 degrees C, and the time for a 50% loss of activity at 70 degrees C under anaerobic conditions was 22 h. The optimum pH for a 2-oxoglutarate oxidation reaction was 7.6 to 7.8. The apparent Km values for 2-oxoglutarate and coenzyme A at 70 degrees C were 1.42 mM and 80 microM, respectively. PMID:8655524

  10. Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake

    SciTech Connect

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; Pati, Amrita; Kyrpides, Nikos; Goodwin, Lynne A.; Woyke, Tanja; Muyzer, Gerard

    2015-11-19

    Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. Moreover, this organism was sequenced as part of the community science program at the DOE Joint Genome Institute.

  11. Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

    SciTech Connect

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; Pati, Amrita; Kyrpides, Nikos; Goodwin, Lynne A.; Woyke, Tanja; Muyzer, Gerard

    2015-10-26

    Thioalkalivibrio thiocyanodenitrificans strain ARhD 1T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete denitrification under anaerobic conditions. In addition, the draft genome sequence consists of 3,746,647 bp in 3 scaffolds, containing 3558 protein-coding and 121 RNA genes. T. thiocyanodenitrificans ARhD 1T was sequenced as part of the DOE Joint Genome Institute Community Science Program.

  12. Magnesium insertion by magnesium chelatase in the biosynthesis of zinc bacteriochlorophyll a in an aerobic acidophilic bacterium Acidiphilium rubrum.

    PubMed

    Masuda, T; Inoue, K; Masuda, M; Nagayama, M; Tamaki, A; Ohta, H; Shimada, H; Takamiya, K

    1999-11-19

    To elucidate the mechanism for formation of zinc-containing bacteriochlorophyll a in the photosynthetic bacterium Acidiphilium rubrum, we isolated homologs of magnesium chelatase subunits (bchI, -D, and -H). A. rubrum bchI and -H were encoded by single genes located on the clusters bchP-orf168-bchI-bchD-orf320-crtI and bchF-N-B-H-L as in Rhodobacter capsulatus, respectively. The deduced sequences of A. rubrum bchI, -D, and -H had overall identities of 59. 8, 40.5, and 50.7% to those from Rba. capsulatus, respectively. When these genes were introduced into bchI, bchD, and bchH mutants of Rba. capsulatus for functional complementation, all mutants were complemented with concomitant synthesis of bacteriochlorophyll a. Analyses of bacteriochlorophyll intermediates showed that A. rubrum cells accumulate magnesium protoporphyrin IX monomethyl ester without detectable accumulation of zinc protoporphyrin IX or its monomethyl ester. These results indicate that a single set of magnesium chelatase homologs in A. rubrum catalyzes the insertion of only Mg(2+) into protoporphyrin IX to yield magnesium protoporphyrin IX monomethyl ester. Consequently, it is most likely that zinc-containing bacteriochlorophyll a is formed by a substitution of Zn(2+) for Mg(2+) at a step in the bacteriochlorophyll biosynthesis after formation of magnesium protoporphyrin IX monomethyl ester.

  13. Sulfuriferula thiophila sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium, and correction of the name Sulfuriferula plumbophilusWatanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig.

    PubMed

    Watanabe, Tomohiro; Kojima, Hisaya; Fukui, Manabu

    2016-05-01

    A novel sulfur-oxidizing bacterium designated strain mst6T was isolated from spring water of Masutomi hot spring in Japan. The cells were rod-shaped (1.2-4.0 × 0.5-0.7 μm) and Gram-stain-negative. The G+C content of genomic DNA was around 52.6 mol%. The isolate possessed summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 as major cellular fatty acids. Strain mst6T grew by inorganic carbon fixation and oxidation of inorganic sulfur compounds with oxygen as an electron acceptor. The isolate grew over a temperature range of 5-34 °C, a NaCl concentration range of 0-110 mM and a pH range of 4.6-8.1. Optimum growth occurred at 32 °C, in the absence of NaCl and at pH 5.9-6.2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain mst6T belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relative was Sulfuriferula multivorans TTNT with a 16S rRNA gene sequence similarity of 97.0 %. On the basis of the data obtained in this study, strain mst6T represents a novel species of the genus Sulfuriferula, for which the name Sulfuriferula thiophila sp. nov. is proposed. The type strain is mst6T ( = NBRC 111150T = DSM 101871T). In addition, we propose correcting the name Sulfuriferula plumbophilus Watanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig. based on Rule 12c, Rule 61 and Appendix 9 of the International Code of Nomenclature of Prokaryotes.

  14. Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas.

    PubMed

    Mori, Koji; Suzuki, Ken-ichiro; Yamaguchi, Kaoru; Urabe, Tetsuro; Hanada, Satoshi

    2015-01-01

    A novel, obligately chemolithoautotrophic, sulfur-oxidizing bacterial strain, designated strain gps52(T), was isolated from a rock sample collected near the hydrothermal vents of the Suiyo Seamount in the Pacific Ocean. The cells possessed a Gram-stain-negative-type cell wall and contained menaquinone-8(H4) and menaquinone-9(H4) as respiratory quinones, and C16 : 1ω7c, C16 : 0 and C18 : 1ω7c as major cellular fatty acids. Neither storage compounds nor extensive internal membranes were observed in the cells. Strain gps52(T) grew using carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as electron acceptor. Optimal growth was observed at 32 °C, pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain gps52(T) belongs to the family Ectothiorhodospiraceae and is different from any other known bacteria, with sequence similarities of less than 93 %. Based on phenotypic and phylogenetic findings, the isolate is considered to represent a novel genus and species in the family Ectothiorhodospiraceae, and the name Thiogranum longum gen. nov., sp. nov. is proposed. The type strain is gps52(T) ( = NBRC 101260(T) = DSM 19610(T)). An emended description of the genus Thiohalomonas is also proposed.

  15. Impact of Different In Vitro Electron Donor/Acceptor Conditions on Potential Chemolithoautotrophic Communities from Marine Pelagic Redoxclines

    PubMed Central

    Labrenz, Matthias; Jost, Günter; Pohl, Christa; Beckmann, Sabrina; Martens-Habbena, Willm; Jürgens, Klaus

    2005-01-01

    Anaerobic or microaerophilic chemolithoautotrophic bacteria have been considered to be responsible for CO2 dark fixation in different pelagic redoxclines worldwide, but their involvement in redox processes is still not fully resolved. We investigated the impact of 17 different electron donor/acceptor combinations in water of pelagic redoxclines from the central Baltic Sea on the stimulation of bacterial CO2 dark fixation as well as on the development of chemolithoautotrophic populations. In situ, the highest CO2 dark fixation rates, ranging from 0.7 to 1.4 μmol liter−1 day−1, were measured directly below the redoxcline. In enrichment experiments, chemolithoautotrophic CO2 dark fixation was maximally stimulated by the addition of thiosulfate, reaching values of up to 9.7 μmol liter−1 CO2 day−1. Chemolithoautotrophic nitrate reduction proved to be an important process, with rates of up to 33.5 μmol liter−1 NO3− day−1. Reduction of Fe(III) or Mn(IV) was not detected; nevertheless, the presence of these potential electron acceptors influenced the development of stimulated microbial assemblages. Potential chemolithoautotrophic bacteria in the enrichment experiments were displayed on 16S ribosomal complementary DNA single-strand-conformation polymorphism fingerprints and identified by sequencing of excised bands. Sequences were closely related to chemolithoautotrophic Thiomicrospira psychrophila and Maorithyas hadalis gill symbiont (both Gammaproteobacteria) and to an uncultured nitrate-reducing Helicobacteraceae bacterium (Epsilonproteobacteria). Our data indicate that this Helicobacteraceae bacterium could be of general importance or even a key organism for autotrophic nitrate reduction in pelagic redoxclines. PMID:16269695

  16. Genetic transfer in acidophilic bacteria

    SciTech Connect

    Roberto, F.F.; Glenn, A.W.; Bulmer, D.; Ward, T.E.

    1990-01-01

    There is increasing interest in the use of microorganisms to recover metals from ores, as well as to remove sulfur from coal. These so-called bioleaching processes are mediated by a number of bacteria. The best-studied of these organisms are acidophiles including Thiobacillus and Acidiphilium species. Our laboratory has focused on developing genetic strategies to allow the manipulation of acidophilic bacteria to improve and augment their utility in large scale operations. We have recently been successful in employing conjugation for interbacterial transfer of genetic information, as well as in directly transforming Acidiphilium by use of electroporation. We are now testing the properties of IncPl, IncW and IncQ plasmid vectors in Acidiphilium to determine their relative usefulness in routine manipulation of acidophiles and transfer between organisms. This study also allows us to determine the natural ability of these bacteria to transfer genetic material amongst themselves in their particular environment. 21 refs., 3 figs., 2 tabs.

  17. Draft Genome Sequence of a Novel Acidophilic Iron-Oxidizing Firmicutes Species, “Acidibacillus ferrooxidans” (SLC66T)

    PubMed Central

    Ñancucheo, Ivan; Oliveira, Renato; Dall’Agnol, Hivana; Johnson, D. Barrie; Grail, Barry; Holanda, Roseanne; Nunes, Gisele Lopes; Cuadros-Orellana, Sara

    2016-01-01

    Here, we present the draft genome sequence of the type strain of “Acidibacillus ferrooxidans,” a mesophilic, heterotrophic, and acidophilic bacterium that was isolated from mine spoilage subjected to accelerated weathering in humidity cell tests carried out by the former U.S. Bureau of Mines in Salt Lake City, UT. PMID:27198020

  18. Carbon Fixation Driven by Molecular Hydrogen Results in Chemolithoautotrophically Enhanced Growth of Helicobacter pylori

    PubMed Central

    Kuhns, Lisa G.; Benoit, Stéphane L.; Bayyareddy, Krishnareddy; Johnson, Darryl; Orlando, Ron; Evans, Alexandra L.; Waldrop, Grover L.

    2016-01-01

    ABSTRACT A molecular hydrogen (H2)-stimulated, chemolithoautotrophic growth mode for the gastric pathogen Helicobacter pylori is reported. In a culture medium containing peptides and amino acids, H2-supplied cells consistently achieved 40 to 60% greater growth yield in 16 h and accumulated 3-fold more carbon from [14C]bicarbonate (on a per cell basis) in a 10-h period than cells without H2. Global proteomic comparisons of cells supplied with different atmospheric conditions revealed that addition of H2 led to increased amounts of hydrogenase and the biotin carboxylase subunit of acetyl coenzyme A (acetyl-CoA) carboxylase (ACC), as well as other proteins involved in various cellular functions, including amino acid metabolism, heme synthesis, or protein degradation. In agreement with this result, H2-supplied cells contained 3-fold more ACC activity than cells without H2. Other possible carbon dioxide (CO2) fixation enzymes were not up-expressed under the H2-containing atmosphere. As the gastric mucus is limited in carbon and energy sources and the bacterium lacks mucinase, this new growth mode may contribute to the persistence of the pathogen in vivo. This is the first time that chemolithoautotrophic growth is described for a pathogen. IMPORTANCE Many pathogens must survive within host areas that are poorly supplied with carbon and energy sources, and the gastric pathogen Helicobacter pylori resides almost exclusively in the nutritionally stringent mucus barrier of its host. Although this bacterium is already known to be highly adaptable to gastric niches, a new aspect of its metabolic flexibility, whereby molecular hydrogen use (energy) is coupled to carbon dioxide fixation (carbon acquisition) via a described carbon fixation enzyme, is shown here. This growth mode, which supplements heterotrophy, is termed chemolithoautotrophy and has not been previously reported for a pathogen. PMID:26929299

  19. 1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum.

    SciTech Connect

    Cort, John R.; Swenson, Michael; Magnuson, Timothy S.

    2011-03-04

    We report the 1H, 13C, and 15N chemical shift assignments of both oxidized and reduced forms of an abundant periplasmic c-type cytochrome, designated ApcA, from the acidophilic gram-negative facultatively anaerobic metal-reducing alpha-proteobacterium Acidiphilium cryptum. These resonance assignments prove that ApcA is a monoheme cytochrome c2 and the product of the Acry_2099 gene. An absence of resonance peaks in the NMR spectra for the 21 N-terminal residues suggests that a predicted N-terminal signal sequence is cleaved. We also describe the preparation and purification of the protein in labeled form from laboratory cultures of A. cryptum growing on 13C- and 15N- labeled substrates.

  20. Acidophilic algae isolated from mine-impacted environments and their roles in sustaining heterotrophic acidophiles.

    PubMed

    Nancucheo, Ivan; Barrie Johnson, D

    2012-01-01

    Two acidophilic algae, identified as strains of Chlorella protothecoides var. acidicola and Euglena mutabilis, were isolated in pure culture from abandoned copper mines in Spain and Wales and grown in pH- and temperature-controlled bioreactors. The Chlorella isolate grew optimally at pH 2.5 and 30°C, with a corresponding culture doubling time of 9 h. The isolates displayed similar tolerance (10-50 mM) to four transition metals tested. Growth of the algae in liquid media was paralleled with increasing concentrations of dissolved organic carbon (DOC). Glycolic acid was identified as a significant component (12-14%) of total DOC. Protracted incubation resulted in concentrations of glycolic acid declining in both cases, and glycolic acid added to a culture of Chlorella incubated in the dark was taken up by the alga (~100% within 3 days). Two monosaccharides were identified in cell-free liquors of each algal isolate: fructose and glucose (Chlorella), and mannitol and glucose (Euglena). These were rapidly metabolized by acidophilic heterotrophic bacteria (Acidiphilium and Acidobacterium spp.) though only fructose was utilized by the more fastidious heterotroph "Acidocella aromatica." The significance of algae in promoting the growth of iron- (and sulfate-) reducing heterotrophic acidophiles that are important in remediating mine-impacted waters (MIWs) is discussed.

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

    PubMed

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

    2017-03-16

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

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

    PubMed Central

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

    2017-01-01

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

  3. Oxidation of Molecular Hydrogen by a Chemolithoautotrophic Beggiatoa Strain

    PubMed Central

    2016-01-01

    ABSTRACT A chemolithoautotrophic strain of the family Beggiatoaceae, Beggiatoa sp. strain 35Flor, was found to oxidize molecular hydrogen when grown in a medium with diffusional gradients of oxygen, sulfide, and hydrogen. Microsensor profiles and rate measurements suggested that the strain oxidized hydrogen aerobically when oxygen was available, while hydrogen consumption under anoxic conditions was presumably driven by sulfur respiration. Beggiatoa sp. 35Flor reached significantly higher biomass in hydrogen-supplemented oxygen-sulfide gradient media, but hydrogen did not support growth of the strain in the absence of reduced sulfur compounds. Nevertheless, hydrogen oxidation can provide Beggiatoa sp. 35Flor with energy for maintenance and assimilatory purposes and may support the disposal of internally stored sulfur to prevent physical damage resulting from excessive sulfur accumulation. Our knowledge about the exposure of natural populations of Beggiatoaceae to hydrogen is very limited, but significant amounts of hydrogen could be provided by nitrogen fixation, fermentation, and geochemical processes in several of their typical habitats such as photosynthetic microbial mats and submarine sites of hydrothermal fluid flow. IMPORTANCE Reduced sulfur compounds are certainly the main electron donors for chemolithoautotrophic Beggiatoaceae, but the traditional focus on this topic has left other possible inorganic electron donors largely unexplored. In this paper, we provide evidence that hydrogen oxidation has the potential to strengthen the ecophysiological plasticity of Beggiatoaceae in several ways. Moreover, we show that hydrogen oxidation by members of this family can significantly influence biogeochemical gradients and therefore should be considered in environmental studies. PMID:26896131

  4. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    PubMed

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments.

  5. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus “Ferrovum”

    PubMed Central

    Ullrich, Sophie R.; Poehlein, Anja; Tischler, Judith S.; González, Carolina; Ossandon, Francisco J.; Daniel, Rolf; Holmes, David S.; Schlömann, Michael; Mühling, Martin

    2016-01-01

    Background Members of the genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain “Ferrovum myxofaciens” P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus “Ferrovum” is extremely scarce. Objective In order to access the wider genetic pool of the genus “Ferrovum” we sequenced the genome of a “Ferrovum”-containing mixed culture and successfully assembled the almost complete genome sequence of the novel “Ferrovum” strain JA12. Phylogeny and Lifestyle The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct “Ferrovum” species. “Ferrovum” strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that “Ferrovum” strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively. Unique Metabolic Features The potential utilisation of urea by “Ferrovum” strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs “Ferrovum” strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus

  6. Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea.

    PubMed

    Patwardhan, Sushmita; Vetriani, Costantino

    2016-09-01

    A mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic bacterium, designated strain TC8T, was isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, in the Tyrrhenian Sea, Italy. Cells were Gram-stain-negative curved rods with one or more polar flagella. Cells were approximately 1-1.5 µm in length and 0.6 µm in width. Strain TC8T grew between 20 and 35 °C (optimum 30 °C), with between 5 and 45 g NaCl l-1 (optimum 15-20 g l-1) and between pH 4.5 and 8.5 (optimum pH 6.0-7.0). The generation time under optimal conditions was 8 h. Strain TC8T was a facultative chemolithoautotroph also capable of using organic substrates as electron donors and carbon sources. Chemolithoautotrophic growth occurred with sulfur and thiosulfate as the electron donors, CO2 as the carbon source, and nitrate, oxygen (5 %, v/v) and ferric iron as the electron acceptors. Chemoorganoheterotrophic growth occurred with tryptone, peptone, Casamino acids, pyruvate and glycerol as substrates, while chemolithoherotrophic growth occurred with d(+)-glucose, sucrose, yeast extract, acetate, lactate, citrate and l-glutamine. The G+C content of the genomic DNA was 59.9 mol%. Phylogenetic analysis of the 16S rRNA gene sequence of strain TC8T showed that this organism formed a lineage within the family Rhodospirillaceae, which branched separately from the two closest relatives, Magnetovibrio blakemoreiMV1T (91.25 % similarity) and Magnetospira thiophilaMMS-1T (90.13 %). Based on phylogenetic, physiological and chemotaxonomic characteristics, it is proposed that the organism represents a novel species of a new genus within the family Rhodospirillaceae,Varunaivibrio sulfuroxidans gen. nov., sp. nov. The type strain of Varunaivibrio sulfuroxidans is TC8T (=DSM 101688T=JCM 31027T).

  7. Acidophilic Methanotrophic Communities from Sphagnum Peat Bogs

    PubMed Central

    Dedysh, Svetlana N.; Panikov, Nicolai S.; Tiedje, James M.

    1998-01-01

    Highly enriched methanotrophic communities (>25 serial transfers) were obtained from acidic ombrotrophic peat bogs from four boreal forest sites. The enrichment strategy involved using media conditions that were associated with the highest rates of methane uptake by the original peat samples, namely, the use of diluted mineral medium of low buffering capacity, moderate incubation temperature (20°C), and pH values of 3 to 6. Enriched communities contained a mixture of rod-shaped bacteria arranged in aggregates with a minor contribution of Hyphomicrobium-like cells. The growth stoichiometry of isolates was characteristic of methanotrophic bacteria (CH4/O2/CO2=1:1.1:0.59), with an average apparent yield of 0.41 ± 0.03 g of biomass C/g of CH4-C. DNA from each enrichment yielded a PCR product of the expected size with primers for both mmoX and mmoY genes of soluble methane monooxygenase. Two types of sequences were obtained for PCR-amplified fragments of mmoX. One of them exhibited high identity to the mmoX protein of the Methylocystis-Methylosinus group, whereas the other showed an equal level of divergence from both the Methylosinus-Methylocystis group and Methylococcus capsulatus (Bath) and formed a distinct branch. The pH optimum for growth and for CH4 uptake was 4.5 to 5.5, which is very similar to that for the optimum CH4 uptake observed in the original peat samples. These methanotrophs are moderate acidophiles rather than acidotolerant organisms, since their growth rate and methane uptake were much lower at neutral pH. The growth of the methanotrophic community was enhanced by using media with a very low salt content (20 to 200 mg/liter), more typical of their natural environment. All four enriched communities grew on N-free medium. PMID:9501432

  8. From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources

    PubMed Central

    Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

    2015-01-01

    At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe2+ ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD+ through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats. PMID:26500609

  9. Chemolithoautotrophic arsenite oxidation by a thermophilic Anoxybacillus flavithermus strain TCC9-4 from a hot spring in Tengchong of Yunnan, China

    PubMed Central

    Jiang, Dawei; Li, Ping; Jiang, Zhou; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Guo, Qinghai; Wang, Yanxin

    2015-01-01

    A new facultative chemolithoautotrophic arsenite (AsIII)-oxidizing bacterium TCC9-4 was isolated from a hot spring microbial mat in Tengchong of Yunnan, China. This strain could grow with AsIII as an energy source, CO2–HCO3- as a carbon source and oxygen as the electron acceptor in a minimal salts medium. Under chemolithoautotrophic conditions, more than 90% of 100 mg/L AsIII could be oxidized by the strain TCC9-4 in 36 h. Temperature was an important environmental factor that strongly influenced the AsIII oxidation rate and AsIII oxidase (Aio) activity; the highest Aio activity was found at the temperature of 40∘C. Addition of 0.01% yeast extract enhanced the growth significantly, but delayed the AsIII oxidation. On the basis of 16S rRNA phylogenetic sequence analysis, strain TCC9-4 was identified as Anoxybacillus flavithermus. To our best knowledge, this is the first report of arsenic (As) oxidation by A. flavithermus. The Aio gene in TCC9-4 might be quite novel relative to currently known gene sequences. The results of this study expand our current understanding of microbially mediated As oxidation in hot springs. PMID:25999920

  10. From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources.

    PubMed

    Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

    2015-01-01

    At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe(2+) ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD(+) through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats.

  11. Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems

    NASA Technical Reports Server (NTRS)

    Shock, Everett L.; Mccollom, Thomas; Schulte, Mithell D.

    1995-01-01

    Thermodynamic calculations provide the means to quantify the chemical disequilibrium inherent in the mixing of reduced hydrothermal fluids with seawater. The chemical energy available for metabolic processes in these environments can be evaluated by taking into account the pressure and temperature dependence of the apparent standard Gibbs free energies of reactions in the S-H2-H2O system together with geochemical constraints on pH, activities of aqueous sulfur species and fugacities of H2 and/or O2. Using present-day mixing of hydrothermal fluids and seawater as a starting point, it is shown that each mole of H2S entering seawater from hydrothermal fluids represents about 200,000 calories of chemical energy for metabolic systems able to catalyze H2S oxidation. Extrapolating to the early Earth, which was likely to have had an atmosphere more reduced than at present, shows that this chemical energy may have been a factor of two or so less. Nevertheless, mixing of hydrothermal fluids with seawater would have been an abundant source of chemical energy, and an inevitable consequence of the presence of an ocean on an initially hot Earth. The amount of energy available was more than enough for organic synthesis from CO2 or CO, and/or polymer formation, indicating that the vicinity of hydrothermal systems at the sea floor was an ideal location for the emergence of the first chemolithoautotrophic metabolic systems.

  12. Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems

    NASA Astrophysics Data System (ADS)

    Shock, Everett L.; McCollom, Thomas; Schulte, Mitchell D.

    1995-06-01

    Thermodynamic calculations provide the means to quantify the chemical disequilibrium inherent in the mixing of redeuced hydrothermal fluids with seawater. The chemical energy available for metabolic processes in these environments can be evaluated by taking into account the pressure and temperature dependence of the apparent standard Gibbs free energies of reactions in the S-H2-H2O system together with geochemical constraints on pH, activities of aqueous sulfur species and fugacities of H2 and/or O2. Using present-day mixing of hydrothermal fluids and seawater as a starting point, it is shown that each mole of H2S entering seawater from hydrothermal fluids represents about 200,000 calories of chemical energy for metabolic systems able to catalyze H2S oxidation. Extrapolating to the early Earth, which was likely to have had an atmosphere more reduced than at present, shows that this chemical energy may have been a factor of two or so less. Nevertheless, mixing of hydrothermal fluids with seawater would have been an abundant source of chemical energy, and an inevitable consequence of the presence of an ocean on an initially hot Earth. The amount of energy available was more than enough for organic synthesis from CO2 or CO, and/or polymer formation, indicating that the vicinity of hydrothermal systems at the sea floor was an ideal location for the emergence of the first chemolithoautotrophic metabolic systems.

  13. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions.

    PubMed

    Belnap, Christopher P; Pan, Chongle; Denef, Vincent J; Samatova, Nagiza F; Hettich, Robert L; Banfield, Jillian F

    2011-07-01

    Extensive genomic characterization of multi-species acid mine drainage microbial consortia combined with laboratory cultivation has enabled the application of quantitative proteomic analyses at the community level. In this study, quantitative proteomic comparisons were used to functionally characterize laboratory-cultivated acidophilic communities sustained in pH 1.45 or 0.85 conditions. The distributions of all proteins identified for individual organisms indicated biases for either high or low pH, and suggests pH-specific niche partitioning for low abundance bacteria and archaea. Although the proteome of the dominant bacterium, Leptospirillum group II, was largely unaffected by pH treatments, analysis of functional categories indicated proteins involved in amino acid and nucleotide metabolism, as well as cell membrane/envelope biogenesis were overrepresented at high pH. Comparison of specific protein abundances indicates higher pH conditions favor Leptospirillum group III, whereas low pH conditions promote the growth of certain archaea. Thus, quantitative proteomic comparisons revealed distinct differences in community composition and metabolic function of individual organisms during different pH treatments. Proteomic analysis revealed other aspects of community function. Different numbers of phage proteins were identified across biological replicates, indicating stochastic spatial heterogeneity of phage outbreaks. Additionally, proteomic data were used to identify a previously unknown genotypic variant of Leptospirillum group II, an indication of selection for a specific Leptospirillum group II population in laboratory communities. Our results confirm the importance of pH and related geochemical factors in fine-tuning acidophilic microbial community structure and function at the species and strain level, and demonstrate the broad utility of proteomics in laboratory community studies.

  14. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions

    SciTech Connect

    Belnap, Christopher P.; Pan, Chongle; Denef, Vincent; Samatova, Nagiza F; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2011-01-01

    Extensive genomic characterization of multi-species acid mine drainage microbial consortia combined with laboratory cultivation has enabled the application of quantitative proteomic analyses at the community level. In this study, quantitative proteomic comparisons were used to functionally characterize laboratory-cultivated acidophilic communities sustained in pH 1.45 or 0.85 conditions. The distributions of all proteins identified for individual organisms indicated biases for either high or low pH, and suggests pH-specific niche partitioning for low abundance bacteria and archaea. Although the proteome of the dominant bacterium, Leptospirillum group II, was largely unaffected by pH treatments, analysis of functional categories indicated proteins involved in amino acid and nucleotide metabolism, as well as cell membrane/envelope biogenesis were overrepresented at high pH. Comparison of specific protein abundances indicates higher pH conditions favor Leptospirillum group III, whereas low pH conditions promote the growth of certain archaea. Thus, quantitative proteomic comparisons revealed distinct differences in community composition and metabolic function of individual organisms during different pH treatments. Proteomic analysis revealed other aspects of community function. Different numbers of phage proteins were identified across biological replicates, indicating stochastic spatial heterogeneity of phage outbreaks. Additionally, proteomic data were used to identify a previously unknown genotypic variant of Leptospirillum group II, an indication of selection for a specific Leptospirillum group II population in laboratory communities. Our results confirm the importance of pH and related geochemical factors in fine-tuning acidophilic microbial community structure and function at the species and strain level, and demonstrate the broad utility of proteomics in laboratory community studies.

  15. Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses.

    PubMed

    Kip, Nardy; Ouyang, Wenjing; van Winden, Julia; Raghoebarsing, Ashna; van Niftrik, Laura; Pol, Arjan; Pan, Yao; Bodrossy, Levente; van Donselaar, Elly G; Reichart, Gert-Jan; Jetten, Mike S M; Damsté, Jaap S Sinninghe; Op den Camp, Huub J M

    2011-08-15

    Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses.

  16. Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals.

    PubMed

    Nybo, S Eric; Khan, Nymul E; Woolston, Benjamin M; Curtis, Wayne R

    2015-07-01

    The ability of autotrophic organisms to fix CO2 presents an opportunity to utilize this 'greenhouse gas' as an inexpensive substrate for biochemical production. Unlike conventional heterotrophic microorganisms that consume carbohydrates and amino acids, prokaryotic chemolithoautotrophs have evolved the capacity to utilize reduced chemical compounds to fix CO2 and drive metabolic processes. The use of chemolithoautotrophic hosts as production platforms has been renewed by the prospect of metabolically engineered commodity chemicals and fuels. Efforts such as the ARPA-E electrofuels program highlight both the potential and obstacles that chemolithoautotrophic biosynthetic platforms provide. This review surveys the numerous advances that have been made in chemolithoautotrophic metabolic engineering with a focus on hydrogen oxidizing bacteria such as the model chemolithoautotrophic organism (Ralstonia), the purple photosynthetic bacteria (Rhodobacter), and anaerobic acetogens. Two alternative strategies of microbial chassis development are considered: (1) introducing or enhancing autotrophic capabilities (carbon fixation, hydrogen utilization) in model heterotrophic organisms, or (2) improving tools for pathway engineering (transformation methods, promoters, vectors etc.) in native autotrophic organisms. Unique characteristics of autotrophic growth as they relate to bioreactor design and process development are also discussed in the context of challenges and opportunities for genetic manipulation of organisms as production platforms.

  17. Protection of chemolithoautotrophic bacteria exposed to simulated Mars environmental conditions

    NASA Astrophysics Data System (ADS)

    Gómez, Felipe; Mateo-Martí, Eva; Prieto-Ballesteros, Olga; Martín-Gago, Jose; Amils, Ricardo

    2010-10-01

    Current surface conditions (strong oxidative atmosphere, UV radiation, low temperatures and xeric conditions) on Mars are considered extremely challenging for life. The question is whether there are any features on Mars that could exert a protective effect against the sterilizing conditions detected on its surface. Potential habitability in the subsurface would increase if the overlaying material played a protective role. With the aim of evaluating this possibility we studied the viability of two microorganisms under different conditions in a Mars simulation chamber. An acidophilic chemolithotroph isolated from Río Tinto belonging to the Acidithiobacillus genus and Deinococcus radiodurans, a radiation resistant microorganism, were exposed to simulated Mars conditions under the protection of a layer of ferric oxides and hydroxides, a Mars regolith analogue. Samples of these microorganisms were exposed to UV radiation in Mars atmospheric conditions at different time intervals under the protection of 2 and 5 mm layers of oxidized iron minerals. Viability was evaluated by inoculation on fresh media and characterization of their growth cultures. Here we report the survival capability of both bacteria to simulated Mars environmental conditions.

  18. Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant.

    PubMed

    Ghosh, Wriddhiman; Roy, Pradosh

    2006-01-01

    The bacterial strain SJT(T), along with 15 other mesophilic, neutrophilic and facultatively sulfur-oxidizing chemolithotrophic isolates, was isolated by enrichment on reduced sulfur compounds as the sole energy and electron source from soils immediately adjacent to the roots of Clitoria ternatea, a slender leguminous herb of the Lower Gangetic plains of India. Strain SJT(T) was able to oxidize thiosulfate and elemental sulfur for chemolithoautotrophic growth. 16S rRNA and recA gene sequence-based phylogenetic analyses showed that the Gram-negative rod-shaped bacterium belonged to the genus Mesorhizobium and was most closely related to Mesorhizobium loti, Mesorhizobium plurifarium, Mesorhizobium amorphae and Mesorhizobium chacoense. Unequivocally low 16S rRNA (<97 %) and recA (< or =88 %) gene sequence similarities to all existing species of the most closely related genera, a unique fatty acid profile, a distinct G+C content (59.6 mol%) and phenotypic characteristics all suggested that strain SJT(T) represents a novel species. DNA-DNA hybridization and SDS-PAGE analysis of whole-cell proteins also confirmed the taxonomic uniqueness of SJT(T). It is therefore proposed that isolate SJT(T) (= LMG 22697T = MTCC 7001T) be classified as the type strain of a novel species, Mesorhizobium thiogangeticum sp. nov.

  19. Novel thermo-acidophilic bacteria isolated from geothermal sites in Yellowstone National Park: physiological and phylogenetic characteristics.

    PubMed

    Johnson, D Barrie; Okibe, Naoko; Roberto, Francisco F

    2003-07-01

    Moderately thermophilic acidophilic bacteria were isolated from geothermal (30-83 degrees C) acidic (pH 2.7-3.7) sites in Yellowstone National Park. The temperature maxima and pH minima of the isolates ranged from 50 to 65 degrees C, and pH 1.0-1.9. Eight of the bacteria were able to catalyze the dissimilatory oxidation of ferrous iron, and eleven could reduce ferric iron to ferrous iron in anaerobic cultures. Several of the isolates could also oxidize tetrathionate. Six of the iron-oxidizing isolates, and one obligate heterotroph, were low G+C gram-positive bacteria ( Firmicutes). The former included three Sulfobacillus-like isolates (two closely related to a previously isolated Yellowstone strain, and the third to a mesophilic bacterium isolated from Montserrat), while the other three appeared to belong to a different genus. The other two iron-oxidizers were an Actinobacterium (related to Acidimicrobium ferrooxidans) and a Methylobacterium-like isolate (a genus within the alpha -Proteobacteria that has not previously been found to contain either iron-oxidizers or acidophiles). The other three (heterotrophic) isolates were also alpha-Proteobacteria and appeared be a novel thermophilic Acidisphaera sp. An ARDREA protocol was developed to discriminate between the iron-oxidizing isolates. Digestion of amplified rRNA genes with two restriction enzymes ( SnaBI and BsaAI) separated these bacteria into five distinct groups; this result was confirmed by analysis of sequenced rRNA genes.

  20. Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin.

    PubMed

    Albert, Richard A; Archambault, Julieta; Rosselló-Mora, Ramón; Tindall, Brian J; Matheny, Mike

    2005-09-01

    A mesophilic, acidophilic, spore-forming bacterium, strain 105-2(T), was isolated from an acidic Sphagnum peat bog in Wisconsin, USA. Strain 105-2(T) has 16S rRNA gene sequence similarity to Bacillus sporothermodurans DSM 10599(T) and Bacillus oleronius DSM 9356(T) of 97.4 and 97.8%, respectively. The primary lipoquinone is MK-7 and the major fatty acids are 15:0 iso, 15:0 anteiso and 17:0 anteiso. The predominant polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a glycolipid. The DNA G+C content was found to be 43.2 mol%. The phenotypic, chemotaxonomic and molecular analyses identified strain 105-2(T) as a novel Bacillus species, for which the name Bacillus acidicola is proposed. The type strain is 105-2(T) (=DSM 14745(T)=ATCC BAA-366(T)=NRRL B-23453(T)).

  1. Genomics and Metagenomics of Extreme Acidophiles in Biomining Environments

    NASA Astrophysics Data System (ADS)

    Holmes, D. S.

    2015-12-01

    Over 160 draft or complete genomes of extreme acidophiles (pH < 3) have been published, many of which are from bioleaching and other biomining environments, or are closely related to such microorganisms. In addition, there are over 20 metagenomic studies of such environments. This provides a rich source of latent data that can be exploited for understanding the biology of biomining environments and for advancing biotechnological applications. Genomic and metagenomic data are already yielding valuable insights into cellular processes, including carbon and nitrogen management, heavy metal and acid resistance, iron and sulfur oxido-reduction, linking biogeochemical processes to organismal physiology. The data also allow the construction of useful models of the ecophysiology of biomining environments and provide insight into the gene and genome evolution of extreme acidophiles. Additionally, since most of these acidophiles are also chemoautolithotrophs that use minerals as energy sources or electron sinks, their genomes can be plundered for clues about the evolution of cellular metabolism and bioenergetic pathways during the Archaean abiotic/biotic transition on early Earth. Acknowledgements: Fondecyt 1130683.

  2. Engineering the iron-oxidizing chemolithoautotroph Acidithiobacillus ferrooxidans for biochemical production.

    PubMed

    Kernan, Timothy; Majumdar, Sudipta; Li, Xiaozheng; Guan, Jingyang; West, Alan C; Banta, Scott

    2016-01-01

    There is growing interest in developing non-photosynthetic routes for the conversion of CO2 to fuels and chemicals. One underexplored approach is the transfer of energy to the metabolism of genetically modified chemolithoautotrophic bacteria. Acidithiobacillus ferrooxidans is an obligate chemolithoautotroph that derives its metabolic energy from the oxidation of iron or sulfur at low pH. Two heterologous biosynthetic pathways have been expressed in A. ferrooxidans to produce either isobutyric acid or heptadecane from CO2 and the oxidation of Fe(2+). A sevenfold improvement in productivity of isobutyric acid was obtained through improved media formulations in batch cultures. Steady-state efficiencies were lower in continuous cultures, likely due to ferric inhibition. If coupled to solar panels, the photon-to-fuel efficiency of this proof-of-principle process approaches estimates for agriculture-derived biofuels. These efforts lay the foundation for the utilization of this organism in the exploitation of electrical energy for biochemical synthesis.

  3. Mycobacteria Isolated from Angkor Monument Sandstones Grow Chemolithoautotrophically by Oxidizing Elemental Sulfur

    PubMed Central

    Kusumi, Asako; Li, Xian Shu; Katayama, Yoko

    2011-01-01

    To characterize sulfate-producing microorganisms from the deteriorated sandstones of Angkor monuments in Cambodia, strains of Mycobacterium spp. were isolated from most probable number-positive cultures. All five strains isolated were able to use both elemental sulfur (S0) for chemolithoautotrophic growth and organic substances for chemoorganoheterotrophic growth. Results of phylogenetic and phenotypic analyses indicated that all five isolates were rapid growers of the genus Mycobacterium and were most similar to Mycobacterium cosmeticum and Mycobacterium pallens. Chemolithoautotrophic growth was further examined in the representative strain THI503. When grown in mineral salts medium, strain THI503 oxidized S0 to thiosulfate and sulfate; oxidation was accompanied by a decrease in the pH of the medium from 4.7 to 3.6. The link between sulfur oxidation and energy metabolism was confirmed by an increase in ATP. Fluorescence microscopy of DAPI-stained cells revealed that strain THI503 adheres to and proliferates on the surface of sulfur particles. The flexible metabolic ability of facultative chemolithoautotrophs enables their survival in nutrient-limited sandstone environments. PMID:21747806

  4. Novel Thermo-Acidophilic Bacteria Isolated from Geothermal Sites in Yellowstone National Park: Physiological and Phylogenetic Characteristics

    SciTech Connect

    D. B. Johnson; N. Okibe; F. F. Roberto

    2003-07-01

    Moderately thermophilic acidophilic bacteria were isolated from geothermal (30–83 °C) acidic (pH 2.7– 3.7) sites in Yellowstone National Park. The temperature maxima and pH minima of the isolates ranged from 50 to 65 °C, and pH 1.0–1.9. Eight of the bacteria were able to catalyze the dissimilatory oxidation of ferrous iron, and eleven could reduce ferric iron to ferrous iron in anaerobic cultures. Several of the isolates could also oxidize tetrathionate. Six of the iron-oxidizing isolates, and one obligate heterotroph, were low G+C gram-positive bacteria (Firmicutes). The former included three Sulfobacillus-like isolates (two closely related to a previously isolated Yellowstone strain, and the third to a mesophilic bacterium isolated from Montserrat), while the other three appeared to belong to a different genus. The other two iron-oxidizers were an Actinobacterium (related to Acidimicrobium ferrooxidans) and a Methylobacterium-like isolate (a genus within the a-Proteobacteria that has not previously been found to contain either iron-oxidizers or acidophiles). The other three (heterotrophic) isolates were also a-Proteobacteria and appeared be a novel thermophilic Acidisphaera sp. An ARDREA protocol was developed to discriminate between the iron-oxidizing isolates. Digestion of amplified rRNA genes with two restriction enzymes (SnaBI and BsaAI) separated these bacteria into five distinct groups; this result was confirmed by analysis of sequenced rRNA genes.

  5. [Study on fast discrimination of varieties of acidophilous milk using near infrared spectra].

    PubMed

    He, Yong; Feng, Shui-juan; Li, Xiao-li; Qiu, Zheng-jun

    2006-11-01

    A new method for the discrimination of varieties of near acidophilous milk by means of near infrared spectroscopy (NIRS) was developed. Firstly, through the principal component analysis (PCA) of spectroscopic curves of 5 typical kinds of acidophilous milk, the clustering of acidophilous milk varieties was processed. The analysis results showed that the cumulate reliabilities of PC1 and PC2 (the first two principal components) reached 98.96%, and the cumulate reliabilities of PC1 to PC7 (the first seven principal components) were 99.97%. Secondly, a discrimination model of artificial neural network (ANN-BP) was set up. The first seven principal components of the samples were applied as ANN-BP inputs, and the values of type of acidophilous milk were applied as outputs, then the three layer ANN-BP model was build. In this model, every variety of acidophilous milk includes 27 samples, the total number of samples is 135, and the rest 25 samples were used as prediction set. Calculation results showed that the distinguishing rate of the five acidophilous milk varieties was 100%. This model is reliable and practicable. So a new approach to the rapid and lossless discrimination of varieties of acidophilous milk was put forward.

  6. Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: comparison of growing- and energy-starved cells.

    PubMed

    Pellitteri-Hahn, Molly C; Halligan, Brian D; Scalf, Mark; Smith, Lloyd; Hickey, William J

    2011-04-01

    Obligately aerobic ammonia-oxidizing bacteria (AOB) like Nitrosomonas europaea play a pivotal role in the global nitrogen cycle. Although starvation tolerance is a key environmental adaptation, little is known about this response in AOB. The goal of these studies was to compare the composition of the N. europaea proteome in growing- and energy-starved cells using ¹⁵N labeling and HPLC-ESI-MS/MS. More than 6500 peptides were sequenced with high confidence, and matched to 876 proteins (34% of the protein coding genes). Of these, 126 proteins had two or more peptide forms identified by 10 or more scans, and were used in quantitative analysis and 27 were found to be significantly different in abundance between growing and starved cells. Proteins showing greater abundance in growing cells are geared toward biosynthesis, particularly DNA replication. Energy-starved cells were shifted away from biosynthesis and toward survival functions that included: cell envelope modification, protein protection/degradation, detoxification, and implementation of alternative energy generation mechanisms. Most of these activities have not previously been reported as associated with energy-starvation stress in N. europaea. This study provides insights into the potential effects of fluctuating environmental conditions on the regulation of physiological networks in N. europaea.

  7. A Description of an Acidophilic, Iron Reducer, Geobacter sp. FeAm09 Isolated from Tropical Soils

    NASA Astrophysics Data System (ADS)

    Healy, O.; Souchek, J.; Heithoff, A.; LaMere, B.; Pan, D.; Hollis, G.; Yang, W. H.; Silver, W. L.; Weber, K. A.

    2014-12-01

    Iron (Fe) is the fourth most abundant element in the Earth's crust and plays a significant role controlling the geochemistry in soils, sediments, and aquatic systems. As part of a study to understand microbially-catalysed iron biogeochemical cycling in tropical soils, an iron reducing isolate, strain FeAm09, was obtained. Strain FeAm09 was isolated from acidic, Fe-rich soils collected from a tropical forest (Luquillo Experimental Forest, Puerto Rico). Strain FeAm09 is a rod-shaped, motile, Gram-negative bacterium. Taxonomic analysis of the near complete 16S rRNA gene sequence revealed that strain FeAm09 is 94.7% similar to Geobacter lovleyi, placing it in the genus Geobacter within the Family Geobacteraceae in the Deltaproteobacteria. Characterization of the optimal growth conditions revealed that strain FeAm09 is a moderate acidophile with an optimal growth pH of 5.0. The optimal growth temperature was 37°C. Growth of FeAm09 was coupled to the reduction of soluble Fe(III), Fe(III)-NTA, with H2, fumarate, ethanol, and various organic acids and sugars serving as the electron donor. Insoluble Fe(III), in the form of synthetic ferrihydrite, was reduced by strain FeAm09 using acetate or H2 as the electron donor. The use of H2 as an electron donor in the presence of CO2 and absence of organic carbon and assimilation of 14C-labelled CO2 into biomass indicate that strain FeAm09 is an autotrophic Fe(III)-reducing bacterium. Together, these data describe the first acidophilic, autotrophic Geobacter species. Iron reducing bacteria were previously shown to be as abundant in tropical soils as in saturated sediments (lake-bottoms) and saturated soils (wetlands) where Fe(III) reduction is more commonly recognized as a dominant mode of microbial respiration. Furthermore, Fe(III) reduction was identified as a primary driver of carbon mineralization in these tropical soils (Dubinsky et al. 2010). In addition to mineralizing organic carbon, Geobacter sp. FeAm09 is likely to also

  8. Thiomicrospira hydrogeniphila sp. nov., an aerobic, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a seawater tank containing a block of beef tallow.

    PubMed

    Watsuji, Tomo-O; Hada, Emi; Miyazaki, Masayuki; Ichimura, Masako; Takai, Ken

    2016-09-01

    A moderately psychrophilic, aerobic, hydrogen- and sulfur-oxidizing bacterium, designated strain MAS2T, was isolated from a tank containing coastal seawater from Tokyo Bay and a block of beef tallow added as organic material. Growth occurred under aerobic chemolithoautotrophic conditions in the presence of molecular hydrogen, thiosulfate, tetrathionate, elemental sulfur or sulfide as the sole energy source and bicarbonate as a carbon source. The isolate represented a Gram-staining-negative rod with a single polar flagellum and grew in artificial seawater medium with thiosulfate at 2-40 °C (optimum 30 °C). The isolate grew in media with thiosulfate at Na+ concentrations between 30 and 1380 mM (optimum 270 mM). MAS2T possessed C16 : 0, C16 : 1 and C18 : 1 as the major fatty acids. The G+C content of the genomic DNA was 39.6 mol%. The 16S rRNA gene sequence similarity analysis showed that the isolate represented a member of the genus Thiomicrospira within the class Gammaproteobacteria and was most closely related to Thiomicrospira frisia JB-A2T. On the basis of phenotypic and molecular properties, the isolate represents a novel species of the genus Thiomicrospira, for which the name Thiomicrospira hydrogeniphila sp. nov. is proposed (type strain, MAS2T=JCM 30760T=DSM 100274T).

  9. In Situ Gene Expression Responsible for Sulfide Oxidation and CO2 Fixation of an Uncultured Large Sausage-Shaped Aquificae Bacterium in a Sulfidic Hot Spring

    PubMed Central

    Tamazawa, Satoshi; Yamamoto, Kyosuke; Takasaki, Kazuto; Mitani, Yasuo; Hanada, Satoshi; Kamagata, Yoichi; Tamaki, Hideyuki

    2016-01-01

    We investigated the in situ gene expression profile of sulfur-turf microbial mats dominated by an uncultured large sausage-shaped Aquificae bacterium, a key metabolic player in sulfur-turfs in sulfidic hot springs. A reverse transcription-PCR analysis revealed that the genes responsible for sulfide, sulfite, and thiosulfate oxidation and carbon fixation via the reductive TCA cycle were continuously expressed in sulfur-turf mats taken at different sampling points, seasons, and years. These results suggest that the uncultured large sausage-shaped bacterium has the ability to grow chemolithoautotrophically and plays key roles as a primary producer in the sulfidic hot spring ecosystem in situ. PMID:27297893

  10. In Situ Gene Expression Responsible for Sulfide Oxidation and CO2 Fixation of an Uncultured Large Sausage-Shaped Aquificae Bacterium in a Sulfidic Hot Spring.

    PubMed

    Tamazawa, Satoshi; Yamamoto, Kyosuke; Takasaki, Kazuto; Mitani, Yasuo; Hanada, Satoshi; Kamagata, Yoichi; Tamaki, Hideyuki

    2016-06-25

    We investigated the in situ gene expression profile of sulfur-turf microbial mats dominated by an uncultured large sausage-shaped Aquificae bacterium, a key metabolic player in sulfur-turfs in sulfidic hot springs. A reverse transcription-PCR analysis revealed that the genes responsible for sulfide, sulfite, and thiosulfate oxidation and carbon fixation via the reductive TCA cycle were continuously expressed in sulfur-turf mats taken at different sampling points, seasons, and years. These results suggest that the uncultured large sausage-shaped bacterium has the ability to grow chemolithoautotrophically and plays key roles as a primary producer in the sulfidic hot spring ecosystem in situ.

  11. Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog.

    PubMed

    Mamani, Sigde; Moinier, Danielle; Denis, Yann; Soulère, Laurent; Queneau, Yves; Talla, Emmanuel; Bonnefoy, Violaine; Guiliani, Nicolas

    2016-01-01

    While a functional quorum sensing system has been identified in the acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 23270(T) and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in A. ferrooxidans (T), the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL (N-acyl homoserine lactones) analog has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analog, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy. A fast adherence of A. ferrooxidans (T) cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signaling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the A. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that quorum sensing network represents at least 4.5% (141 genes) of the ATCC 23270(T) genome of which 42.5% (60 genes) are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of A. ferrooxidans to quorum sensing and on biofilm biogenesis.

  12. Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog

    PubMed Central

    Mamani, Sigde; Moinier, Danielle; Denis, Yann; Soulère, Laurent; Queneau, Yves; Talla, Emmanuel; Bonnefoy, Violaine; Guiliani, Nicolas

    2016-01-01

    While a functional quorum sensing system has been identified in the acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 23270T and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in A. ferrooxidansT, the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL (N-acyl homoserine lactones) analog has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analog, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy. A fast adherence of A. ferrooxidansT cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signaling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the A. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that quorum sensing network represents at least 4.5% (141 genes) of the ATCC 23270T genome of which 42.5% (60 genes) are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of A. ferrooxidans to quorum sensing and on biofilm biogenesis. PMID:27683573

  13. The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2

    SciTech Connect

    Scott, K M; Sievert, S M; Abril, F N; Ball, L A; Barrett, C J; Blake, R A; Boller, A J; Chain, P G; Clark, J A; Davis, C R; Detter, C; Do, K F; Dobrinski, K P; Faza, B I; Fitzpatrick, K A; Freyermuth, S K; Harmer, T L; Hauser, L J; Hugler, M; Kerfeld, C A; Klotz, M G; Kong, W W; Land, M; Lapidus, A; Larimer, F W; Longo, D L; Lucas, S; Malfatti, S A; Massey, S E; Martin, D D; McCuddin, Z; Meyer, F; Moore, J L; Ocampo Jr., L H; Paul, J H; Paulsen, I T; Reep, D K; Ren, Q; Ross, R L; Sato, P Y; Thomas, P; Tinkham, L E; Zerugh, G T

    2007-01-10

    Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 bp), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of CDSs encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. T. crunogena XCL-2 is unusual among obligate sulfur oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. A 38 kb prophage is present, and a high level of prophage induction was observed, which may play a role in keeping competing populations of close relatives in check. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.

  14. Organization and regulation of the arsenite oxidase operon of the moderately acidophilic and facultative chemoautotrophic Thiomonas arsenitoxydans.

    PubMed

    Slyemi, Djamila; Moinier, Danielle; Talla, Emmanuel; Bonnefoy, Violaine

    2013-11-01

    Thiomonas arsenitoxydans is an acidophilic and facultatively autotrophic bacterium that can grow by oxidizing arsenite to arsenate. A comparative genomic analysis showed that the T. arsenitoxydans aioBA cluster encoding the two subunits of arsenite oxidase is distinct from the other clusters, with two specific genes encoding a cytochrome c and a metalloregulator belonging to the ArsR/SmtB family. These genes are cotranscribed with aioBA, suggesting that these cytochromes c are involved in arsenite oxidation and that this operon is controlled by the metalloregulator. The growth of T. arsenitoxydans in the presence of thiosulfate and arsenite, or arsenate, is biphasic. Real-time PCR experiments showed that the operon is transcribed during the second growth phase in the presence of arsenite or arsenate, whereas antimonite had no effect. These results suggest that the expression of the aioBA operon of T. arsenitoxydans is regulated by the electron donor present in the medium, i.e., is induced in the presence of arsenic but is repressed by more energetic substrates. Our data indicate that the genetic organization and regulation of the aioBA operon of T. arsenitoxydans differ from those of the other arsenite oxidizers.

  15. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community

    SciTech Connect

    Verberkmoes, Nathan C; Singer, Steven; Shah, Manesh B; Thelen, Michael P.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2008-01-01

    We have discovered and characterized a novel membrane cytochrome of an iron oxidizing microbial biofilm obtained from the surface of extremely acidic mine water. This protein was initially identified through proteogenomic analysis as one of many novel gene products of Leptospirillum group II, the dominant bacterium of this community (Ram et al, 2005, Science 308, 1915-20). Extraction of proteins directly from environmental biofilm samples followed by membrane fractionation, detergent solubilization and gel filtration chromatography resulted in the purification of an abundant yellow-red protein. Covalently bound to heme, the purified cytochrome has a unique spectral signature at 572 nm and is thus called Cyt572. It readily oxidizes Fe2+ even in the presence of Fe3+ over a pH range from 0.95 to 3.4. Independent experiments involving 2D blue-native polyacrylamide gel electrophoresis and chemical crosslinking establish a homotetrameric structure for Cyt572. Also, circular dichroism spectroscopy indicates that the protein is largely beta-stranded, consistent with an outer membrane location. Although no significant sequence homology to the full-length cytochrome is detected in protein databases, environmental DNA sequences from both Leptospirillum groups II and III reveal at least 17 strain variants of Cyt572. Due to its abundance, cellular location and Fe2+ oxidation activity, we propose Cyt572 is the iron oxidase of the Leptospirillum bacteria, providing a critical function for fitness within the ecological niche of this acidophilic microbial community.

  16. Cultivation and quantitative proteomic analyses of acidophilic microbial communities

    SciTech Connect

    Belnap, Christopher P.; Pan, Chongle; Verberkmoes, Nathan C; Power, Mary E.; Samatova, Nagiza F; Carver, Rudolf L.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.

  17. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    PubMed Central

    Bollmann, Annette; Sedlacek, Christopher J.; Norton, Jeanette; Laanbroek, Hendrikus J.; Suwa, Yuichi; Stein, Lisa Y.; Klotz, Martin G.; Arp, Daniel; Sayavedra-Soto, Luis; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, James; Woyke, Tanja; Lucas, Susan M.; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L.; Huntemann, Marcel; Deshpande, Shweta; Han, Cliff; Chen, Amy; Kyrpides, Nikos; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Peters, Lin; Ovchinnikova, Galina; Goodwin, Lynne A.

    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 chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006. PMID:24019993

  18. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    SciTech Connect

    Bollmann, Annette; Sedlacek, Christopher J; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Klotz, Martin G; Arp, D J; Sayavedra-Soto, LA; Lu, Megan; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, James; Woyke, Tanja; Lucas, Susan; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L; Huntemann, Marcel; Deshpande, Shweta; Han, Cliff; Chen, Amy; Kyrpides, Nikos C; Mavromatis, K; Markowitz, Victor; Szeto, Ernest; Ivanova, N; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Peters, Lin; Ovchinnikova, Galina; Goodwin, Lynne A.

    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 chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

  19. Iron and carbon metabolism by a mineral-oxidizing Alicyclobacillus-like bacterium.

    PubMed

    Yahya, Adibah; Hallberg, Kevin B; Johnson, D Barrie

    2008-04-01

    A novel iron-oxidizing, moderately thermophilic, acidophilic bacterium (strain "GSM") was isolated from mineral spoil taken from a gold mine in Montana. Biomolecular analysis showed that it was most closely related to Alicyclobacillus tolerans, although the two bacteria differed in some key respects, including the absence (in strain GSM) of varpi-alicyclic fatty acids and in their chromosomal base compositions. Isolate GSM was able to grow in oxygen-free media using ferric iron as terminal electron acceptor confirming that it was a facultative anaerobe, a trait not previously described in Alicyclobacillus spp.. The acidophile used both organic and inorganic sources of energy and carbon, although growth and iron oxidation by isolate GSM was uncoupled in media that contained both fructose and ferrous iron. Fructose utilization suppressed iron oxidation, and oxidation of ferrous iron occurred only when fructose was depleted. In contrast, fructose catabolism was suppressed when bacteria were harvested while actively oxidizing iron, suggesting that both ferrous iron- and fructose-oxidation are inducible in this acidophile. Isolate GSM accelerated the oxidative dissolution of pyrite in liquid media either free of, or amended with, organic carbon, although redox potentials were significantly different in these media. The potential of this isolate for commercial mineral processing is discussed.

  20. Genomics of the thermo-acidophilic red alga Galdieria sulphuraria

    NASA Astrophysics Data System (ADS)

    Barbier, Guillaume G.; Zimmermann, Marc; Weber, Andreas P. M.

    2005-09-01

    Extremophilic organisms dwell in environments that are characterized by high or low temperatures (thermophiles or psychrophiles), very low or high pH-values (acidophiles or alkalophiles), high salt concentrations (halophiles), high pressure (barophiles), or extreme drought (xerophiles). Many extremophiles are microbes, and many also belong to the prokaryota. Galdieria sulphuraria, however, is a member of a group of extremophilic eukaryotes that are named Cyanidiales. Cyanidiales are unicellular red micro-algae that occur worldwide in hot acidic waters, volcanic calderas, and in human-made acidic environments such as acidic mine drainage. G. sulphuraria has a unique position within the Cyanidiales because, in contrast to the other obligate photoautotrophic members of this group, it is able to grow photoautotrophically, mixotrophically, and heterotrophically. It is not only resistant to acid (pH 0) and heat (56oC), but also to high salt (1.5 M NaCl), toxic metals, and many other abiotic stressors. This unusual combination of features such as thermophily, acidophily, resistance to a wide array of abiotic stressors, and an extraordinary metabolic plasticity make G. sulphuraria highly interesting model organism to study adaptation to extreme environments. We have started a genomics approach to gain insight into the biology of G. sulphuraria and to identify genes and gene products critical for survival under extreme conditions. To this end, we pursue a whole-genome, shotgun sequencing approach towards unraveling the genome sequence of G. sulphuraria. We report here on the status quo of the genome-sequencing project and we summarize what we have learned to date from the genome sequence about the biology of this truly unique extremophile.

  1. Population structure of deep-sea chemolithoautotrophs: identification of phenotypic and genotypic correlations

    NASA Astrophysics Data System (ADS)

    Mino, S.; Nakagawa, S.; Sawabe, T.; Miyazaki, J.; Makita, H.; Nunoura, T.; Yamamoto, M.; Takai, K.

    2012-12-01

    Deep-sea hydrothermal fields are areas on the seafloor of high biological productivity fueled primarily by microbial chemosynthesis. Chemolithoautotrophic Epsilonproteobacteria and Persephonella with an ability to utilize inorganic substrates such as elemental sulfur and hydrogen are important members in wide range of temperature conditions in deep-sea hydrothermal vents. However, little is known about their population genetic structure such as intraspecific genetic diversity, distribution pattern, and phenotypic characteristics. Previously, using genetic approach based on multi-locus sequence analysis (MLSA), we clarified that Epsilonproteobacteria Group A, B, F, and Persephonella populations were geographically separated, and Epsilonproteobacteria appeared to diverge by mutation rather than recombination. Contrary to genetic evidence for allopatric segregation in deep-sea chemoautotrophs, however, phenotypic evidence has never been found. In addition, analyzing such a phenotypic characteristic may lead to a better understanding of the interactions microbes have with their environment. In this study, we present a metabolomic approach based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to reveal phenotypic biogeographical discrimination. We demonstrated the whole-cell MALDI-TOF MS method on Epsilonproteobacteria and Persephonella populations. These chemoautotrophic strains used in this study were isolated from chimney structures, vent fluids, and hydrothermal sediments. These hydrothermal samples were collected from geographically separated hydrothermal areas of the South Mariana Trough, Okinawa Trough and Central Indian Ridge. Based on mass peaks (signal/noise >10) within the m/z range of 2000-14000, phenotypic analysis was carried out by cluster analysis. The result of phenotypic analysis was compared with the genotypic clusters. The whole-cell MALDI-TOF MS revealed that Persephonella population was identified to

  2. Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system.

    PubMed

    Takai, Ken; Nakagawa, Satoshi; Sako, Yoshihiko; Horikoshi, Koki

    2003-11-01

    A novel, extremely thermophilic bacterium, designated strain 17S(T), was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. The cells were rods with no apparent motility, most of which were narrow in the middle in the exponential-growth phase and had several polar flagella at both ends. Growth was observed between 45 and 80 degrees C (optimum temperature, 70-75 degrees C; doubling time, 80 min) and between pH 5.0 and 7.0 (optimum pH, 5.4). The isolate was a strictly anaerobic chemolithoautotroph that was capable of using molecular hydrogen as its sole energy source and carbon dioxide as its sole carbon source. Elemental sulfur (S(0)) was required for growth as an electron acceptor. The G+C content of the genomic DNA was 34.6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was related to Thermovibrio ruber ED11/3LLK(T) and Desulfurobacterium thermolithotrophum BSA(T), whilst it appeared to be a novel lineage prior to the divergence of these genera. This isolate could also be differentiated from both T. ruber ED11/3LLK(T) and D. thermolithotrophum BSA(T) on the basis of physiological properties. The name Balnearium lithotrophicum gen. nov., sp. nov. is proposed for this isolate (type strain, 17S(T)=JCM 11970(T)=ATCC BAA-736(T)).

  3. Acidiferrobacter thiooxydans, gen. nov. sp. nov.; an acidophilic, thermo-tolerant, facultatively anaerobic iron- and sulfur-oxidizer of the family Ectothiorhodospiraceae.

    PubMed

    Hallberg, Kevin B; Hedrich, Sabrina; Johnson, D Barrie

    2011-03-01

    A comprehensive physiological and phylogenetic characterisation was carried out of "Thiobacillus ferrooxidans" m-1, an acidophilic iron-oxidizing bacterium first described over 25 years ago. Phylogenetically, strain m-1 is a gammaproteobacterium, most closely related to alkaliphilic Ectothiorhodospira spp. and only distantly to iron-oxidizing acidithiobacilli. Physiological examination confirmed that strain m-1 can grow autotrophically not only by ferrous iron oxidation but also, in contrast to previous reports, by oxidation of elemental sulfur, sulfide and tetrathionate, using either oxygen or ferric iron as terminal electron acceptor. The bacterium was also found to be thermo-tolerant, growing optimally at 38°C and up to a maximum of 47°C. Growth in liquid media required an external osmotic potential of >2 bar, and was optimal at ~5 bar, though no growth occurred where the medium osmotic potential was close to that of sea water (~26 bar). From this, it was concluded that strain m-1 is a moderate osmophile. Strain m-1 was also shown to be diazotrophic and tolerant of elevated concentrations of many metals typically found in mine-impacted environments. On the basis of these data, m-1 is proposed as the type strain of a new genus and species of bacteria, Acidiferrobacter thiooxydans (DSM 2392, JCM 17358).

  4. Detection, Isolation, and Characterization of Acidophilic Methanotrophs from Sphagnum Mosses ▿ †

    PubMed Central

    Kip, Nardy; Ouyang, Wenjing; van Winden, Julia; Raghoebarsing, Ashna; van Niftrik, Laura; Pol, Arjan; Pan, Yao; Bodrossy, Levente; van Donselaar, Elly G.; Reichart, Gert-Jan; Jetten, Mike S. M.; Sinninghe Damsté, Jaap S.; Op den Camp, Huub J. M.

    2011-01-01

    Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses. PMID:21724892

  5. Genome Sequence of the Acidophilic Iron Oxidizer Ferrimicrobium acidiphilum Strain T23T.

    PubMed

    Eisen, Sebastian; Poehlein, Anja; Johnson, D Barrie; Daniel, Rolf; Schlömann, Michael; Mühling, Martin

    2015-04-30

    Extremely acidophilic iron-oxidizing bacteria have largely been characterized for the phyla Proteobacteria and Nitrospira. Here, we report the draft genome of an iron-oxidizing and -reducing heterotrophic mesophile of the Actinobacteria, Ferrimicrobium acidiphilum, which was isolated from an abandoned pyrite mine. The genome sequence comprises 3.08 Mb.

  6. Diffusion susceptibility demonstrates relative inhibition potential of sorbent-immobilized heavy metals against sulfur oxidizing acidophiles.

    PubMed

    Caicedo-Ramirez, Alejandro; Ling, Alison L; Hernandez, Mark

    2016-12-01

    A new generation of laminates and cementitious materials incorporate antimicrobial metals into domestic infrastructure. Conventional culturing approaches are unsuitable for assessing the inhibitory properties of these materials. Modifications to the radial Kirby-Bauer antibiotic assay, which incorporate metal impregnated activated carbon in linear formats, reveal relative metal sensitivities of destructive acidophiles.

  7. A method of genetically engineering acidophilic, heterotrophic, bacteria by electroporation and conjugation

    SciTech Connect

    Roberto, F.F.; Glenn, A.W.; Ward, T.E.

    1990-08-07

    A method of genetically manipulating an acidophilic bacteria is provided by two different procedures. Using electroporation, chimeric and broad-host range plasmids are introduced into Acidiphilium. Conjugation is also employed to introduce broad-host range plasmids into Acidiphilium at neutral pH.

  8. Enhanced Productivity of a Lutein-Enriched Novel Acidophile Microalga Grown on Urea

    PubMed Central

    Casal, Carlos; Cuaresma, Maria; Vega, Jose Maria; Vilchez, Carlos

    2011-01-01

    Coccomyxa acidophila is an extremophile eukaryotic microalga isolated from the Tinto River mining area in Huelva, Spain. Coccomyxa acidophila accumulates relevant amounts of β-carotene and lutein, well-known carotenoids with many biotechnological applications, especially in food and health-related industries. The acidic culture medium (pH < 2.5) that prevents outdoor cultivation from non-desired microorganism growth is one of the main advantages of acidophile microalgae production. Conversely, acidophile microalgae growth rates are usually very low compared to common microalgae growth rates. In this work, we show that mixotrophic cultivation on urea efficiently enhances growth and productivity of an acidophile microalga up to typical values for common microalgae, therefore approaching acidophile algal production towards suitable conditions for feasible outdoor production. Algal productivity and potential for carotenoid accumulation were analyzed as a function of the nitrogen source supplied. Several nitrogen conditions were assayed: nitrogen starvation, nitrate and/or nitrite, ammonia and urea. Among them, urea clearly led to the best cell growth (~4 × 108 cells/mL at the end of log phase). Ammonium led to the maximum chlorophyll and carotenoid content per volume unit (220 μg·mL·1 and 35 μg·mL·1, respectively). Interestingly, no significant differences in growth rates were found in cultures grown on urea as C and N source, with respect to those cultures grown on nitrate and CO2 as nitrogen and carbon sources (control cultures). Lutein accumulated up to 3.55 mg·g·1 in the mixotrophic cultures grown on urea. In addition, algal growth in a shaded culture revealed the first evidence for an active xanthophylls cycle operative in acidophile microalgae. PMID:21339944

  9. Enhanced productivity of a lutein-enriched novel acidophile microalga grown on urea.

    PubMed

    Casal, Carlos; Cuaresma, Maria; Vega, Jose Maria; Vilchez, Carlos

    2010-12-24

    Coccomyxa acidophila is an extremophile eukaryotic microalga isolated from the Tinto River mining area in Huelva, Spain. Coccomyxa acidophila accumulates relevant amounts of β-carotene and lutein, well-known carotenoids with many biotechnological applications, especially in food and health-related industries. The acidic culture medium (pH < 2.5) that prevents outdoor cultivation from non-desired microorganism growth is one of the main advantages of acidophile microalgae production. Conversely, acidophile microalgae growth rates are usually very low compared to common microalgae growth rates. In this work, we show that mixotrophic cultivation on urea efficiently enhances growth and productivity of an acidophile microalga up to typical values for common microalgae, therefore approaching acidophile algal production towards suitable conditions for feasible outdoor production. Algal productivity and potential for carotenoid accumulation were analyzed as a function of the nitrogen source supplied. Several nitrogen conditions were assayed: nitrogen starvation, nitrate and/or nitrite, ammonia and urea. Among them, urea clearly led to the best cell growth (~4 × 10(8) cells/mL at the end of log phase). Ammonium led to the maximum chlorophyll and carotenoid content per volume unit (220 μg·mL(·1) and 35 μg·mL(·1), respectively). Interestingly, no significant differences in growth rates were found in cultures grown on urea as C and N source, with respect to those cultures grown on nitrate and CO(2) as nitrogen and carbon sources (control cultures). Lutein accumulated up to 3.55 mg·g(·1) in the mixotrophic cultures grown on urea. In addition, algal growth in a shaded culture revealed the first evidence for an active xanthophylls cycle operative in acidophile microalgae.

  10. Comparing chemolithoautotrophic subseafloor communities across geochemical gradients using meta-omics and RNA-SIP

    NASA Astrophysics Data System (ADS)

    Fortunato, C. S.; Huber, J. A.

    2015-12-01

    The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. Past studies have shown that the taxonomic structure of subseafloor communities differs based on the geochemical signatures of individual vents. In this study, we expanded beyond phylogeny and used a combination of metagenomic, metatranscriptomic, and RNA-based stable isotope probing (RNA-SIP) analyses to identify the metabolic potential, expression patterns, and the active autotrophic players and genomic pathways present in venting fluids from Axial Seamount, an active submarine volcano off the coast of Oregon, USA. Low-temperature diffuse vent fluids from three hydrothermal vents, Marker 113, Marker 33, and Anemone, were filtered and preserved on the seafloor for metagenome and metatranscriptome analyses. Fluid for RNA-SIP was also collected and incubated shipboard with 13C-labeled sodium bicarbonate at 30ºC, 55ºC, and 80ºC for each vent. Taxonomically, Epsilonproteobacteria comprised a significant proportion of the community at all three vents, but each vent also had distinct groups that were abundant including SUP05 at Anemone and Methanococcus at Marker 113. Functionally, vents shared many metabolic processes including genes for denitrification, sulfur reduction and sulfur, hydrogen, and ammonium oxidation, which were present and expressed in similar abundance across all three vents. One metabolic difference between vents was the presence and expression of genes for methanogenesis, which were highly abundant and expressed at Marker 113, in lower abundance and expression at Marker 33, and not present at Anemone. RNA-SIP analysis is ongoing but initial results from Marker 113 revealed that at mesophilic, thermophilic, or hyperthemophilic temperatures, different genera and autotrophic metabolisms dominated

  11. Preferential Use of an Anode as an Electron Acceptor by an Acidophilic Bacterium in the Presence of Oxygen▿

    PubMed Central

    Malki, Moustafa; De Lacey, Antonio L.; Rodríguez, Nuria; Amils, Ricardo; Fernandez, Victor M.

    2008-01-01

    Several anaerobic metal-reducing bacteria have been shown to be able to donate electrons directly to an electrode. This property is of great interest for microbial fuel cell development. To date, microbial fuel cell design requires avoiding O2 diffusion from the cathodic compartment to the sensitive anodic compartment. Here, we show that Acidiphilium sp. strain 3.2 Sup 5 cells that were isolated from an extreme acidic environment are able to colonize graphite felt electrodes. These bacterial electrodes were able to produce high-density electrocatalytic currents, up to 3 A/m2 at a poised potential of +0.15 V (compared to the value for the reference standard calomel electrode) in the absence of redox mediators, by oxidizing glucose even at saturating air concentrations and very low pHs. PMID:18487393

  12. Cobalamin Protection against Oxidative Stress in the Acidophilic Iron-oxidizing Bacterium Leptospirillum Group II CF-1

    PubMed Central

    Ferrer, Alonso; Rivera, Javier; Zapata, Claudia; Norambuena, Javiera; Sandoval, Álvaro; Chávez, Renato; Orellana, Omar; Levicán, Gloria

    2016-01-01

    Members of the genus Leptospirillum are aerobic iron-oxidizing bacteria belonging to the phylum Nitrospira. They are important members of microbial communities that catalyze the biomining of sulfidic ores, thereby solubilizing metal ions. These microorganisms live under extremely acidic and metal-loaded environments and thus must tolerate high concentrations of reactive oxygen species (ROS). Cobalamin (vitamin B12) is a cobalt-containing tetrapyrrole cofactor involved in intramolecular rearrangement reactions and has recently been suggested to be an intracellular antioxidant. In this work, we investigated the effect of the exogenous addition of cobalamin on oxidative stress parameters in Leptospirillum group II strain CF-1. Our results revealed that the external supplementation of cobalamin reduces the levels of intracellular ROSs and the damage to biomolecules, and also stimulates the growth and survival of cells exposed to oxidative stress exerted by ferric ion, hydrogen peroxide, chromate and diamide. Furthermore, exposure of strain CF-1 to oxidative stress elicitors resulted in the transcriptional activation of the cbiA gene encoding CbiA of the cobalamin biosynthetic pathway. Altogether, these data suggest that cobalamin plays an important role in redox protection of Leptospirillum strain CF-1, supporting survival of this microorganism under extremely oxidative environmental conditions. Understanding the mechanisms underlying the protective effect of cobalamin against oxidative stress may help to develop strategies to make biomining processes more effective. PMID:27242761

  13. Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1AT)

    PubMed Central

    Anderson, Iain; Göker, Markus; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Brambilla, Evelyne-Marie; Huber, Harald; Yasawong, Montri; Rohde, Manfred; Spring, Stefan; Abt, Birte; Sikorski, Johannes; Wirth, Reinhard; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2011-01-01

    Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106°C). This is the first completed genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on September 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21886865

  14. Distribution of Thermophilic Acidophiles at Cerro Negro, Nicaragua, an Analog for Acid-Sulfate Weathering Environments on Early Mars

    NASA Astrophysics Data System (ADS)

    Rogers, K. L.; Stephenson, S.; McCollom, T. M.; Hynek, B. M.

    2010-04-01

    Cerro Negro, Nicaragua is an excellent terrestrial analog for putative acid-sulfate weathering systems on early Mars. Sulfur- and sulfate-reducing acidophiles are found throughout Cerro Negro and can further elucidate the habitability of early Mars.

  15. Bioleaching kinetics and multivariate analysis of spent petroleum catalyst dissolution using two acidophiles.

    PubMed

    Pradhan, Debabrata; Mishra, Debaraj; Kim, Dong J; Ahn, Jong G; Chaudhury, G Roy; Lee, Seoung W

    2010-03-15

    Bioleaching studies were conducted to evaluate the recovery of metal values from waste petroleum catalyst using two different acidophilic microorganisms, Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. Various leaching parameters such as contact time, pH, oxidant concentration, pulp densities, particle size, and temperature were studied in detail. Activation energy was evaluated from Arrhenius equation and values for Ni, V and Mo were calculated in case of both the acidophiles. In both cases, the dissolution kinetics of Mo was lower than those of V and Ni. The lower dissolution kinetics may have been due to the formation of a sulfur product layer, refractoriness of MoS(2) or both. Multivariate statistical data were presented to interpret the leaching data in the present case. The significance of the leaching parameters was derived through principle component analysis and multi linear regression analyses for both iron and sulfur oxidizing bacteria.

  16. [An Acidophilic Desulfosporosinus Isolated from the Oxidized Mining Wastes in the Transbaikal Area].

    PubMed

    Karnachuk, O V; Kurganskaya, I A; Avakyan, M R; Frank, Y A; Ikkert, O P; Filenko, R A; Danilovac, E V; Pimenov, N V

    2015-01-01

    Dissimilatory sulfate reduction plays an important role in removal of dissolved metals from acidic mine waters. Although this process was convincingly shown to occur in acidic waste of metal recovery, few isolates of acid-tolerant sulfate rducers are known. We isolated a new acidophilic sulfidogen, strain BG, from the oxidized acidic waste of the Bom-Gorkhon tungsten deposit, Transbaikalia, Russia. Phylogenetic analysis of its 16S rRNA gene sequence made it possible to identify it as a member of the genus Desulfosporosinus. Unlike other known acidophilic sulfate reducers of this genus, strain BG was tolerant to high copper concentrations (up to 5 g/L), could grow on organic acids at low ambient pH, and formed crystalline copper sulfides (covellite and chalcopyrite). Molecular analysis of the phenotypes predominating in oxidized waste and in enrichment cultures confirmed the presence of various Desulfosporosinus strains.

  17. Evaluation of a fluorescent lectin-based staining technique for some acidophilic mining bacteria

    SciTech Connect

    Fife, D.J.; Bruhn, D.F.; Miller, K.S.; Stoner, D.L.

    2000-05-01

    A fluorescence-labeled wheat germ agglutinin staining technique was modified and found to be effective for staining gram-positive, acidophilic mining bacteria. Bacteria identified by others as being gram positive through 16S rRNA sequence analyses, yet clustering near the divergence of that group, stained weakly. Gram-negative bacteria did not stain. Background staining of environmental samples was negligible, and pyrite and soil particles in the samples did not interfere with the staining procedure.

  18. Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the epsilon-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field.

    PubMed

    Takai, Ken; Nealson, Kenneth H; Horikoshi, Koki

    2004-01-01

    A novel thermophilic bacterium, strain EP1-55-1%T, was isolated from an in-situ colonization system deployed in a superheated, deep-sea, hydrothermal vent emission at the Kairei Field on the Central Indian Ridge in the Indian Ocean. The cells were highly motile rods, each possessing a single polar flagellum. Growth was observed between 35 and 65 degrees C (optimum temperature, 55 degrees C; 70 min doubling time) and between pH 4.9 and 7.2 (optimum, pH 5.9). The isolate was a microaerobic-to-anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Molecular oxygen, nitrate or elemental sulfur (S0) could serve as electron acceptors to support growth. The G+C content of the genomic DNA was 34.6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that strain EP1-55-1%T represents the first strain for which taxonomic properties have been characterized within the previously uncultivated phylogroup classified as belonging to the uncultivated epsilon-Proteobacteria group A; the name Hydrogenimonas thermophila gen. nov., sp. nov. is proposed, with strain EP1-55-1%T (=JCM 11971T=ATCC BAA-737T) as the type strain.

  19. Permanent draft genome of Thiobacillus thioparus DSM 505(T), an obligately chemolithoautotrophic member of the Betaproteobacteria.

    PubMed

    Hutt, Lee P; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, Tatiparthi; Daum, Chris; Shapiro, Nicole; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Boden, Rich

    2017-01-01

    Thiobacillus thioparus DSM 505(T) is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C(T) (=DSM 505(T) = ATCC 8158(T)) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.

  20. Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria

    PubMed Central

    Ňancucheo, Ivan; Johnson, D. Barrie

    2012-01-01

    Summary Two continuous‐flow bench‐scale bioreactor systems populated by mixed communities of acidophilic sulfate‐reducing bacteria were constructed and tested for their abilities to promote the selective precipitation of transition metals (as sulfides) present in synthetic mine waters, using glycerol as electron donor. The objective with the first system (selective precipitation of copper from acidic mine water containing a variety of soluble metals) was achieved by maintaining a bioreactor pH of ∼2.2–2.5. The second system was fed with acidic (pH 2.5) synthetic mine water containing 3 mM of both zinc and ferrous iron, and varying concentrations (0.5–30 mM) of aluminium. Selective precipitation of zinc sulfide was possible by operating the bioreactor at pH 4.0 and supplementing the synthetic mine water with 4 mM glycerol. Analysis of the microbial populations in the bioreactors showed that they changed with varying operational parameters, and novel acidophilic bacteria (including one sulfidogen) were isolated from the bioreactors. The acidophilic sulfidogenic bioreactors provided ‘proof of principle’ that segregation of metals present in mine waters is possible using simple online systems within which controlled pH conditions are maintained. The modular units are versatile and robust, and involve minimum engineering complexity. PMID:21895996

  1. Heavy metal bioleaching and sludge stabilization in a single-stage reactor using indigenous acidophilic heterotrophs.

    PubMed

    Mehrotra, Akanksha; Sreekrishnan, T R

    2017-01-10

    Simultaneous sludge digestion and metal leaching (SSDML) have been reported at mesophilic temperature. It is generally perceived that while sludge stabilization is effected by heterotrophs at neutral pH, metal bioleaching is done by acidophilic autotrophs. However, little information is available on the microbial communities involved in the process. This study carried out SSDML in a single-stage reactor using sludge indigenous microorganisms and looked at the bacterial communities responsible for the process. Volatile suspended solids were reduced by more than 40%. The concentration of zinc, copper, chromium, cadmium and nickel decreased by more than 45% in the dry sludge. Acidophilic species of Alicyclobacillus genus were the dominant heterotrophs. A few heterotrophic bacteria were detected which can oxidize iron (Alicyclobacillus ferrooxydans, Alicyclobacillus ferripilum and Ferrimicrobium acidiphilum). Acidithiobacillus ferrooxidans (autotroph) was responsible for the oxidation of both iron and sulfur which lead to a change in the pH from neutral to acidic. The presence of acidophilic heterotrophs, which can oxidize either iron or sulfur, enhanced the efficiency of SSDML process with respect to sludge stabilization and metal leaching. This study shows that it is possible to carry out the SSDML in a single-stage reactor with indigenous microorganisms.

  2. α-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans.

    PubMed

    Lefimil, C; Jedlicki, E; Holmes, D S

    2014-03-01

    A large non-coding RNA, termed α-Fur, of ~1000 nt has been detected in the extreme acidophile Acidithiobacillus ferrooxidans encoded on the antisense strand to the iron-responsive master regulator fur (ferric uptake regulator) gene. A promoter for α-fur was predicted bioinformatically and validated using gene fusion experiments. The promoter is situated within the coding region and in the same sense as proB, potentially encoding a glutamate 5-kinase. The 3' termination site of the α-fur transcript was determined by 3' rapid amplification of cDNA ends to lie 7 nt downstream of the start of transcription of fur. Thus, α-fur is antisense to the complete coding region of fur, including its predicted ribosome-binding site. The genetic context of α-fur is conserved in several members of the genus Acidithiobacillus but not in all acidophiles, indicating that it is monophyletic but not niche specific. It is hypothesized that α-Fur regulates the cellular level of Fur. This is the fourth example of an antisense RNA to fur, although it is the first in an extreme acidophile, and underscores the growing importance of cis-encoded non-coding RNAs as potential regulators involved in the microbial iron-responsive stimulon.

  3. Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria.

    PubMed

    Nancucheo, Ivan; Johnson, D Barrie

    2012-01-01

    Two continuous-flow bench-scale bioreactor systems populated by mixed communities of acidophilic sulfate-reducing bacteria were constructed and tested for their abilities to promote the selective precipitation of transition metals (as sulfides) present in synthetic mine waters, using glycerol as electron donor. The objective with the first system (selective precipitation of copper from acidic mine water containing a variety of soluble metals) was achieved by maintaining a bioreactor pH of ≈ 2.2-2.5. The second system was fed with acidic (pH 2.5) synthetic mine water containing 3 mM of both zinc and ferrous iron, and varying concentrations (0.5-30 mM) of aluminium. Selective precipitation of zinc sulfide was possible by operating the bioreactor at pH 4.0 and supplementing the synthetic mine water with 4 mM glycerol. Analysis of the microbial populations in the bioreactors showed that they changed with varying operational parameters, and novel acidophilic bacteria (including one sulfidogen) were isolated from the bioreactors. The acidophilic sulfidogenic bioreactors provided 'proof of principle' that segregation of metals present in mine waters is possible using simple online systems within which controlled pH conditions are maintained. The modular units are versatile and robust, and involve minimum engineering complexity.

  4. Indirect Redox Transformations of Iron, Copper, and Chromium Catalyzed by Extremely Acidophilic Bacteria

    PubMed Central

    Johnson, D. Barrie; Hedrich, Sabrina; Pakostova, Eva

    2017-01-01

    Experiments were carried out to examine redox transformations of copper and chromium by acidophilic bacteria (Acidithiobacillus, Leptospirillum, and Acidiphilium), and also of iron (III) reduction by Acidithiobacillus spp. under aerobic conditions. Reduction of iron (III) was found with all five species of Acidithiobacillus tested, grown aerobically on elemental sulfur. Cultures maintained at pH 1.0 for protracted periods displayed increasing propensity for aerobic iron (III) reduction, which was observed with cell-free culture liquors as well as those containing bacteria. At. caldus grown on hydrogen also reduced iron (III) under aerobic conditions, confirming that the unknown metabolite(s) responsible for iron (III) reduction were not (exclusively) sulfur intermediates. Reduction of copper (II) by aerobic cultures of sulfur-grown Acidithiobacillus spp. showed similar trends to iron (III) reduction in being more pronounced as culture pH declined, and occurring in both the presence and absence of cells. Cultures of Acidithiobacillus grown anaerobically on hydrogen only reduced copper (II) when iron (III) (which was also reduced) was also included; identical results were found with Acidiphilium cryptum grown micro-aerobically on glucose. Harvested biomass of hydrogen-grown At. ferridurans oxidized iron (II) but not copper (I), and copper (I) was only oxidized by growing cultures of Acidithiobacillus spp. when iron (II) was also included. The data confirmed that oxidation and reduction of copper were both mediated by acidophilic bacteria indirectly, via iron (II) and iron (III). No oxidation of chromium (III) by acidophilic bacteria was observed even when, in the case of Leptospirillum spp., the redox potential of oxidized cultures exceeded +900 mV. Cultures of At. ferridurans and A. cryptum reduced chromium (VI), though only when iron (III) was also present, confirming an indirect mechanism and contradicting an earlier report of direct chromium reduction by A

  5. Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent

    PubMed Central

    Fortunato, Caroline S; Huber, Julie A

    2016-01-01

    The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched 13C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent. PMID:26872039

  6. Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent.

    PubMed

    Fortunato, Caroline S; Huber, Julie A

    2016-08-01

    The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched (13)C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.

  7. Culture-independent detection of "TM7" bacteria in a streptomycin-resistant acidophilic nitrifying process

    NASA Astrophysics Data System (ADS)

    Kurogi, T.; Linh, N. T. T.; Kuroki, T.; Yamada, T.; Hiraishi, A.

    2014-02-01

    Nitrification in biological wastewater treatment processes has been believed for long time to take place under neutral conditions and is inhibited under acidic conditions. However, we previously constructed acidophilic nitrifying sequencing-batch reactors (ANSBRs) being capable of nitrification at < pH 4 and harboring bacteria of the candidate phylum "TM7" as the major constituents of the microbial community. In light of the fact that the 16S rRNA of TM7 bacteria has a highly atypical base substitution possibly responsible for resistance to streptomycin at the ribosome level, this study was undertaken to construct streptomycin-resistant acidophilic nitrifying (SRAN) reactors and to demonstrate whether TM7 bacteria are abundant in these reactors. The SRAN reactors were constructed by seeding with nitrifying sludge from an ANSBR and cultivating with ammonium-containing mineral medium (pH 4.0), to which streptomycin at a concentration of 10, 30 and 50 mg L-1 was added. In all reactors, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate in every batch cycle. PCR-aided denaturing gradient gel electrophoresis (DGGE) targeting 16S rRNA genes revealed that some major clones assigned to TM7 bacteria and Gammaproteobacteria were constantly present during the overall period of operation. Fluorescence in situ hybridization (FISH) with specific oligonucleotide probes also showed that TM7 bacteria predominated in all SRAN reactors, accounting for 58% of the total bacterial population on average. Although the biological significance of the TM7 bacteria in the SRAN reactors are unknown, our results suggest that these bacteria are possibly streptomycin-resistant and play some important roles in the acidophilic nitrifying process.

  8. Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants.

    PubMed

    Poomthongdee, Nalin; Duangmal, Kannika; Pathom-aree, Wasu

    2015-02-01

    Three hundred and fifty-one isolates of actinomycetes were recovered from 21 rhizospheric soil samples using acidified media of pH 5.5. They were evaluated for their antifungal, siderophore production and phosphate solubilization activities. The total count of actinomycetes growing on acidified starch casein agar and Gause no. 1 agar were below 2.48 × 10(4) CFU g(-1) soil. Two hundred and twelve isolates were assigned to acidophiles and the remaining 139 isolates were neutrophiles. Of these actinomycetes, 57.8, 32.5 and 50.4%, showed antagonistic activity against three rice pathogenic fungi; Fusarium moniliforme, Helminthosporium oryzae and Rhizoctonia solani, respectively. More than half of the isolates (68.1%) inhibited at least one tested pathogenic fungus, whereas 25.9% exhibited antifungal activities against all tested fungi. Three hundred and thirty-eight isolates (96.3%) produced siderophore and 266 isolates (75.8%) solubilized phosphate. A greater proportion of the acidophilic actinomycetes exhibited antifungal, siderophore production and phosphate solubilization activity compared with the neutrophiles. Three hundred and twenty-five isolates (92.6%) were classified as streptomycetes based on their morphological characteristics and the presence of the LL-isomeric form of diaminopimelic acid in whole-cell hydrolysates. The 16S ribosomal RNA (rRNA) gene analysis of representative non-streptomycete strains showed that the isolates belonged to seven genera, that is, Allokutzneria, Amycolatopsis, Mycobacterium, Nocardia, Nonomuraea, Saccharopolyspora and Verrucosispora. The potential antifungal acidophilic isolates, R9-4, R14-1, R14-5 and R20-5, showed close similarity to Streptomyces misionensis NBRC 13063(T) (AB184285) in terms of morphological characteristics and 16S rRNA gene sequences.

  9. Culture-independent detection of 'TM7' bacteria in a streptomycin-resistant acidophilic nitrifying process

    SciTech Connect

    Kurogi, T.; Linh, N. T. T.; Kuroki, T.; Yamada, T.; Hiraishi, A.

    2014-02-20

    Nitrification in biological wastewater treatment processes has been believed for long time to take place under neutral conditions and is inhibited under acidic conditions. However, we previously constructed acidophilic nitrifying sequencing-batch reactors (ANSBRs) being capable of nitrification at < pH 4 and harboring bacteria of the candidate phylum 'TM7' as the major constituents of the microbial community. In light of the fact that the 16S rRNA of TM7 bacteria has a highly atypical base substitution possibly responsible for resistance to streptomycin at the ribosome level, this study was undertaken to construct streptomycin-resistant acidophilic nitrifying (SRAN) reactors and to demonstrate whether TM7 bacteria are abundant in these reactors. The SRAN reactors were constructed by seeding with nitrifying sludge from an ANSBR and cultivating with ammonium-containing mineral medium (pH 4.0), to which streptomycin at a concentration of 10, 30 and 50 mg L{sup −1} was added. In all reactors, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate in every batch cycle. PCR-aided denaturing gradient gel electrophoresis (DGGE) targeting 16S rRNA genes revealed that some major clones assigned to TM7 bacteria and Gammaproteobacteria were constantly present during the overall period of operation. Fluorescence in situ hybridization (FISH) with specific oligonucleotide probes also showed that TM7 bacteria predominated in all SRAN reactors, accounting for 58% of the total bacterial population on average. Although the biological significance of the TM7 bacteria in the SRAN reactors are unknown, our results suggest that these bacteria are possibly streptomycin-resistant and play some important roles in the acidophilic nitrifying process.

  10. [Preparation of Copper and Nickel from Metallurgical Waste Products with the Use of Acidophilic Chemolithotrophic Microorganisms].

    PubMed

    Fomchenko, N V; Murav'ev, M I

    2015-01-01

    The study concerns the leaching of copper, nickel, and cobalt from metallurgical production slag with trivalent iron sulphates prepared in the process of oxidation of bivalent iron ions with the use of associations of acidophilic chemolithotrophic microorganisms. At the same time, copper extraction in the solution reached 91.2%, nickel reached 74.9%, and cobalt reached 90.1%. Copper was extracted by cementation, and nickel as sulphate was extracted by electrolysis. Associations of microorganisms can then completely bioregenerate the solution obtained after leaching.

  11. The Importance of CO2 Utilizing Chemolithoautotrophic Microorganisms for Carbon Sequestration and Isotope Signatures of SOM in Tropical Rainforest Soils

    NASA Astrophysics Data System (ADS)

    Nowak, M. E.; Behrendt, T.; Quesada, B.; Yanez Serrano, A. M.; Trumbore, S.

    2015-12-01

    Soil organic matter (SOM) is a major compartment of the tropical carbon cycle with up to 26 % of global carbon stocks stored in tropical soils. Understanding factors and processes driving SOM dynamics under changing climate conditions is crucial for predicting the role of tropical forest ecosystems to act as a carbon sink or source. Soil microorganisms are major drivers of the belowground carbon cycle by releasing CO2 by soil respiration but also by stabilizing and storing SOM, as indicated by recent research. Our investigations focus on chemolithoautotrophic microorganisms, a group that relies on CO2 as their carbon source. Chemolithoautotrophic microorganisms have been shown to be highly abundant in soils, whereas their role in SOM sequestration is still poorly understood. In tropical soils, the activity of chemolithoautotropic microbes might be important for generating and stabilizing carbon, especially in the deeper soil, which is rich in CO2 and reduced energy sources like Fe2+. They further might impact carbon isotope signatures (13C and 14C) of SOM, because of enzymatic fractionation during carboxylation and the use of carbon, which has a distinct isotopic composition than other carbon sources at the same depth. In order to study the activity of chemolithoautotropic microbes and their importance for SOM, we conducted isotope and isotope-labelling studies, gas measurements as well as molecular analyses at soils from the Atto site from 0 to 1 meter depth. These soils are classified as Ferralsols and Alisols and represent the most abundant soil types in the Amazon. With this we will be able to gain knowledge about the function and identity of an important group of microorganisms and their contribution to crucial biogeochemical cycles in the world`s most important ecosystem.

  12. Whole-Genome Transcriptional Analysis of Chemolithoautotrophic Thiosulfate Oxidation by Thiobacillus denitrificans Under Aerobic vs. Denitrifying Conditions

    SciTech Connect

    Beller, H R; Letain, T E; Chakicherla, A; Kane, S R; Legler, T C; Coleman, M A

    2006-04-22

    Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with ke chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends.

  13. Bioleaching of spent hydro-processing catalyst using acidophilic bacteria and its kinetics aspect.

    PubMed

    Mishra, Debaraj; Kim, Dong J; Ralph, David E; Ahn, Jong G; Rhee, Young H

    2008-04-15

    Bioleaching of metals from hazardous spent hydro-processing catalysts was attempted in the second stage after growing the bacteria with sulfur in the first stage. The first stage involved transformation of elemental sulfur particles to sulfuric acid through an oxidation process by acidophilic bacteria. In the second stage, the acidic medium was utilized for the leaching process. Nickel, vanadium and molybdenum contained within spent catalyst were leached from the solid materials to liquid medium by the action of sulfuric acid that was produced by acidophilic leaching bacteria. Experiments were conducted varying the reaction time, amount of spent catalysts, amount of elemental sulfur and temperature. At 50 g/L spent catalyst concentration and 20 g/L elemental sulfur, 88.3% Ni, 46.3% Mo, and 94.8% V were recovered after 7 days. Chemical leaching with commercial sulfuric acid of the similar amount that produced by bacteria was compared. Thermodynamic parameters were calculated and the nature of reaction was found to be exothermic. Leaching kinetics of the metals was represented by different reaction kinetic equations, however, only diffusion controlled model showed the best correlation here. During the whole process Mo showed low dissolution because of substantiate precipitation with leach residues as MoO3. Bioleach residues were characterized by EDX and XRD.

  14. Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.

    PubMed

    Ni, Gaofeng; Christel, Stephan; Roman, Pawel; Wong, Zhen Lim; Bijmans, Martijn F M; Dopson, Mark

    2016-09-01

    Sulfide mineral processing often produces large quantities of wastewaters containing acid-generating inorganic sulfur compounds. If released untreated, these wastewaters can cause catastrophic environmental damage. In this study, microbial fuel cells were inoculated with acidophilic microorganisms to investigate whether inorganic sulfur compound oxidation can generate an electrical current. Cyclic voltammetry suggested that acidophilic microorganisms mediated electron transfer to the anode, and that electricity generation was catalyzed by microorganisms. A cation exchange membrane microbial fuel cell, fed with artificial wastewater containing tetrathionate as electron donor, reached a maximum whole cell voltage of 72 ± 9 mV. Stepwise replacement of the artificial anolyte with real mining process wastewater had no adverse effect on bioelectrochemical performance and generated a maximum voltage of 105 ± 42 mV. 16S rRNA gene sequencing of the microbial consortia resulted in sequences that aligned within the genera Thermoplasma, Ferroplasma, Leptospirillum, Sulfobacillus and Acidithiobacillus. This study opens up possibilities to bioremediate mining wastewater using microbial fuel cell technology.

  15. Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.

    PubMed

    Baker-Austin, Craig; Dopson, Mark; Wexler, Margaret; Sawers, R Gary; Stemmler, Ann; Rosen, Barry P; Bond, Philip L

    2007-05-01

    'Ferroplasma acidarmanus' Fer1 is an arsenic-hypertolerant acidophilic archaeon isolated from the Iron Mountain mine, California; a site characterized by heavy metals contamination. The presence of up to 10 g arsenate per litre [As(V); 133 mM] did not significantly reduce growth yields, whereas between 5 and 10 g arsenite per litre [As(III); 67-133 mM] significantly reduced the yield. Previous bioinformatic analysis indicates that 'F. acidarmanus' Fer1 has only two predicted genes involved in arsenic resistance and lacks a recognizable gene for an arsenate reductase. Biochemical analysis suggests that 'F. acidarmanus' Fer1 does not reduce arsenate indicating that 'F. acidarmanus' Fer1 has an alternative resistance mechanism to arsenate other than reduction to arsenite and efflux. Primer extension analysis of the putative ars transcriptional regulator (arsR) and efflux pump (arsB) demonstrated that these genes are co-transcribed, and expressed in response to arsenite, but not arsenate. Two-dimensional polyacrylamide gel electrophoresis analysis of 'F. acidarmanus' Fer1 cells exposed to arsenite revealed enhanced expression of proteins associated with protein refolding, including the thermosome Group II HSP60 family chaperonin and HSP70 DnaK type heat shock proteins. This report represents the first molecular and proteomic study of arsenic resistance in an acidophilic archaeon.

  16. Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1

    SciTech Connect

    Baker-Austin, C., M. Dopson, M. Wexler, R. G. Sawers, A. Stemmler, B.P. Rosen and P.L. Bond

    2007-01-01

    'Ferroplasma acidarmanus' Fer1 is an arsenic-hypertolerant acidophilic archaeon isolated from the Iron Mountain mine, California; a site characterized by heavy metals contamination. The presence of up to 10 g arsenate per litre [As(V); 133 mM] did not significantly reduce growth yields, whereas between 5 and 10 g arsenite per litre [As(III); 67-133 mM] significantly reduced the yield. Previous bioinformatic analysis indicates that 'F. acidarmanus' Fer1 has only two predicted genes involved in arsenic resistance and lacks a recognizable gene for an arsenate reductase. Biochemical analysis suggests that 'F. acidarmanus' Fer1 does not reduce arsenate indicating that 'F. acidarmanus' Fer1 has an alternative resistance mechanism to arsenate other than reduction to arsenite and efflux. Primer extension analysis of the putative ars transcriptional regulator (arsR) and efflux pump (arsB) demonstrated that these genes are co-transcribed, and expressed in response to arsenite, but not arsenate. Two-dimensional polyacrylamide gel electrophoresis analysis of 'F. acidarmanus' Fer1 cells exposed to arsenite revealed enhanced expression of proteins associated with protein refolding, including the thermosome Group II HSP60 family chaperonin and HSP70 DnaK type heat shock proteins. This report represents the first molecular and proteomic study of arsenic resistance in an acidophilic archaeon.

  17. Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent.

    PubMed

    Slobodkina, G B; Kolganova, T V; Chernyh, N A; Querellou, J; Bonch-Osmolovskaya, E A; Slobodkin, A I

    2009-06-01

    A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50(T)) was isolated from a hydrothermal sample collected at the Mid-Atlantic Ridge from the deepest of the known World ocean hydrothermal fields, Ashadze field (1 degrees 58' 21'' N 4 degrees 51' 47'' W) at a depth of 4100 m. Cells of strain SL50(T) were motile, straight to bent rods with one polar flagellum, 0.5-0.6 mum in width and 3.0-3.5 mum in length. The temperature range for growth was 25-75 degrees C, with an optimum at 60 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.5. Growth of strain SL50(T) was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v) with an optimum at 2.5 % (w/v). The generation time under optimal growth conditions for strain SL50(T) was 60 min. Strain SL50(T) used molecular hydrogen, acetate, lactate, succinate, pyruvate and complex proteinaceous compounds as electron donors, and Fe(III), Mn(IV), nitrate or elemental sulfur as electron acceptors. The G+C content of the DNA of strain SL50(T) was 28.7 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of strain SL50(T) was Deferribacter abyssi JR(T) (95.5 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Deferribacter autotrophicus sp. nov. is proposed. The type strain is SL50(T) (=DSM 21529(T)=VKPM B-10097(T)). Deferribacter autotrophicus sp. nov. is the first described deep-sea bacterium capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor and ferric iron as electron acceptor and CO(2) as the carbon source.

  18. Draft Genome Sequence of the Acidophilic, Halotolerant, and Iron/Sulfur-Oxidizing Acidihalobacter prosperus DSM 14174 (Strain V6)

    PubMed Central

    Khaleque, Himel Nahreen; Ramsay, Joshua P.; Murphy, Riley J. T.; Kaksonen, Anna H.; Boxall, Naomi J.

    2017-01-01

    ABSTRACT The principal genomic features of Acidihalobacter prosperus DSM 14174 (strain V6) are presented here. This is a mesophilic, halotolerant, and iron/sulfur-oxidizing acidophile that was isolated from seawater at Vulcano, Italy. It has potential for use in biomining applications in regions where high salinity exists in the source water and ores. PMID:28104654

  19. Differential bioleaching of copper by mesophilic and moderately thermophilic acidophilic consortium enriched from same copper mine water sample.

    PubMed

    Marhual, N P; Pradhan, N; Kar, R N; Sukla, L B; Mishra, B K

    2008-11-01

    Three acidophilic enrichment consortium were developed from mine water sample of copper mine site at Khetri, India were compared for their copper leaching efficiency. Out of these one was mesophilic (35 degrees C) and two were moderately thermophilic (50 degrees C). Consortia were named as mesophilic acidophilic chemolithotrophic consortia (MACC), thermophilic acidophilic chemolithotrophic consortia (TACC), and Sulfobacillus acidophilic consortia (SAC). Copper extraction ability of both the thermophilic consortia (77-78% extraction) was almost double to that of mesophilic consortia (40% extraction) at 10% pulp density after 55 days. Both the thermophilic consortia were equally effective in leaching of other metals like Ni, Co, Zn, Mn. After 55 days, the percentage of extractions of copper by TACC was 76, 74, 67, 48 and 45 at 5%, 10%, 15%, 20% and 30% pulp density, respectively. Total number of bacteria was maximum at 5% pulp density which decreases with increase in pulp density. Sulfobacillus-like bacteria were seen in the Sulfobacillus enrichment cultures. Moderately thermophilic consortia proved to be better in leaching performance than the mesophilic counterpart.

  20. 13C-isotope analyses reveal that chemolithoautotrophic Gamma- and Epsilonproteobacteria feed a microbial food web in a pelagic redoxcline of the central Baltic Sea.

    PubMed

    Glaubitz, Sabine; Lueders, Tillmann; Abraham, Wolf-Rainer; Jost, Günter; Jürgens, Klaus; Labrenz, Matthias

    2009-02-01

    Marine pelagic redoxclines are zones of high dark CO(2) fixation rates, which can correspond up to 30% of the surface primary production. However, despite this significant contribution to the pelagic carbon cycle, the identity of most chemolithoautotrophic organisms is still unknown. Therefore, the aim of this study was to directly link the dark CO(2) fixation capacity of a pelagic redoxcline in the central Baltic Sea (Landsort Deep) with the identity of the main chemolithoautotrophs involved. Our approach was based on the analysis of natural carbon isotope signatures in fatty acid methyl esters (FAMEs) and on measurements of CO(2) incorporation in (13)C-bicarbonate pulse experiments. The incorporation of (13)C into chemolithoautotrophic cells was investigated by rRNA-based stable isotope probing (RNA-SIP) and FAME analysis after incubation for 24 and 72 h under in situ conditions. Our results demonstrated that fatty acids indicative of Proteobacteria were significantly enriched in (13)C slightly below the chemocline. RNA-SIP analyses revealed that two different Gammaproteobacteria and three closely related Epsilonproteobacteria of the Sulfurimonas cluster were active dark CO(2)-fixing microorganisms, with a time-dependent community shift between these groups. Labelling of Archaea was not detectable, but after 72 h of incubation the (13)C-label had been transferred to a potentially bacterivorous ciliate related to Euplotes sp. Thus, RNA-SIP provided direct evidence for the contribution of chemolithoautotrophic production to the microbial food web in this marine pelagic redoxcline, emphasizing the importance of dark CO(2)-fixing Proteobacteria within this habitat.

  1. Column bioleaching of uranium embedded in granite porphyry by a mesophilic acidophilic consortium.

    PubMed

    Qiu, Guanzhou; Li, Qian; Yu, Runlan; Sun, Zhanxue; Liu, Yajie; Chen, Miao; Yin, Huaqun; Zhang, Yage; Liang, Yili; Xu, Lingling; Sun, Limin; Liu, Xueduan

    2011-04-01

    A mesophilic acidophilic consortium was enriched from acid mine drainage samples collected from several uranium mines in China. The performance of the consortium in column bioleaching of low-grade uranium embedded in granite porphyry was investigated. The influences of several chemical parameters on uranium extraction in column reactor were also investigated. A uranium recovery of 96.82% was achieved in 97 days column leaching process including 33 days acid pre-leaching stage and 64 days bioleaching stage. It was reflected that indirect leaching mechanism took precedence over direct. Furthermore, the bacterial community structure was analyzed by using Amplified Ribosomal DNA Restriction Analysis. The results showed that microorganisms on the residual surface were more diverse than that in the solution. Acidithiobacillus ferrooxidans was the dominant species in the solution and Leptospirillum ferriphilum on the residual surface.

  2. Optimized Production of Xylitol from Xylose Using a Hyper-Acidophilic Candida tropicalis.

    PubMed

    Tamburini, Elena; Costa, Stefania; Marchetti, Maria Gabriella; Pedrini, Paola

    2015-08-19

    The yeast Candida tropicalis DSM 7524 produces xylitol, a natural, low-calorie sweetener, by fermentation of xylose. In order to increase xylitol production rate during the submerged fermentation process, some parameters-substrate (xylose) concentration, pH, aeration rate, temperature and fermentation strategy-have been optimized. The maximum xylitol yield reached at 60-80 g/L initial xylose concentration, pH 5.5 at 37 °C was 83.66% (w/w) on consumed xylose in microaerophilic conditions (kLa = 2·h(-1)). Scaling up on 3 L fermenter, with a fed-batch strategy, the best xylitol yield was 86.84% (w/w), against a 90% of theoretical yield. The hyper-acidophilic behaviour of C. tropicalis makes this strain particularly promising for industrial application, due to the possibility to work in non-sterile conditions.

  3. Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays

    SciTech Connect

    Frank F. Roberto

    2008-08-01

    Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means of rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.

  4. Optimized Production of Xylitol from Xylose Using a Hyper-Acidophilic Candida tropicalis

    PubMed Central

    Tamburini, Elena; Costa, Stefania; Marchetti, Maria Gabriella; Pedrini, Paola

    2015-01-01

    The yeast Candida tropicalis DSM 7524 produces xylitol, a natural, low-calorie sweetener, by fermentation of xylose. In order to increase xylitol production rate during the submerged fermentation process, some parameters-substrate (xylose) concentration, pH, aeration rate, temperature and fermentation strategy-have been optimized. The maximum xylitol yield reached at 60–80 g/L initial xylose concentration, pH 5.5 at 37 °C was 83.66% (w/w) on consumed xylose in microaerophilic conditions (kLa = 2·h−1). Scaling up on 3 L fermenter, with a fed-batch strategy, the best xylitol yield was 86.84% (w/w), against a 90% of theoretical yield. The hyper-acidophilic behaviour of C. tropicalis makes this strain particularly promising for industrial application, due to the possibility to work in non-sterile conditions. PMID:26295411

  5. Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum".

    PubMed

    Ullrich, Sophie R; González, Carolina; Poehlein, Anja; Tischler, Judith S; Daniel, Rolf; Schlömann, Michael; Holmes, David S; Mühling, Martin

    2016-01-01

    Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus "Ferrovum" are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of "Ferrovum" has proven to be extremely difficult and has so far only been successful for the designated type strain "Ferrovum myxofaciens" P3G. In this study, the genomes of two novel strains of "Ferrovum" (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of "Ferrovum" sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three "Ferrovum" species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the "F. myxofaciens" strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed

  6. Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus

    PubMed Central

    Acuña, Lillian G.; Cárdenas, Juan Pablo; Covarrubias, Paulo C.; Haristoy, Juan José; Flores, Rodrigo; Nuñez, Harold; Riadi, Gonzalo; Shmaryahu, Amir; Valdés, Jorge; Dopson, Mark; Rawlings, Douglas E.; Banfield, Jillian F.; Holmes, David S.; Quatrini, Raquel

    2013-01-01

    Background Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. Principal Findings Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. Significance For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular

  7. Reduction of Cr(VI) under acidic conditions by the facultative Fe(III)-reducing bacterium Acidiphilium cryptum

    SciTech Connect

    David E. Cummings; Scott Fendorf; Rajesh K. Sani; Brent M. Peyton; Timothy S. Magnuson

    2007-01-01

    The potential for biological reduction of Cr(VI) under acidic conditions was evaluated with the acidophilic, facultatively metal-reducing bacterium Acidiphilium cryptum strain JF-5 to explore the role of acidophilic microorganisms in the Cr cycle in low-pH environments. An anaerobic suspension of washed A. cryptum cells rapidly reduced 50 M Cr(VI) at pH 3.2; biological reduction was detected from pH 1.7-4.7. The reduction product, confirmed by XANES analysis, was entirely Cr(III) that was associated predominantly with the cell biomass (70-80%) with the residual residing in the aqueous phase. Reduction of Cr(VI) showed a pH optimum similar to that for growth and was inhibited by 5 mM HgCl2, suggesting that the reaction was enzyme-mediated. Introduction of O2 into the reaction medium slowed the reduction rate only slightly, whereas soluble Fe(III) (as ferric sulfate) increased the rate dramatically, presumably by the shuttling of electrons from bioreduced Fe(II) to Cr(VI) in a coupled biotic-abiotic cycle. Starved cells could not reduce Cr(VI) when provided as sole electron acceptor, indicating that Cr(VI) reduction is not an energy-conserving process in A. cryptum. We speculate, rather, that Cr(VI) reduction is used here as a detoxification mechanism.

  8. Chemolithoautotrophic production mediating the cycling of the greenhouses gases N2O and CH4 in an upwelling ecosystem

    NASA Astrophysics Data System (ADS)

    Farías, L.; Fernández, C.; Faúndez, J.; Cornejo, M.; Alcaman, M. E.

    2009-06-01

    Coastal upwelling ecosystems with marked oxyclines (redoxclines) present high availability of electron donors that favour chemoautotrophy, leading in turn to high N2O and CH4 cycling associated with aerobic NH4+ (AAO) and CH4 oxidation (AMO). This is the case of the highly productive coastal upwelling area off Central Chile (36° S), where we evaluated the importance of total chemolithoautotrophic vs. photoautotrophic production, the specific contributions of AAO and AMO to chemosynthesis and their role in gas cycling. Chemoautotrophy (involving bacteria and archaea) was studied at a time-series station during monthly (2002-2009) and seasonal cruises (January 2008, September 2008, January 2009) and was assessed in terms of dark carbon assimilation (CA), N2O and CH4 cycling, and the natural C isotopic ratio of particulate organic carbon (δ13POC). Total Integrated dark CA fluctuated between 19.4 and 2.924 mg C m-2 d-1. It was higher during active upwelling and represented on average 27% of the integrated photoautotrophic production (from 135 to 7.626 mg C m-2d-1). At the oxycline, δ13POC averaged -22.209‰ this was significantly lighter compared to the surface (-19.674‰) and bottom layers (-20.716‰). This pattern, along with low NH4+ content and high accumulations of N2O, NO2- and NO3- within the oxycline indicates that chemolithoautotrophs and specifically AA oxydisers were active. Dark CA was reduced from 27 to 48% after addition of a specific AAO inhibitor (ATU) and from 24 to 76% with GC7, a specific archaea inhibitor, indicating that AAO and maybe AMO microbes (most of them archaea) were performing dark CA through oxidation of NH4+ and CH4. AAO produced N2O at rates from 8.88 to 43 nM d-1 and a fraction of it was effluxed into the atmosphere (up to 42.85 μmol m-2 d-1). AMO on the other hand consumed CH4 at rates between 0.41 and 26.8 nM d-1 therefore preventing its efflux to the atmosphere (up to 18.69 μmol m-2 d-1). These findings show that chemically

  9. Biodiversity of acidophilic moderate thermophiles isolated from two sites in Yellowstone National Park and their roles in the dissimilatory oxido-reduction of iron

    SciTech Connect

    D. B. Johnson; D.A. Body; T. A. M. Bridge; D. F. Bruhn; F. F. Roberto

    2001-07-01

    Some of the thermal sites within Yellowstone National Park are extremely acidic and are therefore potential sites for isolating novel strains of acidophilic thermophiles, including those that are involved in the biogeochemical cycling of iron. This paper describes the isolation and characterization of thermotolerant, acidophilic “iron bacteria” isolated from two such sites in Yellowstone National Park, and reports the biodiversity of isolates in terms of their physiological traits and their phylogenetic make-up.

  10. Complete genome sequence of the chemolithoautotrophic marine magnetotactic coccus strain MC-1.

    PubMed

    Schübbe, Sabrina; Williams, Timothy J; Xie, Gary; Kiss, Hajnalka E; Brettin, Thomas S; Martinez, Diego; Ross, Christian A; Schüler, Dirk; Cox, B Lea; Nealson, Kenneth H; Bazylinski, Dennis A

    2009-07-01

    The marine bacterium strain MC-1 is a member of the alpha subgroup of the proteobacteria that contains the magnetotactic cocci and was the first member of this group to be cultured axenically. The magnetotactic cocci are not closely related to any other known alphaproteobacteria and are only distantly related to other magnetotactic bacteria. The genome of MC-1 contains an extensive (102 kb) magnetosome island that includes numerous genes that are conserved among all known magnetotactic bacteria, as well as some genes that are unique. Interestingly, certain genes that encode proteins considered to be important in magnetosome assembly (mamJ and mamW) are absent from the genome of MC-1. Magnetotactic cocci exhibit polar magneto-aerotaxis, and the MC-1 genome contains a relatively large number of identified chemotaxis genes. Although MC-1 is capable of both autotrophic and heterotrophic growth, it does not appear to be metabolically versatile, with heterotrophic growth confined to the utilization of acetate. Central carbon metabolism is encoded by genes for the citric acid cycle (oxidative and reductive), glycolysis, and gluconeogenesis. The genome also reveals the presence or absence of specific genes involved in the nitrogen, sulfur, iron, and phosphate metabolism of MC-1, allowing us to infer the presence or absence of specific biochemical pathways in strain MC-1. The pathways inferred from the MC-1 genome provide important information regarding central metabolism in this strain that could provide insights useful for the isolation and cultivation of new magnetotactic bacterial strains, in particular strains of other magnetotactic cocci.

  11. New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph.

    PubMed

    Barco, Roman A; Emerson, David; Sylvan, Jason B; Orcutt, Beth N; Jacobson Meyers, Myrna E; Ramírez, Gustavo A; Zhong, John D; Edwards, Katrina J

    2015-09-01

    Microaerophilic, neutrophilic, iron-oxidizing bacteria (FeOB) grow via the oxidation of reduced Fe(II) at or near neutral pH, in the presence of oxygen, making them relevant in numerous environments with elevated Fe(II) concentrations. However, the biochemical mechanisms for Fe(II) oxidation by these neutrophilic FeOB are unknown, and genetic markers for this process are unavailable. In the ocean, microaerophilic microorganisms in the genus Mariprofundus of the class Zetaproteobacteria are the only organisms known to chemolithoautotrophically oxidize Fe and concurrently biomineralize it in the form of twisted stalks of iron oxyhydroxides. The aim of this study was to identify highly expressed proteins associated with the electron transport chain of microaerophilic, neutrophilic FeOB. To this end, Mariprofundus ferrooxydans PV-1 was cultivated, and its proteins were extracted, assayed for redox activity, and analyzed via liquid chromatography-tandem mass spectrometry for identification of peptides. The results indicate that a cytochrome c4, cbb3-type cytochrome oxidase subunits, and an outer membrane cytochrome c were among the most highly expressed proteins and suggest an involvement in the process of aerobic, neutrophilic bacterial Fe oxidation. Proteins associated with alternative complex III, phosphate transport, carbon fixation, and biofilm formation were abundant, consistent with the lifestyle of Mariprofundus.

  12. Paracoccus bengalensis sp. nov., a novel sulfur-oxidizing chemolithoautotroph from the rhizospheric soil of an Indian tropical leguminous plant.

    PubMed

    Ghosh, Wriddhiman; Mandal, Sukhendu; Roy, Pradosh

    2006-07-01

    Paracoccus versutus-like isolates from the rhizosphere of Clitoria ternatea, a slender leguminous herb (family--Papilionaceae), found ubiquitously in waste places and village forests of the Lower Gangetic plains of India, presented a case of graduated infraspecific variation that was capped by the identification of a new species Paracoccus bengalensis (type strain JJJ(T) = LMG 22700(T) = MTCC 7003(T)). The diverged phenetic and genetic structure of these sulfur-oxidizing chemolithoautotrophs presented a case of apparent nonconformity of 16S rRNA gene sequence similarities with results of DNA-DNA hybridization. Despite high 16S rRNA gene sequence similarity with P. versutus one of the newly isolated strains, viz., JJJ(T) was identified as a new species of Paracoccus by virtue of its explicitly low DNA-DNA hybridization (42-45%) with the type strain of the closest species P. versutus (), distinct G + C content (65.3 mol%), physiological and biochemical differences amounting to <60% phenetic similarity with strains of P. versutus as well as new isolates akin to the species. The newly described species also had a unique fatty acid profile that was distinguished by the absence of 18:1 omega9c, unique possession of Summed feature 3 (16:1omega7c & 15:0 iso 2-OH), 19:0 10 methyl, and a much higher concentration of 19:0 cycloomega8c.

  13. New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph

    PubMed Central

    Emerson, David; Sylvan, Jason B.; Orcutt, Beth N.; Jacobson Meyers, Myrna E.; Ramírez, Gustavo A.; Zhong, John D.; Edwards, Katrina J.

    2015-01-01

    Microaerophilic, neutrophilic, iron-oxidizing bacteria (FeOB) grow via the oxidation of reduced Fe(II) at or near neutral pH, in the presence of oxygen, making them relevant in numerous environments with elevated Fe(II) concentrations. However, the biochemical mechanisms for Fe(II) oxidation by these neutrophilic FeOB are unknown, and genetic markers for this process are unavailable. In the ocean, microaerophilic microorganisms in the genus Mariprofundus of the class Zetaproteobacteria are the only organisms known to chemolithoautotrophically oxidize Fe and concurrently biomineralize it in the form of twisted stalks of iron oxyhydroxides. The aim of this study was to identify highly expressed proteins associated with the electron transport chain of microaerophilic, neutrophilic FeOB. To this end, Mariprofundus ferrooxydans PV-1 was cultivated, and its proteins were extracted, assayed for redox activity, and analyzed via liquid chromatography-tandem mass spectrometry for identification of peptides. The results indicate that a cytochrome c4, cbb3-type cytochrome oxidase subunits, and an outer membrane cytochrome c were among the most highly expressed proteins and suggest an involvement in the process of aerobic, neutrophilic bacterial Fe oxidation. Proteins associated with alternative complex III, phosphate transport, carbon fixation, and biofilm formation were abundant, consistent with the lifestyle of Mariprofundus. PMID:26092463

  14. Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.

    PubMed

    Vasilyeva, Lina V; Omelchenko, Marina V; Berestovskaya, Yulia Y; Lysenko, Anatolii M; Abraham, Wolf-Rainer; Dedysh, Svetlana N; Zavarzin, George A

    2006-09-01

    A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023(T). Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023(T) was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 degrees Celsius (optimum 15-20 degrees Celsius) and between pH 4.5 and 8.0 (optimum 5.6-6.0). The major phospholipid fatty acid was 18 : 1omega7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023(T) was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA-DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023(T) (=DSM 16100(T)=ATCC BAA-896(T)).

  15. Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane.

    PubMed

    Krukenberg, Viola; Harding, Katie; Richter, Michael; Glöckner, Frank Oliver; Gruber-Vodicka, Harald R; Adam, Birgit; Berg, Jasmine S; Knittel, Katrin; Tegetmeyer, Halina E; Boetius, Antje; Wegener, Gunter

    2016-09-01

    The anaerobic oxidation of methane (AOM) is mediated by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. In thermophilic AOM consortia enriched from Guaymas Basin, members of the ANME-1 clade are associated with bacteria of the HotSeep-1 cluster, which likely perform direct electron exchange via nanowires. The partner bacterium was enriched with hydrogen as sole electron donor and sulfate as electron acceptor. Based on phylogenetic, genomic and metabolic characteristics we propose to name this chemolithoautotrophic sulfate reducer Candidatus Desulfofervidus auxilii. Ca. D. auxilii grows on hydrogen at temperatures between 50°C and 70°C with an activity optimum at 60°C and doubling time of 4-6 days. Its genome draft encodes for canonical sulfate reduction, periplasmic and soluble hydrogenases and autotrophic carbon fixation via the reductive tricarboxylic acid cycle. The presence of genes for pili formation and cytochromes, and their similarity to genes of Geobacter spp., indicate a potential for syntrophic growth via direct interspecies electron transfer when the organism grows in consortia with ANME. This first ANME-free enrichment of an AOM partner bacterium and its characterization opens the perspective for a deeper understanding of syntrophy in anaerobic methane oxidation.

  16. Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134(T), a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia.

    PubMed

    Boden, Rich; Hutt, Lee P; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, Tatiparthi; Ngan, Chew Yee; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Woyke, Tanja; Kyrpides, Nikos

    2016-01-01

    Thermithiobacillus tepidarius DSM 3134(T) was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.

  17. RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.

    PubMed

    Christel, Stephan; Fridlund, Jimmy; Buetti-Dinh, Antoine; Buck, Moritz; Watkin, Elizabeth L; Dopson, Mark

    2016-04-01

    Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.

  18. Regulation of photosynthesis in the unicellular acidophilic red alga Galdieria sulphuraria.

    PubMed

    Oesterhelt, Christine; Schmälzlin, Elmar; Schmitt, Jürgen M; Lokstein, Heiko

    2007-08-01

    Extremophilic organisms are gaining increasing interest because of their unique metabolic capacities and great biotechnological potential. The unicellular acidophilic and mesothermophilic red alga Galdieria sulphuraria (074G) can grow autotrophically in light as well as heterotrophically in the dark. In this paper, the effects of externally added glucose on primary and secondary photosynthetic reactions are assessed to elucidate mixotrophic capacities of the alga. Photosynthetic O2 evolution was quantified in an open system with a constant supply of CO2 to avoid rapid volatilization of dissolved inorganic carbon at low pH levels. In the presence of glucose, O2 evolution was repressed even in illuminated cells. Ratios of variable to maximum chlorophyll fluorescence (Fv/Fm) and 77 K fluorescence spectra indicated a reduced photochemical efficiency of photosystem II. The results were corroborated by strongly reduced levels of the photosystem II reaction centre protein D1. The downregulation of primary photosynthetic reactions was accompanied by reduced levels of the Calvin Cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Both effects depended on functional sugar uptake and are thus initiated by intracellular rather than extracellular glucose. Following glucose depletion, photosynthetic O2 evolution of illuminated cells commenced after 15 h and Rubisco levels again reached the levels of autotrophic cells. It is concluded that true mixotrophy, involving electron transport across both photosystems, does not occur in G. sulphuraria 074G, and that heterotrophic growth is favoured over autotrophic growth if sufficient organic carbon is available.

  19. Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds

    PubMed Central

    Lehtovirta-Morley, Laura E; Ge, Chaorong; Ross, Jenna; Yao, Huaiying; Nicol, Graeme W; Prosser, James I

    2014-01-01

    Autotrophic ammonia oxidation is performed by two distinct groups of microorganisms: ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB). AOA outnumber their bacterial counterparts in many soils, at times by several orders of magnitude, but relatively little is known of their physiology due to the lack of cultivated isolates. Although a number of AOA have been cultivated from soil, Nitrososphaera viennensis was the sole terrestrial AOA in pure culture and requires pyruvate for growth in the laboratory. Here, we describe isolation in pure culture and characterisation of two acidophilic terrestrial AOA representing the Candidatus genus Nitrosotalea and their responses to organic acids. Interestingly, despite their close phylogenetic relatedness, the two Nitrosotalea strains exhibited differences in physiological features, including specific growth rate, temperature preference and to an extent, response to organic compounds. In contrast to N. viennensis, both Nitrosotalea isolates were inhibited by pyruvate but their growth yield increased in the presence of oxaloacetate. This study demonstrates physiological diversity within AOA species and between different AOA genera. Different preferences for organic compounds potentially influence the favoured localisation of ammonia oxidisers within the soil and the structure of ammonia-oxidising communities in terrestrial ecosystems. PMID:24909965

  20. Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds.

    PubMed

    Lehtovirta-Morley, Laura E; Ge, Chaorong; Ross, Jenna; Yao, Huaiying; Nicol, Graeme W; Prosser, James I

    2014-09-01

    Autotrophic ammonia oxidation is performed by two distinct groups of microorganisms: ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB). AOA outnumber their bacterial counterparts in many soils, at times by several orders of magnitude, but relatively little is known of their physiology due to the lack of cultivated isolates. Although a number of AOA have been cultivated from soil, Nitrososphaera viennensis was the sole terrestrial AOA in pure culture and requires pyruvate for growth in the laboratory. Here, we describe isolation in pure culture and characterisation of two acidophilic terrestrial AOA representing the Candidatus genus Nitrosotalea and their responses to organic acids. Interestingly, despite their close phylogenetic relatedness, the two Nitrosotalea strains exhibited differences in physiological features, including specific growth rate, temperature preference and to an extent, response to organic compounds. In contrast to N. viennensis, both Nitrosotalea isolates were inhibited by pyruvate but their growth yield increased in the presence of oxaloacetate. This study demonstrates physiological diversity within AOA species and between different AOA genera. Different preferences for organic compounds potentially influence the favoured localisation of ammonia oxidisers within the soil and the structure of ammonia-oxidising communities in terrestrial ecosystems.

  1. Bioleaching of metal concentrates of waste printed circuit boards by mixed culture of acidophilic bacteria.

    PubMed

    Zhu, Nengwu; Xiang, Yun; Zhang, Ting; Wu, Pingxiao; Dang, Zhi; Li, Ping; Wu, Jinhua

    2011-08-30

    Metal concentrates of printed circuit boards (PCBs) are the residue valuable metals from which non-metallic components are removed. The non-metallic components show bacterial toxicity in bioleaching process and can be recycled as well. In this study, the effects of initial pH, initial Fe(II) concentration, metal concentrate dosage, particle size, and inoculation quantity on the bioleaching were investigated so as to determine the optimum conditions and evaluate the feasibility of bioleaching of metal concentrates of PCBs by mixed culture of acidophilic bacteria (MCAB). The results showed that the initial pH and Fe(II) concentration played an important role in copper extraction and precipitate formation. Under the optimized conditions of initial pH 2.00, 12g/L initial Fe(II), 12g/L metal concentrate dosage, 10% inoculation quantity, and 60-80 mesh particle size, 96.8% the copper leaching efficiency was achieved in 45h, and aluminum and zinc 88.2% and 91.6% in 98h, respectively. All findings demonstrated that metals could be efficiently leached from metal concentrates of waste PCBs by using the MCAB, and the leaching period was shorten from about 8 days to 45h.

  2. Use of lectins to in situ visualize glycoconjugates of extracellular polymeric substances in acidophilic archaeal biofilms

    PubMed Central

    Zhang, R Y; Neu, T R; Bellenberg, S; Kuhlicke, U; Sand, W; Vera, M

    2015-01-01

    Biofilm formation and the production of extracellular polymeric substances (EPS) by meso- and thermoacidophilic metal-oxidizing archaea on relevant substrates have been studied to a limited extent. In order to investigate glycoconjugates, a major part of the EPS, during biofilm formation/bioleaching by archaea on pyrite, a screening with 75 commercially available lectins by fluorescence lectin-binding analysis (FLBA) has been performed. Three representative archaeal species, Ferroplasma acidiphilum DSM 28986, Sulfolobus metallicus DSM 6482T and a novel isolate Acidianus sp. DSM 29099 were used. In addition, Acidianus sp. DSM 29099 biofilms on elemental sulfur were studied. The results of FLBA indicate (i) 22 lectins bound to archaeal biofilms on pyrite and 21 lectins were binding to Acidianus sp. DSM 29099 biofilms on elemental sulfur; (ii) major binding patterns, e.g. tightly bound EPS and loosely bound EPS, were detected on both substrates; (iii) the three archaeal species produced various EPS glycoconjugates on pyrite surfaces. Additionally, the substratum induced different EPS glycoconjugates and biofilm structures of cells of Acidianus sp. DSM 29099. Our data provide new insights into interactions between acidophilic archaea on relevant surfaces and also indicate that FLBA is a valuable tool for in situ investigations on archaeal biofilms. PMID:25488256

  3. Vulcanisaeta thermophila sp. nov., a hyperthermophilic and acidophilic crenarchaeon isolated from solfataric soil.

    PubMed

    Yim, Kyung June; Cha, In-Tae; Rhee, Jin-Kyu; Song, Hye Seon; Hyun, Dong-Wook; Lee, Hae-Won; Kim, Daekyung; Kim, Kil-Nam; Nam, Young-Do; Seo, Myung-Ji; Bae, Jin-Woo; Roh, Seong Woon

    2015-01-01

    An anaerobic, rod-shaped, hyperthermophilic and acidophilic crenarchaeon, designated strain CBA1501(T), was isolated from solfataric soil of the Mayon volcano in the Republic of the Philippines. Phylogenetic analysis showed that strain CBA1501(T) is affiliated with the genus Vulcanisaeta in the phylum Crenarchaeota. DNA sequence similarities between the 16S rRNA gene of strain CBA1501(T) and those of Vulcanisaeta distributa IC-017(T) and Vulcanisaeta souniana IC-059(T) were 98.5 and 97.4 %, respectively. Strain CBA1501(T) grew between 75-90 °C, over a pH range of 4.0-6.0 and in the presence of 0-1.0 % (w/v) NaCl, with optimal growth occurring at 85 °C, pH 5.0, and with 0 % (w/v) NaCl. Fumarate, malate, oxidized glutathione, sulfur and thiosulfate were used as final electron acceptors, but FeCl3, nitrate and sulfate were not. The DNA G+C content of strain CBA1501(T) was 43.1 mol%. On the basis of polyphasic taxonomic analysis, strain CBA1501(T) represents a novel species of the genus Vulcanisaeta in the phylum Crenarchaeota, for which we propose the name Vulcanisaeta thermophila sp. nov. The type strain is CBA1501(T) ( = ATCC BAA-2415(T) = JCM 17228(T)).

  4. Solar Radiation Stress in Natural Acidophilic Biofilms of Euglena mutabilis Revealed by Metatranscriptomics and PAM Fluorometry.

    PubMed

    Puente-Sánchez, Fernando; Olsson, Sanna; Gómez-Rodriguez, Manuel; Souza-Egipsy, Virginia; Altamirano-Jeschke, Maria; Amils, Ricardo; Parro, Victor; Aguilera, Angeles

    2016-02-01

    The daily photosynthetic performance of a natural biofilm of the extreme acidophilic Euglena mutabilis from Río Tinto (SW, Spain) under full solar radiation was analyzed by means of pulse amplitude-modulated (PAM) fluorescence measurements and metatrascriptomic analysis. Natural E. mutabilis biofilms undergo large-scale transcriptomic reprogramming during midday due to a dynamic photoinhibition and solar radiation stress. Photoinhibition is due to UV radiation and not to light intensity, as revealed by PAM fluorometry analysis. In order to minimize the negative effects of solar radiation, our data supports the presence of a circadian rhythm in this euglenophyte that increases their opportunity to survive. Differential gene expression throughout the day (at 12:00, 20:00 and night) was monitored by massive Illumina parallel sequencing of metatranscriptomic libraries. The transcription pattern was altered in genes involved in Photosystem II stability and repair, UV damaged DNA repair, non-photochemical quenching and oxidative stress, supporting the photoinhibition detected by PAM fluorometry at midday.

  5. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

    SciTech Connect

    Denef, Vincent; Kalnejals, Linda; Muller, R; Wilmes, P; Baker, Brett J.; Thomas, Brian; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillumgroup II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.

  6. Effect of physical characteristics on bioleaching using indigenous acidophilic bacteria for recovering the valuable resources

    NASA Astrophysics Data System (ADS)

    Wi, D.; Kim, B.; Cho, K.; Choi, N.; Park, C.

    2011-12-01

    Bioleaching technology which is based on the ability of bacteria to transform solid compounds into soluble or extractable elements that can be recovered, has developed rapidly in recent decades for its advantages, such as mild reaction, low energy consumption, simple process, environmentally friendly and suitable for low-grade mine tailing and residues. This study investigated the bioleaching efficiency of copper matte under batch experimental conditions (various mineral particle size) using the indigenous acidophilic bacteria collected from acidic hot spring in Hatchnobaru, Japan. We conducted the batch experiments at three different mineral particle sizes: 0.06, 0.16 and 1.12mm. The results showed that the pH in the bacteria inoculating sample increased than initial condition, possibly due to buffer effects by phosphate ions in growth medium. After 22 days from incubation the leached accumulation content of Cu was 0.06 mm - 1,197 mg/L, 0.16 mm - 970 mg/L and 1.12 mm - 704 mg/L. Additionally, through SEM analysis we found of gypsum formed crystals which coated the copper matte surface 6 days after inoculation in 1.12mm case. This study informs basic knowledge when bacteria apply to eco-/economic resources utilization studies including the biomining and the recycling of mine waste system.

  7. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil.

    PubMed

    Lehtovirta-Morley, Laura E; Stoecker, Kilian; Vilcinskas, Andreas; Prosser, James I; Nicol, Graeme W

    2011-09-20

    Nitrification is a fundamental component of the global nitrogen cycle and leads to significant fertilizer loss and atmospheric and groundwater pollution. Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world's soils, equal or exceed those of neutral soils. Paradoxically, autotrophic ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture below pH 6.5, at which ammonia availability is reduced by ionization. Here we report the discovery and cultivation of a chemolithotrophic, obligately acidophilic thaumarchaeal ammonia oxidizer, "Candidatus Nitrosotalea devanaterra," from an acidic agricultural soil. Phylogenetic analysis places the organism within a previously uncultivated thaumarchaeal lineage that has been observed in acidic soils. Growth of the organism is optimal in the pH range 4 to 5 and is restricted to the pH range 4 to 5.5, unlike all previously cultivated ammonia oxidizers. Growth of this organism and associated ammonia oxidation and autotrophy also occur during nitrification in soil at pH 4.5. The discovery of Nitrosotalea devanaterra provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling. Growth at extremely low ammonia concentration (0.18 nM) also challenges accepted views on ammonia uptake and metabolism and indicates novel mechanisms for ammonia oxidation at low pH.

  8. Single Bacterium Detection Using Sers

    NASA Astrophysics Data System (ADS)

    Gonchukov, S. A.; Baikova, T. V.; Alushin, M. V.; Svistunova, T. S.; Minaeva, S. A.; Ionin, A. A.; Kudryashov, S. I.; Saraeva, I. N.; Zayarny, D. A.

    2016-02-01

    This work is devoted to the study of a single Staphylococcus aureus bacterium detection using surface-enhanced Raman spectroscopy (SERS) and resonant Raman spectroscopy (RS). It was shown that SERS allows increasing sensitivity of predominantly low frequency lines connected with the vibrations of Amide, Proteins and DNA. At the same time the lines of carotenoids inherent to this kind of bacterium are well-detected due to the resonance Raman scattering mechanism. The reproducibility and stability of Raman spectra strongly depend on the characteristics of nanostructured substrate, and molecular structure and size of the tested biological object.

  9. Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria

    PubMed Central

    Mardanov, Andrey V.; Beletsky, Alexey V.; Kadnikov, Vitaly V.; Slobodkin, Alexander I.; Ravin, Nikolai V.

    2016-01-01

    Thermosulfurimonas dismutans S95T, isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5′-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood–Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents. PMID:27379079

  10. Propyl gallate synthesis using acidophilic tannase and simultaneous production of tannase and gallic acid by marine Aspergillus awamori BTMFW032.

    PubMed

    Beena, P S; Basheer, Soorej M; Bhat, Sarita G; Bahkali, Ali H; Chandrasekaran, M

    2011-07-01

    Marine Aspergillus awamori BTMFW032, recently reported by us, produce acidophilic tannase as extracellular enzyme. Here, we report the application of this enzyme for synthesis of propyl gallate by direct transesterification of tannic acid and in tea cream solubilisation besides the simultaneous production of gallic acid along with tannase under submerged fermentation by this fungus. This acidophilic tannase enabled synthesis of propyl gallate by direct transesterification of tannic acid using propanol as organic reaction media under low water conditions. The identity of the product was confirmed with thin layer chromatography and Fourier transform infrared spectroscopy. It was noted that 699 U/ml of enzyme could give 60% solubilisation of tea cream within 1 h. Enzyme production medium was optimized adopting Box-Behnken design for simultaneous synthesis of tannase and gallic acid. Process variables including tannic acid, sodium chloride, ferrous sulphate, dipotassium hydrogen phosphate, incubation period and agitation were recognized as the critical factors that influenced tannase and gallic acid production. The model obtained predicted 4,824.61 U/ml of tannase and 136.206 μg/ml gallic acid after 48 h of incubation, whereas optimized medium supported 5,085 U/ml tannase and 372.6 μg/ml of gallic acid production after 36 and 84 h of incubation, respectively, with a 15-fold increase in both enzyme and gallic acid production. Results indicated scope for utilization of this acidophilic tannase for transesterification of tannic acid into propyl gallate, tea cream solubilisation and simultaneous production of gallic acid along with tannase.

  11. Geochemical niches of iron-oxidizing acidophiles in acidic coal mine drainage.

    PubMed

    Jones, Daniel S; Kohl, Courtney; Grettenberger, Christen; Larson, Lance N; Burgos, William D; Macaladya, Jennifer L

    2015-02-01

    A legacy of coal mining in the Appalachians has provided a unique opportunity to study the ecological niches of iron-oxidizing microorganisms. Mine-impacted, anoxic groundwater with high dissolved-metal concentrations emerges at springs and seeps associated with iron oxide mounds and deposits. These deposits are colonized by iron-oxidizing microorganisms that in some cases efficiently remove most of the dissolved iron at low pH, making subsequent treatment of the polluted stream water less expensive. We used full-cycle rRNA methods to describe the composition of sediment communities at two geochemically similar acidic discharges, Upper and Lower Red Eyes in Somerset County, PA, USA. The dominant microorganisms at both discharges were acidophilic Gallionella-like organisms, “Ferrovum” spp., and Acidithiobacillus spp. Archaea and Leptospirillum spp. accounted for less than 2% of cells. The distribution of microorganisms at the two sites could be best explained by a combination of iron(II) concentration and pH. Populations of the Gallionella-like organisms were restricted to locations with pH>3 and iron(II) concentration of >4 mM, while Acidithiobacillus spp. were restricted to pH<3 and iron(II) concentration of <4 mM. Ferrovum spp. were present at low levels in most samples but dominated sediment communities at pH<3 and iron(II) concentration of >4 mM. Our findings offer a predictive framework that could prove useful for describing the distribution of microorganisms in acid mine drainage, based on readily accessible geochemical parameters.

  12. Photochemical Performance of the Acidophilic Red Alga Cyanidium sp. in a pH Gradient

    NASA Astrophysics Data System (ADS)

    Kvíderová, Jana

    2012-06-01

    The acidophilic red alga Cyanidium sp. is one of the dominant mat-forming species in the highly acidic waters of Río Tinto, Spain. The culture of Cyanidium sp., isolated from a microbial mat sample collected at Río Tinto, was exposed to 9 different pH conditions in a gradient from 0.5 to 5 for 24 h and its physiological status evaluated by variable chlorophyll a fluorescence kinetics measurements. Maximum quantum yield was determined after 30 min, 1 h, 2 h, 4 h, 6 h and 24 h of exposure after 15 min dark adaptation. The effect of pH on photochemical activity of Cyanidium sp. was observable as early as 30 min after exposure and the pattern remained stable or with only minor modifications for 24 h. The optimum pH ranged from 1.5 to 2.5. A steep decrease of the photochemical activity was observed at pH below 1 even after 30 min of exposure. Although the alga had tolerated the exposure to pH = 1 for at least 6 h, longer (24 h) exposure resulted in reduction of the photochemical activity. At pH above 2.5, the decline was more moderate and its negative effect on photochemistry was less severe. According to the fluorescence measurements, the red alga Cyanidium sp. is well-adapted to prevailing pH at its original locality at Río Tinto, i.e. pH of 1 to 3. The short-term survival in pH < 1.5 may be adaptation to rare exposures to such low pH in the field. The tolerance of pH above 3 could be caused by adaptation to the microenvironment of the inner parts of microbial mats in which Cyanidium sp. usually dominates and where higher pH could occur due to photosynthetic oxygen production.

  13. Leaching of pyrite by acidophilic heterotrophic iron-oxidizing bacteria in pure and mixed cultures

    SciTech Connect

    Bacelar-Nicolau, P.; Johnson, D.B.

    1999-02-01

    Seven strains of heterotrophic iron-oxidizing acidophilic bacteria were examined to determine their abilities to promote oxidative dissolution of pyrite (FeS{sub 2}) when they were grown in pure cultures and in mixed cultures with sulfur-oxidizing Thiobacillus spp. Only one of the isolates (strain T-24) oxidized pyrite when it was grown in pyrite-basal salts medium. However, when pyrite-containing cultures were supplemented with 0.02% (wt/vol) yeast extract, most of the isolates oxidized pyrite, and one (strain T-24) promoted rates of mineral dissolution similar to the rates observed with the iron-oxidizing autotroph Thiobacillus ferroxidans. Pyrite oxidation by another isolate (strain T-21) occurred in cultures containing between 0.005 and 0.05% (wt/vol) yeast extract but was completely inhibited in cultures containing 0.5% yeast extract. Ferrous iron was also needed for mineral dissolution by the iron-oxidizing heterotrophs, indicating that these organisms oxidize pyrite via the indirect mechanism. Mixed cultures of three isolates (strains T-21, T-232, and T-24) and the sulfur-oxidizing autotroph Thiobacillus thiooxidans promoted pyrite dissolution; since neither strains T-21 and T-23 nor T. thiooxidans could oxidize this mineral in yeast extract-free media, this was a novel example of bacterial synergism. Mixed cultures of strains T-21 and T-23 and the sulfur-oxidizing mixotroph Thiobacillus acidophilus also oxidized pyrite but to a lesser extent than did mixed cultures containing T. thiooxidans. Pyrite leaching by strain T -23 grown in an organic compound-rich medium and incubated either shaken or unshaken was also assessed. The potential environmental significance of iron-oxidizing heterotrophs in accelerating pyrite oxidation is discussed.

  14. Geochemical Niches of Iron-Oxidizing Acidophiles in Acidic Coal Mine Drainage

    PubMed Central

    Kohl, Courtney; Grettenberger, Christen; Larson, Lance N.; Burgos, William D.

    2014-01-01

    A legacy of coal mining in the Appalachians has provided a unique opportunity to study the ecological niches of iron-oxidizing microorganisms. Mine-impacted, anoxic groundwater with high dissolved-metal concentrations emerges at springs and seeps associated with iron oxide mounds and deposits. These deposits are colonized by iron-oxidizing microorganisms that in some cases efficiently remove most of the dissolved iron at low pH, making subsequent treatment of the polluted stream water less expensive. We used full-cycle rRNA methods to describe the composition of sediment communities at two geochemically similar acidic discharges, Upper and Lower Red Eyes in Somerset County, PA, USA. The dominant microorganisms at both discharges were acidophilic Gallionella-like organisms, “Ferrovum” spp., and Acidithiobacillus spp. Archaea and Leptospirillum spp. accounted for less than 2% of cells. The distribution of microorganisms at the two sites could be best explained by a combination of iron(II) concentration and pH. Populations of the Gallionella-like organisms were restricted to locations with pH >3 and iron(II) concentration of >4 mM, while Acidithiobacillus spp. were restricted to pH <3 and iron(II) concentration of <4 mM. Ferrovum spp. were present at low levels in most samples but dominated sediment communities at pH <3 and iron(II) concentration of >4 mM. Our findings offer a predictive framework that could prove useful for describing the distribution of microorganisms in acid mine drainage, based on readily accessible geochemical parameters. PMID:25501473

  15. Microalgae as a safe food source for animals: nutritional characteristics of the acidophilic microalga Coccomyxa onubensis

    PubMed Central

    Navarro, Francisco; Forján, Eduardo; Vázquez, María; Montero, Zaida; Bermejo, Elisabeth; Castaño, Miguel Ángel; Toimil, Alberto; Chagüaceda, Enrique; García-Sevillano, Miguel Ángel; Sánchez, Marisa; Domínguez, María José; Pásaro, Rosario; Garbayo, Inés; Vílchez, Carlos; Vega, José María

    2016-01-01

    Background Edible microalgae are marine or fresh water mesophilic species. Although the harvesting of microalgae offers an abundance of opportunities to the food and pharmaceutical industries, the possibility to use extremophilic microalgae as a food source for animals is not well-documented. Objective We studied the effects of dietary supplementation of a powdered form of the acidophilic microalga Coccomyxa onubensis on growth and health parameters of laboratory rats. Method Four randomly organized groups of rats (n=6) were fed a standard diet (Diet 1, control) or with a diet in which 0.4% (Diet 2), 1.25% (Diet 3), or 6.25% (Diet 4) (w/w) of the standard diet weight was substituted with dried microalgae powder, respectively. The four groups of animals were provided ad libitum access to feed for 45 days. Results C. onubensis biomass is rich in protein (44.60% of dry weight) and dietary fiber (15.73%), and has a moderate carbohydrate content (24.8%) and a low lipid content (5.4%) in which polyunsaturated fatty acids represent 65% of the total fatty acid. Nucleic acids are present at 4.8%. No significant difference was found in growth rates or feed efficiency ratios of the four groups of rats. Histological studies of liver and kidney tissue revealed healthy organs in control and C. onubensis-fed animals, while plasma hematological and biochemical parameters were within healthy ranges for all animals. Furthermore, animals fed a microalgae-enriched diet exhibited a statistically significant decrease in both blood cholesterol and triglyceride levels. The blood triglyceride content and very low density lipoprotein-cholesterol levels decreased by about 50% in rats fed Diet 4. Conclusions These data suggest that C. onubensis may be useful as a food supplement for laboratory animals and may also serve as a nutraceutical in functional foods. In addition, microalgae powder-supplemented diets exerted a significant hypocholesterolemic and hypotriglyceridemic effect in animals

  16. Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples.

    PubMed

    Yamauchi, Yuto; Minegishi, Hiroaki; Echigo, Akinobu; Shimane, Yasuhiro; Kamekura, Masahiro; Itoh, Takashi; Ohkuma, Moriya; Doukyu, Noriyuki; Inoue, Akira; Usami, Ron

    2013-09-01

    Six halo-acidophilic archaeal strains were isolated from four commercial salt samples obtained from seawater in the Philippines, Indonesia (Bali) and Japan (Okinawa) on agar plates at pH 4.5. Cells of the six strains were pleomorphic, and stained Gram-negative. Two strains were pink-red pigmented, while four other strains were orange-pink pigmented. Strain MH1-16-3(T) was able to grow at 9-30% (w/v) NaCl [with optimum at 18% (w/v) NaCl], at pH 4.5-6.8 (optimum, pH 5.5) and at 20-50 °C (optimum, 42 °C). The five other strains grew at slightly different ranges. The six strains required at least 1 mM Mg(2+) for growth. The 16S rRNA gene sequences of the six strains were almost identical, sharing 99.9 (1-2 nt differences) to 100% similarity. The closest relatives were Halarchaeum acidiphilum MH1-52-1(T) and Halarchaeum salinum MH1-34-1(T) with 97.7% similarity. The DNA G+C contents of the six strains were 63.2-63.7 mol%. Levels of DNA-DNA relatedness amongst the six strains were 79-86%, while those between MH1-16-3(T) and H. acidiphilum MH1-52-1(T) and H. salinum MH1-34-1(T) were both 43 and 45% (reciprocally), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the six isolates represent a novel species of the genus Halarchaeum, for which the name Halarchaeum rubridurum sp. nov. is proposed. The type strain is MH1-16-3(T) ( =JCM 16108(T) =CECT 7535(T)).

  17. Acidophilic actinobacteria synthesised silver nanoparticles showed remarkable activity against fungi-causing superficial mycoses in humans.

    PubMed

    Anasane, N; Golińska, P; Wypij, M; Rathod, D; Dahm, H; Rai, M

    2016-03-01

    Superficial mycoses are limited to the most external part of the skin and hair and caused by Malassezia sp., Trichophyton sp. and Candida sp. We report extracellular biosynthesis of silver nanoparticles (AgNPs) by acidophilic actinobacteria (SF23, C9) and its in vitro antifungal activity against fungi-causing superficial mycoses. The phylogenetic analysis based on the 16S rRNA gene sequence of strains SF23 and C9 showed that they are most closely related to Pilimelia columellifera subsp. pallida GU269552(T). The detection of AgNPs was confirmed by visual observation of colour changes from colourless to brown, and UV-vis spectrophotometer analysis, which showed peaks at 432 and 427 nm, respectively. These AgNPs were further characterised by nanoparticle tracking analysis (NTA), Zeta potential, Fourier-transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM). The FTIR analysis exhibited the presence of proteins as capping agents. The TEM analysis revealed the formation of spherical and polydispersed nanoparticles in the size range of 4-36 nm and 8-60 nm, respectively. The biosynthesised AgNPs were screened against fungi-causing superficial mycoses viz., Malassezia furfur, Trichophyton rubrum, Candida albicans and C. tropicalis. The highest antifungal activity of AgNPs from SF23 and C9 against T. rubrum and the least against M. furfur and C. albicans was observed as compared to other tested fungi. The biosynthesised AgNPs were found to be potential anti-antifungal agent against fungi-causing superficial mycoses.

  18. Chemolithoautotrophic production mediating the cycling of the greenhouse gases N2O and CH4 in an upwelling ecosystem

    NASA Astrophysics Data System (ADS)

    Farías, L.; Fernández, C.; Faúndez, J.; Cornejo, M.; Alcaman, M. E.

    2009-12-01

    The high availability of electron donors occurring in coastal upwelling ecosystems with marked oxyclines favours chemoautotrophy, in turn leading to high N2O and CH4 cycling associated with aerobic NH4+ (AAO) and CH4 oxidation (AMO). This is the case of the highly productive coastal upwelling area off central Chile (36° S), where we evaluated the importance of total chemolithoautotrophic vs. photoautotrophic production, the specific contributions of AAO and AMO to chemosynthesis and their role in gas cycling. Chemolithoautotrophy was studied at a time-series station during monthly (2007-2009) and seasonal cruises (January 2008, September 2008, January 2009) and was assessed in terms of the natural C isotopic ratio of particulate organic carbon (δ13POC), total and specific (associated with AAO and AMO) dark carbon assimilation (CA), and N2O and CH4 cycling experiments. At the oxycline, δ13POC averaged -22.2‰; this was significantly lighter compared to the surface (-19.7‰) and bottom layers (-20.7‰). Total integrated dark CA in the whole water column fluctuated between 19.4 and 2.924 mg C m-2 d-1, was higher during active upwelling, and contributed 0.7 to 49.7% of the total integrated autotrophic CA (photo plus chemoautotrophy), which ranged from 135 to 7.626 mg C m-2 d-1, and averaged 20.3% for the whole sampling period. Dark CA was reduced by 27 to 48% after adding a specific AAO inhibitor (ATU) and by 24 to 76% with GC7, a specific archaea inhibitor. This indicates that AAO and AMO microbes (most of them archaea) were performing dark CA through the oxidation of NH4+ and CH4. Net N2O cycling rates varied between 8.88 and 43 nM d-1, whereas net CH4 cycling rates ranged from -0.41 to -26.8 nM d-1. The addition of both ATU and GC7 reduced N2O accumulation and increased CH4 consumption, suggesting that AAO and AMO were responsible, in part, for the cycling of these gases. These findings show that chemically driven chemolithoautotrophy (with NH4+ and CH4 acting

  19. Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH

    PubMed Central

    Mühling, Martin; Poehlein, Anja; Stuhr, Anna; Voitel, Matthias; Daniel, Rolf; Schlömann, Michael

    2016-01-01

    Bacterial community analyses of samples from a pilot plant for the treatment of acid mine drainage (AMD) from the lignite-mining district in Lusatia (East Germany) had previously demonstrated the dominance of two groups of acidophilic iron oxidizers: the novel candidate genus “Ferrovum” and a group comprising Gallionella-like strains. Since pure culture had proven difficult, previous studies have used genome analyses of co-cultures consisting of “Ferrovum” and a strain of the heterotrophic acidophile Acidiphilium in order to obtain insight into the life style of these novel bacteria. Here we report on attempts to undertake a similar study on Gallionella-like acidophiles from AMD. Isolates belonging to the family Gallionellaceae are still restricted to the microaerophilic and neutrophilic iron oxidizers Sideroxydans and Gallionella. Availability of genomic or metagenomic sequence data of acidophilic strains of these genera should, therefore, be relevant for defining adaptive strategies in pH homeostasis. This is particularly the case since complete genome sequences of the neutrophilic strains G. capsiferriformans ES-2 and S. lithotrophicus ES-1 permit the direct comparison of the metabolic capacity of neutrophilic and acidophilic members of the same genus and, thus, the detection of biochemical features that are specific to acidophilic strains to support life under acidic conditions. Isolation attempts undertaken in this study resulted in the microaerophilic enrichment culture ADE-12-1 which, based on 16S rRNA gene sequence analysis, consisted of at least three to four distinct Gallionellaceae strains that appear to be closely related to the neutrophilic iron oxidizer S. lithotrophicus ES-1. Key hypotheses inferred from the metabolic reconstruction of the metagenomic sequence data of these acidophilic Sideroxydans strains include the putative role of urea hydrolysis, formate oxidation and cyanophycin decarboxylation in pH homeostasis. PMID:28066396

  20. Investigation of energy gene expressions and community structures of free and attached acidophilic bacteria in chalcopyrite bioleaching.

    PubMed

    Zhu, Jianyu; Jiao, Weifeng; Li, Qian; Liu, Xueduan; Qin, Wenqing; Qiu, Guanzhou; Hu, Yuehua; Chai, Liyuan

    2012-12-01

    In order to better understand the bioleaching mechanism, expression of genes involved in energy conservation and community structure of free and attached acidophilic bacteria in chalcopyrite bioleaching were investigated. Using quantitative real-time PCR, we studied the expression of genes involved in energy conservation in free and attached Acidithiobacillus ferrooxidans during bioleaching of chalcopyrite. Sulfur oxidation genes of attached A. ferrooxidans were up-regulated while ferrous iron oxidation genes were down-regulated compared with free A. ferrooxidans in the solution. The up-regulation may be induced by elemental sulfur on the mineral surface. This conclusion was supported by the results of HPLC analysis. Sulfur-oxidizing Acidithiobacillus thiooxidans and ferrous-oxidizing Leptospirillum ferrooxidans were the members of the mixed culture in chalcopyrite bioleaching. Study of the community structure of free and attached bacteria showed that A. thiooxidans dominated the attached bacteria while L. ferrooxidans dominated the free bacteria. With respect to available energy sources during bioleaching of chalcopyrite, sulfur-oxidizers tend to be on the mineral surfaces whereas ferrous iron-oxidizers tend to be suspended in the aqueous phase. Taken together, these results indicate that the main role of attached acidophilic bacteria was to oxidize elemental sulfur and dissolution of chalcopyrite involved chiefly an indirect bioleaching mechanism.

  1. The lowering of external pH in confined environments by thermo-acidophilic algae (class: Cyanidiophyceae).

    PubMed

    Lowell, Christina; Castenholz, Richard W

    2013-10-01

    The unicellular, asexual thermo-acidophilic algae of the class Cyanidiophyceae, order Cyanidiales (the 'cyanidia') include only three genera, walled Cyanidium and Galdieria, and 'naked' Cyanidioschyzon, names based on morphological and cytological characters. Most species and strains of this class live in acid hot springs or acid soils or steam vents associated with these springs at pH 0.5 to ~ 4.0 at temperatures of ~ 38-56 °C. No other phototrophs live in this combination of factors in these habitats, except for a small overlap with other acidophilic algae at the highest pH and the lowest temperature. The optimum pH for growth of the 'cyanidia' in this study was ~ 2.3. Galdieria-like walled cells of Cyanidioschyzon and naked Cyanidioschyzon cells were exposed in culture to higher pH conditions of 6.0, 5.5 and 5.0 in confined, illuminated environments (cotton plugged flasks). The subsequent acidification of the medium towards or to 2.3 occurred as growth and biomass increased. There was a direct correlation with final biomass (Chl a) and lower pH. All eight strains isolated from Yellowstone acidic conditions were able to lower the supra-optimal pH of their medium, while only two from other continents and none of the three from Japan were competent. It is probable that the ability to lower pH to an optimal level has survival value in some niches in natural habitats.

  2. Biochemistry and Ecology of Novel Cytochromes Catalyzing Fe(II) Oxidation by an Acidophilic Microbial Community

    NASA Astrophysics Data System (ADS)

    Singer, S. W.; Jeans, C. J.; Thelen, M. P.; Verberkmoes, N. C.; Hettich, R. C.; Chan, C. S.; Banfield, J. F.

    2007-12-01

    An acidophilic microbial community found in the Richmond Mine at Iron Mountain, CA forms abundant biofilms in extremely acidic (pH<1) and toxic metal conditions. In this ecosystem, biological Fe(II) oxidation is critical to the metabolic functioning of the community, and in turn this process generates acid mine drainage, causing an environmental catastrophe. Two conspicuous novel proteins isolated from these biofilms were identified as gene products of Leptospirillum group II and were characterized as cytochromes with unique properties. Sulfuric acid extraction of biofilm samples liberated one of these proteins, a 16 kDa cytochrome with an unusual alpha-band absorption at 579 (Cyt579). Genomic sequencing of multiple biofilms indicated that several variants of Cyt579 were present in Leptospirillum strains. Intact protein MS analysis identified the dominant variants in each biofilm and documented multiple N-terminal cleavage sites for Cyt579. By combining biochemical, geochemical and microbiological data, we established that the sequence variation and N-terminal processing of Cyt579 are selected by ecological conditions. In addition to the soluble Cyt579, the second cytochrome appears as a much larger protein complex of ~210 kDa predominant in the biofilm membrane fraction, and has an alpha-band absorption at 572 nm. The 60 kDa cytochrome subunit, Cyt572, resides in the outer membrane of LeptoII, and readily oxidizes Fe(II) at low pH (0.95 - 3.0). Several genes encoding Cyt572 were localized within a recombination hotspot between two strains of LeptoII, causing a large range of variation in the sequences. Genomic sequencing and MS proteomic studies established that the variants were also selected by ecological conditions. A general mechanistic model for Fe(II) oxidation has been developed from these studies. Initial Fe(II) oxidation by Cyt572 occurs at the outer membrane. Cyt572 then transfers electrons to Cyt579, perhaps representing an initial step in energy flow

  3. Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt.

    PubMed

    Minegishi, Hiroaki; Yamauchi, Yuto; Echigo, Akinobu; Shimane, Yasuhiro; Kamekura, Masahiro; Itoh, Takashi; Ohkuma, Moriya; Usami, Ron

    2013-11-01

    Two halophilic moderately acidophilic archaeal strains, MH1-136-2(T) and MH1-370-1 were isolated from commercial salt samples made from seawater in Japan and Indonesia, respectively. Cells of the two strains were pleomorphic and Gram-stain-negative. Strain MH1-136-2(T) was pink pigmented, while MH1-370-1 was orange-red pigmented. Strain MH1-136-2(T) was able to grow at 9-30 % (w/v) NaCl (with optimum, 21 % NaCl, w/v) at pH 4.5-6.2 (optimum, pH 5.2-5.5) and at 18-55 °C (optimum, 45 °C). Strain MH1-370-1 was able to grow at 12-30 % (w/v) NaCl (optimum, 18 %, w/v) at pH 4.2-6.0 (optimum, pH 5.2-5.5) and 20-50 °C (optimum, 45 °C). Strain MH1-136-2(T) required at least 1 mM Mg(2+), while MH1-370-1 required at least 10 mM for growth. Both strains reduced nitrate and nitrite under aerobic conditions. The 16S rRNA gene sequences of strains MH1-136-2(T) and MH1-370-1 were identical, and the closest relative was Halarchaeum rubridurum MH1-16-3(T) with 98.3 % similarity. The level of DNA-DNA relatedness between these strains was 90.9 % and 92.4 % (reciprocally), while that between MH1-136-2(T) and Halarchaeum acidiphilum MH1-52-1(T), Halarchaeum salinum MH1-34-1(T) and Halarchaeum rubridurum MH1-16-3(T) was 37.7 %, 44.3 % and 41.1 % (each an average), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of the genus Halarchaeum, for which the name Halarchaeum nitratireducens sp. nov. is proposed. The type strain is MH1-136-2(T) ( = JCM 16331(T) = CECT 7573(T)) isolated from solar salt produced in Japan.

  4. Long term performance of an AMD treatment bioreactor using chemolithoautotrophic sulfate reduction and ferrous iron precipitation under in situ groundwater conditions.

    PubMed

    Bilek, F; Wagner, S

    2012-01-01

    Chemolithoautotrophic sulfate reduction (CSR) was tested to treat natural acid mine drainage influenced groundwaters. The long term behavior was studied for more than 3 years under groundwater conditions (10 °C, autochthonous sulfate reducing bacteria (SRB)) without biomass replenishment in a 190 L bench scale reactor. The process produces water with alkalinity >10 mM. pH can be controlled by p(CO(2)) for all expectable water qualities. SRB were immobilized using an expanded clay bed. After 1.3 years of operation, a constant biomass content and sulfate reduction rate of 0.25-0.30 mmol(so)₄(Lh)⁻¹ were established. The sulfate reduction rate was limited by biomass content. Most of the electrons were used for sulfate reduction (98%). The hydrogen turn over in competing processes like methanogenesis and homoacetogenesis was successfully suppressed by adjusting the sulfate concentration to be >2 mM in the runoff.

  5. Sulfurihydrogenibium rodmanii sp. nov., a sulfur-oxidizing chemolithoautotroph from the Uzon Caldera, Kamchatka Peninsula, Russia, and emended description of the genus Sulfurihydrogenibium.

    PubMed

    O'Neill, Andrew H; Liu, Yitai; Ferrera, Isabel; Beveridge, Terry J; Reysenbach, Anna-Louise

    2008-05-01

    Four thermophilic, sulfur-oxidizing, chemolithoautotrophic strains with >99 % 16S rRNA gene sequence similarity were isolated from terrestrial hot springs in the Geyser Valley and the Uzon Caldera, Kamchatka, Russia. One strain, designated UZ3-5T, was characterized fully. Cells of UZ3-5T were Gram-negative, motile, slightly oval rods (about 0.7 microm wide and 1.0 microm long) with multiple polar flagella. All four strains were obligately microaerophilic chemolithoautotrophs and could use elemental sulfur or thiosulfate as electron donors and oxygen (1-14 %, v/v) as the electron acceptor. Strain UZ3-5T grew at temperatures between 55 and 80 degrees C (optimally at 75 degrees C; 1.1 h doubling time), at pH 5.0-7.2 (optimally at pH 6.0-6.3) and at 0-0.9 % NaCl (optimally in the absence of NaCl). The G+C content of the genomic DNA of strain UZ3-5T was 35 mol%. Phylogenetic analysis revealed that strain UZ3-5T was a member of the genus Sulfurihydrogenibium, its closest relative in culture being Sulfurihydrogenibium azorense Az-Fu1T (98.3 % 16S rRNA gene sequence similarity). On the basis of its physiological and molecular characteristics, strain UZ3-5T represents a novel species of the genus Sulfurihydrogenibium, for which the name Sulfurihydrogenibium rodmanii sp. nov. is proposed. The type strain is UZ3-5T (=OCM 900T =ATCC BAA-1536T =DSM 19533T).

  6. Caldimicrobium rimae gen. nov., sp. nov., an extremely thermophilic, facultatively lithoautotrophic, anaerobic bacterium from the Uzon Caldera, Kamchatka.

    PubMed

    Miroshnichenko, Margarita L; Lebedinsky, Alexander V; Chernyh, N A; Tourova, Tatyana P; Kolganova, Tatyana V; Spring, Stefan; Bonch-Osmolovskaya, Elizaveta A

    2009-05-01

    An extremely thermophilic, strictly anaerobic, facultatively chemolithoautotrophic bacterium designated strain DS(T) was isolated from Treshchinnyi Spring, one of the hottest springs of the Uzon Caldera (Kamchatka, Russia). Cells of the novel organism were Gram-negative rods, about 1.0-1.2 microm long and 0.5 microm wide. The temperature range for growth was 52-82 degrees C, with an optimum at 75 degrees C. Growth was observed at pH 6.8-7.4, and the optimum pH was 7.0-7.2. Strain DS(T) was able to grow lithoautotrophically with hydrogen in the presence of CO(2) as a carbon source and thiosulfate or elemental sulfur as an electron acceptor. It also grew well with ethanol, fumarate, succinate or malate in the presence of thiosulfate. Yeast extract was not required for growth and did not stimulate growth. The genomic DNA G+C content was 35.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the novel organism was a member of the family Thermodesulfobacteriaceae. On the basis of phylogenetic and physiological considerations, it is proposed that strain DS(T) represents a new genus and species, Caldimicrobium rimae gen. nov., sp. nov. The type strain of Caldimicrobium rimae is DS(T) (=DSM 19393(T) =VKM B-2460(T)).

  7. [Leaching of copper ore of the Udokanskoe deposit at low temperatures by an association of acidophilic chemolithotrophic microorganisms].

    PubMed

    Kondrat'eva, T F; Pivovarova, T A; Krylova, L N; Melamud, V S; Adamov, E V; Karavaĭko, G I

    2011-01-01

    Pure cultures of indigenous microorganisms Acidithiobacillus ferrooxidans strain TFUd, Leptospirillum ferrooxidans strain LUd, and Sulfobacillus thermotolerans strain SUd have been isolated from the oxidation zone of sulfide copper ore of the Udokanskoe deposit. Regimes of bacterial-chemical leaching of ore have been studied over a temperature range from -10 to +20 degrees C. Effects of pH, temperature, and the presence of microorganisms on the extraction of copper have been shown. Bacterial leaching has been detected only at positive values of temperature, and has been much more active at +20 than at +4 degrees C. The process of leaching was more active when the ore contained more hydrophilic and oxidized minerals. The possibility of copper ore leaching of the Udokanskoe deposit using sulfuric acid with pH 0.4 at negative values of temperature and applying acidophilic chemolithotrophic microorganisms at positive values of temperature and low pH values was shown.

  8. Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”

    PubMed Central

    Ullrich, Sophie R.; González, Carolina; Poehlein, Anja; Tischler, Judith S.; Daniel, Rolf; Schlömann, Michael; Holmes, David S.; Mühling, Martin

    2016-01-01

    Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus “Ferrovum” are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of “Ferrovum” has proven to be extremely difficult and has so far only been successful for the designated type strain “Ferrovum myxofaciens” P3G. In this study, the genomes of two novel strains of “Ferrovum” (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of “Ferrovum” sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three “Ferrovum” species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the “F. myxofaciens” strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features

  9. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.

    PubMed

    Ziegler, Sibylle; Dolch, Kerstin; Geiger, Katharina; Krause, Susanne; Asskamp, Maximilian; Eusterhues, Karin; Kriews, Michael; Wilhelms-Dick, Dorothee; Goettlicher, Joerg; Majzlan, Juraj; Gescher, Johannes

    2013-09-01

    Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.

  10. Acidophilic denitrifiers dominate the N2O production in a 100-year-old tea orchard soil.

    PubMed

    Huang, Ying; Long, Xi-En; Chapman, Stephen J; Yao, Huaiying

    2015-03-01

    Aerobic denitrification is the main process for high N2O production in acid tea field soil. However, the biological mechanisms for the high emission are not fully understood. In this study, we examined N2O emission and denitrifier communities in 100-year-old tea soils with four pH levels (3.71, 5.11, 6.19, and 7.41) and four nitrate concentration (0, 50, 200, and 1000 mg kg(-1) of NO3 (-)-N) addition. Results showed the highest N2O emission (10.1 mg kg(-1) over 21 days) from the soil at pH 3.71 with 1000 mg kg(-1) NO3 (-) addition. The N2O reduction and denitrification enzyme activity in the acid soils (pH <7.0) were significantly higher than that of soils at pH 7.41. Moreover, TRF 78 of nirS and TRF 187 of nosZ dominated in soils of pH 3.71, suggesting an important role of acidophilic denitrifiers in N2O production and reduction. CCA analysis also showed a negative correlation between the dominant denitrifier ecotypes (nirS TRF 78, nosZ TRF 187) and soil pH. The representative sequences were identical to those of cultivated denitrifiers from acidic soils via phylogenetic tree analysis. Our results showed that the acidophilic denitrifier adaptation to the acid environment results in high N2O emission in this highly acidic tea soil.

  11. A "MICROTUBULE" IN A BACTERIUM

    PubMed Central

    van Iterson, Woutera; Hoeniger, Judith F. M.; van Zanten, Eva Nijman

    1967-01-01

    A study of the anchorage of the flagella in swarmers of Proteus mirabilis led to the incidental observation of microtubules. These microtubules were found in thin sections and in whole mount preparations of cells from which most of the content had been released by osmotic shock before staining negatively with potassium phosphotungstate (PTA). The microtubules are in negatively stained preparations about 200 A wide, i.e. somewhat thicker than the flagella (approximately 130 A). They are thus somewhat thinner than most microtubules recorded for other cells. They are referred to as microtubules because of their smooth cylindrical wall, or cortex, surrounding a hollow core which is readily filled with PTA when stained negatively. Since this is probably the first time that such a structure is described inside a bacterium, we do not know for certain whether it represents a normal cell constituent or an abnormality, for instance of the type of "polysheaths" (16). PMID:10976198

  12. Production of glycolic acid by chemolithotrophic iron- and sulfur-oxidizing bacteria and its role in delineating and sustaining acidophilic sulfide mineral-oxidizing consortia.

    PubMed

    Nancucheo, Ivan; Johnson, D Barrie

    2010-01-01

    Glycolic acid was detected as an exudate in actively growing cultures of three chemolithotrophic acidophiles that are important in biomining operations, Leptospirillum ferriphilum, Acidithiobacillus (At.) ferrooxidans, and At. caldus. Although similar concentrations of glycolic acid were found in all cases, the concentrations corresponded to ca. 24% of the total dissolved organic carbon (DOC) in cultures of L. ferriphilum but only ca. 5% of the total DOC in cultures of the two Acidithiobacillus spp. Rapid acidification (to pH 1.0) of the culture medium of At. caldus resulted in a large increase in the level of DOC, although the concentration of glycolic acid did not change in proportion. The archaeon Ferroplasma acidiphilum grew in the cell-free spent medium of At. caldus; glycolic acid was not metabolized, although other unidentified compounds in the DOC pool were metabolized. Glycolic acid exhibited levels of toxicity with 21 strains of acidophiles screened similar to those of acetic acid. The most sensitive species were chemolithotrophs (L. ferriphilum and At. ferrivorans), while the most tolerant species were chemoorganotrophs (Acidocella, Acidobacterium, and Ferroplasma species), and the ability to metabolize glycolic acid appeared to be restricted (among acidophiles) to Firmicutes (chiefly Sulfobacillus spp.). Results of this study help explain why Sulfobacillus spp. rather than other acidophiles are the main organic carbon-degrading bacteria in continuously fed stirred tanks used to bioprocess sulfide mineral concentrates and also why temporary cessation of pH control in these systems, resulting in rapid acidification, often results in a plume of the archaeon Ferroplasma.

  13. Biodegradation of polycyclic aromatic hydrocarbons by an acidophilic Stenotrophomonas maltophilia strain AJH1 isolated from a mineral mining site in Saudi Arabia.

    PubMed

    Arulazhagan, P; Al-Shekri, K; Huda, Q; Godon, J J; Basahi, J M; Jeyakumar, D

    2017-01-01

    The present study aims at analyzing the degradation of polycyclic aromatic hydrocarbons (PAHs) at acidic conditions (pH = 2) by acidophilic Stenotrophomonas maltophilia strain AJH1 (KU664513). The strain AJH1 was obtained from an enrichment culture obtained from soil samples of mining area in the presence of PAH as sole sources of carbon and energy. Strain AJH1was able to degrade low (anthracene, phenanthrene, naphthalene, fluorene) and high (pyrene, benzo(e)pyrene and benzo(k)fluoranthene) molecular weight PAHs in acidophilic mineral salt medium at pH 2, with removal rates of up to 95% (LMW PAH) and 80% (HMW PAH), respectively. In addition, strain AJH1 treated petroleum wastewater with 89 ± 1.1% COD removal under acidic condition (pH 2) in a continuously stirred reactor. Acidophilic S. maltophilia strain AJH1, hence holds the promise as an effective degrader for biological treatment of PAHs contaminated wastewater at acidic pH.

  14. Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment.

    PubMed

    Cai, Lin; Shao, Ming-Fei; Zhang, Tong

    2014-06-15

    Here, we report a type strain AST-10 representing a novel species Sulfurimonas hongkongensis within Epsilonproteobacteria, which is involved in marine sedimentary sulfur oxidation and denitrification. Strain AST-10(T) (= DSM 22096(T) = JCM 18418(T)) was isolated from the coastal sediment at the Kai Tak Approach Channel connected to Victoria Harbour in Hong Kong. It grew chemolithoautotrophically using thiosulfate, sulfide or hydrogen as the sole electron donor and nitrate as the electron acceptor under anoxic conditions. It was rod-shaped and grew at 15-35°C (optimum at 30°C), pH 6.5-8.5 (optimum at 7.0-7.5), and 10-60 g L(-1) NaCl (optimum at 30 g L(-1)). Genome sequencing and annotation of strain AST-10(T) showed a 2,302,023 bp genome size, with 34.9% GC content, 2,290 protein-coding genes, and 42 RNA genes, including 3 rRNA genes.

  15. Biofilm formation and interspecies interactions in mixed cultures of thermo-acidophilic archaea Acidianus spp. and Sulfolobus metallicus.

    PubMed

    Castro, Camila; Zhang, Ruiyong; Liu, Jing; Bellenberg, Sören; Neu, Thomas R; Donati, Edgardo; Sand, Wolfgang; Vera, Mario

    2016-09-01

    The understanding of biofilm formation by bioleaching microorganisms is of great importance for influencing mineral dissolution rates and to prevent acid mine drainage (AMD). Thermo-acidophilic archaea such as Acidianus, Sulfolobus and Metallosphaera are of special interest due to their ability to perform leaching at high temperatures, thereby enhancing leaching rates. In this work, leaching experiments and visualization by microscopy of cell attachment and biofilm formation patterns of the crenarchaeotes Sulfolobus metallicus DSM 6482(T) and the Acidianus isolates DSM 29038 and DSM 29099 in pure and mixed cultures on sulfur or pyrite were studied. Confocal laser scanning microscopy (CLSM) combined with fluorescent dyes as well as fluorescently labeled lectins were used to visualize different components (e.g. DNA, proteins or glycoconjugates) of the aforementioned species. The data indicate that cell attachment and the subsequently formed biofilms were species- and substrate-dependent. Pyrite leaching experiments coupled with pre-colonization and further inoculation with a second species suggest that both species may negatively influence each other during pyrite leaching with respect to initial attachment and pyrite dissolution rates. In addition, the investigation of binary biofilms on pyrite showed that both species were heterogeneously distributed on pyrite surfaces in the form of individual cells or microcolonies. Physical contact between the two species seems to occur, as revealed by specific lectins able to specifically bind single species within mixed cultures.

  16. Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon

    PubMed Central

    Kawamura, Takuya; Hirata, Akira; Ohno, Satoshi; Nomura, Yuichiro; Nagano, Tomoko; Nameki, Nobukazu; Yokogawa, Takashi; Hori, Hiroyuki

    2016-01-01

    Archaeosine (G+), which is found only at position 15 in many archaeal tRNA, is formed by two steps, the replacement of the guanine base with preQ0 by archaeosine tRNA-guanine transglycosylase (ArcTGT) and the subsequent modification of preQ0 to G+ by archaeosine synthase. However, tRNALeu from Thermoplasma acidophilum, a thermo-acidophilic archaeon, exceptionally has two G+13 and G+15 modifications. In this study, we focused on the biosynthesis mechanism of G+13 and G+15 modifications in this tRNALeu. Purified ArcTGT from Pyrococcus horikoshii, for which the tRNA recognition mechanism and structure were previously characterized, exchanged only the G15 base in a tRNALeu transcript with 14C-guanine. In contrast, T. acidophilum cell extract exchanged both G13 and G15 bases. Because T. acidophilum ArcTGT could not be expressed as a soluble protein in Escherichia coli, we employed an expression system using another thermophilic archaeon, Thermococcus kodakarensis. The arcTGT gene in T. kodakarensis was disrupted, complemented with the T. acidophilum arcTGT gene, and tRNALeu variants were expressed. Mass spectrometry analysis of purified tRNALeu variants revealed the modifications of G+13 and G+15 in the wild-type tRNALeu. Thus, T. acidophilum ArcTGT has a multisite specificity and is responsible for the formation of both G+13 and G+15 modifications. PMID:26721388

  17. A novel acidophilic, thermophilic iron and sulfur-oxidizing archaeon isolated from a hot spring of tengchong, yunnan, China

    PubMed Central

    Ding, Jiannan; Zhang, Ruiyong; Yu, Yizun; Jin, Decai; Liang, Changli; Yi, Yang; Zhu, Wei; Xia, Jinlan

    2011-01-01

    A novel thermoacidophilic iron and sulfur-oxidizing archaeon, strain YN25, was isolated from an in situ enriched acid hot spring sample collected in Yunnan, China. Cells were irregular cocci, about 0.9–1.02 µm × 1.0–1.31 µm in the medium containing elemental sulfur and 1.5–2.22 µm × 1.8–2.54 µm in ferrous sulfate medium. The ranges of growth and pH were 50–85 (optimum 65) and pH 1.0–6.0 (optimum 1.5–2.5). The acidophile was able to grow heterotrophically on several organic substrates, including various monosaccharides, alcohols and amino acids, though the growth on single substrate required yeast extract as growth factor. Growth occurred under aerobic conditions or via anaerobic respiration using elemental sulfur as terminal electron acceptor. Results of morphology, physiology, fatty acid analysis and analysis based on 16S rRNA gene sequence indicated that the strain YN25 should be grouped in the species Acidianus manzaensis. Bioleaching experiments indicated that this strain had excellent leaching capacity, with a copper yielding ratio up to 79.16% in 24 d. The type strain YN25 was deposited in China Center for Type Culture Collection (=CCTCCZNDX0050). PMID:24031663

  18. [Basic proteins in the granules of mast cells. Demonstration of masked proteins, acidophilic staining of the granules].

    PubMed

    Anikó, K; Lajos, K

    1976-07-01

    Basic proteins of the granules of mast cells in nativ, formalin-, alcohol- and aceton fixed preparations without any preliminary treatment, when stained with acidic dye at the pH 9 cytochemically seem to be masked. After various preliminary treatment (treatment with acid, with cetylpiridinumchlorid, CPC) mast-cell granula stained with acidic-dye at pH 9 appear intensively acidophile. This phenomenon can be explained by the presence of basic proteins in the mast cell granula. Preliminary treatment with CPC inhibits acid radicals of the heparin. This may lead to the disintegration of the linkage between proteins of the heparin, thus amino-group of the basic proteins become reactivated and can be identified by acidic dyes. It can not be excluded as well, that CPC linked to the heparin with free positive radicals reveals acidic-dye-binding capacity. In cases of preliminary treatment with various acids this mechanism does not seem possible to lay on the base of changing of the dye binding capacity.

  19. Insights into glycogen metabolism in chemolithoautotrophic bacteria from distinctive kinetic and regulatory properties of ADP-glucose pyrophosphorylase from Nitrosomonas europaea.

    PubMed

    Machtey, Matías; Kuhn, Misty L; Flasch, Diane A; Aleanzi, Mabel; Ballicora, Miguel A; Iglesias, Alberto A

    2012-11-01

    Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO(2) via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms.

  20. Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats.

    PubMed

    Tourova, Tatjana P; Kovaleva, Olga L; Sorokin, Dimitry Yu; Muyzer, Gerard

    2010-07-01

    The presence and diversity of the cbb genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) (a key enzyme of the Calvin-Benson cycle of autotrophic CO(2) assimilation) were investigated in pure cultures of seven genera of halophilic chemolithoautotrophic sulfur-oxidizing bacteria (SOB) and in sediments from a hypersaline lake in which such bacteria have been recently discovered. All of the halophilic SOB strains (with the exception of Thiohalomonas nitratireducens) possessed the cbbL gene encoding RuBisCO form I, while the cbbM gene encoding RuBisCO form II was detected only in some of the pure cultures. The general topologies of the CbbL/CbbM trees and the 16S rRNA gene tree were different, but both markers showed that the halophilic SOB genera formed independent lineages in the Gammaproteobacteria. In some cases, such as with several strains of the genus Thiohalospira and with Thioalkalibacter halophilus, the cbbL clustering was incongruent with the positions of these strains on the ribosomal tree. In the cbbM tree, the clustering of Thiohalospira and Thiohalorhabdus strains was incongruent with their branching in both cbbL and 16S rRNA gene trees. cbbL and cbbM genes related to those found in the analysed halophilic SOB were also detected in a sediment from a hypersaline lake in Kulunda Steppe (Russia). Most of the cbbL and cbbM genes belonged to members of the genus Thiohalorhabdus. In the cbbL clone library, sequences related to those of Halothiobacillus and Thiohalospira were detected as minor components. Some of the environmental cbbM sequences belonged to as yet unknown phylotypes, representing deep lineages of halophilic autotrophs.

  1. Insights into Glycogen Metabolism in Chemolithoautotrophic Bacteria from Distinctive Kinetic and Regulatory Properties of ADP-Glucose Pyrophosphorylase from Nitrosomonas europaea

    PubMed Central

    Machtey, Matías; Kuhn, Misty L.; Flasch, Diane A.; Aleanzi, Mabel; Ballicora, Miguel A.

    2012-01-01

    Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO2 via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms. PMID:22961847

  2. Unmodified prolactin (PRL) promotes PRL secretion and acidophil hypertrophy and is associated with pituitary hyperplasia in female rats.

    PubMed

    Johnson, Terence E; Vue, Mayza; Brekhus, Sharyn; Khong, Amy; Ho, Timothy W C; Walker, Ameae M

    2003-01-01

    In this study, we have tested the hypothesis that unmodified prolactin (U-PRL) and phosphorylated prolactin (P-PRL) have differential roles in the autoregulation of PRL secretion in vivo. Recombinant human U-PRL and a molecular mimic of P-PRL (S179D PRL) were administered to male rats and to female rats in different physiological states and the effect on rat PRL release was measured. Administration of U-PRL elevated rat PRL in all female animals, but was without effect in males. By contrast, S179D PRL was inactive in females, but inhibited PRL release in males. Morphometric and immunohistochemical analyses demonstrated acidophil hypertrophy and evidence of increased PRL secretion in the pituitaries of U-PRL-treated females. Analysis of the two forms of PRL during prolactinoma induction in two differentially susceptible strains of rats found a strong temporal correlation among increased ratios of U-PRL: P-PRL, increased circulating PRL, and increased cell proliferation. We conclude (1). that the autoregulatory mechanism(s) can distinguish between the two major forms of PRL and that higher proportions of U-PRL not only allow for higher circulating levels of PRL, but are also autostimulatory, (2). that the autoregulatory mechanism( s) are set differently in males and females such that females are more sensitive to autostimulation by U-PRL and less sensitive to inhibition by P-PRL, and (3). that U-PRL and P-PRL may also have differential roles in the regulation of pituitary cell proliferation.

  3. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community.

    PubMed

    Jeans, Chris; Singer, Steven W; Chan, Clara S; Verberkmoes, Nathan C; Shah, Manesh; Hettich, Robert L; Banfield, Jillian F; Thelen, Michael P

    2008-05-01

    Recently, there has been intense interest in the role of electron transfer by microbial communities in biogeochemical systems. We examined the process of iron oxidation by microbial biofilms in one of the most extreme environments on earth, where the inhabited water is pH 0.5-1.2 and laden with toxic metals. To approach the mechanism of Fe(II) oxidation as a means of cellular energy acquisition, we isolated proteins from natural samples and found a conspicuous and novel cytochrome, Cyt(572), which is unlike any known cytochrome. Both the character of its covalently bound prosthetic heme group and protein sequence are unusual. Extraction of proteins directly from environmental biofilm samples followed by membrane fractionation, detergent solubilization and gel filtration chromatography resulted in the purification of an abundant yellow-red protein. The purified protein has a cytochrome c-type heme binding motif, CxxCH, but a unique spectral signature at 572 nm, and thus is called Cyt(572). It readily oxidizes Fe(2+) in the physiologically relevant acidic regime, from pH 0.95-3.4. Other physical characteristics are indicative of a membrane-bound multimeric protein. Circular dichroism spectroscopy indicates that the protein is largely beta-stranded, and 2D Blue-Native polyacrylamide gel electrophoresis and chemical crosslinking independently point to a multi-subunit structure for Cyt(572). By analyzing environmental genomic information from biofilms in several distinctly different mine locations, we found multiple genetic variants of Cyt(572). MS proteomics of extracts from these biofilms substantiated the prevalence of these variants in the ecosystem. Due to its abundance, cellular location and Fe(2+) oxidation activity at very low pH, we propose that Cyt(572) provides a critical function for fitness within the ecological niche of these acidophilic microbial communities.

  4. Synthesis of silver nanoparticles from two acidophilic strains of Pilimelia columellifera subsp. pallida and their antibacterial activities.

    PubMed

    Golińska, Patrycja; Wypij, Magdalena; Rathod, Dnyaneshwar; Tikar, Sagar; Dahm, Hanna; Rai, Mahendra

    2016-05-01

    Biosynthesis of silver nanoparticles (AgNPs) is an eco-friendly approach by using different biological sources; for example, plants and microorganisms such as bacteria, fungi, and actinobacteria. In this report, we present the biological synthesis of silver nanoparticles (AgNPs) by acidophilic actinomycetes SL19 and SL24 strains isolated from pine forest soil (pH < 4.0). The isolates based on 16S rRNA gene sequence were identified as Pilimelia columellifera subsp. pallida. The synthesized AgNPs were characterized by visual observations of colour change from light-yellow to dark-brown. The UV-vis spectra of AgNPs were recorded at 425 and 430 nm. The AgNPs were further characterized by Nanoparticle tracking analysis (NTA), Zeta potential, Fourier transform infrared spectroscopy (FTIR) and Transmission electron microscopy (TEM). FTIR analysis revealed the presence of proteins as a capping agent. TEM analysis confirmed the formation of spherical and polydispersed NPs of 12.7 and 15.9 nm sizes. The in vitro antibacterial activity of AgNPs alone and in combination with antibiotics was evaluated against clinical bacteria viz., Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and uropathogens such as Enterobacter, S. aureus, P. aeruginosa, K. pneumoniae, and E. coli. The lowest MIC (40 μg ml(-1) ) was demonstrated by AgNPs synthesized from SL24 against E. coli. However, the AgNPs of SL19 showed lowest MIC (70 μg ml(-1) ) against S. aureus. The activity of antibiotic was enhanced, when tested in combination with silver nanoparticles synthesized from both actinobacterial strains.

  5. Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost.

    PubMed

    Steven, Blaire; Chen, Min Qun; Greer, Charles W; Whyte, Lyle G; Niederberger, Thomas D

    2008-06-01

    A Gram-positive, aerobic, rod-shaped bacterium (strain Eur1 9.5(T)) was isolated from a 9-m-deep permafrost sample from the Canadian high Arctic. Strain Eur1 9.5(T) could not be cultivated in liquid medium and grew over the temperature range 5-37 degrees C; no growth was observed at 42 degrees C and only slow growth was observed at 5 degrees C following 1 month of incubation. Eur1 9.5(T) grew over the pH range 5.5-8.9 and tolerated NaCl concentrations of 0-0.5 % (w/v). Eur1 9.5(T) grew heterotrophically on complex carbon substrates and chemolithoautotrophically on inorganic sulfur compounds, as demonstrated by growth on sodium thiosulfate and sulfite as sole electron donors. Eur1 9.5(T) contained iso-C(15 : 0) as the major cellular fatty acid and menaquinone 7 (MK-7) as the major respiratory quinone. The cell-wall peptidoglycan was of type A1gamma. The DNA G+C content was 53.1 mol%. The 16S rRNA gene sequence of strain Eur1 9.5(T) was only distantly related (

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

    PubMed

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

    2013-03-01

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

  7. Thermosulfurimonas dismutans gen. nov., sp. nov., an extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent.

    PubMed

    Slobodkin, A I; Reysenbach, A-L; Slobodkina, G B; Baslerov, R V; Kostrikina, N A; Wagner, I D; Bonch-Osmolovskaya, E A

    2012-11-01

    An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S95(T)) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center, Pacific Ocean, at a depth of 1910 m. Cells of strain S95(T) were oval to short Gram-negative rods, 0.5-0.6 µm in diameter and 1.0-1.5 µm in length, growing singly or in pairs. Cells were motile with a single polar flagellum. The temperature range for growth was 50-92 °C, with an optimum at 74 °C. The pH range for growth was 5.5-8.0, with an optimum at pH 7.0. Growth of strain S95(T) was observed at NaCl concentrations ranging from 1.5 to 3.5% (w/v). Strain S95(T) grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO(2) as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline iron(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S95(T) was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the phylum Thermodesulfobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents the sole species of a new genus, Thermosulfurimonas dismutans gen. nov., sp. nov.; S95(T) (=DSM 24515(T)=VKM B-2683(T)) is the type strain of the type species. This is the first description of a thermophilic micro-organism that disproportionates elemental sulfur.

  8. Novel Waddlia Intracellular Bacterium in Artibeus intermedius Fruit Bats, Mexico

    PubMed Central

    Pierlé, Sebastián Aguilar; Morales, Cirani Obregón; Martínez, Leonardo Perea; Ceballos, Nidia Aréchiga; Rivero, Juan José Pérez; Díaz, Osvaldo López; Brayton, Kelly A.

    2015-01-01

    An intracellular bacterium was isolated from fruit bats (Artibeus intermedius) in Cocoyoc, Mexico. The bacterium caused severe lesions in the lungs and spleens of bats and intracytoplasmic vacuoles in cell cultures. Sequence analyses showed it is related to Waddlia spp. (order Chlamydiales). We propose to call this bacterium Waddlia cocoyoc. PMID:26583968

  9. Acidophilic Green Alga Pseudochlorella sp. YKT1 Accumulates High Amount of Lipid Droplets under a Nitrogen-Depleted Condition at a Low-pH

    PubMed Central

    Hirooka, Shunsuke; Higuchi, Sumio; Uzuka, Akihiro; Nozaki, Hisayoshi; Miyagishima, Shin-ya

    2014-01-01

    Microalgal storage lipids are considered to be a promising source for next-generation biofuel feedstock. However, microalgal biodiesel is not yet economically feasible due to the high cost of production. One of the reasons for this is that the use of a low-cost open pond system is currently limited because of the unavoidable contamination with undesirable organisms. Extremophiles have an advantage in culturing in an open pond system because they grow in extreme environments toxic to other organisms. In this study, we isolated the acidophilic green alga Pseudochlorella sp. YKT1 from sulfuric acid mine drainage in Nagano Prefecture, Japan. The vegetative cells of YKT1 display the morphological characteristics of Trebouxiophyceae and molecular phylogenetic analyses indicated it to be most closely related to Pseudochlorella pringsheimii. The optimal pH and temperature for the growth of YKT1 are pH 3.0–5.0 and a temperature 20–25°C, respectively. Further, YKT1 is able to grow at pH 2.0 and at 32°C, which corresponds to the usual water temperature in the outdoors in summer in many countries. YKT1 accumulates a large amount of storage lipids (∼30% of dry weigh) under a nitrogen-depleted condition at low-pH (pH 3.0). These results show that acidophilic green algae will be useful for industrial applications by acidic open culture systems. PMID:25221913

  10. Lipase production from a novel thermo-tolerant and extreme acidophile Bacillus pumilus using palm oil as the substrate and treatment of palm oil-containing wastewater.

    PubMed

    Saranya, P; Sukanya Kumari, H; Prasad Rao, B; Sekaran, G

    2014-03-01

    The thermo-tolerant and extreme acidophilic microorganism Bacillus pumilus was isolated from the soil collected from a commercial edible-oil extraction industry. Optimisation of conditions for the lipase production was conducted using response surface methodology. The optimum conditions for obtaining the maximum activity (1,100 U/mL) of extremely acidic thermostable lipase were fermentation time, 96 h; pH, 1; temperature, 50 °C; and concentration of palm oil, 50 g/L. After purification, a 7.1-fold purity of lipase with specific activity of 5,173 U/mg protein was obtained. The molecular weight of the thermo-tolerant acidophilic lipase (TAL) was 55 kDa. The predominant amino acid in the TAL was glycine. The functional groups of lipase were determined by Fourier transform infrared spectroscopy. TAL exhibited enhanced activity (114 %) with dimethyl sulphoxide (20 %, v/v), and it showed a moderate activity with methanol, hexane and benzene. The optimum conditions for the treatment of palm oil in wastewater using the TAL were found to be time, 3 h; pH, 1; temperature, 50 °C with pseudo second-order kinetic constant of 1.88 × 10(-3) L mol(-1) min(-1). The Michaelis-Menten enzyme kinetic model and the nonlinear kinetic model were evaluated for the TAL. TAL established hydrolysis efficiency of 96 % for palm oil in wastewater at 50 °C.

  11. The response of an acidophilic and circumneutral clone of the planktonic diatom Asterionella to aluminum: The importance of pH and trace metal interactions

    SciTech Connect

    Riseng, C.M.; Gensemer, R.W. )

    1987-06-01

    The growth rates of an acidophilic and a circumneutral clone of Asterionella were assessed over a range of total aluminum concentrations from 0 to 800 {mu}g/L, and a pH range from 5 to 7. Increasing Al levels stimulated the growth of both clones in the growth medium FRAQUIL, and the growth optima for these effects were pH dependent. Maximum growth stimulation for the circumneutral clone occurred from 200 to 400 {mu}g/L total Al at pH 6, whereas at pH 7, increasing Al levels corresponded to increasing growth rates up to the maximum treatment concentration of 80 {mu}g/L total Al. Similar qualitative responses were observed for the acidophilic clone, but at one pH unit lower than the circumneutral clone. This growth stimulation probably results from Al ions replacing apparently growth limiting trace elements from the media chelator EDTA. The same growth responses can be achieved by manipulating trace mental ion activities by altering total EDTA levels.

  12. "Use of acidophilic bacteria of the genus Acidithiobacillus to biosynthesize CdS fluorescent nanoparticles (quantum dots) with high tolerance to acidic pH".

    PubMed

    Ulloa, G; Collao, B; Araneda, M; Escobar, B; Álvarez, S; Bravo, D; Pérez-Donoso, J M

    2016-12-01

    The use of bacterial cells to produce fluorescent semiconductor nanoparticles (quantum dots, QDs) represents a green alternative with promising economic potential. In the present work, we report for the first time the biosynthesis of CdS QDs by acidophilic bacteria of the Acidithiobacillus genus. CdS QDs were obtained by exposing A. ferrooxidans, A. thiooxidans and A. caldus cells to sublethal Cd(2+) concentrations in the presence of cysteine and glutathione. The fluorescence of cadmium-exposed cells moves from green to red with incubation time, a characteristic property of QDs associated with nanocrystals growth. Biosynthesized nanoparticles (NPs) display an absorption peak at 360nm and a broad emission spectra between 450 and 650nm when excited at 370nm, both characteristic of CdS QDs. Average sizes of 6 and 10nm were determined for green and red NPs, respectively. The importance of cysteine and glutathione on QDs biosynthesis in Acidithiobacillus was related with the generation of H2S. Interestingly, QDs produced by acidophilic bacteria display high tolerance to acidic pH. Absorbance and fluorescence properties of QDs was not affected at pH 2.0, a condition that totally inhibits the fluorescence of QDs produced chemically or biosynthesized by mesophilic bacteria (stable until pH 4.5-5.0). Results presented here constitute the first report of the generation of QDs with improved properties by using extremophile microorganisms.

  13. [Hydrocarbon-Oxidizing potential and the genes for n-alkane biodegradation in a new acidophilic mycobacterial association from sulfur blocks].

    PubMed

    Ivanova, I E; Sukhacheva, M V; Kanat'eva, A Yu; Kravchenko, I K; Kurganov, A A

    2014-01-01

    Capacity of AG(S10), a new aerobic acidophilic (growing within the pH range from 1.3 to 4.5 with the optimum at 2.0-2.5) bacterial association from sulfur blocks of the Astrakhan gas-processing complex (AGC), for oxidation of hydrocarbons of various chemical structure was investigated. A broad spectrum of normal (C10-C21) and iso-alkanes, toluene, naphthalene, andphenanthrene, as well as isoprenoids resistant to microbial degradation, pristane and phytane (components of paraffin oil), and 2,2,4,4,6,8,8,-heptamethylnonane, a branched hydrocarbon, were biodegraded under acidic conditions. Microbiological investigation revealed the dominance of mycobacteria in the AGS10 association, which was confirmed by analysis of the 16S rRNA gene clone library. In the phylogenetic tree, the 16S rRNA sequences formed a branch within the cluster of slow-growing mycobacteria, with 98% homology to the closest species Mycobacterium florentinum. Genomic DNA of AG(S10) culture grown on C14-C17 n-alkanes at pH 2.5 was found to contain the genes of two hydroxylase families, alkB and Cyp 153, indicating their combined involvement in hydrocarbon biodegradation. The high hydrocarbon-oxidizing potential of the AGS10 bacterial association, indicated that further search for the genes responsible for degradation of various hydrocarbons in acidophilic mycobacteria could be promising.

  14. Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

    PubMed Central

    Sedlacek, Christopher J.; Nielsen, Susanne; Greis, Kenneth D.; Haffey, Wendy D.; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J.

    2016-01-01

    ABSTRACT Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCE Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to

  15. Cultivation of Acidophilic Algae Galdieria sulphuraria and Pseudochlorella sp. YKT1 in Media Derived from Acidic Hot Springs.

    PubMed

    Hirooka, Shunsuke; Miyagishima, Shin-Ya

    2016-01-01

    Microalgae possess a high potential for producing pigments, antioxidants, and lipophilic compounds for industrial applications. However, the cultivation of microalgae comes at a high cost. To reduce the cost, changes from a closed bioreactor to open pond system and from a synthetic medium to environmental or wastewater-based medium are being sought. However, the use of open pond systems is currently limited because of contamination by undesirable organisms. To overcome this issue, one strategy is to combine acidophilic algae and acidic drainage in which other organisms are unable to thrive. Here, we tested waters from sulfuric acidic hot springs (Tamagawa, pH 1.15 and Tsukahara, pH 1.14) in Japan for the cultivation of the red alga Galdieria sulphuraria 074G and the green alga Pseudochlorella sp. YKT1. Both of these spring waters are rich in phosphate (0.043 and 0.145 mM, respectively) compared to other environmental freshwater sources. Neither alga grew in the spring water but they grew very well when the waters were supplemented with an inorganic nitrogen source. The algal yields were ∼2.73 g dry weight/L for G. sulphuraria and ∼2.49 g dry weight/L for P. sp. YKT1, which were comparable to those in an autotrophic synthetic medium. P. sp. YKT1 grew in the spring waters supplemented either of NH4(+), NO3(-) or urea, while G. sulphuraria grew only when NH4(+) was supplemented. For P. sp. YKT1, the spring water was adjusted to pH 2.0, while for G. sulphuraria, no pH adjustment was required. In both cases, no additional pH-buffering compound was required. The phycocyanin of the thermophilic G. sulphuraria is known to be more thermostable than that from the Spirulina platensis currently used in phycocyanin production for commercial use. The phycocyanin content in G. sulphuraria in the Tsukahara water supplemented with NH4(+) was 107.42 ± 1.81 μg/mg dry weight, which is comparable to the level in S. platensis (148.3 μg/mg dry weight). P. sp. YKT1 cells in the

  16. Cultivation of Acidophilic Algae Galdieria sulphuraria and Pseudochlorella sp. YKT1 in Media Derived from Acidic Hot Springs

    PubMed Central

    Hirooka, Shunsuke; Miyagishima, Shin-ya

    2016-01-01

    Microalgae possess a high potential for producing pigments, antioxidants, and lipophilic compounds for industrial applications. However, the cultivation of microalgae comes at a high cost. To reduce the cost, changes from a closed bioreactor to open pond system and from a synthetic medium to environmental or wastewater-based medium are being sought. However, the use of open pond systems is currently limited because of contamination by undesirable organisms. To overcome this issue, one strategy is to combine acidophilic algae and acidic drainage in which other organisms are unable to thrive. Here, we tested waters from sulfuric acidic hot springs (Tamagawa, pH 1.15 and Tsukahara, pH 1.14) in Japan for the cultivation of the red alga Galdieria sulphuraria 074G and the green alga Pseudochlorella sp. YKT1. Both of these spring waters are rich in phosphate (0.043 and 0.145 mM, respectively) compared to other environmental freshwater sources. Neither alga grew in the spring water but they grew very well when the waters were supplemented with an inorganic nitrogen source. The algal yields were ∼2.73 g dry weight/L for G. sulphuraria and ∼2.49 g dry weight/L for P. sp. YKT1, which were comparable to those in an autotrophic synthetic medium. P. sp. YKT1 grew in the spring waters supplemented either of NH4+, NO3- or urea, while G. sulphuraria grew only when NH4+ was supplemented. For P. sp. YKT1, the spring water was adjusted to pH 2.0, while for G. sulphuraria, no pH adjustment was required. In both cases, no additional pH-buffering compound was required. The phycocyanin of the thermophilic G. sulphuraria is known to be more thermostable than that from the Spirulina platensis currently used in phycocyanin production for commercial use. The phycocyanin content in G. sulphuraria in the Tsukahara water supplemented with NH4+ was 107.42 ± 1.81 μg/mg dry weight, which is comparable to the level in S. platensis (148.3 μg/mg dry weight). P. sp. YKT1 cells in the Tamagawa

  17. Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample made in Okinawa, Japan.

    PubMed

    Shimane, Yasuhiro; Minegishi, Hiroaki; Echigo, Akinobu; Kamekura, Masahiro; Itoh, Takashi; Ohkuma, Moriya; Tsubouchi, Taishi; Usui, Keiko; Maruyama, Tadashi; Usami, Ron; Hatada, Yuji

    2015-08-03

    Three moderately acidophilic, halophilic archaeal strains, MH1-243-3T, MH1-243-5 and MH1-243-6 were isolated from a commercial salt sample made from seawater in Okinawa, Japan. Cells of the three strains were pleomorphic, and stained Gram-negative. Colonies of the strains were orange-red pigmented. Strain MH1-243-3T was able to grow at 15-27 % (w/v) NaCl (optimum at 24 %), at pH 4.5-6.5 (pH 5.5) and at 35-50 °C (45 °C). Strains MH1-243-5 and MH1-243-6 grew in slightly different ranges (shown in text). The 16S rRNA gene sequences of the three strains were identical, and the closest relative was Halarchaeum salinum MH1-34-1T with 97.0 % similarities. The rpoB' gene sequences of the three strains were also identical, and the closest relative was Hla. acidiphilum JCM 16109T with 92.0 % similarities. The DNA G+C contents of MH1-243-3T, MH1-243-5 and MH1-243-6 were 65.2 mol%. The levels of DNA-DNA relatedness amongst the three strains were 84.1-99.8 %, while that between MH1-243-3T and Halarchaeum salinum MH1-34-1 T was 30.6 % and 31.6 % (reciprocally), and those between MH1-243-3T and type strains of other species in the genus Halarchaeum were 42.3-29.4 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a new species of the genus Halarchaeum, for which the name Halarchaeum grantii sp. nov. is proposed. The type strain is MH1-243-3T (= JCM 19585T = KCTC 4142T) isolated from commercial sea salt produced in Okinawa, Japan. MH1-243-5 (= JCM 19586) and MH1-243-6 (= JCM 18422) are additional strains of the species.

  18. Paradigms: examples from the bacterium Xylella fastidiosa.

    PubMed

    Purcell, Alexander

    2013-01-01

    The history of advances in research on Xylella fastidiosa provides excellent examples of how paradigms both advance and limit our scientific understanding of plant pathogens and the plant diseases they cause. I describe this from a personal perspective, having been directly involved with many persons who made paradigm-changing discoveries, beginning with the discovery that a bacterium, not a virus, causes Pierce's disease of grape and other plant diseases in numerous plant species, including important crop and forest species.

  19. Pneumonia caused by a previously undescribed bacterium.

    PubMed Central

    Hopfer, R L; Mills, K; Fainstein, V; Fischer, H E; Luna, M P

    1982-01-01

    A new and as yet unidentified bacterium was isolated from the lung tissue of a cancer patient with bilateral pneumonia. Clinically, the pneumonia was consistent with legionellosis; the organism cultured from the lung grew only on the charcoal-yeast extract agar routinely used for Legionella isolation. Subsequent testing, however, showed the organism to be quite distinct from the known Legionella species in its biochemical, antigenic, and growth characteristics. Images PMID:7130363

  20. Characterization of a novel extremely alkalophilic bacterium

    NASA Technical Reports Server (NTRS)

    Souza, K. A.; Deal, P. H.

    1977-01-01

    A new alkalophilic bacterium, isolated from a natural spring of high pH is characterized. It is a Gram-positive, non-sporulating, motile rod requiring aerobic and alkaline conditions for growth. The characteristics of this organism resemble those of the coryneform group of bacteria; however, there are no accepted genera within this group with which this organism can be closely matched. Therefore, a new genus may be warranted.

  1. Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine.

    PubMed

    Guo, Xu; You, Xiao-Yan; Liu, Li-Jun; Zhang, Jia-Yue; Liu, Shuang-Jiang; Jiang, Cheng-Ying

    2009-10-01

    A novel mesophilic, acidophilic, endospore-forming bacterium, designated strain ZJ-6(T), was isolated from Zi-Jin copper mine in Inner Mongolia, China. Cells of strain ZJ-6(T) were rod-shaped, stained Gram-positive or were Gram-variable, and grew aerobically at 25-35 degrees C (optimum, 30 degrees C) and pH 2.0-6.0 (optimum, pH 3.5). 16S rRNA gene sequence analysis showed that strain ZJ-6(T) was related phylogenetically to members of the genus Alicyclobacillus, with 16S rRNA gene sequence similarities of 89.5-94.2 %. Cells contained MK-7 as the major quinone and the DNA G+C content was 51.2 mol%. Strain ZJ-6(T) possessed a number of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including its growth temperature, assimilation of various carbon sources, production of acids from a range of compounds, and the ability to grow chemoautotrophically using ferrous iron, elemental sulfur and tetrathionate as electron donors. The predominant cellular fatty acids of strain ZJ-6(T) were anteiso-C(15 : 0) (67.1 %), iso-C(16 : 0) (7.7 %) and anteiso-C(17 : 0) (7.4 %); omega-alicyclic fatty acids were not found. On the basis of these results, it is concluded that strain ZJ-6(T) represents a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus aeris sp. nov. is proposed; the type strain is ZJ-6(T) (=CGMCC 1.7072(T)=NBRC 104953(T)).

  2. Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov., two acidophilic, psychrotolerant members of the Alphaproteobacteria from acidic northern wetlands.

    PubMed

    Belova, Svetlana E; Pankratov, Timofei A; Detkova, Ekaterina N; Kaparullina, Elena N; Dedysh, Svetlana N

    2009-09-01

    Three obligately aerobic, heterotrophic bacteria, designated strains WM1T, TPB606T and TPB621, were isolated from acidic Sphagnum-dominated tundra and Siberian wetlands in Russia. Cells of these isolates were Gram-negative, non-motile coccobacilli that occurred singly, in pairs or in chains, and were covered by large capsules. The novel strains were moderately acidophilic and psychrotolerant organisms capable of growth at pH 3.0-7.6 and 2-30 degrees C. Cells contained numerous intracellular poly-beta-hydroxybutyrate granules (3-4 per cell). The major cellular fatty acid was cyclo C19:0omega8c and the predominant quinone was Q-10. Strains TPB606T and TPB621, isolated from Siberian wetland, possessed almost identical 16S rRNA gene sequences and shared 97.2% sequence similarity with tundra strain WM1T. The three strains were shown to belong to the Alphaproteobacteria, but were related only distantly to the type strains of acidophilic bacteria Acidisphaera rubrifaciens (93.4-94.3% 16S rRNA gene sequence similarity), Rhodopila globiformis (92.2-93.3%), and members of the genera Acidiphilium (91.3-93%) and Acidocella (91.8-92.4%). The DNA G+C contents of the novel strains were 60.5-61.9 mol%. The low levels of DNA-DNA relatedness (37%) and a number of phenotypic differences between the Siberian strains TPB606T and TPB621 and the tundra strain WM1T indicated that they represent two separate species. As the three isolates are clearly distinct from all recognized acidophilic members of the Alphaproteobacteria, they are considered to represent two novel species of a new genus, for which the names Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov. are proposed. The type strain of Acidisoma sibiricum is TPB606T (=DSM 21000T=VKM B-2487T) and the type strain of Acidisoma tundrae is WM1T (=DSM 19999T=VKM B-2488T).

  3. Generation of a large, protonophore-sensitive proton motive force and pH difference in the acidophilic bacteria Thermoplasma acidophilum and Bacillus acidocaldarius.

    PubMed Central

    Michels, M; Bakker, E P

    1985-01-01

    The mechanism by which acidophilic bacteria generate and maintain their cytoplasmic pH close to neutrality was investigated. For this purpose we determined the components of proton motive force in the eubacterium Bacillus acidocaldarius and the archaebacterium Thermoplasma acidophilum. After correction for probe binding, the proton motive force of untreated cells was 190 to 240 mV between external pH 2 and 4. Anoxia diminished total proton motive force and the transmembrane pH difference by 60 to 80 mV. The protonophore 2,4-dinitrophenol abolished the total proton motive force almost completely and diminished the transmembrane pH difference by at least two units. However, even after correction for probe binding, protonophore-treated cells maintained a pH difference of approximately one unit. PMID:2981803

  4. Detection of Salmonella bacterium in drinking water using microring resonator.

    PubMed

    Bahadoran, Mahdi; Noorden, Ahmad Fakhrurrazi Ahmad; Mohajer, Faeze Sadat; Abd Mubin, Mohamad Helmi; Chaudhary, Kashif; Jalil, Muhammad Arif; Ali, Jalil; Yupapin, Preecha

    2016-01-01

    A new microring resonator system is proposed for the detection of the Salmonella bacterium in drinking water, which is made up of SiO2-TiO2 waveguide embedded inside thin film layer of the flagellin. The change in refractive index due to the binding of the Salmonella bacterium with flagellin layer causes a shift in the output signal wavelength and the variation in through and drop port's intensities, which leads to the detection of Salmonella bacterium in drinking water. The sensitivity of proposed sensor for detecting of Salmonella bacterium in water solution is 149 nm/RIU and the limit of detection is 7 × 10(-4)RIU.

  5. Draft Genome Sequence of the Suttonella ornithocola Bacterium

    PubMed Central

    Waldman Ben-Asher, Hiba; Yerushalmi, Rebecca; Wachtel, Chaim; Barbiro-Michaely, Efrat

    2017-01-01

    ABSTRACT   We report here the draft genome sequence of the Suttonella ornithocola bacterium. To date, this bacterium, found in birds, passed only phylogenetic and phenotypic analyses. To our knowledge, this is the first publication of the Suttonella ornithocola genome sequence. The genetic profile provides a basis for further analysis of its infection pathways. PMID:28209820

  6. Desulfonauticus autotrophicus sp. nov., a novel thermophilic sulfate-reducing bacterium isolated from oil-production water and emended description of the genus Desulfonauticus.

    PubMed

    Mayilraj, Shanmugam; Kaksonen, Anna H; Cord-Ruwisch, Ralf; Schumann, Peter; Spröer, Cathrin; Tindall, Brian J; Spring, Stefan

    2009-03-01

    A novel moderately thermophilic and halophilic sulfate-reducing bacterium, strain TeSt(T), was isolated from production water of an oil field in Northern Germany near Hamburg. The cells were Gram-negative, straight to slightly curved rods and motile by a single polar flagellum. Only hydrogen and formate served as electron donors, whereas a wide variety of organic substrates and CO(2) could be used as carbon sources. Sulfate, sulfite, thiosulfate and sulfur were used as electron acceptors, but not nitrate or ferric iron. The novel isolate was negative for oxidase, catalase and desulfoviridin enzyme activity. Cytochromes were present and predominantly of the c-type. Whole-cells fatty acid patterns were dominated by the branched-chain fatty acids anteiso-C(15:0), iso-C(15:0), iso-C(17:0) and anteiso-C(17:0). As major respiratory lipoquinones partially saturated derivates of menaquinone 6 [MK-6(H(2)) and probably MK-6(H(4))] were identified. The G + C content of the genomic DNA was 41.3 mol% (HPLC method). An analysis of the 16S rRNA gene sequence indicated that strain TeSt(T) belongs to the family Desulfohalobiaceae within the class Deltaproteobacteria. The most closely related species with a sequence similarity of 95.0% was Desulfonauticus submarinus suggesting an affiliation of TeSt(T) to the genus Desulfonauticus. The novel isolate could be clearly distinguished from Desulfonauticus submarinus by its ability to grow chemolithoautotrophically and hence should be assigned to a novel species for which the name Desulfonauticus autotrophicus sp. nov. is proposed. The type strain is TeSt(T) (=DSM 4206(T)=JCM 13028(T)).

  7. Carboxydothermus pertinax sp. nov., a thermophilic, hydrogenogenic, Fe(III)-reducing, sulfur-reducing carboxydotrophic bacterium from an acidic hot spring.

    PubMed

    Yoneda, Yasuko; Yoshida, Takashi; Kawaichi, Satoshi; Daifuku, Takashi; Takabe, Keiji; Sako, Yoshihiko

    2012-07-01

    A novel anaerobic, Fe(III)-reducing, hydrogenogenic, carboxydotrophic bacterium, designated strain Ug1(T), was isolated from a volcanic acidic hot spring in southern Kyushu Island, Japan. Cells of the isolate were rod-shaped (1.0-3.0 µm long) and motile due to peritrichous flagella. Strain Ug1(T) grew chemolithoautotrophically on CO (100% in the gas phase) with reduction of ferric citrate, amorphous iron (III) oxide, 9,10-anthraquinone 2,6-disulfonate, thiosulfate or elemental sulfur. No carboxydotrophic growth occurred with sulfate, sulfite, nitrate or fumarate as electron acceptor. During growth on CO, H(2) and CO(2) were produced. Growth occurred on molecular hydrogen as an energy source and carbon dioxide as a sole carbon source. Growth was observed on various organic compounds under an N(2) atmosphere with the reduction of ferric iron. The temperature range for carboxydotrophic growth was 50-70 °C, with an optimum at 65 °C. The pH(25 °C) range for growth was 4.6-8.6, with an optimum between 6.0 and 6.5. The doubling time under optimum conditions using CO with ferric citrate was 1.5 h. The DNA G+C content was 42.2 mol%. Analysis of 16S rRNA gene sequences demonstrated that this strain belongs to the thermophilic carboxydotrophic bacterial genus Carboxydothermus, with sequence similarities of 94.1-96.6% to members of this genus. The isolate can be distinguished from other members of the genus Carboxydothermus by its ability to grow with elemental sulfur or thiosulfate coupled to CO oxidation. On the basis of phylogenetic analysis and unique physiological features, the isolate represents a novel species of the genus Carboxydothermus for which the name Carboxydothermus pertinax sp. nov. is proposed; the type strain of the novel species is Ug1(T) (=DSM 23698(T)=NBRC 107576(T)).

  8. Deferrisoma paleochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea

    USGS Publications Warehouse

    Perez-Rodriguez, Ileana M.; Rawls, Matthew; Coykendall, Dolly K.; Foustoukos, Dionysis I.

    2016-01-01

    A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30–70 °C (optimum 60 °C), 0–50 g NaCl l− 1 (optimum 15–20 g l− 1) and pH 5.5–8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( − )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T). 

  9. Agrobacterium tumefaciens is a diazotrophic bacterium

    SciTech Connect

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

    1990-07-01

    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 {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} 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.

  10. Characterizations of intracellular arsenic in a bacterium

    NASA Astrophysics Data System (ADS)

    Wolfe-Simon, F.; Yannone, S. M.; Tainer, J. A.

    2011-12-01

    Life requires a key set of chemical elements to sustain growth. Yet, a growing body of literature suggests that microbes can alter their nutritional requirements based on the availability of these chemical elements. Under limiting conditions for one element microbes have been shown to utilize a variety of other elements to serve similar functions often (but not always) in similar molecular structures. Well-characterized elemental exchanges include manganese for iron, tungsten for molybdenum and sulfur for phosphorus or oxygen. These exchanges can be found in a wide variety of biomolecules ranging from protein to lipids and DNA. Recent evidence suggested that arsenic, as arsenate or As(V), was taken up and incorporated into the cellular material of the bacterium GFAJ-1. The evidence was interpreted to support As(V) acting in an analogous role to phosphate. We will therefore discuss our ongoing efforts to characterize intracellular arsenate and how it may partition among the cellular fractions of the microbial isolate GFAJ-1 when exposed to As(V) in the presence of various levels of phosphate. Under high As(V) conditions, cells express a dramatically different proteome than when grown given only phosphate. Ongoing studies on the diversity and potential role of proteins and metabolites produced in the presence of As(V) will be reported. These investigations promise to inform the role and additional metabolic potential for As in biology. Arsenic assimilation into biomolecules contributes to the expanding set of chemical elements utilized by microbes in unusual environmental niches.

  11. Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control*

    PubMed Central

    Kent, Lisa M.; Loo, Trevor S.; Melton, Laurence D.; Mercadante, Davide; Williams, Martin A. K.; Jameson, Geoffrey B.

    2016-01-01

    Many pectin methylesterases (PMEs) are expressed in plants to modify plant cell-wall pectins for various physiological roles. These pectins are also attacked by PMEs from phytopathogens and phytophagous insects. The de-methylesterification by PMEs of the O6-methyl ester groups of the homogalacturonan component of pectin, exposing galacturonic acids, can occur processively or non-processively, respectively, describing sequential versus single de-methylesterification events occurring before enzyme-substrate dissociation. The high resolution x-ray structures of a PME from Aspergillus niger in deglycosylated and Asn-linked N-acetylglucosamine-stub forms reveal a 10⅔-turn parallel β-helix (similar to but with less extensive loops than bacterial, plant, and insect PMEs). Capillary electrophoresis shows that this PME is non-processive, halophilic, and acidophilic. Molecular dynamics simulations and electrostatic potential calculations reveal very different behavior and properties compared with processive PMEs. Specifically, uncorrelated rotations are observed about the glycosidic bonds of a partially de-methyl-esterified decasaccharide model substrate, in sharp contrast to the correlated rotations of processive PMEs, and the substrate-binding groove is negatively not positively charged. PMID:26567911

  12. Dynamic of active microorganisms inhabiting a bioleaching industrial heap of low‐grade copper sulfide ore monitored by real‐time PCR and oligonucleotide prokaryotic acidophile microarray

    PubMed Central

    Remonsellez, Francisco; Galleguillos, Felipe; Moreno‐Paz, Mercedes; Parro, Víctor; Acosta, Mauricio; Demergasso, Cecilia

    2009-01-01

    Summary The bioleaching of metal sulfide has developed into a very important industrial process and understanding the microbial dynamic is key to advancing commercial bioleaching operations. Here we report the first quantitative description of the dynamic of active communities in an industrial bioleaching heap. Acidithiobacillus ferrooxidans was the most abundant during the first part of the leaching cycle, while the abundance of Leptospirillum ferriphilum and Ferroplasma acidiphilum increased with age of the heap. Acidithiobacillus thiooxidans kept constant throughout the leaching cycle, and Firmicutes group showed a low and a patchy distribution in the heap. The Acidiphilium‐like bacteria reached their highest abundance corresponding to the amount of autotrophs. The active microorganisms in the leaching system were determined using two RNA‐based sensitive techniques. In most cases, the 16S rRNA copy numbers of At. ferrooxidans, L. ferriphilum, At. thiooxidans and F. acidiphilum, was concomitant with the DNA copy numbers, whereas Acidiphilium‐like bacteria and some Firmicutes members did not show a clear correlation between 16S rRNA accumulation and DNA copy numbers. However, the prokaryotic acidophile microarray (PAM) analysis showed active members of Alphaproteobacteria in all samples and of Sulfobacillus genus in older ones. Also, new active groups such as Actinobacteria and Acidobacterium genus were detected by PAM. The results suggest that changes during the leaching cycle in chemical and physical conditions, such as pH and Fe3+/Fe2+ ion rate, are primary factors shaping the microbial dynamic in the heap. PMID:21255296

  13. [An autopsy case with peculiar acidophilic bodies in the dentate nucleus and brain stem, associated with degeneration of the pyramidal-extrapyramidal systems].

    PubMed

    Kato, Y; Kashima, H; Tominaga, I; Nojima, T; Yanai, K; Takayama, K; Tamazawa, A; Miura, I; Oyanagi, S

    1985-12-01

    Case S.S. 59 years of age, male. At the age of 25, he had admitted to sanatorium for 7 years because of pulmonary tuberculosis. After his discharge, at the age of 45, he had started complaining of depressive mood or the idea of suicide and admitted to a mental hospital. Psychiatric diagnosis was depression and slight mental retardation. Shortly after, his depressive mood was improved, but his hypochondriac attitude was unchanged. No tendency toward dementia was proven. At the age of 54, he became enable to walk. Neurologically, pyramidal and some sort of extrapyramidal signs, dysarthria, disturbance of swallowing, fecal and urinary incontinence became apparent. Laboratory data showed scarcely any abnormality. At the age of 59, he died of bronchopneumonia. Neuropathologically, moderate degeneration of dentate nucleus, slight degeneration of pyramidal tract from medulla oblongata to spinal cord, striatum, substantia nigra were found. Neither senile plaques nor neurofibrillary changes could be seen throughout central nervous system. The most important finding is the presence of peculiar acidophilic bodies. They are round or oval, 10 approximately 20 mu in diameter and distributed in dentate nucleus, oculomotor nucleus, central grey of midbrain, superior colliculus, putamen, pallidum, subthalamic nucleus, Zona incerta, hypothalamus, Locus coeruleus, reticular formation of midbrain and pons, pontine nucleus, raphe nucleus, vestibular nucleus, inferior olive in order of number of the bodies. These bodies are scattered in so-called ground substance, and have no relations to any cell bodies or cell processes.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Adaptation of a mixed culture of acidophiles for a tank biooxidation of refractory gold concentrates containing a high concentration of arsenic.

    PubMed

    Hong, Jeongsik; Silva, Rene A; Park, Jeonghyun; Lee, Eunseong; Park, Jayhyun; Kim, Hyunjung

    2016-05-01

    We adapted a mixed culture of acidophiles to high arsenic concentrations to confirm the possibility of achieving more than 70% biooxidation of refractory gold concentrates containing high arsenic (As) concentration. The biooxidation process was applied to refractory gold concentrates containing approximately 139.67 g/kg of total As in a stirred tank reactor using an adapted mixed culture of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. The percentage of the biooxidation process was analyzed based on the total As removal efficiency. The As removal was monitored by inductively coupled plasma (ICP) analysis, conducted every 24 h. The results obtained with the adapted culture were compared with the percentage of biooxidation obtained with a non-adapted mixed culture of A. ferrooxidans and A. thiooxidans, and with their respective pure cultures. The percentages of biooxidation obtained during 358 h of reaction were 72.20%, 38.20%, 27.70%, and 11.45% for adapted culture, non-adapted culture, and pure cultures of A. thiooxidans and A. ferrooxidans, respectively. The adapted culture showed a peak maximum percentage of biooxidation of 77% at 120 h of reaction, confirming that it is possible to obtain biooxidation percentages over 70% in gold concentrates containing high As concentrations.

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

    SciTech Connect

    Dees, C.; Ringleberg, D.; Scott, T.C.; Phelps, T.

    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.

  16. Thioprofundum hispidum sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing gammaproteobacterium isolated from the hydrothermal field on Suiyo Seamount, and proposal of Thioalkalispiraceae fam. nov. in the order Chromatiales.

    PubMed

    Mori, Koji; Suzuki, Ken-ichiro; Urabe, Tetsuro; Sugihara, Maki; Tanaka, Kenji; Hamada, Moriyuki; Hanada, Satoshi

    2011-10-01

    A novel mesophilic, facultatively anaerobic, sulfur-oxidizing bacterial strain, designated gps61(T), was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. Cells of the isolate were rod-shaped with a single sheathed polar flagellum. Neither extensive internal membranes nor storage materials were present in the cells. In a 20 % CO(2) atmosphere, strain gps61(T) grew using thiosulfate, sulfur or tetrathionate as electron donors and oxygen or nitrate as electron acceptors. Other substrates, including organic acids and sugars, did not support growth, indicating that strain gps61(T) was an obligate chemolithoautotroph. 16S rRNA gene sequence analysis revealed that strain gps61(T) was closely related to Thioprofundum lithotrophicum 106(T) (98.5 % sequence similarity) in the order Chromatiales. Phylogenetic trees grouped strain gps61(T) and Thioprofundum lithotrophicum in the same cluster along with Thioalkalispira microaerophila and Thiohalophilus thiocyanoxidans, but it was apparent from the analysis that the novel strain had definitely departed from the family lineage. On the basis of its phylogenetic position along with its morphological and physiological characteristics, strain gps61(T) ( = NBRC 101261(T)  = DSM 18546(T)) represents a novel species of the genus Thioprofundum, for which the name Thioprofundum hispidum sp. nov. is proposed. In addition, we propose a novel family name, Thioalkalispiraceae, in the order Chromatiales, to accommodate the genera Thioalkalispira, Thiohalophilus and Thioprofundum.

  17. Pangenome Evolution in the Marine Bacterium Alteromonas

    PubMed Central

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  18. Morphological and ultrastructural characterization of the acidophilic and lipid-producer strain Chlamydomonas acidophila LAFIC-004 (Chlorophyta) under different culture conditions.

    PubMed

    Souza, Luana Dos S; Simioni, Carmen; Bouzon, Zenilda L; Schneider, Rosana de Cassia da S; Gressler, Pablo; Miotto, Maria Cecília; Rossi, Marcio J; Rörig, Leonardo R

    2016-09-30

    Chlamydomonas acidophila LAFIC-004 is an acidophilic strain of green microalgae isolated from coal mining drainage. In the present work, this strain was cultivated in acidic medium (pH 3.6) under phototrophic, mixotrophic, and heterotrophic regimes to determine the best condition for growth and lipid production, simultaneously assessing possible morphological and ultrastructural alterations in the cells. For heterotrophic and mixotrophic treatments, two organic carbon sources were tested: 1 % glucose and 1 % sodium acetate. Lipid content and fatty acid profiles were only determined in phototrophic condition. The higher growth rates were achieved in phototrophic conditions, varying from 0.18 to 0.82 day(-1). Glucose did not result in significant growth increase in either mixotrophic or heterotrophic conditions, and acetate proved to be toxic to the strain in both conditions. Oil content under phototrophic condition was 15.9 % at exponential growth phase and increased to 54.63 % at stationary phase. Based on cell morphology (flow cytometry and light microscopy) and ultrastructure (transmission electron microscopy), similar characteristics were observed between phototrophic and mixotrophic conditions with glucose evidencing many lipid bodies, starch granules, and intense fluorescence. Under the tested conditions, mixotrophic and heterotrophic modes did not result in increased neutral lipid fluorescence. It can be concluded that the strain is a promising lipid producer when grown until stationary phase in acidic medium and under a phototrophic regime, presenting a fatty acid profile suitable for biodiesel production. The ability to grow this strain in acidic mining residues suggests a potential for bioremediation with production of useful biomass.

  19. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

    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.

  20. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

    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.

  1. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana

    PubMed Central

    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

  2. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana.

    PubMed

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

    2015-06-04

    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.

  3. Thiobacillus cuprinus sp. nov. , a novel facultatively organotrophic metal-mobilizing bacterium

    SciTech Connect

    Huber, H.; Stetter, K.O. )

    1990-02-01

    Five strains of mesophilic, facultatively organotrophic, ore-leaching eubacteria were isolated from solfatara fields in Iceland and a uranium mine in the Federal Republic of Germany. The new organisms are aerobic gram-negative rods. They can use sulfidic ores or elemental sulfur as sole energy source, indicating that they belong to the genus Thiobacillus. Alternatively, they grow on organic substrates such as yeast extract, peptone, and pyruvate. In contrast to the other leaching bacteria known so far, the new isolates are unable to oxidize ferrous iron. They consist of extreme and moderate acidophiles growing optimally at pH 3 and 4, respectively. The extreme acidophiles showed leaching characteristics similar to those shown by Thiobacillus ferrooxidans, while the moderate acidophiles exhibited a pronounced preference for copper leaching on some chalcopyrite ores. The G+C content of the DNA is between 66 and 69 mol%, depending on the isolate. In DNA-DNA hybridization experiments, the new strains showed homologies among each other of >70%, indicating that they belong to the same species. No significant DNA homology to Thiobacillus reference strains was detectable. Therefore, the new isolates represent a new species of Thiobacillus, which the authors named Thiobacillus cuprinus. Isolate Hoe5 is designated as the type strain (DSM 5495).

  4. Thiobacillus cuprinus sp. nov., a Novel Facultatively Organotrophic Metal-Mobilizing Bacterium

    PubMed Central

    Huber, Harald; Stetter, Karl O.

    1990-01-01

    Five strains of mesophilic, facultatively organotrophic, ore-leaching eubacteria were isolated from solfatara fields in Iceland and a uranium mine in the Federal Republic of Germany. The new organisms are aerobic gram-negative rods. They can use sulfidic ores or elemental sulfur as sole energy source, indicating that they belong to the genus Thiobacillus. Alternatively, they grow on organic substrates such as yeast extract, peptone, and pyruvate. In contrast to the other leaching bacteria known so far, the new isolates are unable to oxidize ferrous iron. They consist of extreme and moderate acidophiles growing optimally at pH 3 and 4, respectively. The extreme acidophiles showed leaching characteristics similar to those shown by Thiobacillus ferrooxidans, while the moderate acidophiles exhibited a pronounced preference for copper leaching on some chalcopyrite ores. The G+C content of the DNA is between 66 and 69 mol%, depending on the isolate. In DNA-DNA hybridization experiments, the new strains showed homologies among each other of >70%, indicating that they belong to the same species. No significant DNA homology to Thiobacillus reference strains was detectable. Therefore, the new isolates represent a new species of Thiobacillus, which we name Thiobacillus cuprinus. Isolate Hö5 is designated as the type strain (DSM 5495). Images PMID:16348110

  5. Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7

    SciTech Connect

    Suen, Garret; Stevenson, David M; Bruce, David; Chertkov, Olga; Copeland, A; Cheng, Jan-Fang; Detter, J. Chris; Goodwin, Lynne A.; Han, Cliff; Hauser, Loren John; Ivanova, N; Kyrpides, Nikos C; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Ovchinnikova, Galina; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Boyum, Julie; Mead, David; Weimer, Paul J

    2011-01-01

    Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.

  6. Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ruminococcus albus 7 is a highly cellulolytic rumen bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome for this microbe. This genome will be useful for rumen microbiology, cellulosome biology, and in biofuel production, as one of its major fermentation product...

  7. Gut bacterium of Dendrobaena veneta (Annelida: Oligochaeta) possesses antimycobacterial activity.

    PubMed

    Fiołka, Marta J; Zagaja, Mirosław P; Piersiak, Tomasz D; Wróbel, Marek; Pawelec, Jarosław

    2010-09-01

    The new bacterial strain with antimycobacterial activity has been isolated from the midgut of Dendrobaena veneta (Annelida). Biochemical and molecular characterization of isolates from 18 individuals identified all as Raoultella ornithinolytica genus with 99% similarity. The bacterium is a possible symbiont of the earthworm D. veneta. The isolated microorganism has shown the activity against four strains of fast-growing mycobacteria: Mycobacterium butiricum, Mycobacterium jucho, Mycobacterium smegmatis and Mycobacterium phlei. The multiplication of the gut bacterium on plates with Sauton medium containing mycobacteria has caused a lytic effect. After the incubation of the cell free extract prepared from the gut bacterium with four strains of mycobacteria in liquid Sauton medium, the cells of all tested strains were deformed and divided to small oval forms and sometimes created long filaments. The effect was observed by the use of light, transmission and scanning microscopy. Viability of all examined species of mycobacteria was significantly decreased. The antimycobacterial effect was probably the result of the antibiotic action produced by the gut bacterium of the earthworm. The application of ultrafiltration procedure allowed to demonstrate that antimicrobial substance with strong antimycobacterial activity from bacterial culture supernatant, is a protein with the molecular mass above 100 kDa.

  8. Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs.

    PubMed

    Pankratov, Timofey A; Dedysh, Svetlana N

    2010-12-01

    Five strains of strictly aerobic, heterotrophic bacteria that form pink-red colonies and are capable of hydrolysing pectin, xylan, laminarin, lichenan and starch were isolated from acidic Sphagnum peat bogs and were designated OB1010(T), LCBR1, TPB6011(T), TPB6028(T) and TPO1014(T). Cells of these isolates were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance. Old cultures contained spherical bodies of varying sizes, which represent starvation forms. Cells of all five strains were acidophilic and psychrotolerant, capable of growth at pH 3.0-7.5 (optimum pH 3.8-4.5) and at 2-33°C (optimum 15-22°C). The major fatty acids were iso-C(15 : 0), C(16 : 0) and summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH). The major menaquinone detected was MK-8. The pigments were carotenoids. The genomic DNA G+C contents were 57.3-59.3 mol%. The five isolates were found to be members of subdivision 1 of the phylum Acidobacteria and displayed 95.3-98.9 % 16S rRNA gene sequence similarity to each other. The closest described relatives to strains OB1010(T), LCBR1, TPB6011(T), TPB6028(T), and TPO1014(T) were members of the genera Terriglobus (94.6-95.8 % 16S rRNA gene sequence similarity) and Edaphobacter (94.2-95.4 %). Based on differences in cell morphology, phenotypic characteristics and hydrolytic capabilities, we propose a novel genus, Granulicella gen. nov., containing four novel species, Granulicella paludicola sp. nov. with type strain OB1010(T) (=DSM 22464(T) =LMG 25275(T)) and strain LCBR1, Granulicella pectinivorans sp. nov. with type strain TPB6011(T) (=VKM B-2509(T) =DSM 21001(T)), Granulicella rosea sp. nov. with type strain TPO1014(T) (=DSM 18704(T) =ATCC BAA-1396(T)) and Granulicella aggregans sp. nov. with type strain TPB6028(T) (=LMG 25274(T) =VKM B-2571(T)).

  9. The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales

    PubMed Central

    Lünsdorf, Heinrich; Kublanov, Ilya V.; Goldenstein, Nadine I.; Hinrichs, Kai-Uwe; Golyshin, Peter N.

    2016-01-01

    Two novel cell-wall-less, acidophilic, mesophilic, organotrophic and facultatively anaerobic archaeal strains were isolated from acidic streamers formed on the surfaces of copper-ore-containing sulfidic deposits in south-west Spain and North Wales, UK. Cells of the strains varied from 0.1 to 2 μm in size and were pleomorphic, with a tendency to form filamentous structures. The optimal pH and temperature for growth for both strains were 1.0–1.2 and 37–40 °C, with the optimal substrates for growth being beef extract (3 g l− 1) for strain S5T and beef extract with tryptone (3 and 1 g l− 1, respectively) for strain PM4. The lipid composition was dominated by intact polar lipids consisting of a glycerol dibiphytanyl glycerol tetraether (GDGT) core attached to predominantly glycosidic polar headgroups. In addition, free GDGT and small relative amounts of intact and core diether lipids were present. Strains S5T and PM4 possessed mainly menaquinones with minor fractions of thermoplasmaquinones. The DNA G+C content was 37.3 mol% in strain S5T and 37.16 mol% for strain PM4. A similarity matrix of 16S rRNA gene sequences (identical for both strains) showed their affiliation to the order Thermoplasmatales, with 73.9–86.3 % identity with sequences from members of the order with validly published names. The average nucleotide identity between genomes of the strains determined in silico was 98.75 %, suggesting, together with the 16S rRNA gene-based phylogenetic analysis, that the strains belong to the same species. A novel family, Cuniculiplasmataceae fam. nov., genus Cuniculiplasma gen. nov. and species Cuniculiplasma divulgatum sp. nov. are proposed based on the phylogenetic, chemotaxonomic analyses and physiological properties of the two isolates, S5T and PM4 ( = JCM 30641 = VKM B-2940). The type strain of Cuniculiplasma divulgatum is S5T ( = JCM 30642T = VKM B-2941T). PMID:26518885

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

    SciTech Connect

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

    1983-11-01

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

  11. A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium

    SciTech Connect

    Elias, Dwayne A; Wall, Judy D.; Mormile, Dr. Melanie R.; Begemann, Matthew B

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  12. Thermostable purified endoglucanase from thermophilic bacterium acidothermus cellulolyticus

    DOEpatents

    Tucker, Melvin P.; Grohmann, Karel; Himmel, Michael E.; Mohagheghi, Ali

    1992-01-01

    A substantially purified high molecular weight cellulase enzyme having a molecular weight of between about 156,000 to about 203,400 daltons isolated from the bacterium Acidothermus cellulolyticus (ATCC 43068) and a method of producing it are disclosed. The enzyme is water soluble, possesses both C.sub.1 and C.sub.x types of enzymatic activity, has a high degree of stability toward heat and exhibits both a high optimum temperature activity and high inactivation characteristics.

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

    PubMed Central

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

    1997-01-01

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

  14. Initiation of Chromosomal Replication in Predatory Bacterium Bdellovibrio bacteriovorus

    PubMed Central

    Makowski, Łukasz; Donczew, Rafał; Weigel, Christoph; Zawilak-Pawlik, Anna; Zakrzewska-Czerwińska, Jolanta

    2016-01-01

    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/T)TCCACA-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, Escherichia coli or Pseudomonas aeruginosa) systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium. PMID:27965633

  15. [Fractionation of sulfur isotopes by phototrophic sulfur bacterium Ectothiorhodospira shaposhnikovii].

    PubMed

    Ivanov, M V; Gogotova, G I; Matrosov, A G; Ziakun, A M

    1976-01-01

    Two processes of sulphur isotope fractionation have been found in experiments with the sulphur purple bacterium Ectothiorhodospira shaposhnikovii. As a result, a light isotope, 32S, is concentrated in residual hydrogen sulphide, and a heavy isotope, 34S, in elementary suphur which is deposited outside the cell. The sulphate produced is lighter than elementary sulphur. Fractionation of sulphur isotopes is observed in natural conditions and is confined to places of mass growth of photosynthetic sulphur bacteria.

  16. Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome

    PubMed Central

    Brito, José A.; Gutierres, André; Denkmann, Kevin; Dahl, Christiane; Archer, Margarida

    2014-01-01

    The ability to perform the very simple oxidation of two molecules of thiosulfate to tetrathionate is widespread among prokaryotes. Despite the prevalent occurrence of tetrathionate formation and its well documented significance within the sulfur cycle, little is known about the enzymes that catalyze the oxidative condensation of two thiosulfate anions. To fill this gap, the thiosulfate dehydrogenase (TsdA) enzyme from the purple sulfur bacterium Allochromatium vinosum was recombinantly expressed in Escherichia coli, purified and crystallized, and a crystallographic data set was collected. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 79.2, b = 69.9, c = 57.9 Å, β = 129.3°, contained one monomer per asymmetric unit and diffracted to a resolution of 1.98 Å. PMID:25286955

  17. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans

    SciTech Connect

    Sievert, Stefan M; Scott, Kathleen M; Klotz, Martin G; Chain, Patrick S. G.; Hauser, Loren John; Hemp, James; Hugler, Michael; Land, Miriam L; Lapidus, Alla L.; Larimer, Frank W; Lucas, Susan; Malfatti, Stephanie; Meyer, Folker; Paulsen, Ian T; Ren, Qinghu; Simon, Jorg

    2008-01-01

    Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.

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

    PubMed

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

    PubMed

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

    2005-03-11

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

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

    PubMed Central

    Johansson, B C; Gest, H

    1976-01-01

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

  1. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    PubMed Central

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

    1984-01-01

    The photoaffinity herbicide azidoatrazine (2-azido-4-ethylamino-6-isopropylamino-s-triazine) selectively labels the L subunit of the reaction center of the photosynthetic bacterium Rhodopseudomonas sphaeroides. Herbicide-resistant mutants retain the L subunit and have altered binding properties for methylthio- and chloro-substituted triazines as well as altered equilibrium constants for electron transfer between primary and secondary electron acceptors. We suggest that a subtle alteration in the L subunit is responsible for herbicide resistance and that the L subunit is the functional analog of the 32-kDa QB protein of chloroplast membranes. Images PMID:16593520

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

    SciTech Connect

    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.

  3. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE PAGES

    Gardner, Jeffrey G.

    2016-06-04

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. Furthermore, this review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkablemore » ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.« less

  4. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus.

    PubMed

    Gardner, Jeffrey G

    2016-07-01

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.

  5. Molybdate Reduction to Molybdenum Blue by an Antarctic Bacterium

    PubMed Central

    Ahmad, S. A.; Shukor, M. Y.; Shamaan, N. A.; Mac Cormack, W. P.; Syed, M. A.

    2013-01-01

    A molybdenum-reducing bacterium from Antarctica has been isolated. The bacterium converts sodium molybdate or Mo6+ to molybdenum blue (Mo-blue). Electron donors such as glucose, sucrose, fructose, and lactose supported molybdate reduction. Ammonium sulphate was the best nitrogen source for molybdate reduction. Optimal conditions for molybdate reduction were between 30 and 50 mM molybdate, between 15 and 20°C, and initial pH between 6.5 and 7.5. The Mo-blue produced had a unique absorption spectrum with a peak maximum at 865 nm and a shoulder at 710 nm. Respiratory inhibitors such as antimycin A, sodium azide, potassium cyanide, and rotenone failed to inhibit the reducing activity. The Mo-reducing enzyme was partially purified using ion exchange and gel filtration chromatography. The partially purified enzyme showed optimal pH and temperature for activity at 6.0 and 20°C, respectively. Metal ions such as cadmium, chromium, copper, silver, lead, and mercury caused more than 95% inhibition of the molybdenum-reducing activity at 0.1 mM. The isolate was tentatively identified as Pseudomonas sp. strain DRY1 based on partial 16s rDNA molecular phylogenetic assessment and the Biolog microbial identification system. The characteristics of this strain would make it very useful in bioremediation works in the polar and temperate countries. PMID:24381945

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

    PubMed

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

    2004-01-01

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

  7. Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

    USGS Publications Warehouse

    Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

    1990-01-01

    Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-09-08

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

  10. Genome Sequence of the Antarctic Psychrophile Bacterium Planococcus antarcticus DSM 14505

    PubMed Central

    Margolles, Abelardo; Gueimonde, Miguel

    2012-01-01

    Planococcus antarcticus DSM 14505 is a psychrophile bacterium that was isolated from cyanobacterial mat samples, originally collected from ponds in McMurdo, Antarctica. This orange-pigmented bacterium grows at 4°C and may possess interesting enzymatic activities at low temperatures. Here we report the first genomic sequence of P. antarcticus DSM 14505. PMID:22843594

  11. Near-complete genome sequence of the cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603

    DOE PAGES

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; ...

    2015-09-24

    We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

  12. Kinetic study of trichloroethylene and toluene degradation by a bioluminescent reporter bacterium

    SciTech Connect

    Kelly, C.J.; Sanseverino, J.; Bienkowski, P.R.; Sayler, G.S.

    1995-12-31

    A constructed bioluminescent reporter bacterium, Pseudomonas putida B2, is very briefly described in this paper. The bacterium degrades toluene and trichloroethylene (TCE), and produces light in the presence of toluene. The light response is an indication of cellular viability and expression of the genes encoding toluene and TCE degrading enzymes.

  13. Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles.

    PubMed

    Ayano, Hiroyuki; Kuroda, Masashi; Soda, Satoshi; Ike, Michihiko

    2014-05-15

    Pseudomonas aeruginosa strain RB is a bacterium capable of synthesizing cadmium selenide (CdSe) nanoparticles and was isolated from a soil sample. Here, we present the draft genome sequence of P. aeruginosa strain RB. To the best of our knowledge, this is the first report of a draft genome of a CdSe-synthesizing bacterium.

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

    SciTech Connect

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

    1997-06-06

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

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

    PubMed

    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.

  16. Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

    SciTech Connect

    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.

  17. Characterization of the quinones in purple sulfur bacterium Thermochromatium tepidum.

    PubMed

    Kimura, Yuuka; Kawakami, Tomoaki; Yu, Long-Jiang; Yoshimura, Miku; Kobayashi, Masayuki; Wang-Otomo, Zheng-Yu

    2015-07-08

    Quinone distributions in the thermophilic purple sulfur bacterium Thermochromatium tepidum have been investigated at different levels of the photosynthetic apparatus. Here we show that, on average, the intracytoplasmic membrane contains 18 ubiquinones (UQ) and 4 menaquinones (MQ) per reaction center (RC). About one-third of the quinones are retained in the light-harvesting-reaction center core complex (LH1-RC) with a similar ratio of UQ to MQ. The numbers of quinones essentially remains unchanged during crystallization of the LH1-RC. There are 1-2 UQ and 1 MQ associated with the RC-only complex in the purified solution sample. Our results suggest that a large proportion of the quinones are confined to the core complex and at least five UQs remain invisible in the current LH1-RC crystal structure.

  18. Real-time RNA profiling within a single bacterium.

    PubMed

    Le, Thuc T; Harlepp, Sébastien; Guet, Calin C; Dittmar, Kimberly; Emonet, Thierry; Pan, Tao; Cluzel, Philippe

    2005-06-28

    Characterizing the dynamics of specific RNA levels requires real-time RNA profiling in a single cell. We show that the combination of a synthetic modular genetic system with fluorescence correlation spectroscopy allows us to directly measure in real time the activity of any specific promoter in prokaryotes. Using a simple inducible gene expression system, we found that induced RNA levels within a single bacterium of Escherichia coli exhibited a pulsating profile in response to a steady input of inducer. The genetic deletion of an efflux pump system, a key determinant of antibiotic resistance, altered the pulsating transcriptional dynamics and caused overexpression of induced RNA. In contrast with population measurements, real-time RNA profiling permits identifying relationships between genotypes and transcriptional dynamics that are accessible only at the level of the single cell.

  19. Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus

    PubMed Central

    Lonhienne, Thierry G. A.; Sagulenko, Evgeny; Webb, Richard I.; Lee, Kuo-Chang; Franke, Josef; Devos, Damien P.; Nouwens, Amanda; Carroll, Bernard J.; Fuerst, John A.

    2010-01-01

    Endocytosis is a process by which extracellular material such as macromolecules can be incorporated into cells via a membrane-trafficking system. Although universal among eukaryotes, endocytosis has not been identified in Bacteria or Archaea. However, intracellular membranes are known to compartmentalize cells of bacteria in the phylum Planctomycetes, suggesting the potential for endocytosis and membrane trafficking in members of this phylum. Here we show that cells of the planctomycete Gemmata obscuriglobus have the ability to uptake proteins present in the external milieu in an energy-dependent process analogous to eukaryotic endocytosis, and that internalized proteins are associated with vesicle membranes. Occurrence of such ability in a bacterium is consistent with autogenous evolution of endocytosis and the endomembrane system in an ancestral noneukaryote cell. PMID:20566852

  20. The domestication of the probiotic bacterium Lactobacillus acidophilus.

    PubMed

    Bull, Matthew J; Jolley, Keith A; Bray, James E; Aerts, Maarten; Vandamme, Peter; Maiden, Martin C J; Marchesi, Julian R; Mahenthiralingam, Eshwar

    2014-11-26

    Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.

  1. Mechanism of anaerobic degradation of triethanolamine by a homoacetogenic bacterium.

    PubMed

    Speranza, Giovanna; Morelli, Carlo F; Cairoli, Paola; Müller, Britta; Schink, Bernhard

    2006-10-20

    Triethanolamine (TEA) is converted into acetate and ammonia by a strictly anaerobic, gram-positive Acetobacterium strain LuTria3. Fermentation experiments with resting cell suspensions and specifically deuterated substrates indicate that in the acetate molecule the carboxylate and the methyl groups correspond to the alcoholic function and to its adjacent methylene group, respectively, of the 2-hydroxyethyl unit of TEA. A 1,2 shift of a hydrogen (deuterium) atom from -CH2-O- to =N-CH2- without exchange with the medium was observed. This fact gives evidence that a radical mechanism occurs involving the enzyme and/or coenzyme molecule as a hydrogen carrier. Such a biodegradation appears analogous to the conversion of 2-phenoxyethanol into acetate mediated by another strain of the anaerobic homoacetogenic bacterium Acetobacterium.

  2. Mechanism of anaerobic degradation of triethanolamine by a homoacetogenic bacterium

    SciTech Connect

    Speranza, Giovanna . E-mail: giovanna.speranza@unimi.it; Morelli, Carlo F.; Cairoli, Paola; Mueller, Britta; Schink, Bernhard

    2006-10-20

    Triethanolamine (TEA) is converted into acetate and ammonia by a strictly anaerobic, gram-positive Acetobacterium strain LuTria3. Fermentation experiments with resting cell suspensions and specifically deuterated substrates indicate that in the acetate molecule the carboxylate and the methyl groups correspond to the alcoholic function and to its adjacent methylene group, respectively, of the 2-hydroxyethyl unit of TEA. A 1,2 shift of a hydrogen (deuterium) atom from -CH{sub 2} -O- to =N-CH{sub 2} - without exchange with the medium was observed. This fact gives evidence that a radical mechanism occurs involving the enzyme and/or coenzyme molecule as a hydrogen carrier. Such a biodegradation appears analogous to the conversion of 2-phenoxyethanol into acetate mediated by another strain of the anaerobic homoacetogenic bacterium Acetobacterium.

  3. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

    PubMed

    White, O; Eisen, J A; Heidelberg, J F; Hickey, E K; Peterson, J D; Dodson, R J; Haft, D H; Gwinn, M L; Nelson, W C; Richardson, D L; Moffat, K S; Qin, H; Jiang, L; Pamphile, W; Crosby, M; Shen, M; Vamathevan, J J; Lam, P; McDonald, L; Utterback, T; Zalewski, C; Makarova, K S; Aravind, L; Daly, M J; Minton, K W; Fleischmann, R D; Ketchum, K A; Nelson, K E; Salzberg, S; Smith, H O; Venter, J C; Fraser, C M

    1999-11-19

    The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.

  4. Genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)

    SciTech Connect

    Anderson, Iain; Saunders, Elizabeth H; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Tice, Hope; Glavina Del Rio, Tijana; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Chang, Yun-Juan; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2012-01-01

    Thermodesulfatator indicus Moussard et al. 2004 is a member of the genomically so far poorly characterized family Thermodesulfobacteriaceae in the phylum Thermodesulfobacteria. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)

    PubMed Central

    Anderson, Iain; Saunders, Elizabeth; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Chang, Yun-juan; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2012-01-01

    Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:22768359

  6. Self-trapping of a single bacterium in its own chemoattractant

    NASA Astrophysics Data System (ADS)

    Tsori, Y.; de Gennes, P.-G.

    2004-05-01

    Bacteria (e.g., E. coli) are very sensitive to certain chemoattractants (e.g., asparate) which they themselves produce. This leads to chemical instabilities in a uniform population. We discuss here the different case of a single bacterium, following the general scheme of Brenner, Levitov and Budrene. We show that in one and two dimensions (in a capillary or in a thin film) the bacterium can become self-trapped in its cloud of attractant. This should occur if a certain coupling constant g is larger than unity. We then estimate the reduced diffusion Deff of the bacterium in the strong-coupling limit, and find Deff ~ g-1.

  7. Ecology and metabolism of the beneficial intestinal commensal bacterium Faecalibacterium prausnitzii.

    PubMed

    Miquel, Sylvie; Martín, Rebeca; Bridonneau, Chantal; Robert, Véronique; Sokol, Harry; Bermúdez-Humarán, Luis G; Thomas, Muriel; Langella, Philippe

    2014-01-01

    Faecalibacterium prausnitzii is a major commensal bacterium, and its prevalence is often decreased in conditions of intestinal dysbiosis. The phylogenic identity of this bacterium was described only recently. It is still poorly characterized, and its specific growth requirements in the human gastrointestinal tract are not known. In this review, we consider F. prausnitzii metabolism, its ecophysiology in both humans and animals, and the effects of drugs and nutrition on its population. We list important questions about this beneficial and ubiquitous commensal bacterium that it would be valuable to answer.

  8. Presence of an unusual methanogenic bacterium in coal gasification waste.

    PubMed

    Tomei, F A; Rouse, D; Maki, J S; Mitchell, R

    1988-12-01

    Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of Methanosarcina barkeri, but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics d-cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37 degrees C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with Methanosarcina sp. Cells were 1 mum wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed.

  9. Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus

    PubMed Central

    Petroff, Alexander; Libchaber, Albert

    2014-01-01

    The ecology and dynamics of many microbial systems, particularly in mats and soils, are shaped by how bacteria respond to evolving nutrient gradients and microenvironments. Here we show how the response of the sulfur-oxidizing bacterium Thiovulum majus to changing oxygen gradients causes cells to organize into large-scale fronts. To study this phenomenon, we develop a technique to isolate and enrich these bacteria from the environment. Using this enrichment culture, we observe the formation and dynamics of T. majus fronts in oxygen gradients. We show that these dynamics can be understood as occurring in two steps. First, chemotactic cells moving up the oxygen gradient form a front that propagates with constant velocity. We then show, through observation and mathematical analysis, that this front becomes unstable to changes in cell density. Random perturbations in cell density create oxygen gradients. The response of cells magnifies these gradients and leads to the formation of millimeter-scale fluid flows that actively pull oxygenated water through the front. We argue that this flow results from a nonlinear instability excited by stochastic fluctuations in the density of cells. Finally, we show that the dynamics by which these modes interact can be understood from the chemotactic response of cells. These results provide a mathematically tractable example of how collective phenomena in ecological systems can arise from the individual response of cells to a shared resource. PMID:24459183

  10. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    SciTech Connect

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G.; Pienkos, Philip T.; Guarnieri, Michael T.

    2016-02-23

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels.

  11. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    DOE PAGES

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; ...

    2016-02-23

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resultedmore » in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels.« less

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

    USGS Publications Warehouse

    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.

  13. Novel Rickettsiella bacterium in the leafhopper Orosius albicinctus (Hemiptera: Cicadellidae).

    PubMed

    Iasur-Kruh, Lilach; Weintraub, Phyllis G; Mozes-Daube, Netta; Robinson, Wyatt E; Perlman, Steve J; Zchori-Fein, Einat

    2013-07-01

    Bacteria in the genus Rickettsiella (Coxiellaceae), which are mainly known as arthropod pathogens, are emerging as excellent models to study transitions between mutualism and pathogenicity. The current report characterizes a novel Rickettsiella found in the leafhopper Orosius albicinctus (Hemiptera: Cicadellidae), a major vector of phytoplasma diseases in Europe and Asia. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to survey the main symbionts of O. albicinctus, revealing the obligate symbionts Sulcia and Nasuia, and the facultative symbionts Arsenophonus and Wolbachia, in addition to Rickettsiella. The leafhopper Rickettsiella is allied with bacteria found in ticks. Screening O. albicinctus from the field showed that Rickettsiella is highly prevalent, with over 60% of individuals infected. A stable Rickettsiella infection was maintained in a leafhopper laboratory colony for at least 10 generations, and fluorescence microscopy localized bacteria to accessory glands of the female reproductive tract, suggesting that the bacterium is vertically transmitted. Future studies will be needed to examine how Rickettsiella affects host fitess and its ability to vector phytopathogens.

  14. Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus.

    PubMed

    Petroff, Alexander; Libchaber, Albert

    2014-02-04

    The ecology and dynamics of many microbial systems, particularly in mats and soils, are shaped by how bacteria respond to evolving nutrient gradients and microenvironments. Here we show how the response of the sulfur-oxidizing bacterium Thiovulum majus to changing oxygen gradients causes cells to organize into large-scale fronts. To study this phenomenon, we develop a technique to isolate and enrich these bacteria from the environment. Using this enrichment culture, we observe the formation and dynamics of T. majus fronts in oxygen gradients. We show that these dynamics can be understood as occurring in two steps. First, chemotactic cells moving up the oxygen gradient form a front that propagates with constant velocity. We then show, through observation and mathematical analysis, that this front becomes unstable to changes in cell density. Random perturbations in cell density create oxygen gradients. The response of cells magnifies these gradients and leads to the formation of millimeter-scale fluid flows that actively pull oxygenated water through the front. We argue that this flow results from a nonlinear instability excited by stochastic fluctuations in the density of cells. Finally, we show that the dynamics by which these modes interact can be understood from the chemotactic response of cells. These results provide a mathematically tractable example of how collective phenomena in ecological systems can arise from the individual response of cells to a shared resource.

  15. The lipopolysaccharide of a chloridazon-degrading bacterium.

    PubMed

    Weisshaar, R; Lingens, F

    1983-12-01

    Lipopolysaccharide of a chloridazon-degrading bacterium was obtained by a two-stage extraction procedure with phenol/EDTA in a yield of 0.3% of dried bacteria. The carbohydrate moiety consisted of heptose, 3-deoxyoctulosonic acid and D-glucose in a molar ratio of 1:2:2 X 3. Lipid A was composed of 1 mol 2,3-diamino-2,3-dideoxy-D-glucose, 2 mol amide-bound and 2.6 mol ester-bound fatty acids/mol. Amide-bound fatty acids were 3-hydroxydodecanoic acid and 3-hydroxyhexadecanoic acid; dodecanoic acid and R-(-)-3-hydroxydodec-5-cis-enoic acid were found to be present in ester linkage. Under conditions of acidic hydrolysis, the latter was converted into the cis and trans isomers of 5-hexyltetrahydrofuran-2-acetic acid. Dodecanoic acid was demonstrated to be linked with the hydroxy groups of the amide-bound fatty acids. The taxonomic significance of these results, especially the demonstration of 2,3-diamino-2, 3-dideoxy-D-glucose, is discussed.

  16. Bioconversion of methane to lactate by an obligate methanotrophic bacterium.

    PubMed

    Henard, Calvin A; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G; Pienkos, Philip T; Guarnieri, Michael T

    2016-02-23

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to "green" chemicals and fuels.

  17. Novel Trypanosomatid-Bacterium Association: Evolution of Endosymbiosis in Action

    PubMed Central

    Kostygov, Alexei Y.; Dobáková, Eva; Grybchuk-Ieremenko, Anastasiia; Váhala, Dalibor; Maslov, Dmitri A.; Votýpka, Jan

    2016-01-01

    ABSTRACT We describe a novel symbiotic association between a kinetoplastid protist, Novymonas esmeraldas gen. nov., sp. nov., and an intracytoplasmic bacterium, “Candidatus Pandoraea novymonadis” sp. nov., discovered as a result of a broad-scale survey of insect trypanosomatid biodiversity in Ecuador. We characterize this association by describing the morphology of both organisms, as well as their interactions, and by establishing their phylogenetic affinities. Importantly, neither partner is closely related to other known organisms previously implicated in eukaryote-bacterial symbiosis. This symbiotic association seems to be relatively recent, as the host does not exert a stringent control over the number of bacteria harbored in its cytoplasm. We argue that this unique relationship may represent a suitable model for studying the initial stages of establishment of endosymbiosis between a single-cellular eukaryote and a prokaryote. Based on phylogenetic analyses, Novymonas could be considered a proxy for the insect-only ancestor of the dixenous genus Leishmania and shed light on the origin of the two-host life cycle within the subfamily Leishmaniinae. PMID:26980834

  18. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    PubMed Central

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G.; Pienkos, Philip T.; Guarnieri, Michael T.

    2016-01-01

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels. PMID:26902345

  19. Kinetics of a chlorate-accumulating, perchlorate-reducing bacterium.

    PubMed

    Dudley, Margaret; Salamone, Anna; Nerenberg, Robert

    2008-05-01

    Kinetics parameters for perchlorate and chlorate reduction were determined for Dechlorosoma sp. HCAP-C, also known as Dechlorosoma sp. PCC, a novel perchlorate-reducing bacterium (PCRB) that accumulates significant amounts of chlorate during perchlorate reduction. This is the first report of such behavior, and we hypothesized the perchlorate reduction kinetics would be markedly different from other PCRB. In batch tests with initial perchlorate concentrations ranging from 200 to around 1400 mg/L, maximum chlorate accumulation ranged from 41 to 279 mg/L, and were consistently around 20% of the initial perchlorate concentration. For perchlorate, parameters were determined using a competitive inhibition model. The maximum specific substrate degradation rate qmaxP was 11.5mgClO4-/mgdry weight (DW)-d, and the half-maximum rate constant KP was 193 mgClO4-/L. For chlorate, the qmaxC was 8.3 mgClO3-/mgDW-d and the KC was 58.3 mgClO3-/L. The high KP values relative to conventional PCRB, values suggests that HCAP-C does not play a significant role at low perchlorate concentrations. However, the relatively high qmaxP, and the potential for syntrophic relationships with chlorate-reducing bacteria that relieve the effects of chlorate inhibition, suggest that HCAP-C could play a significant role at high perchlorate concentrations.

  20. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7.

    PubMed

    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.

  1. Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans

    PubMed Central

    Reith, Frank; Etschmann, Barbara; Grosse, Cornelia; Moors, Hugo; Benotmane, Mohammed A.; Monsieurs, Pieter; Grass, Gregor; Doonan, Christian; Vogt, Stefan; Lai, Barry; Martinez-Criado, Gema; George, Graham N.; Nies, Dietrich H.; Mergeay, Max; Pring, Allan; Southam, Gordon; Brugger, Joël

    2009-01-01

    While the role of microorganisms as main drivers of metal mobility and mineral formation under Earth surface conditions is now widely accepted, the formation of secondary gold (Au) is commonly attributed to abiotic processes. Here we report that the biomineralization of Au nanoparticles in the metallophillic bacterium Cupriavidus metallidurans CH34 is the result of Au-regulated gene expression leading to the energy-dependent reductive precipitation of toxic Au(III)-complexes. C. metallidurans, which forms biofilms on Au grains, rapidly accumulates Au(III)-complexes from solution. Bulk and microbeam synchrotron X-ray analyses revealed that cellular Au accumulation is coupled to the formation of Au(I)-S complexes. This process promotes Au toxicity and C. metallidurans reacts by inducing oxidative stress and metal resistances gene clusters (including a Au-specific operon) to promote cellular defense. As a result, Au detoxification is mediated by a combination of efflux, reduction, and possibly methylation of Au-complexes, leading to the formation of Au(I)-C-compounds and nanoparticulate Au0. Similar particles were observed in bacterial biofilms on Au grains, suggesting that bacteria actively contribute to the formation of Au grains in surface environments. The recognition of specific genetic responses to Au opens the way for the development of bioexploration and bioprocessing tools. PMID:19815503

  2. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7

    PubMed Central

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

    2015-01-01

    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. PMID:26426011

  3. Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum.

    PubMed

    Hensen, Daniela; Sperling, Detlef; Trüper, Hans G; Brune, Daniel C; Dahl, Christiane

    2006-11-01

    Two different pathways for thiosulphate oxidation are present in the purple sulphur bacterium Allochromatium vinosum: oxidation to tetrathionate and complete oxidation to sulphate with obligatory formation of sulphur globules as intermediates. The tetrathionate:sulphate ratio is strongly pH-dependent with tetrathionate formation being preferred under acidic conditions. Thiosulphate dehydrogenase, a constitutively expressed monomeric 30 kDa c-type cytochrome with a pH optimum at pH 4.2 catalyses tetrathionate formation. A periplasmic thiosulphate-oxidizing multienzyme complex (Sox) has been described to be responsible for formation of sulphate from thiosulphate in chemotrophic and phototrophic sulphur oxidizers that do not form sulphur deposits. In the sulphur-storing A. vinosum we identified five sox genes in two independent loci (soxBXA and soxYZ). For SoxA a thiosulphate-dependent induction of expression, above a low constitutive level, was observed. Three sox-encoded proteins were purified: the heterodimeric c-type cytochrome SoxXA, the monomeric SoxB and the heterodimeric SoxYZ. Gene inactivation and complementation experiments proved these proteins to be indispensable for thiosulphate oxidation to sulphate. The intermediary formation of sulphur globules in A. vinosum appears to be related to the lack of soxCD genes, the products of which are proposed to oxidize SoxY-bound sulphane sulphur. In their absence the latter is instead transferred to growing sulphur globules.

  4. Characterization of a Neochlamydia-like Bacterium Associated with Epitheliocystis in Cultured Artic Char Salvelinus alpinus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic char (Salvelinus alpinus). To characterize a bacterium associated with epitheliocystis in cultured char, gills were sampled for histopathologic examination, conventional...

  5. Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1.

    PubMed

    Masuda, Hisako; Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J

    2014-12-04

    The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence.

  6. Enhancement of xylose utilization from corn stover by a recombinant bacterium for ethanol production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombinant ethanologenic Escherichia coli ferments glucose, xylose and arabinose to ethanol. However, the bacterium preferentially utilizes glucose first, then arabinose and finally xylose (sequential utilization of sugars) during fermentation of lignocellulosic hydrolyzates to ethanol making the p...

  7. Draft Genome Sequence of the Fast-Growing Bacterium Vibrio natriegens Strain DSMZ 759.

    PubMed

    Maida, Isabel; Bosi, Emanuele; Perrin, Elena; Papaleo, Maria Cristiana; Orlandini, Valerio; Fondi, Marco; Fani, Renato; Wiegel, Juergen; Bianconi, Giovanna; Canganella, Francesco

    2013-08-22

    Vibrio natriegens is a Gram-negative bacterium known for its extremely short doubling time. Here we present the annotated draft genome sequence of Vibrio natriegens strain DSMZ 759, with the aim of providing insights about its high growth rate.

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

    EPA Science Inventory

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

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

    PubMed

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

    2015-07-20

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

  10. Vibrio damsela, a Marine Bacterium, Causes Skin Ulcers on the Damselfish Chromis punctipinnis.

    PubMed

    Love, M; Teebken-Fisher, D; Hose, J E; Farmer, J J; Hickman, F W; Fanning, G R

    1981-12-04

    A previously undescribed marine bacterium, Vibrio damsela, was isolated from naturally occurring skin ulcers on a species of temperate-water damselfish, the blacksmith (Chromis punctipinnis). Laboratory infection of the blacksmith with Vibrio damsela produced similar ulcers. Vibrio damsela was pathogenic for four other species of damselfish but not for members of other families of fish. The bacterium has also been isolated from water and from two human wounds and may be a cause of human disease.

  11. Naphthalecin, a novel antibiotic produced by the anaerobic bacterium, Sporotalea colonica sp. nov.

    PubMed

    Ezaki, Masami; Muramatsu, Hideyuki; Takase, Shigehiro; Hashimoto, Michizane; Nagai, Koji

    2008-04-01

    A novel antibiotic naphthalecin was purified and isolated from the cells of an anaerobic bacterium isolated from a soil sample. This antibiotic contained a naphthalene moiety, so named as naphthalecin, and showed antibacterial activity against gram positive species. The producing strain, an obligate anaerobe, was identified as a new species of the genus Sporotalea. Identification of the bacterium, cultivation, purification, structure determination, and antibacterial activity are shown.

  12. Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena.

    PubMed

    Sun, Jinchun; Jin, Jinshan; Beger, Richard D; Cerniglia, Carl E; Yang, Maocheng; Chen, Huizhong

    2016-10-01

    The association between exposure to smokeless tobacco products (STP) and oral diseases is partially due to the physiological and pathological changes in the composition of the oral microbiome and its metabolic profile. However, it is not clear how STPs affect the physiology and ecology of oral microbiota. A UPLC/QTof-MS-based metabolomics study was employed to analyze metabolic alterations in oral bacterium, Capnocytophaga sputigena as a result of smokeless tobacco exposure and to assess the capability of the bacterium to metabolize nicotine. Pathway analysis of the metabolome profiles indicated that smokeless tobacco extracts caused oxidative stress in the bacterium. The metabolomics data also showed that the arginine-nitric oxide pathway was perturbed by the smokeless tobacco treatment. Results also showed that LC/MS was useful in identifying STP constituents and additives, including caffeine and many flavoring compounds. No significant changes in levels of nicotine and its major metabolites were found when C. sputigena was cultured in a nutrient rich medium, although hydroxylnicotine and cotinine N-oxide were detected in the bacterial metabolites suggesting that nicotine metabolism might be present as a minor degradation pathway in the bacterium. Study results provide new insights regarding the physiological and toxicological effects of smokeless tobacco on oral bacterium C. sputigena and associated oral health as well as measuring the ability of the oral bacterium to metabolize nicotine.

  13. Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte

    PubMed Central

    Hoffman, Michele T.; Gunatilaka, Malkanthi K.; Wijeratne, Kithsiri; Gunatilaka, Leslie; Arnold, A. Elizabeth

    2013-01-01

    Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA), often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria) have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales), but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales). Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions. PMID:24086270

  14. Comparative Genomics of Two Closely Related Unicellular Thermo-Acidophilic Red Algae, Galdieria sulphuraria and Cyanidioschyzon merolae, Reveals the Molecular Basis of the Metabolic Flexibility of Galdieria sulphuraria and Significant Differences in Carbohydrate Metabolism of Both Algae1

    PubMed Central

    Barbier, Guillaume; Oesterhelt, Christine; Larson, Matthew D.; Halgren, Robert G.; Wilkerson, Curtis; Garavito, R. Michael; Benning, Christoph; Weber, Andreas P.M.

    2005-01-01

    Unicellular algae serve as models for the study and discovery of metabolic pathways, for the functional dissection of cell biological processes such as organellar division and cell motility, and for the identification of novel genes and gene functions. The recent completion of several algal genome sequences and expressed sequence tag collections and the establishment of nuclear and organellar transformation methods has opened the way for functional genomics approaches using algal model systems. The thermo-acidophilic unicellular red alga Galdieria sulphuraria represents a particularly interesting species for a genomics approach owing to its extraordinary metabolic versatility such as heterotrophic and mixotrophic growth on more than 50 different carbon sources and its adaptation to hot acidic environments. However, the ab initio prediction of genes required for unknown metabolic pathways from genome sequences is not trivial. A compelling strategy for gene identification is the comparison of similarly sized genomes of related organisms with different physiologies. Using this approach, candidate genes were identified that are critical to the metabolic versatility of Galdieria. Expressed sequence tags and high-throughput genomic sequence reads covering >70% of the G. sulphuraria genome were compared to the genome of the unicellular, obligate photoautotrophic red alga Cyanidioschyzon merolae. More than 30% of the Galdieria sequences did not relate to any of the Cyanidioschyzon genes. A closer inspection of these sequences revealed a large number of membrane transporters and enzymes of carbohydrate metabolism that are unique to Galdieria. Based on these data, it is proposed that genes involved in the uptake of reduced carbon compounds and enzymes involved in their metabolism are crucial to the metabolic flexibility of G. sulphuraria. PMID:15710685

  15. Carbonate biomineralization induced by soil bacterium Bacillus megaterium

    NASA Astrophysics Data System (ADS)

    Lian, Bin; Hu, Qiaona; Chen, Jun; Ji, Junfeng; Teng, H. Henry

    2006-11-01

    Biogenic carbonates spawned from microbial activities are common occurrences in soils. Here, we investigate the carbonate biomineralization mediated by the bacterium Bacillus megaterium, a dominant strain separated from a loess profile in China. Upon completing bacterial cultivation, the ensuring products are centrifuged, and the resultant supernatant and the concentrated bacterial sludge as well as the un-separated culture are added separately into a Ca-CO 3 containing solution for crystallization experiments. Results of XRD and SEM analysis indicate that calcite is the dominant mineral phase formed when the bacteria are present. When the supernatant alone is used, however, a significant portion of vaterite is also precipitated. Experimental results further reveal that the bacteria have a strong tendency to colonize the center area of the calcite {1 0 1¯ 4} faces. Observed crystal morphology suggests that the bacterial colony may promote the growth normal to each individual {1 0 1¯ 4} face of calcite when the cell concentration is high, but may retard it or even cause dissolution of the immediate substrate surfaces when the concentration is low. SEM images taken at earlier stages of the crystallization experiments demonstrate the nucleation of calcite on the bacterial cell walls but do not show obvious morphological changes on the nanometer- to submicron-sized nuclei. δ 13C measurements unveil that the crystals grown in the presence of bacteria are further enriched in the heavy carbon isotope, implying that the bacterial metabolism may not be the carbon sources for the mineralization. Based upon these findings, we propose a mechanism for the B. megaterium mediated calcite mineralization and conclude that the whole process involves epi- and inter-cellular growth in the local microenvironments whose conditions may be controlled by cell sequestration and proton pumping during bacterial respiration.

  16. Metabolic Evolution of a Deep-Branching Hyperthermophilic Chemoautotrophic Bacterium

    PubMed Central

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere. PMID:24516572

  17. Genomes of “Spiribacter”, a streamlined, successful halophilic bacterium

    PubMed Central

    2013-01-01

    Background Thalassosaline waters produced by the concentration of seawater are widespread and common extreme aquatic habitats. Their salinity varies from that of sea water (ca. 3.5%) to saturation for NaCl (ca. 37%). Obviously the microbiota varies dramatically throughout this range. Recent metagenomic analysis of intermediate salinity waters (19%) indicated the presence of an abundant and yet undescribed gamma-proteobacterium. Two strains belonging to this group have been isolated from saltern ponds of intermediate salinity in two Spanish salterns and were named “Spiribacter”. Results The genomes of two isolates of “Spiribacter” have been fully sequenced and assembled. The analysis of metagenomic datasets indicates that microbes of this genus are widespread worldwide in medium salinity habitats representing the first ecologically defined moderate halophile. The genomes indicate that the two isolates belong to different species within the same genus. Both genomes are streamlined with high coding densities, have few regulatory mechanisms and no motility or chemotactic behavior. Metabolically they are heterotrophs with a subgroup II xanthorhodopsin as an additional energy source when light is available. Conclusions This is the first bacterium that has been proven by culture independent approaches to be prevalent in hypersaline habitats of intermediate salinity (half a way between the sea and NaCl saturation). Predictions from the proteome and analysis of transporter genes, together with a complete ectoine biosynthesis gene cluster are consistent with these microbes having the salt-out-organic-compatible solutes type of osmoregulation. All these features are also consistent with a well-adapted fully planktonic microbe while other halophiles with more complex genomes such as Salinibacter ruber might have particle associated microniches. PMID:24225341

  18. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    PubMed

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.

  19. Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris.

    PubMed

    Oda, Yasuhiro; Star, Bastiaan; Huisman, Louis A; Gottschal, Jan C; Forney, Larry J

    2003-09-01

    The biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris on a local scale was investigated. Thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by BOX-PCR genomic DNA fingerprinting. Cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were repeatedly isolated. Representatives of these four major genotypes were tentatively identified as R. palustris based on phylogentic analyses of 16S rRNA gene sequences. The differences in the genomic fingerprint patterns among the four major genotypes were accompanied by differences in phenotypic characteristics. These phenotypic differences included differences in the kinetics of carbon source use, suggesting that there may be functional differences with possible ecological significance among these clonal linages. Morisita-Horn similarity coefficients (C(MH)), which were used to compare the numbers of common genotypes found at pairs of sampling locations, showed that there was substantial similarity between locations that were 1 cm apart (C(MH), >/=0.95) but there was almost no similarity between locations that were >/=9 m apart (C(MH),

  20. Interaction of Cadmium With the Aerobic Bacterium Pseudomonas Mendocina

    NASA Astrophysics Data System (ADS)

    Schramm, P. J.; Haack, E. A.; Maurice, P. A.

    2006-05-01

    The fate of toxic metals in the environment can be heavily influenced by interaction with bacteria in the vadose zone. This research focuses on the interactions of cadmium with the strict aerobe Pseudomonas mendocina. P. mendocina is a gram-negative bacterium that has shown potential in the bioremediation of recalcitrant organic compounds. Cadmium is a common environmental contaminant of wide-spread ecological consequence. In batch experiments P. mendocina shows typical bacterial growth curves, with an initial lag phase followed by an exponential phase and a stationary to death phase; concomitant with growth was an increase in pH from initial values of 7 to final values at 96 hours of 8.8. Cd both delays the onset of the exponential phase and decreases the maximum population size, as quantified by optical density and microscopic cell counts (DAPI). The total amount of Cd removed from solution increases over time, as does the amount of Cd removed from solution normalized per bacterial cell. Images obtained with transmission electron microscopy (TEM) showed the production of a cadmium, phosphorus, and iron containing precipitate that was similar in form and composition to precipitates formed abiotically at elevated pH. However, by late stationary phase, the precipitate had been re-dissolved, perhaps by biotic processes in order to obtain Fe. Stressed conditions are suggested by TEM images showing the formation of pili, or nanowires, when 20ppm Cd was present and a marked decrease in exopolysaccharide and biofilm material in comparison to control cells (no cadmium added).

  1. Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli

    PubMed Central

    Shrestha, Ram Kumar; Rosenberg, Tally; Makarovsky, Daria; Eckshtain-Levi, Noam; Zelinger, Einat; Kopelowitz, June; Sikorski, Johannes; Burdman, Saul

    2013-01-01

    Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a disease that threatens the cucurbit industry worldwide. Despite the economic importance of BFB, little is known about pathogenicity and fitness strategies of the bacterium. We have observed the phenomenon of phenotypic variation in A. citrulli. Here we report the characterization of phenotypic variants (PVs) of two strains, M6 and 7a1, isolated from melon and watermelon, respectively. Phenotypic variation was observed following growth in rich medium, as well as upon isolation of bacteria from inoculated plants or exposure to several stresses, including heat, salt and acidic conditions. When grown on nutrient agar, all PV colonies possessed a translucent appearance, in contrast to parental strain colonies that were opaque. After 72 h, PV colonies were bigger than parental colonies, and had a fuzzy appearance relative to parental strain colonies that are relatively smooth. A. citrulli colonies are generally surrounded by haloes detectable by the naked eye. These haloes are formed by type IV pilus (T4P)-mediated twitching motility that occurs at the edge of the colony. No twitching haloes could be detected around colonies of both M6 and 7a1 PVs, and microscopy observations confirmed that indeed the PVs did not perform twitching motility. In agreement with these results, transmission electron microscopy revealed that M6 and 7a1 PVs do not produce T4P under tested conditions. PVs also differed from their parental strain in swimming motility and biofilm formation, and interestingly, all assessed variants were less virulent than their corresponding parental strains in seed transmission assays. Slight alterations could be detected in some DNA fingerprinting profiles of 7a1 variants relative to the parental strain, while no differences at all could be seen among M6 variants and parental strain, suggesting that, at least in the latter, phenotypic variation is mediated by slight genetic and/or epigenetic

  2. The Sulfur Oxygenase Reductase from the Mesophilic Bacterium Halothiobacillus neapolitanus Is a Highly Active Thermozyme

    PubMed Central

    Veith, Andreas; Botelho, Hugo M.; Kindinger, Florian; Gomes, Cláudio M.

    2012-01-01

    A biochemical, biophysical, and phylogenetic study of the sulfur oxygenase reductase (SOR) from the mesophilic gammaproteobacterium Halothiobacillus neapolitanus (HnSOR) was performed in order to determine the structural and biochemical properties of the enzyme. SOR proteins from 14 predominantly chemolithoautotrophic bacterial and archaeal species are currently available in public databases. Sequence alignment and phylogenetic analysis showed that they form a coherent protein family. The HnSOR purified from Escherichia coli after heterologous gene expression had a temperature range of activity of 10 to 99°C with an optimum at 80°C (42 U/mg protein). Sulfite, thiosulfate, and hydrogen sulfide were formed at various stoichiometries in a range between pH 5.4 and 11 (optimum pH 8.4). Circular dichroism (CD) spectroscopy and dynamic light scattering showed that the HnSOR adopts secondary and quaternary structures similar to those of the 24-subunit enzyme from the hyperthermophile Acidianus ambivalens (AaSOR). The melting point of the HnSOR was ≈20°C lower than that of the AaSOR, when analyzed with CD-monitored thermal unfolding. Homology modeling showed that the secondary structure elements of single subunits are conserved. Subtle changes in the pores of the outer shell and increased flexibility might contribute to activity at low temperature. We concluded that the thermostability was the result of a rigid protein core together with the stabilizing effect of the 24-subunit hollow sphere. PMID:22139503

  3. Methylated sulfur compounds in microbial mats: In situ concentrations and metabolism by a colorless sulfur bacterium

    SciTech Connect

    Visscher, P.T. Netherlands Inst. for Sea Research, Den Burg ); Quist, P.; vanGemerden, H. )

    1991-06-01

    The concentrations of the volatile organic sulfur compounds methanethiol, dimethyl disulfide, and dimethyl sulfide (DMS) and the viable population capable of DMS utilization in laminated microbial ecosystems were evaluated. Significant levels of DMS and dimethyl disulfide (maximum concentrations of 220 and 24 nmol cm{sup 3} of sediment{sup {minus}1}, respectively) could be detected only at the top 20 mm of the microbial mat, whereas methanethiol was found only at depth horizons from 20 to 50 mm (maximum concentrations of 42 nmol cm{sup 3} of sediment{sup {minus}1}). DMS concentrations in the surface layer doubled after cold hydrolysis of its precursor, dimethylsulfoniopropioinate. Most-probable-number counts revealed 2.2 {times} 10{sup 5} cells cm{sup 3} of sediment{sup {minus}1}, in the 0- to 5-mm depth horizon, capable of growth on DMS as the sole source of energy. An obligately chemolithoautotrophic bacillus designated strain T5 was isolated from the top layer of the marine sediment. Continuous culture studies in which DMS was the growth-limiting substrate revealed a maximum specific growth rate of 0.10 h{sup {minus}1} and a saturation constant of 90 {mu}mol liter{sup {minus}1} for aerobic growth on this substrate.

  4. Molecular characterization of the nonphotosynthetic partner bacterium in the consortium "Chlorochromatium aggregatum".

    PubMed

    Kanzler, Birgit E M; Pfannes, Kristina R; Vogl, Kajetan; Overmann, Jörg

    2005-11-01

    Phototrophic consortia represent valuable model systems for the study of signal transduction and coevolution between different bacteria. The phototrophic consortium "Chlorochromatium aggregatum" consists of a colorless central rod-shaped bacterium surrounded by about 20 green-pigmented epibionts. Although the epibiont was identified as a member of the green sulfur bacteria, and recently isolated and characterized in pure culture, the central colorless bacterium has been identified as a member of the beta-Proteobacteria but so far could not be characterized further. In the present study, "C. aggregatum" was enriched chemotactically, and the 16S rRNA gene sequence of the central bacterium was elucidated. Based on the sequence information, fluorescence in situ hybridization probes targeting four different regions of the 16S rRNA were designed and shown to hybridize exclusively to cells of the central bacterium. Phylogenetic analyses of the 1,437-bp-long sequence revealed that the central bacterium of "C. aggregatum" represents a so far isolated phylogenetic lineage related to Rhodoferax spp., Polaromonas vacuolata, and Variovorax paradoxus within the family Comamonadaceae. The majority of relatives of this lineage are not yet cultured and were found in low-temperature aquatic environments or aquatic environments containing xenobiotica or hydrocarbons. In CsCl-bisbenzimidazole equilibrium density gradients, genomic DNA of the central bacterium of "Chlorochromatium aggregatum" formed a distinct band which could be detected by quantitative PCR using specific primers. Using this method, the G+C content of the central bacterium was determined to be 55.6 mol%.

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

    PubMed Central

    Quelas, J. I.; Mesa, S.; Mongiardini, E. J.; Jendrossek, D.

    2016-01-01

    ABSTRACT 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

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

    PubMed

    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

  7. Studying the Transfer of Optical Orbital Angular Momentum to a Helical Bacterium

    NASA Astrophysics Data System (ADS)

    Davis, Dana; Horton, Timothy; Reichman, Steven; Link, Justin; Schmitzer, Heidrun; Robbins, Jennifer; Engle, Dorothy

    2014-03-01

    The purpose of this research is to study how the angular momentum of an optical vortex created by a 1064 nm laser is transferred to a helical shaped bacterium. When under the influence of a laser in optical tweezers, the helical shape of the bacteria causes it to spin in the trap. A spatial light modulator reshapes the beam and is twisted either into a left handed or right handed helix. This results in an optical vortex with a diameter which can be adjusted from roughly half a micron to three microns. The rotational speed of a helical bacterium in this type of optical trap should depend on the handedness of the vortex and the handedness of the bacterium being tweezed. When both the tweezing beam and the bacterium have the same handedness, a slight reduction in rotational speed should be observed; when the tweezing beam has the opposite handedness of the bacterium, a slight increase in rotational speed should be expected. We present our first experiments with magnetospirillum magnetotacticum and rhodospirillum rubrum.

  8. A plant growth-promoting bacterium that decreases nickel toxicity in seedlings

    SciTech Connect

    Burd, G.I.; Dixon, D.G.; Glick, B.R.

    1998-10-01

    A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni{sup 2+}, Pb{sup 2+}, Zn{sup 2+}, and CrO{sub 4}{sup {minus}}, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence of K. ascorbata SUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.

  9. Proposal of six species of moderately thermophilic, acidophilic, endospore-forming bacteria: Alicyclobacillus contaminans sp. nov., Alicyclobacillus fastidiosus sp. nov., Alicyclobacillus kakegawensis sp. nov., Alicyclobacillus macrosporangiidus sp. nov., Alicyclobacillus sacchari sp. nov. and Alicyclobacillus shizuokensis sp. nov.

    PubMed

    Goto, Keiichi; Mochida, Kaoru; Kato, Yuko; Asahara, Mika; Fujita, Rieko; An, Sun-Young; Kasai, Hiroaki; Yokota, Akira

    2007-06-01

    Moderately thermophilic, acidophilic, spore-forming bacteria (146 strains) were isolated from various beverages and environments. Based on the results of sequence analysis of the hypervariable region of the 16S rRNA gene, eight of the strains represent novel species of the genus Alicyclobacillus. These strains were designated 3-A191(T), 4-A336(T), 5-A83J(T), 5-A167N, 5-A239-2O-A(T), E-8, RB718(T) and S-TAB(T). Phylogenetic analyses of 16S rRNA and DNA gyrase B subunit (gyrB) nucleotide sequences confirmed that the eight strains belonged to the Alicyclobacillus clade. Cells of the eight strains were Gram-positive or Gram-variable, strictly aerobic and rod-shaped. The strains grew well under acidic and moderately thermal conditions, produced acid from various sugars, contained menaquinone 7 as the major isoprenoid quinone and did not produce guaiacol. omega-Alicyclic fatty acids were the predominant lipid component of strains 4-A336(T), 5-A83J(T), 5-A167N, RB718(T) and S-TAB(T). No omega-alicyclic fatty acids were detected in strains 3-A191(T), 5-A239-2O-A(T) or E-8, but iso- and anteiso-branched fatty acids and small amounts of straight-chain saturated fatty acids were detected instead. According to the DNA-DNA hybridization data and distinct morphological, physiological, chemotaxonomical and genetic traits, the eight strains represent six novel species within the genus Alicyclobacillus, for which the following names are proposed: Alicyclobacillus contaminans sp. nov. (type strain 3-A191(T)=DSM 17975(T)=IAM 15224(T)), Alicyclobacillus fastidiosus sp. nov. (type strain S-TAB(T)=DSM 17978(T)=IAM 15229(T)), Alicyclobacillus kakegawensis sp. nov. (type strain 5-A83J(T)=DSM 17979(T)=IAM 15227(T)), Alicyclobacillus macrosporangiidus sp. nov. (type strain 5-A239-2O-A(T)=DSM 17980(T)=IAM 15370(T)), Alicyclobacillus sacchari sp. nov. (type strain RB718(T)=DSM 17974(T)=IAM 15230(T)) and Alicyclobacillus shizuokensis sp. nov. (type strain 4-A336(T)=DSM 17981(T)=IAM 15226(T)).

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

    PubMed Central

    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

  11. Anaerobic Degradation of Cyanuric Acid, Cysteine, and Atrazine by a Facultative Anaerobic Bacterium

    PubMed Central

    Jessee, J. A.; Benoit, R. E.; Hendricks, A. C.; Allen, G. C.; Neal, J. L.

    1983-01-01

    A facultative anaerobic bacterium that rapidly degrades cyanuric acid (CA) was isolated from the sediment of a stream that received industrial wastewater effluent. CA decomposition was measured throughout the growth cycle by using a high-performance liquid chromatography assay, and the concomitant production of ammonia was also measured. The bacterium used CA or cysteine as a major, if not the sole, carbon and energy source under anaerobic, but not aerobic, conditions in a defined medium. The cell yield was greatly enhanced by the simultaneous presence of cysteine and CA in the medium. Cysteine was preferentially used rather than CA early in the growth cycle, but all of the CA was used without an apparent lag after the cysteine was metabolized. Atrazine was also degraded by this bacterium under anaerobic conditions in a defined medium. PMID:16346187

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

    SciTech Connect

    Xie, Gary; Dalin, Eileen; Tice, Hope; Chertkov, Olga; Land, Miriam L

    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.

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

    SciTech Connect

    Rhee, Mun Su; Moritz, Brelan E.; Xie, Gary; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Chertkov, Olga; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Pitluck, Sam; Land, Miriam L; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, Keelnathan T.

    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.

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

    PubMed

    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

    2011-12-31

    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.

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

    USGS Publications Warehouse

    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.

  16. Investigations of Iron Minerals Formed by Dissimilatory Alkaliphilic Bacterium with {sup 57}Fe Moessbauer Spectroscopy

    SciTech Connect

    Chistyakova, N. I.; Rusakov, V. S.; Shapkin, A. A.; Zhilina, T. N.; Zavarzina, D. G.; Kohout, J.

    2010-07-13

    Anaerobic alkaliphilic bacterium of Geoalkalibacter ferrihydriticus type (strain Z-0531), isolated from a bottom sediment sample from the weakly mineralized soda Lake Khadyn, have been analyzed. The strain uses the amorphous Fe(III)-hydroxide (AFH) as an electron acceptor and acetate CH{sub 3}COO{sup -} as an electron donor. Moessbauer investigations of solid phase samples obtained during the process of the bacterium growth were carried out at room temperature, 77.8 K, 4.2 K without and with the presence of an external magnetic field (6 T) applied perpendicular to the {gamma}-bebam.

  17. Expression of the Bacillus thuringiensis mosquitocidal toxin Cry11Aa in the aquatic bacterium Asticcacaulis excentricus.

    PubMed

    Armengol, Gemma; Guevara, Oscar Enrique; Orduz, Sergio; Crickmore, Neil

    2005-12-01

    A mosquitocidal aquatic bacterium has been developed by introducing an operon containing the cry11Aa, and p20 genes from Bacillus thuringiensis subsp. israelensis (Bti) into the gram-negative aquatic bacterium Asticcacaulis excentricus. After transformation, the cry11Aa gene was successfully expressed in recombinant A. excentricus under the tac promoter, at the level of 0.04 pg/cell. The recombinant bacteria were toxic to Aedes aegypti larvae with an LC(50) of 6.83 x 10(5) cells/mL. We believe that these bacteria may have potential as genetically engineered microorganisms for the control of mosquito larvae.

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

    PubMed

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

    1996-07-01

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

  19. Description of a new anaerobic thermophilic bacterium, Thermoanaerobacterium butyriciformans sp. nov.

    PubMed

    López, G; Cañas-Duarte, S J; Pinzón-Velasco, A M; Vega-Vela, N E; Rodríguez, M; Restrepo, S; Baena, S

    2017-03-01

    Strain USBA-019(T), an anaerobic and thermophilic strain, was identified as a new member of the genus Thermoanaerobacterium. USBA-019(T) cells are gram-positive, strictly anaerobic, thermophilic, chemoorganotrophic, moderately acidophilic, non-motile, endospore-forming, slightly curved, and rod-shaped. Cells measure 0.4×3.0-7.0μm. Optimal growth occurs at 50-55°C (35-65°C). Optimum pH is 5.0-5.5 (4.0-8.5). Thiosulfate, elemental sulfur and nitrate were utilized as electron acceptors. Fermentation of glucose, lactose, cellobiose, galactose, arabinose, xylose, starch and xylan primarily produced acetate and butyrate. Xylan, starch and cellobiose produced ethanol and starch, cellobiose, galactose, arabinose and mannose produced lactic acid. Phylogenetic analyses based on 16S rRNA gene sequence comparison and genomic relatedness indices show the close relation of USBA-019(T) to Thermoanaerobacterium thermostercoris and Thermoanaerobacterium aotearoense (similarity value: 99%). Hybridization of USBA-019(T), Th. thermostercoris DSM22141(T) and Th. aotearoense DMS10170(T) found DNA-DNA relatedness of 33.2% and 18.2%, respectively. Based on phenotypic, chemotaxonomic and phylogenetic evidence, along with low identity at whole genome level, USBA-019(T) is a novel species of the genus Thermoanaerobacterium which we propose to name Thermoanaerobacterium butyriciformans sp. nov. The type strain is USBA-019(T) (=CMPUJ U-019(T)=DSM 101588(T)).

  20. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

    PubMed Central

    Sorokin, Dimitry Y; Lücker, Sebastian; Vejmelkova, Dana; Kostrikina, Nadezhda A; Kleerebezem, Robbert; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Le Paslier, Denis; Muyzer, Gerard; Wagner, Michael; van Loosdrecht, Mark C M; Daims, Holger

    2012-01-01

    Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25–63 °C) and low affinity for nitrite (Ks=1 mℳ), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO2, and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO2 fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems. PMID:22763649

  1. Cadherin Domains in the Polysaccharide-Degrading Marine Bacterium Saccharophagus degradans 2-40 Are Carbohydrate-Binding Modules▿

    PubMed Central

    Fraiberg, Milana; Borovok, Ilya; Bayer, Edward A.; Weiner, Ronald M.; Lamed, Raphael

    2011-01-01

    The complex polysaccharide-degrading marine bacterium Saccharophagus degradans strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium. PMID:21036994

  2. Cadherin domains in the polysaccharide-degrading marine bacterium Saccharophagus degradans 2-40 are carbohydrate-binding modules.

    PubMed

    Fraiberg, Milana; Borovok, Ilya; Bayer, Edward A; Weiner, Ronald M; Lamed, Raphael

    2011-01-01

    The complex polysaccharide-degrading marine bacterium Saccharophagus degradans strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium.

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

    PubMed Central

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

    2013-01-01

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

  4. Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties

    PubMed Central

    El Kafsi, Hela; Binesse, Johan; Loux, Valentin; Buratti, Julien; Boudebbouze, Samira; Dervyn, Rozenn; Hammani, Amal; Maguin, Emmanuelle

    2014-01-01

    Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory properties both in vitro and in vivo. Here, we report the genome sequence of this bacterium, which appears to contain no less than 215 insertion sequence (IS) elements, an exceptionally high number regarding the small genome size of the strain. PMID:25035318

  5. Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium “Candidatus Brocadia sp. 40”

    PubMed Central

    Ali, Muhammad; Haroon, Mohamed Fauzi; Narita, Yuko; Zhang, Lei; Rangel Shaw, Dario; Okabe, Satoshi

    2016-01-01

    The anaerobic ammonium-oxidizing (anammox) bacterium “Candidatus Brocadia sp. 40” demonstrated the fastest growth rate compared to others in this taxon. Here, we report the 2.93-Mb draft genome sequence of this bacterium, which has 2,565 gene-coding regions, 41 tRNAs, and a single rrn operon. PMID:27932661

  6. Robinsoniella peoriensis: A model anaerobic commensal bacterium for acquisition of antibiotic resistance?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: R. peoriensis was characterized in our laboratories from swine manure and feces as a Gram-positive, anaerobic bacterium. Since then strains of this species have been identified from a variety of mammalian and other gastrointestinal (GI) tracts, suggesting it is a member of the commensal ...

  7. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower

    PubMed Central

    Ambrosini, Adriana; Sant’Anna, Fernando Hayashi; de Souza, Rocheli; Tadra-Sfeir, Michele; Faoro, Helisson; Alvarenga, Samuel M.; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi

    2015-01-01

    Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake. PMID:25838494

  8. Draft Genome Sequence of a Benzo[a]pyrene-Degrading Bacterium, Olleya sp. Strain ITB9

    PubMed Central

    Okai, Masahiko; Watanabe, Akihiro; Ishida, Masami

    2015-01-01

    Olleya sp. ITB9 is a benzo[a]pyrene-degrading bacterium, isolated from surface water near a waste treatment plant at Tokyo Bay, Japan. Here, we present the draft genome sequence of this strain, which consists of 58 contigs corresponding to 3.4 Mb and a G+C content of 31.2%. PMID:26564047

  9. Fluoroacetate biosynthesis from the marine-derived bacterium Streptomyces xinghaiensis NRRL B-24674.

    PubMed

    Huang, Sheng; Ma, Long; Tong, Ming Him; Yu, Yi; O'Hagan, David; Deng, Hai

    2014-07-21

    Genome sequencing identified a fluorinase gene in the marine bacterium Streptomyces xinghaiensis NRRL B-24674. Fermentation of the organism with inorganic fluoride (2 mM) demonstrated that the organism could biosynthesise fluoroacetate and that fluoroacetate production is sea-salt dependent. This is the first fluorometabolite producing microorganism identified from the marine environment.

  10. Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium

    PubMed Central

    Jin, Decai; Zhu, Ying; Wang, Xinxin; Kong, Xiao; Liu, Huijun; Wang, Yafeng

    2016-01-01

    Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we report the 5.1-Mb draft genome sequence of this strain, which will provide insights into the diversity of Sphingobium spp. and the mechanism of phthalate ester degradation in the estuary. PMID:27313307

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

    PubMed

    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.

  12. Genome Sequence of Agrobacterium tumefaciens Strain F2, a Bioflocculant-Producing Bacterium

    PubMed Central

    Li, Ang; Geng, Jianing; Cui, Di; Shu, Chang; Zhang, Si; Yang, Jixian; Xing, Jie; Wang, Jinna; Ma, Fang; Hu, Songnian

    2011-01-01

    Agrobacterium tumefaciens F2 is an efficient bioflocculant-producing bacterium. But the genes related to the metabolic pathway of bioflocculant biosynthesis in strain F2 are unknown. We present the draft genome of A. tumefaciens F2. It could provide further insight into the biosynthetic mechanism of polysaccharide-like bioflocculant in strain F2. PMID:21914861

  13. Genome sequence of Agrobacterium tumefaciens strain F2, a bioflocculant-producing bacterium.

    PubMed

    Li, Ang; Geng, Jianing; Cui, Di; Shu, Chang; Zhang, Si; Yang, Jixian; Xing, Jie; Wang, Jinna; Ma, Fang; Hu, Songnian

    2011-10-01

    Agrobacterium tumefaciens F2 is an efficient bioflocculant-producing bacterium. But the genes related to the metabolic pathway of bioflocculant biosynthesis in strain F2 are unknown. We present the draft genome of A. tumefaciens F2. It could provide further insight into the biosynthetic mechanism of polysaccharide-like bioflocculant in strain F2.

  14. Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

    PubMed Central

    Liu, Jin-liang; Hu, Xiao-min

    2013-01-01

    Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

  15. Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9.

    PubMed

    Jiang, Bin-Hui; Liu, Jin-Liang; Hu, Xiao-Min

    2013-04-25

    Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus.

  16. Complete Genome Sequence of Pseudomonas aeruginosa FA-HZ1, an Efficient Dibenzofuran-Degrading Bacterium

    PubMed Central

    Ali, Fawad; Hu, Haiyang; Xu, Ping

    2017-01-01

    ABSTRACT Pseudomonas sp. FA-HZ1, an efficient dibenzofuran-degrading bacterium, was isolated from landfill leachate. Here, we present the complete genome sequence of strain FA-HZ1, which contains only one circular chromosome. The complete genome sequence will be essential for revealing the molecular mechanisms of dibenzofuran degradation. PMID:28209830

  17. Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1

    PubMed Central

    Lai, Qiliang; Li, Weiwei; Wang, Baojiang; Yu, Zhiwei

    2012-01-01

    Cycloclasticus sp. strain P1 was isolated from deep-sea sediments of the Pacific Ocean and characterized as a unique bacterium in the degradation of pyrene, a four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete genome of P1 and genes associated with PAH degradation. PMID:23144416

  18. Genome Sequence of Pseudomonas citronellolis SJTE-3, an Estrogen- and Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

    PubMed Central

    Zheng, Daning; Wang, Xiuli; Wang, Pingping; Peng, Wanli; Ji, Nannan

    2016-01-01

    Pseudomonas citronellolis SJTE-3, isolated from the active sludge of a wastewater treatment plant in China, can utilize a series of environmental estrogens and estrogen-like toxicants. Here, we report its whole-genome sequence, containing one circular chromosome and one circular plasmid. Genes involved in estrogen biodegradation in this bacterium were predicted. PMID:27932659

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

    PubMed Central

    Yang, Jhung-Ahn; Kwon, Kae Kyoung

    2017-01-01

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

  20. Complete genome sequence of the haloalkaliphilic, hydrogen-producing bacterium Halanaerobium hydrogeniformans.

    PubMed

    Brown, Steven D; Begemann, Matthew B; Mormile, Melanie R; Wall, Judy D; Han, Cliff S; Goodwin, Lynne A; Pitluck, Samuel; Land, Miriam L; Hauser, Loren J; Elias, Dwayne A

    2011-07-01

    Halanaerobium hydrogenoformans is an alkaliphilic bacterium capable of biohydrogen production at pH 11 and 7% (wt/vol) salt. We present the 2.6-Mb genome sequence to provide insights into its physiology and potential for bioenergy applications.

  1. Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing Bacterium.

    PubMed

    Regar, Raj Kumar; Gaur, Vivek Kumar; Mishra, Gayatri; Jadhao, Sudhir; Kamthan, Mohan; Manickam, Natesan

    2016-03-03

    We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to form indigo by utilizing indole as the sole carbon source. The Alcaligenes species is increasingly reported for biodegradation of diverse toxicants and thus complete sequencing may provide insight into biodegradation capabilities and other phenotypes.

  2. Complete Genome Sequence of Sphingomonas sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium

    PubMed Central

    Zhu, Xiongyu; Wang, Weiwei; Xu, Ping

    2016-01-01

    Sphingomonas sp. strain NIC1, an efficient nicotine-degrading bacterium, was isolated from tobacco leaves. Here, we present the complete genome sequence of strain NIC1, which contains one circular chromosome and two circular plasmids. The genomic information will provide insights into its molecular mechanism for nicotine degradation. PMID:27417841

  3. Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential.

    PubMed

    Zhang, Xiaobo; Zhao, Chungui; Hong, Xuan; Chen, Shicheng; Yang, Suping

    2016-05-05

    The draft genome sequence of Marichromatium gracile YL-28 contains 3,840,251 bp, with a G+C content of 68.84%. The annotated genome sequence provides the genetic basis for revealing its role as a purple sulfur bacterium in the harvesting of energy and the development of bioremediation applications.

  4. Genome Sequence of the Butyrate-Producing Anaerobic Bacterium Anaerostipes hadrus PEL 85.

    PubMed

    Kant, Ravi; Rasinkangas, Pia; Satokari, Reetta; Pietilä, Taija E; Palva, Airi

    2015-04-02

    Anaerostipes hadrus PEL 85, which was isolated from human feces, is a Gram-positive rod-shaped bacterium. The species may play an important role in gut health, as it was previously reported to produce butyric acid. Here, we present the genome assembly of PEL 85, a novel strain of A. hadrus.

  5. Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium

    PubMed Central

    Rahman, Aminur; Nahar, Noor; Olsson, Björn

    2016-01-01

    Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated from the landfills of tannery industries in Bangladesh. Here, we investigated its genetic composition using massively parallel sequencing and comparative analysis with other known Enterobacter genomes. Assembly of the sequencing reads revealed a genome of ~4.21 Mb in size. PMID:27257201

  6. Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium.

    PubMed

    Rahman, Aminur; Nahar, Noor; Olsson, Björn; Mandal, Abul

    2016-06-02

    Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated from the landfills of tannery industries in Bangladesh. Here, we investigated its genetic composition using massively parallel sequencing and comparative analysis with other known Enterobacter genomes. Assembly of the sequencing reads revealed a genome of ~4.21 Mb in size.

  7. Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.

    PubMed

    Yong, Delicia; Ee, Robson; Lim, Yan-Lue; Yu, Choo-Yee; Ang, Geik-Yong; How, Kah-Yan; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

    2016-01-10

    Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.

  8. Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571(T).

    PubMed

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

    2015-06-20

    Pandoraea vervacti DSM 23571(T) is an oxalate metabolizing bacterium isolated from an uncultivated field soil in Mugla, Turkey. Here, we present the first complete genome sequence of P. vervacti DSM 23571(T). A complete pathway for degradation of oxalate was revealed from the genome analysis. These data are important to path new opportunities for genetic engineering in the field of biotechnology.

  9. Complete genome sequence of the xylan-degrading subseafloor bacterium Microcella alkaliphila JAM-AC0309.

    PubMed

    Kurata, Atsushi; Hirose, Yuu; Misawa, Naomi; Wakazuki, Sachiko; Kishimoto, Noriaki; Kobayashi, Tohru

    2016-03-10

    Here we report the complete genome sequence of Microcella alkaliphila JAM-AC0309, which was newly isolated from the deep subseafloor core sediment from offshore of the Shimokita Peninsula of Japan. An array of genes related to utilization of xylan in this bacterium was identified by whole genome analysis.

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

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

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

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

  12. Study on EDTA-degrading bacterium Burkholderia cepacia YL-6 for bioaugmentation.

    PubMed

    Chen, Shih-Chin; Chen, Szu-Lin; Fang, Hung-Yuan

    2005-11-01

    Bioaugmentation production of EDTA-degrading bacterium Burkholderia cepacia YL-6 was carried out in an aerobic fermentor. Three different carbon sources (ferric-ethylenediaminetetraacetate (Fe-EDTA), potassium acetate, and ethylamine) were used. The bacterium cultivated with Fe-EDTA and maintained in the growth phase could reach the maximum cell concentration on the 38th day. Whereas, the bacterium cultivated with potassium acetate and ethylamine reach the maximum cell concentration at the 76th and 100th hour. The viable-cell counts of the augmentation agents made by feeding Fe-EDTA, potassium acetate, and ethylamine were 8.2x10(10), 6.8x10(11), and 4.3x10(11) CFU/g agent, respectively. The EDTA-degradation time required for the afore-mentioned bioaugmentation agents made by feeding various carbon sources lay in the following order: ethylaminebacterium B. cepacia YL-6.

  13. The construction of an engineered bacterium to remove cadmium from wastewater.

    PubMed

    Chang, S; Shu, H

    2014-01-01

    The removal of cadmium (Cd) from wastewater before it is released from factories is important for protecting human health. Although some researchers have developed engineered bacteria, the resistance of these engineered bacteria to Cd have not been improved. In this study, two key genes involved in glutathione synthesis (gshA and gshB), a serine acetyltransferase gene (cysE), a Thlaspi caerulescens phytochelatin synthase gene (TcPCS1), and a heavy metal ATPase gene (TcHMA3) were transformed into Escherichia coli BL21. The resistance of the engineered bacterium to Cd was significantly greater than that of the initial bacterium and the Cd accumulation in the engineered bacterium was much higher than in the initial bacterium. In addition, the Cd resistance of the bacteria harboring gshB, gshA, cysE, and TcPCS1 was higher than that of the bacteria harboring gshA, cysE, and TcPCS1. This finding demonstrated that gshB played an important role in glutathione synthesis and that the reaction catalyzed by glutathione synthase was the limiting step for producing phytochelatins. Furthermore, TcPCS1 had a greater specificity and a higher capacity for removing Cd than SpPCS1, and TcHMA3 not only played a role in T. caerulescens but also functioned in E. coli.

  14. Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tannins are plant-produced organic compounds that are found in soils, are able to sequester iron, and have antimicrobial properties. We studied the effect of tannic acid on the molecular physiology of the soil-inhabiting biocontrol bacterium Pseudomonas protegens Pf-5 (formerly Pseudomonas fluoresce...

  15. Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T

    PubMed Central

    Castillo Villamizar, Genis Andrés

    2016-01-01

    Here, we report the draft genome sequence of Moorella mulderi DSM 14980T, a thermophilic acetogenic bacterium, which is able to grow autotrophically on H2 plus CO2 using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.99 Mb). PMID:27231372

  16. Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium

    PubMed Central

    Ho, Ying-Ning

    2015-01-01

    An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has shown its abilities for both in planta biocontrol and plant growth promotion. Its draft genome sequence was determined to provide insights into those metabolic pathways involved in plant-beneficial activity. This is the first genome report for endophytic B. cenocepacia. PMID:26564046

  17. Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.

    PubMed

    Ho, Ying-Ning; Huang, Chieh-Chen

    2015-11-12

    An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has shown its abilities for both in planta biocontrol and plant growth promotion. Its draft genome sequence was determined to provide insights into those metabolic pathways involved in plant-beneficial activity. This is the first genome report for endophytic B. cenocepacia.

  18. Response to comments on "A bacterium that can grow using arsenic instead of phosphorus"

    USGS Publications Warehouse

    Wolfe-Simon, Felisa; Blum, Jodi Switzer; 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.

    2011-01-01

    Concerns have been raised about our recent study suggesting that arsenic (As) substitutes for phosphorus in major biomolecules of a bacterium that tolerates extreme As concentrations. We welcome the opportunity to better explain our methods and results and to consider alternative interpretations. We maintain that our interpretation of As substitution, based on multiple congruent lines of evidence, is viable.

  19. Genome sequence of the mycorrhizal helper bacterium Pseudomonas fluorescens BBc6R8

    SciTech Connect

    Deveau, Aurelie; Grob, Harald; Morin, Emmanuelle; Karpinets, Tatiana V; Utturkar, Sagar M; Mehnaz, Samina; Kurz, Sven; Martin, Francis; Frey-Klett, Pascale; Labbe, Jessy L

    2014-01-01

    We report the draft genome sequence of the mycorrhiza helper bacterium Pseudomonas fluorescens strain BBc6R8 . Several traits which could be involved in the mycorrhiza helper ability of the bacterial strain such as multiple secretion systems, auxin metabolism and phosphate mobilization were evidenced in the genome.

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

    PubMed Central

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

    2016-01-01

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

  1. Complete genome sequence of a novel chlorpyrifos degrading bacterium, Cupriavidus nantongensis X1.

    PubMed

    Fang, Lian-Cheng; Chen, Yi-Fei; Zhou, Yan-Long; Wang, Dao-Sheng; Sun, Le-Ni; Tang, Xin-Yun; Hua, Ri-Mao

    2016-06-10

    Cupriavidus nantongensis X1 is a chlorpyrifos degrading bacterium, which was isolated from sludge collected at the drain outlet of a chlorpyrifos manufacture plant. It is the first time to report the complete genome sequence of C. nantongensis species, which has been reported as a novel species of Cupriavidus genus. It could provide further pathway information in chlorpyrifos degradation.

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

    PubMed Central

    Albertsen, Mads

    2017-01-01

    ABSTRACT 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. PMID:28254969

  3. Genome Sequence of the Acetogenic Bacterium Acetobacterium wieringae DSM 1911T

    PubMed Central

    Schiel-Bengelsdorf, Bettina; Daniel, Rolf

    2016-01-01

    Here, we report the draft genome sequence of Acetobacterium wieringae DSM 1911T, an anaerobic, autotrophic, acetogenic, d,l-lactate-utilizing bacterium. The genome consists of a chromosome (3.88 Mb) and 3,620 predicted protein-encoding genes. PMID:28007862

  4. Draft genome sequence of ‘Candidatus Phytoplasma pruni’ strain CX, a plant pathogenic bacterium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Candidatus Phytoplasma pruni’ strain CX, belonging to subgroup 16SrIII-A, is a plant pathogenic bacterium causing economically important diseases in many fruit crops. Here we report the draft genome sequence that consists of 598,508 bases, with a G+C content of 27.21 mol%. ...

  5. Genome Sequence of a Strain of the Human Pathogenic Bacterium Pseudomonas alcaligenes That Caused Bloodstream Infection.

    PubMed

    Suzuki, Masato; Suzuki, Satowa; Matsui, Mari; Hiraki, Yoichi; Kawano, Fumio; Shibayama, Keigo

    2013-10-31

    Pseudomonas alcaligenes, a Gram-negative aerobic bacterium, is a rare opportunistic human pathogen. Here, we report the whole-genome sequence of P. alcaligenes strain MRY13-0052, which was isolated from a bloodstream infection in a medical institution in Japan and is resistant to antimicrobial agents, including broad-spectrum cephalosporins and monobactams.

  6. Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

    DOE PAGES

    Thiel, Vera; Tomsho, Lynn P.; Burhans, Richard; ...

    2015-03-26

    The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus ruber strain A, isolated from a cyanobacterial enrichment culture obtained from Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170 contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding genes, and 2 rRNA operons.

  7. Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes).

    PubMed

    Thiel, Vera; Hamilton, Trinity L; Tomsho, Lynn P; Burhans, Richard; Gay, Scott E; Ramaley, Robert F; Schuster, Stephan C; Steinke, Laurey; Bryant, Donald A

    2014-08-28

    The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes), isolated from Octopus Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in 35 contigs. The draft genome is predicted to encode 2,457 protein coding genes and 37 tRNA encoding genes and two rRNA operons.

  8. Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium

    PubMed Central

    Joshi, M. N.; Sharma, A. C.; Pandya, R. V.; Patel, R. P.; Saiyed, Z. M.; Saxena, A. K.

    2012-01-01

    Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

  9. Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber

    PubMed Central

    Antón, Josefa; Peña, Arantxa; Santos, Fernando; Martínez-García, Manuel; Schmitt-Kopplin, Philippe; Rosselló-Mora, Ramon

    2008-01-01

    Since its discovery in 1998, representatives of the extremely halophilic bacterium Salinibacter ruber have been found in many hypersaline environments across the world, including coastal and solar salterns and solar lakes. Here, we review the available information about the distribution, abundance and diversity of this member of the Bacteroidetes. PMID:18957079

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

    PubMed

    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.

  11. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome

    PubMed Central

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E.; Dong, Qunfeng

    2015-01-01

    We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile. We consider this genome sequence to be a molecular tool for exploring microbial relationships and adaptation strategies to the prevailing extreme conditions at the Atacama Desert. PMID:26294639

  12. Draft Genome Sequence of the Fast-Growing Bacterium Vibrio natriegens Strain DSMZ 759

    PubMed Central

    Maida, Isabel; Bosi, Emanuele; Perrin, Elena; Papaleo, Maria Cristiana; Orlandini, Valerio; Fondi, Marco; Fani, Renato; Wiegel, Juergen; Bianconi, Giovanna

    2013-01-01

    Vibrio natriegens is a Gram-negative bacterium known for its extremely short doubling time. Here we present the annotated draft genome sequence of Vibrio natriegens strain DSMZ 759, with the aim of providing insights about its high growth rate. PMID:23969053

  13. Complete genome sequence of the cellulose-degrading bacterium Cellulosilyticum lentocellum.

    PubMed

    Miller, David A; Suen, Garret; Bruce, David; Copeland, Alex; Cheng, Jan-Feng; Detter, Chris; Goodwin, Lynne A; Han, Cliff S; Hauser, Loren J; Land, Miriam L; Lapidus, Alla; Lucas, Susan; Meincke, Linda; Pitluck, Sam; Tapia, Roxanne; Teshima, Hazuki; Woyke, Tanja; Fox, Brian G; Angert, Esther R; Currie, Cameron R

    2011-05-01

    Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium, which was originally isolated from estuarine sediment of a river that received both domestic and paper mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors that influence degradation rates.

  14. Draft Genome Sequence of a Thermophilic Desulfurization Bacterium, Geobacillus thermoglucosidasius Strain W-2

    PubMed Central

    Zhu, Lin; Li, Mingchang; Guo, Shuyi

    2016-01-01

    Geobacillus thermoglucosidasius strain W-2 is a thermophilic bacterium isolated from a deep-subsurface oil reservoir in northern China, which is capable of degrading organosulfur compounds. Here, we report the draft genome sequence of G. thermoglucosidasius strain W-2, which may help to elucidate the genetic basis of biodegradation of organosulfur pollutants under heated conditions. PMID:27491977

  15. Draft Genome Sequence of Potato ‘Zebra Chip’ Associated Bacterium ‘Candidatus Liberibacter solanacearum’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species of Candidatus Liberibacter, ‘Ca. L. solanacearum’ (Lso) was recently confirmed to be associated with potato zebra chip (ZC) disease. The bacterium belongs to gram negative, phloem-limited, a-Proteobacteria. Because Koch’s postulates have not been fulfilled, information regarding the et...

  16. Bacillus amyloliquefaciens: a mosquitocidal bacterium from mangrove forests of Andaman & Nicobar islands, India.

    PubMed

    Geetha, I; Manonmani, A M; Prabakaran, G

    2011-12-01

    Samples collected from the mangrove forests of Andaman & Nicobar islands yielded a mosquitocidal bacterium, whose extracellular metabolite(s) exhibited mosquito larvicidal and pupicidal activity. The bacterium was isolated using standard microbiological methods and identified using classical biochemical tests and rpoB gene sequences. The mosquitocidal bacterium was identified as Bacillus amyloliquefaciens. Mosquitocidal metabolite(s) was separated from the culture supernatant of the bacterium and its efficacy against the larval and pupal stages of different species of mosquitoes was determined in terms of LC(50) and LC(90). Mosquito larvicidal activity in terms of LC(50) against Anopheles stephensi, Culex quinquefasciatus and Aedes aegypti was respectively, 26.4μg, 22.2μg and 20.5μg/ml and its pupicidal activity was 4.4μg, 8.2μg and 14.5μg/ml respectively. The mosquitocidal metabolite(s) was found to be a biosurfactant. This is the first report of the mosquitocidal activity of B. amyloliquefaciens and it is a new weapon which can be added to the array of microbial agents for use against mosquitoes.

  17. Physiological characterization of an anaerobic ammonium-oxidizing bacterium belonging to the "Candidatus scalindua" group.

    PubMed

    Awata, Takanori; Oshiki, Mamoru; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi; Okabe, Satoshi

    2013-07-01

    The phylogenetic affiliation and physiological characteristics (e.g., Ks and maximum specific growth rate [μmax]) of an anaerobic ammonium oxidation (anammox) bacterium, "Candidatus Scalindua sp.," enriched from the marine sediment of Hiroshima Bay, Japan, were investigated. "Candidatus Scalindua sp." exhibits higher affinity for nitrite and a lower growth rate and yield than the known anammox species.

  18. Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum

    SciTech Connect

    Miller, David A; Suen, Garret; Bruce, David; Copeland, A; Cheng, Jan-Fang; Detter, J. Chris; Goodwin, Lynne A.; Han, Cliff; Hauser, Loren John; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Meincke, Linda; Pitluck, Sam; Tapia, Roxanne; Teshima, Hazuki; Woyke, Tanja; Fox, Brian G.; Angert, Esther R.; Currie, Cameron

    2011-01-01

    Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium; originally isolated from estuarine sediment of a river that received both domestic and paper mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors that influence degradation rates.

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

    PubMed Central

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

    2016-01-01

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

  20. Rhodovulum tesquicola sp. nov., a haloalkaliphilic purple non-sulfur bacterium from brackish steppe soda lakes.

    PubMed

    Kompantseva, Elena I; Komova, Anastasia V; Novikov, Andrey A; Kostrikina, Nadezhda A

    2012-12-01

    Two strains of purple non-sulfur bacteria (A-36s(T) and A-51s) were isolated from brackish steppe soda lakes of southern Siberia. Genetically, the isolates were related most closely to the type strains of Rhodovulum steppense and Rhodovulum strictum, from which they differed at the species level (98.5% 16S rRNA gene sequence similarity, 40-53% DNA-DNA relatedness). Cells of the two strains were ovoid to rod-shaped, 0.4-0.8 µm wide and 1.0-2.5 µm long, and motile by means of a polar flagellum. They contained internal photosynthetic membranes of vesicular type and photosynthetic pigments (bacteriochlorophyll a and carotenoids of the spheroidene series). The strains were obligate haloalkaliphiles, growing over wide ranges of salinity (0.3-10.0% NaCl) and pH (7.5-10.0), with growth optima at 1.0-3.0% NaCl and pH 8.5-9.0. Photoheterotrophic and chemoheterotrophic growth occurred with a number of organic compounds and biotin, p-aminobenzoate, thiamine and niacin as growth factors. No anaerobic respiration on nitrite, nitrate or fumarate and no fermentation were demonstrated. The strains grew photolithoautotrophically and chemolithoautotrophically with sulfide, sulfur and thiosulfate, oxidizing them to sulfate. Sulfide was oxidized via deposition of extracellular elemental sulfur. No growth with H(2) as the electron donor was observed. The major fatty acid was C(18:1) (78%). The major quinone was ubiquinone Q-10. The DNA G+C content of strain A-36s(T) was 65.4 mol% (T(m)). According to genotypic and phenotypic characteristics, the investigated strains were assigned to a novel species of the genus Rhodovulum, for which the name Rhodovulum tesquicola sp. nov. is proposed. The type strain is A-36s(T) ( = VKM B-2491(T) = ATCC BAA-1573(T)), which was isolated from steppe soda lake Sul'fatnoe (Zabaikal'skii Krai, southern Siberia, Russia).

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

    PubMed

    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.

  2. A Streamlined Strategy for Biohydrogen Production with Halanaerobium hydrogeniformans, an Alkaliphilic Bacterium.

    PubMed

    Begemann, Matthew B; Mormile, Melanie R; Sitton, Oliver C; Wall, Judy D; Elias, Dwayne A

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, lignocellulosic biohydrogen production remains inefficient with pretreatments that are heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobiumhydrogeniformans, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. hydrogeniformans ferments a variety of 5- and 6-carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen, acetate, and formate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  3. The bacterium Xenorhabdus nematophila inhibits phospholipases A2 from insect, prokaryote, and vertebrate sources

    NASA Astrophysics Data System (ADS)

    Park, Youngjin; Kim, Yonggyun; Stanley, David

    The bacterium, Xenorhabdus nematophila, is a virulent insect pathogen. Part of its pathogenicity is due to impairing cellular immunity by blocking biosynthesis of eicosanoids, the major recognized signal transduction system in insect cellular immunity. X. nematophila inhibits the first step in eicosanoid biosynthesis, phospholipase A2 (PLA2). Here we report that the bacterium inhibits PLA2 from two insect immune tissues, hemocytes and fat body, as well as PLA2s selected to represent a wide range of organisms, including prokaryotes, insects, reptiles, and mammals. Our finding on a bacterial inhibitor of PLA2 activity contributes new insight into the chemical ecology of microbe-host interactions, which usually involve actions rather than inhibitors of PLA2s.

  4. A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163.

    PubMed

    Mohedano, María de la Luz; Russo, Pasquale; de Los Ríos, Vivian; Capozzi, Vittorio; Fernández de Palencia, Pilar; Spano, Giuseppe; López, Paloma

    2014-02-26

    Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. Oenococcus oeni possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.

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

    PubMed

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

    2011-01-01

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

  6. Inflammasomes Coordinate Pyroptosis and Natural Killer Cell Cytotoxicity to Clear Infection by a Ubiquitous Environmental Bacterium.

    PubMed

    Maltez, Vivien I; Tubbs, Alan L; Cook, Kevin D; Aachoui, Youssef; Falcone, E Liana; Holland, Steven M; Whitmire, Jason K; Miao, Edward A

    2015-11-17

    Defective neutrophils in patients with chronic granulomatous disease (CGD) cause susceptibility to extracellular and intracellular infections. Microbes must first be ejected from intracellular niches to expose them to neutrophil attack, so we hypothesized that inflammasomes detect certain CGD pathogens upstream of neutrophil killing. Here, we identified one such ubiquitous environmental bacterium, Chromobacterium violaceum, whose extreme virulence was fully counteracted by the NLRC4 inflammasome. Caspase-1 protected via two parallel pathways that eliminated intracellular replication niches. Pyroptosis was the primary bacterial clearance mechanism in the spleen, but both pyroptosis and interleukin-18 (IL-18)-driven natural killer (NK) cell responses were required for liver defense. NK cells cleared hepatocyte replication niches via perforin-dependent cytotoxicity, whereas interferon-γ was not required. These insights suggested a therapeutic approach: exogenous IL-18 restored perforin-dependent cytotoxicity during infection by the inflammasome-evasive bacterium Listeria monocytogenes. Therefore, inflammasomes can trigger complementary programmed cell death mechanisms, directing sterilizing immunity against intracellular bacterial pathogens.

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

    PubMed

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

    2015-02-13

    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.

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

    PubMed

    Banerjee, Aulie; Supakar, Subhrangshu; Banerjee, Raja

    2014-01-01

    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 (13)C 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.

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

    PubMed Central

    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. PMID:27610355

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  11. The bacterium endosymbiont of Crithidia deanei undergoes coordinated division with the host cell nucleus.

    PubMed

    Motta, Maria Cristina Machado; Catta-Preta, Carolina Moura Costa; Schenkman, Sergio; de Azevedo Martins, Allan Cezar; Miranda, Kildare; de Souza, Wanderley; Elias, Maria Carolina

    2010-08-26

    In trypanosomatids, cell division involves morphological changes and requires coordinated replication and segregation of the nucleus, kinetoplast and flagellum. In endosymbiont-containing trypanosomatids, like Crithidia deanei, this process is more complex, as each daughter cell contains only a single symbiotic bacterium, indicating that the prokaryote must replicate synchronically with the host protozoan. In this study, we used light and electron microscopy combined with three-dimensional reconstruction approaches to observe the endosymbiont shape and division during C. deanei cell cycle. We found that the bacterium replicates before the basal body and kinetoplast segregations and that the nucleus is the last organelle to divide, before cytokinesis. In addition, the endosymbiont is usually found close to the host cell nucleus, presenting different shapes during the protozoan cell cycle. Considering that the endosymbiosis in trypanosomatids is a mutualistic relationship, which resembles organelle acquisition during evolution, these findings establish an excellent model for the understanding of mechanisms related with the establishment of organelles in eukaryotic cells.

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

    PubMed

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

    2003-02-01

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

  13. Copper-binding characteristics of exopolymers from a freshwater-sediment bacterium

    SciTech Connect

    Mittelman, M.W.; Geesey, G.G.

    1985-04-01

    Copper-binding activity by exopolymers from adherent cells of freshwater-sediment bacterium was demonstrated by a combination of equilibrium dialysis and flameless atomic absorption spectrometry. Crude, cell-free exopolymer preparations containing protein and polysaccharide components bound up to 37 nmol of Cu per mg (dry weight). A highly purified exopolysaccharide preparation bound up to 253 nmol of Cu per mg of carbohydrate. The conditional stability constant for the crude exopolymer-Cu complex was 7.3 x 10/sup 8/. This value was similar to those obtained for Cu complexes formed with humic acids and xanthan, an exopolysaccharide produced by Xanthomonas campestris. Studies conducted at copper concentrations, pHs, and temperatures found in sediments from which the bacterium was isolated indicated that the exopolymers were capable of binding copper under natural conditions.

  14. Discovery of clostrubin, an exceptional polyphenolic polyketide antibiotic from a strictly anaerobic bacterium.

    PubMed

    Pidot, Sacha; Ishida, Keishi; Cyrulies, Michael; Hertweck, Christian

    2014-07-21

    Genome mining of the strictly anaerobic bacterium Clostridium beijerinckii, an industrial producer of solvents, revealed the presence of several cryptic gene clusters for secondary metabolite biosynthesis. To unearth its metabolic potential, a C. beijerinckii strain was cultured under various conditions, which led to the discovery of a deep purple pigment. This novel metabolite, named clostrubin (1), was isolated and its structure was fully elucidated. The pentacyclic polyphenol features a benzo[a]tetraphene ring topology that is unprecedented for natural products. Stable-isotope labeling experiments showed that 1 is an aromatic polyketide that folds in a noncanonical manner to form the unusual perifused ring system. In addition to being the first reported polyketide from an anaerobic bacterium, 1 is a potent antibiotic with pronounced activity against various pathogenic bacteria, such as MRSA, VRE, and mycobacteria, with minimum inhibitory concentrations (MIC) of 0.12-0.97 μM.

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

    PubMed

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

    2015-07-20

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

  16. Effect of Tannic Acid on the Transcriptome of the Soil Bacterium Pseudomonas protegens Pf-5

    PubMed Central

    Lim, Chee Kent; Penesyan, Anahit; Hassan, Karl A.

    2013-01-01

    Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm formation, motility, and secondary metabolite biosynthesis in the soil- and rhizosphere-inhabiting bacterium Pseudomonas protegens Pf-5. PMID:23435890

  17. Draft genome sequence of a strictly anaerobic dichloromethane-degrading bacterium

    DOE PAGES

    Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina; ...

    2016-03-03

    Here, an anaerobic, dichloromethane-degrading bacterium affiliated with novel Peptococcaceae was maintained in a microbial consortium. The organism originated from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto Rico, in October 2009 (latitude 18°21'43.9", longitude –65°46'8.4"). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%.

  18. Draft genome sequence of a strictly anaerobic dichloromethane-degrading bacterium

    SciTech Connect

    Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina; Konstantinidis, Konstantinos T.; Mack, E. Erin; Loffler, Frank E.

    2016-03-03

    Here, an anaerobic, dichloromethane-degrading bacterium affiliated with novel Peptococcaceae was maintained in a microbial consortium. The organism originated from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto Rico, in October 2009 (latitude 18°21'43.9", longitude –65°46'8.4"). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%.

  19. Draft Genome Sequence of Pseudomonas frederiksbergensis SI8, a Psychrotrophic Aromatic-Degrading Bacterium

    PubMed Central

    Brown, Lisa M.; Striebich, Richard C.; Mueller, Susan S.; Gunasekera, Thusitha S.

    2015-01-01

    Pseudomonas frederiksbergensis strain SI8 is a psychrotrophic bacterium capable of efficient aerobic degradation of aromatic hydrocarbons. The draft genome of P. frederiksbergensis SI8 is 6.57 Mb in size, with 5,904 coding sequences and 60.5% G+C content. The isopropylbenzene (cumene) degradation pathway is predicted to be present in P. frederiksbergensis SI8. PMID:26184950

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

    PubMed

    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.

  1. Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine Bacterium.

    PubMed

    Yasuike, Motoshige; Nakamura, Yoji; Kai, Wataru; Fujiwara, Atushi; Fukui, Youhei; Satomi, Masataka; Sano, Motohiko

    2013-07-18

    Agarivorans albus is a Gram-negative, strictly aerobic, and agar-hydrolyzing marine bacterium. We present the draft genome sequence of the A. albus strain MKT 106(T), which is composed of 67 contigs (>500 bp) totaling 4,734,285 bp and containing 4,397 coding DNA sequences (CDSs), four rRNAs, and 64 tRNA sequences.

  2. Permanent draft genome of acetaldehyde degradation bacterium, Shewanella sp. YQH10.

    PubMed

    Liu, Yang; Shang, Xiexie; Zeng, Runying

    2015-02-01

    Shewanella sp. YQH10 isolated from mangrove sediment, was a novel species of Shewanella, which has the ability to degrade acetaldehyde. Here, we present an annotated draft genome sequence of Shewanella sp. YQH10, which contains 4,215,794 bp with a G + C content of 48.1%. This information regarding the genetic basis of this bacterium can greatly advance our understanding of the physiology of this species.

  3. Genome of Bacillus macauensis ZFHKF-1, a long-chain-forming bacterium.

    PubMed

    Cai, Lin; Zhang, Tong

    2012-09-01

    Here, we report the draft genome sequence of Bacillus macauensis ZFHKF-1, a novel long-chain bacterium previously isolated and identified by us (Zhang T, Fan XJ, Hanada S, Kamagata Y, Fang HHP, J. Syst. Evol. Microbiol. 56:349-353, 2006). The genome provides basic genetic information to understand this particular species and explore the potential mechanism of long-chain formation. The type strain is ZFHKF-1 (= JCM 13285 = DSM 17262).

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

    PubMed

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

    1997-09-01

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

  5. Draft Genome Sequence of Gordonia sihwensis Strain 9, a Branched Alkane-Degrading Bacterium

    PubMed Central

    Brown, Lisa M.; Gunasekera, Thusitha S.; Striebich, Richard C.

    2016-01-01

    Gordonia sihwensis strain 9 is a Gram-positive bacterium capable of efficient aerobic degradation of branched and normal alkanes. The draft genome of G. sihwensis S9 is 4.16 Mb in size, with 3,686 coding sequences and 68.1% G+C content. Alkane monooxygenase and P-450 cytochrome genes required for alkane degradation are predicted in G. sihwensis S9. PMID:27340079

  6. Halobacterium saccharovorum sp. nov., a carbohydrate-metabolizing, extremely halophilic bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Hochstein, L. I.

    1976-01-01

    The previously described extremely halophilic bacterium, strain M6, metabolizes a variety of carbohydrates with the production of acid. In addition, the organism produces nitrite (but no gas) from nitrate, is motile, and grows most rapidly at about 50 C. These characteristics distinguish it from all previously described halophilic bacteria in the genus Halobacterium. It is suggested that it be designated as a new species, Halobacterium saccharovorum.

  7. Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes.

    PubMed

    EAGON, R G

    1962-04-01

    Eagon, R. G. (University of Georgia, Athens). Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes. J. Bacteriol. 83:736-737. 1962.-Pseudomonas natriegens, a marine microorganism, was demonstrated to have a generation time of 9.8 min. This is the shortest generation time reported to date. Optimal growth occurred at 37 C in brain heart infusion broth supplemented with 1.5% sea salt.

  8. Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

    PubMed Central

    Thiel, Vera; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Schuster, Stephan C.; Ward, David M.

    2015-01-01

    The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus ruber strain A, isolated from a cyanobacterial enrichment culture obtained from Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170 contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding genes, and 2 rRNA operons. PMID:25814606

  9. Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3

    SciTech Connect

    Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Teshima, Hazuki; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Ivanova, N; Pagani, Ioanna; Vannier, Pauline; Oger, Phil; Bartlett, Douglas; Noll, Kenneth M; Woyke, Tanja; Jebbar, Mohamed

    2012-01-01

    Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

  10. An oleaginous bacterium that intrinsically accumulates long-chain free Fatty acids in its cytoplasm.

    PubMed

    Katayama, Taiki; Kanno, Manabu; Morita, Naoki; Hori, Tomoyuki; Narihiro, Takashi; Mitani, Yasuo; Kamagata, Yoichi

    2014-02-01

    Medium- and long-chain fatty acids are present in organisms in esterified forms that serve as cell membrane constituents and storage compounds. A large number of organisms are known to accumulate lipophilic materials as a source of energy and carbon. We found a bacterium, designated GK12, that intrinsically accumulates free fatty acids (FFAs) as intracellular droplets without exhibiting cytotoxicity. GK12 is an obligatory anaerobic, mesophilic lactic acid bacterium that was isolated from a methanogenic reactor. Phylogenetic analysis based on 16S rRNA gene sequences showed that GK12 is affiliated with the family Erysipelotrichaceae in the phylum Firmicutes but is distantly related to type species in this family (less than 92% similarity in 16S rRNA gene sequence). Saturated fatty acids with carbon chain lengths of 14, 16, 18, and 20 were produced from glucose under stress conditions, including higher-than-optimum temperatures and the presence of organic solvents that affect cell membrane integrity. FFAs were produced at levels corresponding to up to 25% (wt/wt) of the dry cell mass. Our data suggest that FFA accumulation is a result of an imbalance between excess membrane fatty acid biosynthesis due to homeoviscous adaptation and limited β-oxidation activity due to anaerobic growth involving lactic acid fermentation. FFA droplets were not further utilized as an energy and carbon source, even under conditions of starvation. A naturally occurring bacterium that accumulates significant amounts of long-chain FFAs with noncytotoxicity would provide useful strategies for microbial biodiesel production.

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

    PubMed Central

    Khobragade, Chandrahasya N.

    2016-01-01

    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. PMID:27882328

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

    SciTech Connect

    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.

  13. Bioremediation of hexavalent chromium (VI) by a soil-borne bacterium, Enterobacter cloacae B2-DHA.

    PubMed

    Rahman, Aminur; Nahar, Noor; Nawani, Neelu N; Jass, Jana; Hossain, Khaled; Saud, Zahangir Alam; Saha, Ananda K; Ghosh, Sibdas; Olsson, Björn; Mandal, Abul

    2015-01-01

    Chromium and chromium containing compounds are discharged into the nature as waste from anthropogenic activities, such as industries, agriculture, forest farming, mining and metallurgy. Continued disposal of these compounds to the environment leads to development of various lethal diseases in both humans and animals. In this paper, we report a soil borne bacterium, B2-DHA that can be used as a vehicle to effectively remove chromium from the contaminated sources. B2-DHA is resistant to chromium with a MIC value of 1000 µg mL(-1) potassium chromate. The bacterium has been identified as a Gram negative, Enterobacter cloacae based on biochemical characteristics and 16S rRNA gene analysis. TOF-SIMS and ICP-MS analyses confirmed intracellular accumulation of chromium and thus its removal from the contaminated liquid medium. Chromium accumulation in cells was 320 µg/g of cells dry biomass after 120-h exposure, and thus it reduced the chromium concentration in the liquid medium by as much as 81%. Environmental scanning electron micrograph revealed the effect of metals on cellular morphology of the isolates. Altogether, our results indicate that B2-DHA has the potential to reduce chromium significantly to safe levels from the contaminated environments and suggest the potential use of this bacterium in reducing human exposure to chromium, hence avoiding poisoning.

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

    PubMed

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

    2012-09-01

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

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

    PubMed

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

    2008-06-01

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

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

    PubMed Central

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

    2016-01-01

    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. PMID:27748409

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

    NASA Astrophysics Data System (ADS)

    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.

  18. In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment

    PubMed Central

    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. PMID:21701585

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

    PubMed Central

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

    1988-01-01

    Microbiological analyses of sediments located near a point source for petrogenic chemicals resulted in the isolation of a pyrene-mineralizing bacterium. This isolate was identified as a Mycobacterium sp. on the basis of its cellular and colony morphology, gram-positive and strong acid-fast reactions, diagnostic biochemical tests, 66.6% G + C content of the DNA, and high-molecular-weight mycolic acids (C58 to C64). The mycobacterium mineralized pyrene when grown in a mineral salts medium supplemented with nutrients but was unable to utilize pyrene as a sole source of carbon and energy. The mycobacterium grew well at 24 and 30 degrees C and minimally at 35 degrees C. No growth was observed at 5 or 42 degrees C. The mycobacterium grew well at salt concentrations up to 4%. Pyrene-induced Mycobacterium cultures mineralized 5% of the pyrene after 6 h and reached a maximum of 48% mineralization within 72 h. Treatment of induced and noninduced cultures with chloramphenicol showed that pyrene-degrading enzymes were inducible in this Mycobacterium sp. This bacterium could also mineralize other polycyclic aromatic hydrocarbons and alkyl- and nitro-substituted polycyclic aromatic hydrocarbons including naphthalene, phenanthrene, fluoranthene, 3-methylcholanthrene, 1-nitropyrene, and 6-nitrochrysene. This is the first report of a bacterium able to extensively mineralize pyrene and other polycyclic aromatic hydrocarbons containing four aromatic rings. Images PMID:3202633

  20. Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping.

    PubMed

    Johnson, Ethan T; Baron, Daniel B; Naranjo, Belén; Bond, Daniel R; Schmidt-Dannert, Claudia; Gralnick, Jeffrey A

    2010-07-01

    Microorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacterium Shewanella oneidensis strain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containing S. oneidensis expressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments.

  1. The Soil Bacterium Methylococcus capsulatus Bath Interacts with Human Dendritic Cells to Modulate Immune Function

    PubMed Central

    Indrelid, Stine; Kleiveland, Charlotte; Holst, René; Jacobsen, Morten; Lea, Tor

    2017-01-01

    The prevalence of inflammatory bowel disease (IBD) has increased in Western countries during the course of the twentieth century, and is evolving to be a global disease. Recently we showed that a bacterial meal of a non-commensal, non-pathogenic methanotrophic soil bacterium, Methylococcus capsulatus Bath prevents experimentally induced colitis in a murine model of IBD. The mechanism behind the effect has this far not been identified. Here, for the first time we show that M. capsulatus, a soil bacterium adheres specifically to human dendritic cells, influencing DC maturation, cytokine production, and subsequent T cell activation, proliferation and differentiation. We characterize the immune modulatory properties of M. capsulatus and compare its immunological properties to those of another Gram-negative gammaproteobacterium, the commensal Escherichia coli K12, and the immune modulatory Gram-positive probiotic bacterium, Lactobacillus rhamnosus GG in vitro. M. capsulatus induces intermediate phenotypic and functional DC maturation. In a mixed lymphocyte reaction M. capsulatus-primed monocyte-derived dendritic cells (MoDCs) enhance T cell expression of CD25, the γ-chain of the high affinity IL-2 receptor, supports cell proliferation, and induce a T cell cytokine profile different from both E. coli K12 and Lactobacillus rhamnosus GG. M. capsulatus Bath thus interacts specifically with MoDC, affecting MoDC maturation, cytokine profile, and subsequent MoDC directed T cell polarization. PMID:28293233

  2. Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

    PubMed Central

    Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

    2014-01-01

    Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production. PMID:24717418

  3. Whole-Genome Shotgun Sequence of Escherichia coli Strain MN067 from India, a Commensal Bacterium with Potent Pathogenic Ability

    PubMed Central

    Nagarjuna, Daram; Gaind, Rajni; Dhanda, Rakesh Singh

    2017-01-01

    ABSTRACT Escherichia coli is one of the most frequently prevalent pathogens, causing infections in health care settings throughout the world. Here, we report the whole-genome sequence of MN067, a commensal bacterium with a pathogenic potential. PMID:28336596

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

    PubMed Central

    Gilmore, Brendan F.

    2016-01-01

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

  5. Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi.

    PubMed

    Passos da Silva, Daniel; Devescovi, Giulia; Paszkiewicz, Konrad; Moretti, Chiaraluce; Buonaurio, Roberto; Studholme, David J; Venturi, Vittorio

    2013-05-09

    Erwinia toletana was first reported in 2004 as a bacterial species isolated from olive knots caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi. Recent studies have shown that the presence of this bacterium in the olive knot environment increases the virulence of the disease, indicating possible interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft genome sequence of an E. toletana strain.

  6. Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi

    PubMed Central

    Passos da Silva, Daniel; Devescovi, Giulia; Paszkiewicz, Konrad; Moretti, Chiaraluce; Buonaurio, Roberto; Studholme, David J.

    2013-01-01

    Erwinia toletana was first reported in 2004 as a bacterial species isolated from olive knots caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi. Recent studies have shown that the presence of this bacterium in the olive knot environment increases the virulence of the disease, indicating possible interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft genome sequence of an E. toletana strain. PMID:23661482

  7. Complete genome sequence of Photorhabdus temperata subsp. thracensis 39-8 T, an entomopathogenic bacterium for the improved commercial bioinsecticide.

    PubMed

    Kwak, Yunyoung; Shin, Jae-Ho

    2015-11-20

    Photorhabdus temperata subsp. thracensis 39-8(T), a symbiotic bacterium from an entomopathogenic nematode Heterorhabditis bacteriophora, is a novel bacterium harboring insect pathogenicity. Herein, we present the complete genome sequence of strain 39-8(T), which consists of one circular chromosome of 5,147,098 bp with a GC content of 44.10%. This genetic information will provide insights into biotechnological applications of the genus Photorhabdus producing insecticidal toxins, leading to the enhanced commercial bioinsecticide in agricultural pest control.

  8. Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

    PubMed Central

    Gkorezis, Panagiotis; Van Hamme, Jonathan; Bottos, Eric; Thijs, Sofie; Balseiro-Romero, Maria; Monterroso, Carmela; Kidd, Petra Suzan; Rineau, Francois; Weyens, Nele; Sillen, Wouter

    2016-01-01

    We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic Gram-positive bacterium of the family Bacillaceae, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain GB2 is an effective plant-growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:27340073

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

    PubMed Central

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

    2012-01-01

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

  10. Determination of phenanthrene bioavailability by using a self-dying reporter bacterium: test with model solids and soil.

    PubMed

    Shin, Doyun; Nam, Kyoungphile

    2012-02-20

    The present study was conducted to investigate the performance and feasibility of a self-dying reporter bacterium to visualize and quantify phenanthrene bioavailability in soil. The self-dying reporter bacterium was designed to die on the initiation of phenanthrene biodegradation. The viability of the reporter bacterium was determined by a fluorescence live/dead cell staining method and visualized by confocal laser scanning microscopic observation. Phenanthrene was spiked into four types of model solids and a sandy loam. The bioavailability of phenanthrene to the reporter bacterium was remarkably declined with the hydrophobicity of the model solids: essentially no phenanthrene was biodegraded in the presence of 9-nm pores and about 35.8% of initial phenanthrene was biodegraded without pores. Decrease in bioavailability was not evident in the nonporous hydrophilic bead, but a small decrease was observed in the porous hydrophilic bead at 1000 mg/kg of phenanthrene. The fluorescence intensity was commensurate with the extent of phenanthrene biodegradation by the reporter bacterium at the concentration range from 50 to 500 mg/kg. Such a quantitative relationship was also confirmed with a sandy loam spiked up to 1000 mg/kg of phenanthrene. This reporter bacterium may be a useful means to determine phenanthrene bioavailability in soil.

  11. Effect of arsenite-oxidizing bacterium B. laterosporus on arsenite toxicity and arsenic translocation in rice seedlings.

    PubMed

    Yang, Gui-Di; Xie, Wan-Ying; Zhu, Xi; Huang, Yi; Yang, Xiao-Jun; Qiu, Zong-Qing; Lv, Zhen-Mao; Wang, Wen-Na; Lin, Wen-Xiong

    2015-10-01

    Arsenite [As (III)] oxidation can be accelerated by bacterial catalysis, but the effects of the accelerated oxidation on arsenic toxicity and translocation in rice plants are poorly understood. Herein we investigated how an arsenite-oxidizing bacterium, namely Brevibacillus laterosporus, influences As (III) toxicity and translocation in rice plants. Rice seedlings of four cultivars, namely Guangyou Ming 118 (GM), Teyou Hang II (TH), Shanyou 63 (SY) and Minghui 63 (MH), inoculated with or without the bacterium were grown hydroponically with As (III) to investigate its effects on arsenic toxicity and translocation in the plants. Percentages of As (III) oxidation in the solutions with the bacterium (100%) were all significantly higher than those without (30-72%). The addition of the bacterium significantly decreased As (III) concentrations in SY root, GM root and shoot, while increased the As (III) concentrations in the shoot of SY, MH and TH and in the root of MH. Furthermore, the As (III) concentrations in the root and shoot of SY were both the lowest among the treatments with the bacterium. On the other hand, its addition significantly alleviated the As (III) toxicity on four rice cultivars. Among the treatments amended with B. laterosporus, the bacterium showed the best remediation on SY seedlings, with respect to the subdued As (III) toxicity and decreased As (III) concentration in its roots. These results indicated that As (III) oxidation accelerated by B. laterosporus could be an effective method to alleviate As (III) toxicity on rice seedlings.

  12. Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.).

    PubMed

    Anandham, Rangasamy; Indiragandhi, Pandiyan; Kwon, Soon Wo; Sa, Tong Min; Jeon, Che Ok; Kim, Yong Ki; Jee, Hyeong Jin

    2010-01-01

    A facultatively chemolithoautotrophic, thiosulfate-oxidizing, Gram-negative, aerobic, motile, rod-shaped bacterial strain, designated ATSB16(T), was isolated from rhizosphere soils of sesame (Sesamum indicum L.). 16S rRNA gene sequence analysis demonstrated that this strain was closely related to Pandoraea pnomenusa LMG 18087(T) (96.7 % similarity), P. pulmonicola LMG 18016(T) (96.5 %), P. apista LMG 16407(T) (96.2 %), P. norimbergensis LMG 18379(T) (96.1 %) and P. sputorum LMG 18819(T) (96.0 %). Strain ATSB16(T) shared 96.0-96.4 % sequence similarity with four unnamed genomospecies of Pandoraea. The major cellular fatty acids of the strain ATSB16(T) were C(17 : 0) cyclo (33.0 %) and C(16 : 0) (30.6 %). Q-8 was the predominant respiratory quinone. The major polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified aminophospholipids. Hydroxyputrescine and putrescine were the predominant polyamines. The genomic DNA G+C content of the strain was 64.0 mol%. On the basis of the results obtained from this study, strain ATSB16(T) represents a novel species of the genus Pandoraea, for which the name Pandoraea thiooxydans sp. nov. is proposed. The type strain is ATSB16(T) (=KACC 12757(T) =LMG 24779(T)).

  13. Isolation and characterization of alkaliphilic, chemolithoautotrophic, sulphur-oxidizing bacteria.

    PubMed

    Sorokin, D Y; Robertson, L A; Kuenen, J G

    2000-04-01

    Alkaliphilic sulphur-oxidizing bacteria were isolated from samples from alkaline environments including soda soil and soda lakes. Two isolates, currently known as strains AL 2 and AL 3, were characterized. They grew over a pH range 8.0-10.4 with an optimum at 9.5-9.8. Both strains could oxidize thiosulphate, sulphide, polysulphide, elemental sulphur and tetrathionate. Strain AL 3 more actively oxidized thiosulphate and sulphide, while isolate AL 2 had higher activity with elemental sulphur and tetrathionate. Isolate AL 2 was also able to oxidize trithionate. The pH optimum for thiosulphate and sulphide oxidation was between 9-10. Some activity remained at pH 11, but was negligible at pH 7. Metabolism of tetrathionate by isolate AL 2 involved initial anaerobic hydrolysis to form sulphur, thiosulphate and sulphate in a sequence similar to that in other colourless sulphur-oxidizing bacteria. Sulphate was produced by both strains. During batch growth on thiosulphate, elemental sulphur and sulphite transiently accumulated in cultures of isolates AL 2 and AL 3, respectively. At lower pH values, both strains accumulated sulphur during sulphide and thiosulphate oxidation. Both strains contained ribulose bisphosphate carboxylase. Thiosulphate oxidation in isolate AL 3 appeared to be sodium ion-dependent. Isolate AL 2 differed from AL 3 by its high GC mol % value (65.5 and 49.5, respectively), sulphur deposition in its periplasm, the absence of carboxysomes, lower sulphur-oxidizing capacity, growth kinetics (lower growth rate and higher growth yield) and cytochrome composition.

  14. Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

    SciTech Connect

    Walsh, David A.; Zaikova, Elena; Howes, Charles L.; Song, Young; Wright, Jody; Tringe, Susannah G.; Tortell, Philippe D.; Hallam, Steven J.

    2009-07-15

    Oxygen minimum zones (OMZs), also known as oceanic"dead zones", are widespread oceanographic features currently expanding due to global warming and coastal eutrophication. Although inhospitable to metazoan life, OMZs support a thriving but cryptic microbiota whose combined metabolic activity is intimately connected to nutrient and trace gas cycling within the global ocean. Here we report time-resolved metagenomic analyses of a ubiquitous and abundant but uncultivated OMZ microbe (SUP05) closely related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur-oxidation and nitrate respiration responsive to a wide range of water column redox states. Thus, SUP05 plays integral roles in shaping nutrient and energy flow within oxygen-deficient oceanic waters via carbon sequestration, sulfide detoxification and biological nitrogen loss with important implications for marine productivity and atmospheric greenhouse control.

  15. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones.

    PubMed

    Walsh, David A; Zaikova, Elena; Howes, Charles G; Song, Young C; Wright, Jody J; Tringe, Susannah G; Tortell, Philippe D; Hallam, Steven J

    2009-10-23

    Oxygen minimum zones, also known as oceanic "dead zones," are widespread oceanographic features currently expanding because of global warming. Although inhospitable to metazoan life, they support a cryptic microbiota whose metabolic activities affect nutrient and trace gas cycling within the global ocean. Here, we report metagenomic analyses of a ubiquitous and abundant but uncultivated oxygen minimum zone microbe (SUP05) related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate respiration responsive to a wide range of water-column redox states. Our analysis provides a genomic foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential sensitivity to environmental changes.

  16. The Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas dentrificans

    SciTech Connect

    USF Genomics Class; Sievert, Stefan M.; Scott, Kathleen M.; Klotz, Martin G.; Chain, Patrick S.G.; Hauser, Loren J.; Hemp, James; Hugler, Michael; Land, Miriam; Lapidus, Alla; Larimer, Frank W.; Lucas, Susan; Malfatti, Stephanie A.; Meyer, Folker; Paulsen, Ian T.; Ren, Qinghu; Simon, Jorg

    2007-08-08

    Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.

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

    PubMed

    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

  18. Pontibacter diazotrophicus sp. nov., a Novel Nitrogen-Fixing Bacterium of the Family Cytophagaceae

    PubMed Central

    Xu, Linghua; Zeng, Xian-Chun; Nie, Yao; Luo, Xuesong; Zhou, Enmin; Zhou, Lingli; Pan, Yunfan; Li, Wenjun

    2014-01-01

    Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4XT. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4XT displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C15∶0, C16∶1ω5c, summed feature 3 (containing C16∶1ω6c and/or C16∶1ω7c) and summed feature 4 (comprising anteiso-C17∶1B and/or iso-C17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4XT actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4XT is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4XT ( = CCTCC AB 2013049T = NRRL B-59974T). PMID:24647674

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

    PubMed Central

    Watts, Mathew P.; Khijniak, Tatiana V.; Boothman, Christopher

    2015-01-01

    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. PMID:26048926

  20. Development of a Markerless Deletion System for the Fish-Pathogenic Bacterium Flavobacterium psychrophilum

    PubMed Central

    Gómez, Esther; Álvarez, Beatriz; Duchaud, Eric; Guijarro, José A.

    2015-01-01

    Flavobacterium psychrophilum is a Gram-negative fish pathogen that causes important economic losses in aquaculture worldwide. Although the genome of this bacterium has been determined, the function and relative importance of genes in relation to virulence remain to be established. To investigate their respective contribution to the bacterial pathogenesis, effective tools for gene inactivation are required. In the present study, a markerless gene deletion system has been successfully developed for the first time in this bacterium. Using this method, the F. psychrophilum fcpB gene, encoding a predicted cysteine protease homologous to Streptococcus pyogenes streptopain, was deleted. The developed system involved the construction of a conjugative plasmid that harbors the flanking sequences of the fcpB gene and an I-SceI meganuclease restriction site. Once this plasmid was integrated in the genome by homologous recombination, the merodiploid was resolved by the introduction of a plasmid expressing I-SceI under the control of the fpp2 F. psychrophilum inducible promoter. The resulting deleted fcpB mutant presented a decrease in extracellular proteolytic activity compared to the parental strain. However, there were not significant differences between their LD50 in an intramuscularly challenged rainbow trout infection model. The mutagenesis approach developed in this work represents an improvement over the gene inactivation tools existing hitherto for this “fastidious” bacterium. Unlike transposon mutagenesis and gene disruption, gene markerless deletion has less potential for polar effects and allows the mutation of virtually any non-essential gene or gene clusters. PMID:25692569

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

    PubMed

    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. Evolution of a biomass-fermenting bacterium to resist lignin phenolics.

    PubMed

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

    2017-03-31

    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 by changes in gene dosage and regulation, membrane fatty acid structure, and the surface layer. Collectively, this study demonstrates an automated framework for 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 could 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 progressively higher

  3. Haloanaerobium salsugo sp. nov., a moderately halophilic, anaerobic bacterium from a subterranean brine

    SciTech Connect

    Bhupathiraju, V.K.; Sharma, P.K.; Tanner, R.S.; McInerney, M.J.; Oren, A.; Woese, C.R.

    1994-07-01

    A strictly anaerobic, moderately halophilic, gram-negative bacterium was isolated from a highly saline oil field brine. The bacterium was a non-spore-forming, nonmotile rod, appearing singly, in pairs, or occasionally as long chains, and measured 0.3 to 0.4 by 2.6 to 4 {micro}m. The bacterium had a specific requirement for NaCl and grew at NaCl concentrations of between 6 and 24%, with optimal growth at 9% NaCl. The isolate grew at temperatures of between 22 and 51 C and pH values of between 5.6 and 8.0. The doubling time in a complex medium containing 10% NaCl was 9 h. Growth was inhibited by chloramphenicol, tetracycline, and penicillin but not by cycloheximide or azide. Fermentable substrates were predominantly carbohydrates. The end products of glucose fermentation were acetate, ethanol, CO{sub 2}, and H{sub 2}. The major components of the cellular fatty acids were C{sub 14:0}, C{sub 16:0}, C{sub 16:1}, and C{sub 17:0 cyc} acids. The DNA base composition of the isolate was 34 mol% G+C. Oligonucleotide catalog and sequence analyses of the 16S rRNA showed that strain VS-752{sup T} was most closely related to Haloanaerobium praevalens GSL{sup T} (ATCC 33744), the sole member of the genus Haloanaerobium. The authors propose that strain VS-752 (ATCC 51327) by established as the type strain of a new species, Haloanaerobium salsugo, in the genus Haloanaerobium. 40 refs., 3 figs, 5 tabs.

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

    SciTech Connect

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

    1990-05-01

    Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. {sup 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({beta}-aminoethyl ether)-N,N,N{prime}N{prime}-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.

  5. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

    PubMed

    Derrien, Muriel; Vaughan, Elaine E; Plugge, Caroline M; de Vos, Willem M

    2004-09-01

    The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T).

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

    PubMed

    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.

  7. Chitin Utilization by the Insect-Transmitted Bacterium Xylella fastidiosa▿ †

    PubMed Central

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

    2010-01-01

    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. PMID:20656858

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

    USGS Publications Warehouse

    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.

  9. Toxicity on the luminescent bacterium Vibrio fischeri (Beijerinck). I: QSAR equation for narcotics and polar narcotics.

    PubMed

    Vighi, Marco; Migliorati, Sonia; Monti, Gianna Serafina

    2009-01-01

    Toxicity data on chemicals, supposed to have a narcotic or polar narcotic toxicological mode of action, have been produced on the luminescent bacterium Vibrio fischeri using the Microtox test procedure. Advanced statistical methods have been used to calculate statistically sound values for ecotoxicological endpoints. Simple quantitative structure activity relationship (QSAR) equations were developed for narcotics and polar narcotics. These equations were compared with those proposed by the European Technical Guidance Document on Risk Assessment for other aquatic organisms (algae, Daphnia, and fish). Similarities and differences are discussed. The need for including the bacterial component in the ecotoxicological risk assessment for aquatic ecosystems is highlighted.

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

    SciTech Connect

    Maurice, P.

    2004-12-13

    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.

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

    SciTech Connect

    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 the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.

    PubMed

    Wibberg, Daniel; Luque-Almagro, Víctor M; Igeño, Ma Isabel; Bremges, Andreas; Roldán, Ma Dolores; Merchán, Faustino; Sáez, Lara P; Guijo, Ma Isabel; Manso, Ma Isabel; Macías, Daniel; Cabello, Purificación; Becerra, Gracia; Ibáñez, Ma Isabel; Carmona, Ma Isabel; Escribano, Ma María Paz; Castillo, Francisco; Sczyrba, Alexander; Moreno-Vivián, Conrado; Blasco, Rafael; Pühler, Alfred; Schlüter, Andreas

    2014-04-10

    Pseudomonas pseudoalcaligenes CECT5344, a Gram-negative bacterium isolated from the Guadalquir River (Córdoba, Spain), is able to utilize different cyano-derivatives. Here, the complete genome sequence of P. pseudoalcaligenes CECT5344 harboring a 4,686,340bp circular chromosome encoding 4513 genes and featuring a GC-content of 62.34% is reported. Necessarily, remaining gaps in the genome had to be closed by assembly of few long reads obtained from PacBio single molecule real-time sequencing. Here, the first complete genome sequence for the species P. pseudoalcaligenes is presented.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

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

    PubMed

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

    2015-02-01

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

  15. Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus

    SciTech Connect

    Tang, Kuo-Hsiang; Barry, Kerrie; Chertkov, Olga; Dalin, Eileen; Han, Cliff; Hauser, Loren John; Honchak, Barbara M; Karbach, Lauren E; Land, Miriam L; Lapidus, Alla L.; Larimer, Frank W; Mikhailova, Natalia; Pitluck, Sam; Pierson, Beverly K

    2011-01-01

    Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.

  16. Reduction of Uranium(VI) Phosphate during Growth of the Thermophilic Bacterium Thermoterrabacterium ferrireducens

    PubMed Central

    Khijniak, T. V.; Slobodkin, A. I.; Coker, V.; Renshaw, J. C.; Livens, F. R.; Bonch-Osmolovskaya, E. A.; Birkeland, N.-K.; Medvedeva-Lyalikova, N. N.; Lloyd, J. R.

    2005-01-01

    The thermophilic, gram-positive bacterium Thermoterrabacterium ferrireducens coupled organotrophic growth to the reduction of sparingly soluble U(VI) phosphate. X-ray powder diffraction and X-ray absorption spectroscopy analysis identified the electron acceptor in a defined medium as U(VI) phosphate [uramphite; (NH4)(UO2)(PO4) · 3H2O], while the U(IV)-containing precipitate formed during bacterial growth was identified as ningyoite [CaU(PO4)2 · H2O]. This is the first report of microbial reduction of a largely insoluble U(VI) compound. PMID:16204572

  17. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

    DOE PAGES

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; ...

    2015-10-26

    Thioalkalivibrio thiocyanoxidans strain ARh 2T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na+. This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. In conclusion, this organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

  18. Absorbance changes accompanying the fast fluorescence induction in the purple bacterium Rhodobacter sphaeroides.

    PubMed

    Bína, David; Litvín, Radek; Vácha, Frantisek

    2010-08-01

    The authors present a study of the fluorescence and absorbance transients occurring in whole cells of purple nonsulfur bacterium Rhodobacter sphaeroides on the millisecond timescale under pulsed actinic illumination. The fluorescence induction curve is interpreted in terms of combination of effects of redox changes in the reaction center and the membrane potential. The results of this study support the view that the membrane potential act predominantly to increase the fluorescence yield. Advantages of the pulsed actinic illumination for study of the operation of the electron transport chain in vivo are discussed.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  1. Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes

    SciTech Connect

    Lidstrom, Mary E.

    2002-06-10

    The mixture of toxic chemicals, heavy metals, halogenated solvents and radionuclides in many DOE waste materials presents a challenging problem for separating the different species and disposing of individual contaminants. One approach for dealing with mixed wastes is to genetically engineer the radiation-resistant bacterium, Deinococcus radiodurans to survive in and detoxify DOE's mixed waste streams, and to develop process parameters for treating mixed wastes with such constructed strains. The goal for this project is to develop a suite of genetic tools for Deinococcus radiodurans and to use these tools to construct and test stable strains for detoxification of haloorganics in mixed wastes.

  2. Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes

    SciTech Connect

    Lidstrom, Mary E.

    2001-06-11

    The mixture of toxic chemicals, heavy metals, halogenated solvents and radionuclides in many DOE waste materials presents a challenging problem for separating the different species and disposing of individual contaminants. One approach for dealing with mixed wastes is to genetically engineer the radiation-resistant bacterium, Deinococcus radiodurans to survive in and detoxify DOE's mixed waste streams, and to develop process parameters for treating mixed wastes with such constructed strains. The goal for this project is to develop a suite of genetic tools for Deinococcus radiodurans and to use these tools to construct and test stable strains for detoxification of haloorganics in mixed wastes.

  3. Genome Sequence of the Boron-Tolerant and -Requiring Bacterium Bacillus boroniphilus

    PubMed Central

    Çöl, Bekir; Özkeserli, Zeynep; Kumar, Dibyendu; Özdağ, Hilal

    2014-01-01

    Bacillus boroniphilus is a highly boron-tolerant bacterium that also requires this element for its growth. The complete genome sequence of B. boroniphilus was determined by a combination of shotgun sequencing and paired-end sequencing using 454 pyrosequencing technology. A total of 84,872,624 reads from shotgun sequencing and a total of 194,092,510 reads from paired-end sequencing were assembled using Newbler 2.3. The estimated size of the draft genome is 5.2 Mb. PMID:24385571

  4. An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

    PubMed Central

    2014-01-01

    When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome. PMID:25780504

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

    SciTech Connect

    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.

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

    PubMed Central

    Hong, Chi Eun; Jo, Sung Hee

    2016-01-01

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

  7. Microbial Reduction of Structural Fe3+ in Nontronite by a Thermophilic Bacterium and its Role in Promoting the Smectite to Illite Reaction

    DTIC Science & Technology

    2007-01-01

    structural Fe1* was investigated by using a thermophilic metal-reducing bacterium, Thermoanaerobacter ethanolicus, isolated from the deep subsurface...structural Fe’* was investigated by using a thermophilic metal-reducing bacterium, Thermoanaerobacter ethanolicus, isolated from the deep subsurface. T...for sediment diagenesis. MATERIALS AND METHODS Bacterium and clay mineral CCSD_DF2450_MljS8_isolatel was isolated from a circulating drilling

  8. Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22

    PubMed Central

    Kanaly, Robert A; Micheletto, Ruggero; Matsuda, Tomonari; Utsuno, Youko; Ozeki, Yasuhiro; Hamamura, Natsuko

    2015-01-01

    Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2′-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H]+ > [M + H − 116]+ transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2′-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work. PMID:26305056

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

    PubMed

    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.

  10. Accurate Cell Division in Bacteria: How Does a Bacterium Know Where its Middle Is?

    NASA Astrophysics Data System (ADS)

    Howard, Martin; Rutenberg, Andrew

    2004-03-01

    I will discuss the physical principles lying behind the acquisition of accurate positional information in bacteria. A good application of these ideas is to the rod-shaped bacterium E. coli which divides precisely at its cellular midplane. This positioning is controlled by the Min system of proteins. These proteins coherently oscillate from end to end of the bacterium. I will present a reaction-diffusion model that describes the diffusion of the Min proteins, and their binding/unbinding from the cell membrane. The system possesses an instability that spontaneously generates the Min oscillations, which control accurate placement of the midcell division site. I will then discuss the role of fluctuations in protein dynamics, and investigate whether fluctuations set optimal protein concentration levels. Finally I will examine cell division in a different bacteria, B. subtilis. where different physical principles are used to regulate accurate cell division. See: Howard, Rutenberg, de Vet: Dynamic compartmentalization of bacteria: accurate division in E. coli. Phys. Rev. Lett. 87 278102 (2001). Howard, Rutenberg: Pattern formation inside bacteria: fluctuations due to the low copy number of proteins. Phys. Rev. Lett. 90 128102 (2003). Howard: A mechanism for polar protein localization in bacteria. J. Mol. Biol. 335 655-663 (2004).

  11. Acinetobacter sp. strain Ths, a novel psychrotolerant and alkalitolerant bacterium that utilizes hydrocarbon.

    PubMed

    Yamahira, Keiko; Hirota, Kikue; Nakajima, Kenji; Morita, Naoki; Nodasaka, Yoshinobu; Yumoto, Isao

    2008-09-01

    A novel psychrotolerant, alkalitolerant bacterium, strain Ths, was isolated from a soil sample immersed in hot spring water containing hydrocarbons and grown on a chemically defined medium containing n-tetradecane as the sole carbon source. The isolate grew at 0 degrees C but not at temperatures higher than 45 degrees C; its optimum growth temperature was 27 degrees C. It grew in the pH range of 7-9. The strain utilized C(13)-C(30) n-alkane and fluorene at pH 9 and 4 degrees C. To our knowledge, this is the first report on the bacterium that utilizes a wide range of hydrocarbons at a high pH and a low temperature. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ths is closely related to genomic species 6 ATCC 17979 (99.1% similarity), genomic species BJ13/TU14 ATCC 17905 (97.8% similarity), genomic species 9 ATCC 9957 (97.6% similarity) belonging to the genus Acinetobacter and to Acinetobacter calcoaceticus JCM 6842(T) (97.5% similarity). DNA-DNA hybridization revealed that the isolate has 62, 25, 18 and 19% relatedness, respectively, to genomic species 6 ATCC 17979, genomic species BJ13/TU14 ATCC 17905, genomic species 9 ATCC 9957 and A. calcoaceticus, respectively.

  12. Francisella Inflammasomes: Integrated Responses to a Cytosolic Stealth Bacterium.

    PubMed

    Wallet, Pierre; Lagrange, Brice; Henry, Thomas

    2016-01-01

    Francisella tularensis is a facultative intracellular bacterium causing tularemia, a zoonotic disease. Francisella replicates in the macrophage cytosol and eventually triggers cytosolic immune responses. In murine macrophages, Francisella novicida and Francisella tularensis live vaccine strain lyse in the host cytosol and activate the cytosolic DNA receptor Aim2. Here, we review the mechanisms leading or contributing to Aim2 inflammasome activation, including the role of TLRs and of IFN signaling and the implication of the guanylate-binding proteins 2 and 5 in triggering cytosolic bacteriolysis. Furthermore, we present how this cytosolic Gram-negative bacterium escapes recognition by caspase-11 but can trigger a non-canonical caspase-8 inflammasome. In addition, we highlight the differences in inflammasome activation in murine and human cells with pyrin, NLRP3, and AIM2 involved in sensing Francisella in human phagocytes. From a bacterial prospective, we describe the hiding strategy of Francisella to escape recognition by innate sensors and to resist to bacteriolysis in the host cytosol. Finally, we discuss the inability of the inflammasome sensors to detect F. tularensis subspecies tularensis strains, making them highly pathogenic stealth microbes.

  13. The Symbiotic Bacterium Fuels the Energy Metabolism of the Host Trypanosomatid Strigomonas culicis.

    PubMed

    Loyola-Machado, Ana Carolina; Azevedo-Martins, Allan Cézar; Catta-Preta, Carolina Moura Costa; de Souza, Wanderley; Galina, Antonio; Motta, Maria Cristina M

    2017-02-28

    The mutualistic relationship between trypanosomatids and their respective endosymbiotic bacteria represents an excellent model for studying metabolic co-evolution since the symbiont completes essential biosynthetic routes of the host cell. In this work, we investigated the influence of the endosymbiont on the energy metabolism of Strigomonas culicis by comparing the wild strain with aposymbiotic protists. The bacterium maintains a frequent and close association with glycosomes, which are distributed around the prokaryote. Furthermore, 3D reconstructions revealed that the shape and distribution of glycosomes are different in symbiont-bearing protists compared to symbiont-free cells. Results of bioenergetic assays showed that the presence of the symbiont enhances the O2 consumption of the host cell. When the quantity of intracellular or released glycerol was evaluated, the aposymbiotic strain presented higher values when compared to symbiont-containing cells. Furthermore, inhibition of oxidative phosphorylation by potassium cyanide increased the rate of glycerol release and slightly diminished the ATP content in cells without the symbiont, indicating that the host trypanosomatid enhances its fermentative activity when the bacterium is lost.

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

    PubMed

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

    2017-01-03

    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%.

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

    PubMed

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

    2008-02-01

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

  16. Characterization of acetonitrile-tolerant marine bacterium Exiguobacterium sp. SBH81 and its tolerance mechanism.

    PubMed

    Kongpol, Ajiraporn; Kato, Junichi; Tajima, Takahisa; Vangnai, Alisa S

    2012-01-01

    A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. Investigation of its tolerance mechanisms illustrated that it does not rely on solvent inactivation processes or modification of cell surface characteristics, but rather, increase of the cell size lowers solvent partitioning into cells and the extrusion of solvents through the efflux system. A test using efflux pump inhibitors suggested that secondary transporters, i.e. resistance nodulation cell division (RND) and the multidrug and toxic compound extrusion (MATE) family, are involved in acetonitrile tolerance in this strain. In addition, its acetonitrile tolerance ability could be stably and significantly enhanced by repetitive growth in the presence of toxic acetonitrile. The marked acetonitrile tolerance of Exiguobacterium sp. SBH81 indicates its potential use as a host for biotechnological fermentation processes as well as bioremediation.

  17. An O2-sensing stressosome from a Gram-negative bacterium.

    PubMed

    Jia, Xin; Wang, Jian-Bo; Rivera, Shannon; Duong, Duc; Weinert, Emily E

    2016-08-04

    Bacteria have evolved numerous pathways to sense and respond to changing environmental conditions, including, within Gram-positive bacteria, the stressosome complex that regulates transcription of general stress response genes. However, the signalling molecules recognized by Gram-positive stressosomes have yet to be identified, hindering our understanding of the signal transduction mechanism within the complex. Furthermore, an analogous pathway has yet to be described in Gram-negative bacteria. Here we characterize a putative stressosome from the Gram-negative bacterium Vibrio brasiliensis. The sensor protein RsbR binds haem and exhibits ligand-dependent control of the stressosome complex activity. Oxygen binding to the haem decreases activity, while ferrous RsbR results in increased activity, suggesting that the V. brasiliensis stressosome may be activated when the bacterium enters anaerobic growth conditions. The findings provide a model system for investigating ligand-dependent signalling within stressosome complexes, as well as insights into potential pathways controlled by oxygen-dependent signalling within Vibrio species.

  18. An O2-sensing stressosome from a Gram-negative bacterium

    PubMed Central

    Jia, Xin; Wang, Jian-bo; Rivera, Shannon; Duong, Duc; Weinert, Emily E.

    2016-01-01

    Bacteria have evolved numerous pathways to sense and respond to changing environmental conditions, including, within Gram-positive bacteria, the stressosome complex that regulates transcription of general stress response genes. However, the signalling molecules recognized by Gram-positive stressosomes have yet to be identified, hindering our understanding of the signal transduction mechanism within the complex. Furthermore, an analogous pathway has yet to be described in Gram-negative bacteria. Here we characterize a putative stressosome from the Gram-negative bacterium Vibrio brasiliensis. The sensor protein RsbR binds haem and exhibits ligand-dependent control of the stressosome complex activity. Oxygen binding to the haem decreases activity, while ferrous RsbR results in increased activity, suggesting that the V. brasiliensis stressosome may be activated when the bacterium enters anaerobic growth conditions. The findings provide a model system for investigating ligand-dependent signalling within stressosome complexes, as well as insights into potential pathways controlled by oxygen-dependent signalling within Vibrio species. PMID:27488264

  19. Soil-Bacterium Compatibility Model as a Decision-Making Tool for Soil Bioremediation.

    PubMed

    Horemans, Benjamin; Breugelmans, Philip; Saeys, Wouter; Springael, Dirk

    2017-02-07

    Bioremediation of organic pollutant contaminated soil involving bioaugmentation with dedicated bacteria specialized in degrading the pollutant is suggested as a green and economically sound alternative to physico-chemical treatment. However, intrinsic soil characteristics impact the success of bioaugmentation. The feasibility of using partial least-squares regression (PLSR) to predict the success of bioaugmentation in contaminated soil based on the intrinsic physico-chemical soil characteristics and, hence, to improve the success of bioaugmentation, was examined. As a proof of principle, PLSR was used to build soil-bacterium compatibility models to predict the bioaugmentation success of the phenanthrene-degrading Novosphingobium sp. LH128. The survival and biodegradation activity of strain LH128 were measured in 20 soils and correlated with the soil characteristics. PLSR was able to predict the strain's survival using 12 variables or less while the PAH-degrading activity of strain LH128 in soils that show survival was predicted using 9 variables. A three-step approach using the developed soil-bacterium compatibility models is proposed as a decision making tool and first estimation to select compatible soils and organisms and increase the chance of success of bioaugmentation.

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

    PubMed

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

    2016-02-10

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

  1. Thiorhodococcus mannitoliphagus sp. nov., a purple sulfur bacterium from the White Sea.

    PubMed

    Rabold, Sandra; Gorlenko, Vladimir M; Imhoff, Johannes F

    2006-08-01

    A novel purple sulfur bacterium, strain WS(T), was isolated from a microbial mat from an estuary of the White Sea. Individual cells are coccoid shaped, motile by flagella and do not contain gas vesicles. The mean cell diameter is 1.85 mum (range 1.5-2.0 mum). Cell suspensions exhibit a purple-violet colour. They contain bacteriochlorophyll a and carotenoids of the rhodopinal series as photosynthetic pigments. The novel bacterium is an anoxygenic photoautotroph, using sulfide, thiosulfate, sulfite and elemental sulfur as electron donors for photosynthesis and is capable of photoassimilating several organic carbon sources in the presence of carbonate and a reduced sulfur source (sulfide and/or thiosulfate). Sulfur globules, formed during oxidation of sulfide, are stored transiently inside the cells. Optimal salinity and pH for growth are at 0.5-2.0 % NaCl and pH 7.0-7.5. The DNA base composition of strain WS(T) is 61.8 mol% G+C. 16S rRNA gene sequence analysis showed that the new isolate belongs to the genus Thiorhodococcus, with Thiorhodococcus minor CE2203(T) as the nearest relative (sequence similarity of 97.3 %). Several distinct differences from described species necessitate the description of a novel species. Thiorhodococcus mannitoliphagus sp. nov. is the proposed name, with strain WS(T) (=ATCC BAA-1228(T)=VKM B-2393(T)) as the type strain.

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

    PubMed

    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.

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

    PubMed

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

    2014-11-01

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

  4. Genome-scale metabolic reconstruction for the insidious bacterium in aquaculture Piscirickettsia salmonis.

    PubMed

    Fuentealba, Pablo; Aros, Camila; Latorre, Yesenia; Martínez, Irene; Marshall, Sergio; Ferrer, Pau; Albiol, Joan; Altamirano, Claudia

    2017-01-01

    Piscirickettsia salmonis is a fish bacterium that causes the disease piscirickettsiosis in salmonids. This pathology is partially controlled by vaccines. The lack of knowledge has hindered its culture on laboratory and industrial scale. The study describes the metabolic phenotype of P. salmonis in culture. This study presents the first genome-scale model (iPF215) of the LF-89 strain of P. salmonis, describing the central metabolic pathway, biosynthesis and molecule degradation and transport mechanisms. The model was adjusted with experiment data, allowing the identification of the capacities that were not predicted by the automatic annotation of the genome sequences. The iPF215 model is comprised of 417 metabolites, 445 reactions and 215 genes, was used to reproduce the growth of P. salmonis (μmax 0.052±0.005h(-1)). The metabolic reconstruction of the P. salmonis LF-89 strain obtained in this research provides a baseline that describes the metabolic capacities of the bacterium and is the basis for developing improvements to its cultivation for vaccine formulation.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  8. The Bacterium Endosymbiont of Crithidia deanei Undergoes Coordinated Division with the Host Cell Nucleus

    PubMed Central

    Motta, Maria Cristina Machado; Catta-Preta, Carolina Moura Costa; Schenkman, Sergio; de Azevedo Martins, Allan Cezar; Miranda, Kildare; de Souza, Wanderley; Elias, Maria Carolina

    2010-01-01

    In trypanosomatids, cell division involves morphological changes and requires coordinated replication and segregation of the nucleus, kinetoplast and flagellum. In endosymbiont-containing trypanosomatids, like Crithidia deanei, this process is more complex, as each daughter cell contains only a single symbiotic bacterium, indicating that the prokaryote must replicate synchronically with the host protozoan. In this study, we used light and electron microscopy combined with three-dimensional reconstruction approaches to observe the endosymbiont shape and division during C. deanei cell cycle. We found that the bacterium replicates before the basal body and kinetoplast segregations and that the nucleus is the last organelle to divide, before cytokinesis. In addition, the endosymbiont is usually found close to the host cell nucleus, presenting different shapes during the protozoan cell cycle. Considering that the endosymbiosis in trypanosomatids is a mutualistic relationship, which resembles organelle acquisition during evolution, these findings establish an excellent model for the understanding of mechanisms related with the establishment of organelles in eukaryotic cells. PMID:20865129

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

    SciTech Connect

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

    1986-10-01

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

  10. A highly infective plant-associated bacterium influences reproductive rates in pea aphids

    PubMed Central

    Hendry, Tory A.; Clark, Kelley J.; Baltrus, David A.

    2016-01-01

    Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction. PMID:26998321

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

    PubMed

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

    2002-08-01

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

  12. Co-infections and transmission dynamics in a tick-borne bacterium community exposed to songbirds.

    PubMed

    Heylen, Dieter; Fonville, Manoj; van Leeuwen, Arieke Docters; Sprong, Hein

    2016-03-01

    We investigated the transmission dynamics of a community of tick-borne pathogenic bacteria in a common European songbird (Parus major). Tick-naïve birds were infested with three successive batches (spaced 5 days apart) of field-collected Ixodes ricinus nymphs, carrying the following tick-borne bacteria: Rickettsia helvetica (16.9%), Borrelia garinii (1.9%), Borrelia miyamotoi (1.6%), Anaplasma phagocytophilum (1.2%) and Candidatus Neoehrlichia mikurensis (0.4%). Fed ticks were screened for the pathogens after moulting to the next developmental phase. We found evidence for early transmission (within 2.75 days after exposure) of R. helvetica and B. garinii, and to a lesser extent of A. phagocytophilum based on the increased infection rates of ticks during the first infestation. The proportion of ticks infected with R. helvetica remained constant over the three infestations. In contrast, the infection rate of B. garinii in the ticks increased over the three infestations, indicating a more gradual development of host tissue infection. No interactions were found among the different bacterium species during transmission. Birds did not transmit or amplify the other bacterial species. We show that individual birds can transmit several pathogenic bacterium species at the same time using different mechanisms, and that the transmission facilitation by birds increases the frequency of co-infections in ticks.

  13. The Fitness Effects of Spontaneous Mutations Nearly Unseen by Selection in a Bacterium with Multiple Chromosomes.

    PubMed

    Dillon, Marcus M; Cooper, Vaughn S

    2016-11-01

    Mutation accumulation (MA) experiments employ the strategy of minimizing the population size of evolving lineages to greatly reduce effects of selection on newly arising mutations. Thus, most mutations fix within MA lines independently of their fitness effects. This approach, more recently combined with genome sequencing, has detailed the rates, spectra, and biases of different mutational processes. However, a quantitative understanding of the fitness effects of mutations virtually unseen by selection has remained an untapped opportunity. Here, we analyzed the fitness of 43 sequenced MA lines of the multi-chromosome bacterium Burkholderia cenocepacia that had each undergone 5554 generations of MA and accumulated an average of 6.73 spontaneous mutations. Most lineages exhibited either neutral or deleterious fitness in three different environments in comparison with their common ancestor. The only mutational class that was significantly overrepresented in lineages with reduced fitness was the loss of the plasmid, though nonsense mutations, missense mutations, and coding insertion-deletions were also overrepresented in MA lineages whose fitness had significantly declined. Although the overall distribution of fitness effects was similar between the three environments, the magnitude and even the sign of the fitness of a number of lineages changed with the environment, demonstrating that the fitness of some genotypes was environmentally dependent. These results present an unprecedented picture of the fitness effects of spontaneous mutations in a bacterium with multiple chromosomes and provide greater quantitative support for the theory that the vast majority of spontaneous mutations are neutral or deleterious.

  14. Nematode-Bacterium Symbioses - Cooperation and Conflict Revealed in the 'Omics' Age

    PubMed Central

    Murfin, Kristen E.; Dillman, Adler R.; Foster, Jeremy M.; Bulgheresi, Silvia; Slatko, Barton E.; Sternberg, Paul W.; Goodrich-Blair, Heidi

    2012-01-01

    Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for investigating host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a diversity of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions, and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we will discuss the importance and diversity of nematodes, 'omics' studies in nematode-bacterial systems, and the wider implications of the findings. PMID:22983035

  15. Characterization of a Marine Bacterium Associated with Crassostrea virginica (the Eastern Oyster)

    PubMed Central

    Weiner, Ronald M.; Segall, Anca M.; Colwell, Rita R.

    1985-01-01

    A gram-negative bacterium found to be closely associated with oysters has been isolated and characterized. The organism, designated LST, has a generation time of 106 min in Marine broth under optimal growth conditions at 25°C. During the decline phase of growth, it exhibits a morphological transition from a motile rod (ca. 1 μm in length) to an elongated, 3- to 40-μm, nonmotile, tightly coiled helix. LST synthesizes and releases a pigment in the stationary and decline phases of growth. Identified as melanin on the basis of chemical properties and UV absorbance maxima, the pigment comprises polymers of heterogeneous molecular weights, ranging from 12,000 to 120,000. The guanosine-plus-cytosine content of the LST DNA is 46%, and results of phenetic analysis and DNA-DNA hybridization indicate that this bacterium represents a new species. LST adheres to a variety of surfaces, including glass, plastics, and oyster shell, and has been shown to promote the settlement of oyster larvae. Images PMID:16346712

  16. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    SciTech Connect

    Gardner, Jeffrey G.

    2016-06-04

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. Furthermore, this review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.

  17. Inhibitory effect of the natural product betulin and its derivatives against the intracellular bacterium Chlamydia pneumoniae.

    PubMed

    Salin, Olli; Alakurtti, Sami; Pohjala, Leena; Siiskonen, Antti; Maass, Viola; Maass, Matthias; Yli-Kauhaluoma, Jari; Vuorela, Pia

    2010-10-15

    Chlamydia pneumoniae is a universal pathogen that has been indicated to play a part in the development of asthma, atherosclerosis and lung cancer. The complete eradication of this intracellular bacterium is in practice impossible with the antibiotics that are currently in use and studies on new antichlamydial compounds is challenging because Chlamydia research lacks the tools required for the genetic modification of this bacterium. Betulin is a natural lupane-class triterpene derived from plants with a wide variety of biological activities. This compound group thus has wide medical potentials, and in fact has been shown to be active against intracellular pathogens. For this reason, betulin and its derivatives were selected to be assayed against C. pneumoniae in the present study. Thirty-two betulin derivatives were assayed against C. pneumoniae using an acute infection model in vitro. Five promising compounds with potential lead compound characteristics were identified. Compound 24 (betulin dioxime) gave a minimal inhibitory concentration (MIC) of 1 microM against strain CWL-029 and showed activity in nanomolar concentrations, as 50% inhibition was achieved at 290 nM. The antichlamydial effect of 24 was confirmed with a clinical isolate CV-6, showing a MIC of 2.2 microM. Previous research on betulin and its derivatives has not identified such a remarkable inhibition of Gram-negative bacterial growth. Furthermore, we also demonstrated that this antichlamydial activity was not due to PLA(2) (EC 3.1.1.4) inhibition caused by the betulin derivatives.

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

    PubMed

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

    2010-09-01

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

  19. Influence of yeast and lactic acid bacterium on the constituent profile of soy sauce during fermentation.

    PubMed

    Harada, Risa; Yuzuki, Masanobu; Ito, Kotaro; Shiga, Kazuki; Bamba, Takeshi; Fukusaki, Eiichiro

    2017-02-01

    Soy sauce is a Japanese traditional seasoning composed of various constituents that are produced by various microbes during a long-term fermentation process. Due to the complexity of the process, the investigation of the constituent profile during fermentation is difficult. Metabolomics, the comprehensive study of low molecular weight compounds in biological samples, is thought to be a promising strategy for deep understanding of the constituent contribution to food flavor characteristics. Therefore, metabolomics is suitable for the analysis of soy sauce fermentation. Unfortunately, only few and unrefined studies of soy sauce fermentation using metabolomics approach have been reported. Therefore, we investigated changes in low molecular weight hydrophilic and volatile compounds of soy sauce using gas chromatography/mass spectrometry (GC/MS)-based non-targeted metabolic profiling. The data were analyzed by statistical analysis to evaluate influences of yeast and lactic acid bacterium on the constituent profile. Consequently, our results suggested a novel finding that lactic acid bacterium affected the production of several constituents such as cyclotene, furfural, furfuryl alcohol and methional in the soy sauce fermentation process.

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

    NASA Astrophysics Data System (ADS)

    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.