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Sample records for oxidizing bacterium nitrosomonas

  1. 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.

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

    PubMed

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

    2004-01-01

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

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

    PubMed Central

    Nakagawa, Tatsunori; Takahashi, Reiji

    2015-01-01

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

  4. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

    SciTech Connect

    Stein, Lisa Y; Arp, D J; Berube, PM; Chain, Patrick S. G.; Hauser, Loren John; Jetten, MSM; Klotz, Martin G; Larimer, Frank W; Norton, Jeanette M.; Op den Camp, HJM; Shin, M; Wei, Xueming

    2007-12-01

    Analysis of the structure and inventory of the genome of Nitrosomonas eutropha C91 revealed distinctive features that may explain the adaptation of N. eutropha-like bacteria to N-saturated ecosystems. Multiple gene-shuffling events are apparent, including mobilized and replicated transposition, as well as plasmid or phage integration events into the 2.66 Mbp chromosome and two plasmids (65 and 56 kbp) of N. eutropha C91. A 117 kbp genomic island encodes multiple genes for heavy metal resistance, including clusters for copper and mercury transport, which are absent from the genomes of other ammonia-oxidizing bacteria (AOB). Whereas the sequences of the two ammonia monooxygenase and three hydroxylamine oxidoreductase gene clusters in N. eutropha C91 are highly similar to those of Nitrosomonas europaea ATCC 19718, a break of synteny in the regions flanking these clusters in each genome is evident. Nitrosomonas eutropha C91 encodes four gene clusters for distinct classes of haem-copper oxidases, two of which are not found in other aerobic AOB. This diversity of terminal oxidases may explain the adaptation of N. eutropha to environments with variable O2 concentrations and/or high concentrations of nitrogen oxides. As with N. europaea, the N. eutropha genome lacks genes for urease metabolism, likely disadvantaging nitrosomonads in low-nitrogen or acidic ecosystems. Taken together, this analysis revealed significant genomic variation between N. eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization.

  5. Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718.

    PubMed

    Kozlowski, Jessica A; Price, Jennifer; Stein, Lisa Y

    2014-08-01

    Nitrite reductase (NirK) and nitric oxide reductase (NorB) have long been thought to play an essential role in nitrous oxide (N2O) production by ammonia-oxidizing bacteria. However, essential gaps remain in our understanding of how and when NirK and NorB are active and functional, putting into question their precise roles in N2O production by ammonia oxidizers. The growth phenotypes of the Nitrosomonas europaea ATCC 19718 wild-type and mutant strains deficient in expression of NirK, NorB, and both gene products were compared under atmospheric and reduced O2 tensions. Anoxic resting-cell assays and instantaneous nitrite (NO2 (-)) reduction experiments were done to assess the ability of the wild-type and mutant N. europaea strains to produce N2O through the nitrifier denitrification pathway. Results confirmed the role of NirK for efficient substrate oxidation of N. europaea and showed that NorB is involved in N2O production during growth at both atmospheric and reduced O2 tensions. Anoxic resting-cell assays and measurements of instantaneous NO2 (-) reduction using hydrazine as an electron donor revealed that an alternate nitrite reductase to NirK is present and active. These experiments also clearly demonstrated that NorB was the sole nitric oxide reductase for nitrifier denitrification. The results of this study expand the enzymology for nitrogen metabolism and N2O production by N. europaea and will be useful to interpret pathways in other ammonia oxidizers that lack NirK and/or NorB genes. PMID:24907318

  6. Methane oxidation by Nitrosomonas europaea.

    PubMed Central

    Hyman, M R; Wood, P M

    1983-01-01

    Methane inhibited NH4+ utilization by Nitrosomonas europaea with a Ki of 2mM. O2 consumption was not inhibited. In the absence of NH4+, or with hydrazine as reductant, methane caused nearly a doubling in the rate of O2 uptake. The stimulation was abolished by allylthiourea, a sensitive inhibitor of the oxidation of NH4+. Analysis revealed that methanol was being formed in these experiments, with yields approaching 1 mol of methanol per mol of O2 consumed under certain conditions. When cells were incubated with NH4+ under an atmosphere of 50% methane, 50 microM-methanol was generated in 1 h. It is concluded that methane is an alternative substrate for the NH3-oxidizing enzyme (ammonia mono-oxygenase),m albeit with a much lower affinity than for methane mono-oxygenase of methanotrophs. PMID:6870854

  7. 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. PMID:26358065

  8. Specific inhibitors of ammonia oxidation in Nitrosomonas.

    PubMed

    Hooper, A B; Terry, K R

    1973-08-01

    The following compounds or treatments have been shown to inhibit the oxidation of ammonia, but not the oxidation of hydroxylamine in cells of Nitrosomonas: (i) metal-binding agents such as allylthiourea or potassium cyanide; (ii) compounds such as SKF 525 which interact with cytochrome P-450 of mammalian microsomes; (iii) carbon monoxide; (iv) inhibitors of catalase, peroxidase, and amine oxidases such as thiosemicarbazide, ethylxanthate, and iproniazid, respectively; (v) uncouplers of oxidative phosphorylation such as m-chlorocarbonylcyanidephenylhydrazone; (vi) electron acceptors such as phenazine methosulfate; (vii) compounds such as methanol or N(2)O which react with free radicals; and (viii) illumination with 420 lux (5,000 foot candles) of light. PMID:4725614

  9. Specific Inhibitors of Ammonia Oxidation in Nitrosomonas

    PubMed Central

    Hooper, Alan B.; Terry, Kathleen R.

    1973-01-01

    The following compounds or treatments have been shown to inhibit the oxidation of ammonia, but not the oxidation of hydroxylamine in cells of Nitrosomonas: (i) metal-binding agents such as allylthiourea or potassium cyanide; (ii) compounds such as SKF 525 which interact with cytochrome P-450 of mammalian microsomes; (iii) carbon monoxide; (iv) inhibitors of catalase, peroxidase, and amine oxidases such as thiosemicarbazide, ethylxanthate, and iproniazid, respectively; (v) uncouplers of oxidative phosphorylation such as m-chlorocarbonylcyanidephenylhydrazone; (vi) electron acceptors such as phenazine methosulfate; (vii) compounds such as methanol or N2O which react with free radicals; and (viii) illumination with 420 lux (5,000 foot candles) of light. PMID:4725614

  10. Methane Oxidation by Nitrosococcus oceanus and Nitrosomonas europaea†

    PubMed Central

    Jones, Ronald D.; Morita, Richard Y.

    1983-01-01

    Chemolithotrophic ammonium-oxidizing and nitrite-oxidizing bacteria including Nitrosomonas europaea, Nitrosococcus oceanus, Nitrobacter sp., Nitiospina gracilis, and Nitrococcus mobilis were examined as to their ability to oxidize methane in the absence of ammonium or nitrite. All ammonium oxidizers tested had the ability to oxidize significant amounts of methane to CO2 and incorporate various amounts into cellular components. None of the nitrite-oxidizing bacteria were capable of methane oxidation. The methane-oxidizing capabilities of Nitrosococcus oceanus and Nitrosomonas europaea were examined with respect to ammonium and methane concentrations, nitrogen source, and pH. The addition of ammonium stimulated both CO2 production and cellular incorporation of methane-carbon by both organisms. Less than 0.1 mM CH4 in solution inhibited the oxidation of ammonium by Nitrosococcus oceanus by 87%. Methane concentrations up to 1.0 mM had no inhibitory effects on ammonium oxidation by Nitrosomonas europaea. In the absence of NH4-N, Nitrosococcus oceanus achieved a maximum methane oxidation rate of 2.20 × 10−2 μmol of CH4 h−1 mg (dry weight) of cells−1, which remained constant as the methane concentration was increased. In the presence of NH4-N (10 ppm [10 μg/ml]), its maximum rate was 26.4 × 10−2 μmol of CH4 h−1 mg (dry weight) of cells−1 at a methane concentration of 1.19 × 10−2 mM. Increasing the methane concentration above this level decreased CO2 production, whereas cellular incorporation of methane-carbon continued to increase. Nitrosomonas europaea showed a linear response throughout the test range, with an activity of 196.0 × 10−2 μmol of CH4 h−1 mg (dry weight) of cells −1 at a methane concentration of 1.38 × 10−1 mM. Both nitrite and nitrate stimulated the oxidation of methane. The pH range was similar to that for ammonium oxidation, but the points of maximum activity were at lower values for the oxidation of methane. PMID:16346190

  11. Inhibition, Inactivation, and Recovery of Ammonia-Oxidizing Activity in Cometabolism of Trichloroethylene by Nitrosomonas europaea

    PubMed Central

    Hyman, M. R.; Russell, S. A.; Ely, R. L.; Williamson, K. J.; Arp, D. J.

    1995-01-01

    The kinetics of the cometabolism of trichloroethylene (TCE) by the ammonia-oxidizing soil bacterium Nitrosomonas europaea in short-term (<10-min) incubations were investigated. Three individual effects of TCE cometabolism on this bacterium were characterized. First, we observed that TCE is a potent competitive inhibitor of ammonia oxidation by N. europaea. The K(infi) value for TCE (30 (mu)M) is similar to the K(infm) for ammonia (40 (mu)M). Second, we examined the toxicity associated with TCE cometabolism by N. europaea. Stationary-phase cells of N. europaea oxidized approximately 60 nmol of TCE per mg of protein before ammonia-oxidizing activity was completely inactivated by reactive intermediates generated during TCE oxidation. At the TCE concentrations used in these experiments, ammonia did not provide significant protection against inactivation. Third, we have determined the ability of cells to recover ammonia-oxidizing activity after exposure to TCE. Cells recovering from TCE inactivation were compared with cells recovering from the specific inactivation of ammonia-oxidizing activity by light. The recovery kinetics were indistinguishable when 40% or less of the activity was inactivated. However, at increased levels of inactivation, TCE-inactivated cells did not recover as rapidly as light-inactivated cells. The kinetics of recovery appear to be dependent on both the extent of inactivation of ammonia-oxidizing activity and the degree of specificity of the inactivating treatment. PMID:16534997

  12. Toxicity of binary mixtures of metal oxide nanoparticles to Nitrosomonas europaea.

    PubMed

    Yu, Ran; Wu, Junkang; Liu, Meiting; Zhu, Guangcan; Chen, Lianghui; Chang, Yan; Lu, Huijie

    2016-06-01

    Although the widely used metal oxide nanoparticles (NPs) titanium dioxide NPs (n-TiO2), cerium dioxide NPs (n-CeO2), and zinc oxide NPs (n-ZnO) have been well known for their potential cytotoxicities to environmental organisms, their combined effects have seldom been investigated. In this study, the short-term binary effect of n-CeO2 and n-TiO2 or n-ZnO on a model ammonia oxidizing bacterium, Nitrosomonas europaea were evaluated based on the examinations of cells' physiological, metabolic, and transcriptional responses. The addition of n-TiO2 mitigated the negative effect of more toxic n-CeO2 and the binary toxicity (antagonistic toxicity) of n-TiO2 and n-CeO2 was generally lower than the single NPs induced one. While the n-CeO2/n-ZnO mixture exerted higher cytotoxicity (synergistic cytotoxicity) than that from single NPs. The increased addition of the less toxic n-CeO2 exaggerated the binary toxicity of n-CeO2/n-ZnO mixture although the solubility of n-ZnO was not significantly affected, which excluded the contribution of the dissolved Zn ions to the enhancement of the combined cytotoxicity. The cell membrane disturbances and NP internalizations were detected for all the NP impacted cultures and the electrostatic interactions among the two distinct NPs and the cells were expected to play a key role in mediating their direct contacts and the eventual binary nanotoxicity to the cells. PMID:27016814

  13. Anaerobic ammonium oxidation by Nitrosomonas spp. and anammox bacteria in a sequencing batch reactor.

    PubMed

    Lek Noophan, Pongsak; Sripiboon, Siriporn; Damrongsri, Mongkol; Munakata-Marr, Junko

    2009-02-01

    A sequencing batch reactor (SBR) was inoculated with mixed nitrifying bacteria from an anoxic tank at the conventional activated sludge wastewater treatment plant in Nongkhaem, Bangkok, Thailand. This enriched nitrifying culture was maintained under anaerobic conditions using ammonium (NH(4)(+)) as an electron donor and nitrite (NO(2)(-)) as an electron acceptor. Autotrophic ammonium oxidizing bacteria survived under these conditions. The enrichment period for anammox culture was over 100 days. Both ammonium and nitrite conversion rates were proportional to the biomass of ammonium oxidizing bacteria; rates were 0.08 g N/gV SS/d and 0.05 g N/g VSS/d for ammonium and nitrite, respectively, in a culture maintained for 3 months at 42 mg N/L ammonium. The nitrogen transformation rate at a ratio of NH(4)(+)-N to NO(2)(-)-N of 1:1.38 was faster, and effluent nitrogen levels were lower, than at ratios of 1:0.671, 1:2.18, and 1:3.05. Fluorescent in situ hybridization (FISH) was used to identify specific autotrophic ammonium oxidizing bacteria (Nitrosomonas spp., Candidatus Brocadia anammoxidans, and Candidatus Kuenenia stuttgartiensis). The ammonium oxidizing culture maintained at 42 mg N/L ammonium was enriched for Nitrosomonas spp. (30%) over Candidati B. anammoxidans and K. stuttgartiensis (2.1%) while the culture maintained at 210 mg N/L ammonium was dominated by Candidati B. anammoxidans and K. stuttgartiensis (85.6%). The specific nitrogen removal rate of anammox bacteria (0.6 g N/g anammox VSS/d) was significantly higher than that of ammonium oxidizing bacteria (0.4 g N/g Nitrosomonas VSS/d). Anammox bacteria removed up to 979 mg N/L/d of total nitrogen (ammonium:nitrite concentrations, 397:582 mg N/L). These results suggest significant promise of this approach for application to wastewater with high nitrogen but low carbon content, such as that found in Bangkok. PMID:18423965

  14. OXIDATION OF NITROPYRIN TO 6-CHOLORPICOLINIC ACID BY THE AMMONIA-OXIDIZING BACTERIUM NOSTROSOMAS EUROPAEA

    EPA Science Inventory

    Suspensions of Nitrosomonas europaea catalyzed the oxidation of the commercial nitrification inhibitor nitrapyrin [2-chloro-6-(trichloromethyl)-pyridine]. apid oxidation of nitrapyrin (at a concentration of 10 uM) required the concomitant oxidation of ammonia, hydroxylamine, or h...

  15. Monochloramine disinfection kinetics of Nitrosomonas europaea by propidium monoazide quantitative PCR and Live/Dead BacLight Methods

    EPA Science Inventory

    Monochloramine disinfection kinetics were determined for the pure culture ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) by two culture independent methods: (1) LIVE/DEAD® BacLight™ (LD) and (2) propidium monoazide quantitative PCR (PMA-qPCR). Both methods were f...

  16. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm.

    PubMed

    Foesel, Bärbel U; Gieseke, Armin; Schwermer, Carsten; Stief, Peter; Koch, Liat; Cytryn, Eddie; de la Torré, José R; van Rijn, Jaap; Minz, Dror; Drake, Harold L; Schramm, Andreas

    2008-02-01

    Zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. In these systems, water is purified and recycled via microbial biofilters. Here, quantitative data on nitrifier community structure of a trickling filter biofilm associated with a recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amoA) confirmed the results. The most abundant ammonia-oxidizing bacteria (AOB) were members of the Nitrosomonas sp. Nm143-lineage (6.7% of the bacterial biovolume), followed by Nitrosomonas marina-like AOB (2.2% of the bacterial biovolume). Both were outnumbered by nitrite-oxidizing bacteria of the Nitrospira marina-lineage (15.7% of the bacterial biovolume). Although more than eight other nitrifying populations were detected, including Crenarchaeota closely related to the ammonia-oxidizer 'Nitrosopumilus maritimus', their collective abundance was below 1% of the total biofilm volume; their contribution to nitrification in the biofilter is therefore likely to be negligible. PMID:18093145

  17. Ammonia-Oxidizing Bacteria in Biofilters Removing Trihalomethanes Are Related to Nitrosomonas oligotropha

    EPA Science Inventory

    Nitrifying biofilters degrading the four regulated trihalomethanes (THMs) trichloromethane (TCM), bromodichloromethane (BDCM), dibromochloromethane (DBCM), and tribromomethane (TBM) -were analyzed for the presence and activity of ammonia-oxidizing bacteria (AOB). Biofilter perfor...

  18. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.

    PubMed

    Norton, Jeanette M; Klotz, Martin G; Stein, Lisa Y; Arp, Daniel J; Bottomley, Peter J; Chain, Patrick S G; Hauser, Loren J; Land, Miriam L; Larimer, Frank W; Shin, Maria W; Starkenburg, Shawn R

    2008-06-01

    The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196(T)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments. PMID:18390676

  19. Structure of the Nitrosomonas Europaea Rh Protein

    SciTech Connect

    Li, X.; Jayachandran, S.; Nguyen, H.-H.T.; Chan, M.K.

    2009-06-01

    Amt/MEP/Rh proteins are a family of integral membrane proteins implicated in the transport of NH3, CH(2)NH2, and CO2. Whereas Amt/MEP proteins are agreed to transport ammonia (NH3/NH4+), the primary substrate for Rh proteins has been controversial. Initial studies suggested that Rh proteins also transport ammonia, but more recent evidence suggests that they transport CO2. Here we report the first structure of an Rh family member, the Rh protein from the chemolithoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea. This Rh protein exhibits a number of similarities to its Amt cousins, including a trimeric oligomeric state, a central pore with an unusual twin-His site in the middle, and a Phe residue that blocks the channel for small-molecule transport. However, there are some significant differences, the most notable being the presence of an additional cytoplasmic C-terminal alpha-helix, an increased number of internal proline residues along the transmembrane helices, and a specific set of residues that appear to link the C-terminal helix to Phe blockage. This latter linkage suggests a mechanism in which binding of a partner protein to the C terminus could regulate channel opening. Another difference is the absence of the extracellular pi-cation binding site conserved in Amt/Mep structures. Instead, CO2 pressurization experiments identify a CO2 binding site near the intracellular exit of the channel whose residues are highly conserved in all Rh proteins, except those belonging to the Rh30 subfamily. The implications of these findings on the functional role of the human Rh antigens are discussed.

  20. Prevalence of Nitrosomonas cluster 7 populations in the ammonia-oxidizing community of a submerged membrane bioreactor treating urban wastewater under different operation conditions.

    PubMed

    Cerrone, F; Poyatos, J M; Molina-Muñoz, M; Cortés-Lorenzo, C; González-López, J; Rodelas, B

    2013-07-01

    A pilot-scale ultrafiltration membrane bioreactor (MBR) was used for the aerobic treatment of urban wastewater in four experimental stages influenced by seasonal temperature and different sets of operation conditions. The structure of the ammonia-oxidizing bacteria (AOB) community was profiled by temperature gradient gel electrophoresis (TGGE), based on the amplification and separation of partial ammonia-monoxygenase subunit A (amoA) genes. Canonical correspondence analysis revealed that temperature, hydraulic retention time and percentage of ammonia removal had a significant effect on the fingerprints of AOB communities. Phylogenetic analysis conducted on amoA/AmoA sequences of reamplified TGGE bands showed, however, that closely related ammonia-oxidizing populations inhabited the sludge of the MBR in all experimental stages. Nitrosomonas cluster 7 populations (N. europaea-N. eutropha cluster) prevailed under all conditions tested, even when the MBR was operated under complete biomass retention or at low temperatures, suggesting that the high ammonia concentrations in the system were determinant to select r-strategist AOB. PMID:22976820

  1. Energy coupling and respiration in Nitrosomonas europaea.

    PubMed

    Drozd, J W

    1976-11-01

    Intact cells of Nitrosomonas europaea grown in an ammonium salts medium will oxidise ammonium ions, hydroxylamine and ascorbate-TMPD; there is no oxidation of carbon monoxide, methane or methanol. The Km value for ammonia oxidation is highly pH dependent with a minimum value of 0.5 mM above pH 8.0. This suggests that free ammonia is the species crossing the cytoplasmic membrane(s). The measurement of respiration driven proton translocation indicates that there is probably only one proton translocating loop (loop 3) association with hydroxylamine oxidation. The oxidation of "endogenous" substrates is sometimes associated with more than one proton-translocating loop. These results indicate that during growth hydroxylamine oxidation is probably associated with a maximum P/O ratio of 1. PMID:13754

  2. Cytotoxicity of sulfurous acid on cell membrane and bioactivity of Nitrosomonas europaea.

    PubMed

    Jiang, Ruiyu; Wang, Mingqing; Xue, Jianliang; Xu, Ning; Hou, Guihua; Zhang, Wubing

    2015-01-01

    Nitrosomonas europaea, an ammonia oxidizing bacterium, was chosen as a research model to study the alteration of cell membrane in the presence of sulfurous acid and biodegradation of acetochlor. Significant changes of the outer cell membrane were observed in the presence of sulfurous acid using scanning electron microscopy (SEM) and Atomic Force Microscopy (AFM). The fluorescence polarization has shown a significant decrease in membrane fluidity and the increase of permeability of cell membrane. Lysozyme experiment show the cell becomes easily influenced by substance in medium. Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) measurements show considerable amount of Ca(2+) and Mg(2+) in the supernatant from the sulfurous acid exposed cells. Sulfurous acid treatment enhanced the ability of N. europaea to degrade acetochlor. On this basis, it can be concluded that the increased cell permeability is favor for the absorbability of nutrition. As a result, N. europaea grows faster and the biodegradation efficiency was improved. PMID:25240954

  3. Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad

    PubMed Central

    Kozlowski, Jessica A.; Kits, K. Dimitri

    2016-01-01

    The complete genome of Nitrosomonas ureae strain Nm10, a mesophilic betaproteobacterial ammonia oxidizer isolated from Mediterranean soils in Sardinia, Italy, is reported here. This genome represents a cluster 6a nitrosomonad. PMID:26966201

  4. Transformations of Aromatic Compounds by Nitrosomonas europaea

    PubMed Central

    Keener, William K.; Arp, Daniel J.

    1994-01-01

    Benzene and a variety of substituted benzenes inhibited ammonia oxidation by intact cells of Nitrosomonas europaea. In most cases, the inhibition was accompanied by transformation of the aromatic compound to a more oxidized product or products. All products detected were aromatic, and substituents were often oxidized but were not separated from the benzene ring. Most transformations were enhanced by (NH4)2SO4 (12.5 mM) and were prevented by C2H2, a mechanism-based inactivator of ammonia monooxygenase (AMO). AMO catalyzed alkyl substituent hydroxylations, styrene epoxidation, ethylbenzene desaturation to styrene, and aniline oxidation to nitrobenzene (and unidentified products). Alkyl substituents were preferred oxidation sites, but the ring was also oxidized to produce phenolic compounds from benzene, ethylbenzene, halobenzenes, phenol, and nitrobenzene. No carboxylic acids were identified. Ethylbenzene was oxidized via styrene to two products common also to oxidation of styrene; production of styrene is suggestive of an electron transfer mechanism for AMO. Iodobenzene and 1,2-dichlorobenzene were oxidized slowly to halophenols; 1,4-dichlorobenzene was not transformed. No 2-halophenols were detected as products. Several hydroxymethyl (-CH2OH)-substituted aromatics and p-cresol were oxidized by C2H2-treated cells to the corresponding aldehydes, benzaldehyde was reduced to benzyl alcohol, and o-cresol and 2,5-dimethylphenol were not depleted. PMID:16349282

  5. 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

  6. 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.

  7. Crystal structure of a novel red copper protein from Nitrosomonas europaea

    SciTech Connect

    Lieberman, R.L.; Arciero, D.M.; Hooper, A.B.; Rosenzweig, A.C.

    2010-03-08

    Nitrosocyanin (NC) is a mononuclear red copper protein isolated from the ammonia oxidizing bacterium Nitrosomonas europaea. Although NC exhibits some sequence homology to classic blue copper proteins, its spectroscopic and electrochemical properties are drastically different. The 1.65 {angstrom} resolution crystal structure of oxidized NC reveals an unprecedented trimer of single domain cupredoxins. Each copper center is partially covered by an unusual extended {beta}-hairpin structure from an adjacent monomer. The copper ion is coordinated by His 98, His 103, Cys 95, a single side chain oxygen of Glu 60, and a solvent molecule. In the 2.3 {angstrom} resolution structure of reduced NC, His 98 shifts away from the copper ion, and the solvent molecule is not observed. The arrangement of these ligands renders the coordination geometry of the NC red copper center distinct from that of blue copper centers. In particular, the red copper center has a higher coordination number and lacks the long Cu-S(Met) and short Cu-S(Cys) bond distances characteristic of blue copper. Moreover, the red copper center is square pyramidal whereas blue copper is typically distorted tetrahedral. Analysis of the NC structure provides insight into possible functions of this new type of biological copper center.

  8. Superoxide Production by a Manganese-Oxidizing Bacterium Facilitates Iodide Oxidation

    PubMed Central

    Li, Hsiu-Ping; Daniel, Benjamin; Creeley, Danielle; Grandbois, Russell; Zhang, Saijin; Xu, Chen; Ho, Yi-Fang; Schwehr, Kathy A.; Kaplan, Daniel I.; Santschi, Peter H.; Hansel, Colleen M.

    2014-01-01

    The release of radioactive iodine (i.e., iodine-129 and iodine-131) from nuclear reprocessing facilities is a potential threat to human health. The fate and transport of iodine are determined primarily by its redox status, but processes that affect iodine oxidation states in the environment are poorly characterized. Given the difficulty in removing electrons from iodide (I−), naturally occurring iodide oxidation processes require strong oxidants, such as Mn oxides or microbial enzymes. In this study, we examine iodide oxidation by a marine bacterium, Roseobacter sp. AzwK-3b, which promotes Mn(II) oxidation by catalyzing the production of extracellular superoxide (O2−). In the absence of Mn2+, Roseobacter sp. AzwK-3b cultures oxidized ∼90% of the provided iodide (10 μM) within 6 days, whereas in the presence of Mn(II), iodide oxidation occurred only after Mn(IV) formation ceased. Iodide oxidation was not observed during incubations in spent medium or with whole cells under anaerobic conditions or following heat treatment (boiling). Furthermore, iodide oxidation was significantly inhibited in the presence of superoxide dismutase and diphenylene iodonium (a general inhibitor of NADH oxidoreductases). In contrast, the addition of exogenous NADH enhanced iodide oxidation. Taken together, the results indicate that iodide oxidation was mediated primarily by extracellular superoxide generated by Roseobacter sp. AzwK-3b and not by the Mn oxides formed by this organism. Considering that extracellular superoxide formation is a widespread phenomenon among marine and terrestrial bacteria, this could represent an important pathway for iodide oxidation in some environments. PMID:24561582

  9. Factors limiting aliphatic chlorocarbon degradation by Nitrosomonas europaea: Cometabolic inactivation of ammonia monooxygenase and substrate specificity

    SciTech Connect

    Rasche, M.E.; Hyman, M.R.; Arp, D.J. )

    1991-10-01

    The soil nitrifying bacterium Nitrosomonas europaea is capable of degrading trichloroethylene (TCE) and other halogenated hydrocarbons. TCE cometabolism by N. europaea resulted in an irreversible loss of TCE biodegradative capacity, ammonia-oxidizing activity, and ammonia-dependent O{sub 2} uptake by the cells. Inactivation was not observed in the presence of allylthiourea, a specific inhibitor of enzyme ammonia monooxygenase, or under anaerobic conditions, indicating that the TCE-mediated inactivation required ammonia monooxygenase activity. When N. europaea cells were incubated with ({sup 14}C)TCE under conditions which allowed turnover of ammonia monooxygenase, a number of cellular proteins were covalently labeled with {sup 14}C. Treatment of cells with allylthiourea or acetylene prior to incubation with ({sup 14}C)TCE prevented incorporation of {sup 14}C into proteins. The ammonia-oxidizing activity of cells inactivated in the presence of TCE could be recovered through a process requiring de novo protein synthesis. In addition to TCE, a series of chlorinated methanes, ethanes, and other ethylenes were screened as substrates for ammonia monooxygenase and for their ability to inactivate the ammonia-oxidizing system of N. europaea. The chlorocarbons would be divided into three classes depending on their biodegradability and inactivating potential: (1) compounds which were not biodegradable by N. europaea and which had no toxic effect on the cells (2) compounds which were cooxidized by N. europaea and had little or no toxic effect on the cells; and (3) compounds which were cooxidized and produced a turnover-dependent inactivation of ammonia oxidation by N. europaea.

  10. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

    NASA Astrophysics Data System (ADS)

    Frame, C. H.; Casciotti, K. L.

    2010-09-01

    Nitrous oxide (N2O) is a trace gas that contributes to the greenhouse effect and stratospheric ozone depletion. The N2O yield from nitrification (moles N2O-N produced per mole ammonium-N consumed) has been used to estimate marine N2O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O yield from nitrification is not constant. Previous culture-based measurements indicate that N2O yield increases as oxygen (O2) concentration decreases and as nitrite (NO2-) concentration increases. Here, we have measured yields of N2O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM) media. These yields, which were typically between 4 × 10-4 and 7 × 10-4 for cultures with cell densities between 2 × 102 and 2.1 × 104 cells ml-1, were lower than previous reports for ammonia-oxidizing bacteria. The observed impact of O2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5 × 106 cells ml-1), where 160-fold higher yields were observed at 0.5% O2 (5.1 μM dissolved O2) compared with 20% O2 (203 μM dissolved O2). At lower cell densities (2 × 102 and 2.1 × 104 cells ml-1), cultures grown under 0.5% O2 had yields that were only 1.25- to 1.73-fold higher than cultures grown under 20% O2. Thus, previously reported many-fold increases in N2O yield with dropping O2 could be reproduced only at cell densities that far exceeded those of ammonia oxidizers in the ocean. The presence of excess NO2- (up to 1 mM) in the growth medium also increased N2O yields by an average of 70% to 87% depending on O2 concentration. We made stable isotopic measurements on N2O from these cultures to identify the biochemical mechanisms behind variations in N2O yield. Based on measurements of δ15Nbulk, site preference (SP = δ15Nα-δ15Nβ), and δ18O of N2O (δ18O-N2O), we estimate that nitrifier

  11. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

    NASA Astrophysics Data System (ADS)

    Frame, C. H.; Casciotti, K. L.

    2010-04-01

    Nitrous oxide (N2O) is a trace gas that contributes to greenhouse warming of the atmosphere and stratospheric ozone depletion. The N2O yield from nitrification (moles N2O-N produced/mole ammonium-N consumed) has been used to estimate marine N2O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O yield from nitrification is not constant. Previous culture-based measurements indicate that N2O yield increases as oxygen (O2) concentration decreases and as nitrite (NO2-) concentration increases. These results were obtained in substrate-rich conditions and may not reflect N2O production in the ocean. Here, we have measured yields of N2O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM) media. These yields were lower than previous reports, between 4×10-4 and 7×10-4 (moles N/mole N). The observed impact of O2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5×10oxidizers in the ocean. The presence of excess NO2- (up to 1 mM) in the growth medium also increased N2O yields by an average of 70% to 87% depending on O2 concentration. We made stable isotopic measurements on N2O from these cultures to identify the biochemical mechanisms behind variations in N2O yield. Based on measurements of δ15N, site preference (SP=δ15Nα - δ15Nβ), and δ18O, we estimate that nitrifier-denitrification produced between 11% and 26% of N2O from cultures

  12. Inhibition and gene expression of Nitrosomonas europaea biofilms exposed to phenol and toluene.

    PubMed

    Lauchnor, Ellen G; Radniecki, Tyler S; Semprini, Lewis

    2011-04-01

    Pure culture biofilms of the ammonia-oxidizing bacterium Nitrosomonas europaea were grown in a Drip Flow Biofilm Reactor and exposed to the aromatic hydrocarbons phenol and toluene. Ammonia oxidation rates, as measured by nitrite production in the biofilms, were inhibited 50% when exposed to 56 µM phenol or 100 µM toluene, while 50% inhibition of suspended cells occurred at 8 µM phenol or 20 µM toluene. Biofilm-grown cells dispersed into liquid medium and immediately exposed to phenol or toluene experienced similar inhibition levels as batch grown cells, indicating that mass transfer may be a factor in N. europaea biofilm resistance. Whole genome microarray analysis of gene expression was used to detect genes up-regulated in biofilms during toluene and phenol exposure. Two genes, a putative pirin protein (NE1545) and a putative inner membrane protein (NE1546) were up-regulated during phenol exposure, but no genes were up-regulated during toluene exposure. Using qRT-PCR, up-regulation of NE1545 was detected in biofilms and suspended cells exposed to a range of phenol concentrations and levels of inhibition. In the biofilms, NE1545 expression was up-regulated an average of 13-fold over the range of phenol concentrations tested, and was essentially independent of phenol concentration. However, the expression of NE1545 in suspended cells increased from 20-fold at 7 µM phenol up to 80-fold at 30 µM phenol. This study demonstrates that biofilms of N. europaea are more resistant than suspended cells to inhibition of ammonia oxidation by phenol and toluene, even though the global transcriptional responses to the inhibitors do not differ in N. europaea between the suspended and attached growth states. PMID:21404249

  13. Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, “Candidatus Brocadia sinica”

    PubMed Central

    Oshiki, Mamoru; Shinyako-Hata, Kaori; Satoh, Hisashi

    2015-01-01

    A draft genome sequence of an anaerobic ammonium-oxidizing (anammox) bacterium, “Candidatus Brocadia sinica,” was determined by pyrosequencing and by screening a fosmid library. A 4.07-Mb genome sequence comprising 3 contigs was assembled, in which 3,912 gene-coding regions, 47 tRNAs, and a single rrn operon were annotated. PMID:25883286

  14. Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea.

    PubMed

    Bennett, Kristen; Sadler, Natalie C; Wright, Aaron T; Yeager, Chris; Hyman, Michael R

    2016-04-01

    Nitrosomonas europaea is an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2 (-)) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4 (+)-dependent O2 uptake by N. europaea by 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, andde novoprotein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and matrix-assisted laser desorption ionization-tandem time of flight (MALDI-TOF/TOF) analyses also confirmed that the fluorescent 28-kDa polypeptide was AmoA. PMID:26826234

  15. Influence of Water Hardness on Silver Ion and Silver Nanoparticle Fate and Toxicity Toward Nitrosomonas europaea

    PubMed Central

    Anderson, Joseph W.; Semprini, Lewis; Radniecki, Tyler S.

    2014-01-01

    Abstract This study investigated the influence of water hardness (Mg2+ and Ca2+) on the fate and toxicity of 20 nm citrate silver nanoparticles (AgNPs) and Ag+ toward Nitrosomonas europaea, a model ammonia-oxidizing bacterium. Nitrification inhibition of N. europaea by 1 ppm AgNPs and 0.5 ppm Ag+ was reduced from 80% and 83%, respectively, in the absence of Mg2+ to 2% and 33%, respectively, in the presence of 730 μM Mg2+. Introduction of Mg2+ resulted in the rapid aggregation of the AgNP suspensions and reduced the 3 h Ag+ dissolution rates from 30%, in the absence of Mg2+, to 9%, in the presence of 730 μM Mg2+. Reduced AgNP dissolution rates resulted in decreased concentrations of silver that were found adsorbed to N. europaea cells. Increasing AgNP concentrations in the presence of Mg2+ increased the observed inhibition of nitrification, but was always less than what was observed in the absence of Mg2+. The presence of Mg2+ also reduced the adsorption of Ag+ to cells, possibly due to multiple mechanisms, including a reduction in the negative surface charge of the N. europaea membrane and a competition between Mg2+ and Ag+ for membrane binding sites and transport into the cells. Ca2+ demonstrated similar protection mechanisms, as Ag+ toxicity was reduced and AgNP suspensions aggregated and decreased their dissolution rates. These results indicate that the toxicity of Ag+ and AgNPs to nitrifying bacteria in wastewater treatment would be less pronounced in systems with hard water. PMID:25053878

  16. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002.

    PubMed

    Weber, Karrie A; Hedrick, David B; Peacock, Aaron D; Thrash, J Cameron; White, David C; Achenbach, Laurie A; Coates, John D

    2009-06-01

    A lithoautotrophic, Fe(II) oxidizing, nitrate-reducing bacterium, strain 2002 (ATCC BAA-1479; =DSM 18807), was isolated as part of a study on nitrate-dependent Fe(II) oxidation in freshwater lake sediments. Here we provide an in-depth phenotypic and phylogenetic description of the isolate. Strain 2002 is a gram-negative, non-spore forming, motile, rod-shaped bacterium which tested positive for oxidase, catalase, and urease. Analysis of the complete 16S rRNA gene sequence placed strain 2002 in a clade within the family Neisseriaceae in the order Nessieriales of the Betaproteobacteria 99.3% similar to Pseudogulbenkiania subflava. Similar to P. sublfava, predominant whole cell fatty acids were identified as 16:17c, 42.4%, and 16:0, 34.1%. Whole cell difference spectra of the Fe(II) reduced minus nitrate oxidized cyctochrome content revealed a possible role of c-type cytochromes in nitrate-dependent Fe(II) oxidation. Strain 2002 was unable to oxidize aqueous or solid-phase Mn(II) with nitrate as the electron acceptor. In addition to lithotrophic growth with Fe(II), strain 2002 could alternatively grow heterotrophically with long-chain fatty acids, simple organic acids, carbohydrates, yeast extract, or casamino acids. Nitrate, nitrite, nitrous oxide, and oxygen also served as terminal electron acceptors with acetate as the electron donor. PMID:19333599

  17. 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.

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

    PubMed

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

    2013-12-01

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

  19. 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. PMID:26024808

  20. Extracellular haem peroxidases mediate Mn(II) oxidation in a marine Roseobacter bacterium via superoxide production.

    PubMed

    Andeer, Peter F; Learman, Deric R; McIlvin, Matt; Dunn, James A; Hansel, Colleen M

    2015-10-01

    Manganese (Mn) oxides are among the strongest sorbents and oxidants in environmental systems. A number of biotic and abiotic pathways induce the oxidation of Mn(II) to Mn oxides. Here, we use a combination of proteomic analyses and activity assays, to identify the enzyme(s) responsible for extracellular superoxide-mediated Mn oxide formation by a bacterium within the ubiquitous Roseobacter clade. We show that animal haem peroxidases (AHPs) located on the outer membrane and within the secretome are responsible for Mn(II) oxidation. These novel peroxidases have previously been implicated in direct Mn(II) oxidation by phylogenetically diverse bacteria. Yet, we show that in this Roseobacter species, AHPs mediate Mn(II) oxidation not through a direct reaction but by producing superoxide and likely also by degrading hydrogen peroxide. These findings point to a eukaryotic-like oscillatory oxidative-peroxidative enzymatic cycle by these AHPs that leads to Mn oxide formation by this organism. AHP expression appears unaffected by Mn(II), yet the large energetic investment required to produce and secrete these enzymes points to an as yet unknown physiological function. These findings are further evidence that bacterial peroxidases and secreted enzymes, in general, are unappreciated controls on the cycling of metals and reactive oxygen species (ROS), and by extension carbon, in natural systems. PMID:25923595

  1. Anaerobic arsenite oxidation by an autotrophic arsenite-oxidizing bacterium from an arsenic-contaminated paddy soil.

    PubMed

    Zhang, Jun; Zhou, Wuxian; Liu, Bingbing; He, Jian; Shen, Qirong; Zhao, Fang-Jie

    2015-05-19

    Microbe-mediated arsenic (As) redox reactions play an important role in the biogeochemical cycling of As. Reduction of arsenate [As(V)] generally leads to As mobilization in paddy soils and increased As availability to rice plants, whereas oxidation of arsenite [As(III)] results in As immobilization. A novel chemoautotrophic As(III)-oxidizing bacterium, designated strain SY, was isolated from an As-contaminated paddy soil. The isolate was able to derive energy from the oxidation of As(III) to As(V) under both aerobic and anaerobic conditions using O2 or NO3(-) as the respective electron acceptor. Inoculation of the washed SY cells into a flooded soil greatly enhanced As(III) oxidation to As(V) both in the solution and adsorbed phases of the soil. Strain SY is phylogenetically closely related to Paracoccus niistensis with a 16S rRNA gene similarity of 96.79%. The isolate contains both the denitrification and ribulose 1,5-bisphosphate carboxylase/oxygenase gene clusters, underscoring its ability to denitrify and to fix CO2 while coupled to As(III) oxidation. Deletion of the aioA gene encoding the As(III) oxidase subunit A abolished the As(III) oxidation ability of strain SY and led to increased sensitivity to As(III), suggesting that As(III) oxidation is a detoxification mechanism in this bacterium under aerobic and heterotrophic growth conditions. Analysis of the aioA gene clone library revealed that the majority of the As(III)-oxidizing bacteria in the soil were closely related to the genera Paracoccus of α-Proteobacteria. Our results provide direct evidence for As(III) oxidation by Paracoccus species and suggest that these species may play an important role in As(III) oxidation in paddy soils under both aerobic and denitrifying conditions. PMID:25905768

  2. Coupled Mn(II) Oxidation Pathways by a Planktonic Roseobacter-like Bacterium

    NASA Astrophysics Data System (ADS)

    Hansel, C. M.; Francis, C. A.

    2005-12-01

    Bacteria belonging to the Roseobacter clade of the alpha-Proteobacteria are numerically abundant in coastal waters, ecologically significant in the cycling of (in)organic sulfur, and occupy a wide range of environmental niches. Here we reveal that Roseobacter-like bacteria may play a previously unrecognized role in the oxidation and cycling of manganese (Mn) in coastal waters. A diverse array of Mn(II)-oxidizing Roseobacter-like species were isolated from Elkhorn Slough, a coastal estuary adjacent to Monterey Bay, California. One isolate (designated AzwK-3b), in particular, rapidly oxidizes Mn(II) to insoluble Mn(III, IV) oxides. Interestingly, AzwK-3b is 100% identical (at the 16S rRNA level) to a previously reported Pfiesteria-associated Roseobacter-like bacterium, which does not posses the ability to oxidize Mn(II). Manganese(II) oxidation rates by live cultures and cell-free filtrates are substantially higher when incubated in the presence of light. Rates of oxidation by washed cell extracts, however, are light independent, which are actually identical to rates by cell-free filtrates incubated in the dark. Thus, AwwK-3b induces two Mn(II) oxidation mechanisms when incubated in the presence of light as opposed to predominantly direct enzymatic oxidation in the dark. Within the light, production of photochemically-active metabolites is coupled with initial direct enzymatic Mn(II) oxidation, resulting in substantially accelerated Mn(II) oxidation rates. Thus, Roseobacter-like bacteria may not only greatly influence Mn(II) oxidation and cycling within coastal surface waters, but may also induce a novel photo-oxidation pathway providing an alternative means of Mn(II) oxidation within the photic zone.

  3. Coupled Photochemical and Enzymatic Mn(II) Oxidation Pathways of a Planktonic Roseobacter-Like Bacterium

    PubMed Central

    Hansel, Colleen M.; Francis, Chris A.

    2006-01-01

    Bacteria belonging to the Roseobacter clade of the α-Proteobacteria occupy a wide range of environmental niches and are numerically abundant in coastal waters. Here we reveal that Roseobacter-like bacteria may play a previously unrecognized role in the oxidation and cycling of manganese (Mn) in coastal waters. A diverse array of Mn(II)-oxidizing Roseobacter-like species were isolated from Elkhorn Slough, a coastal estuary adjacent to Monterey Bay in California. One isolate (designated AzwK-3b), in particular, rapidly oxidizes Mn(II) to insoluble Mn(III, IV) oxides. Interestingly, AzwK-3b is 100% identical (at the 16S rRNA gene level) to a previously described Pfiesteria-associated Roseobacter-like bacterium, which is not able to oxidize Mn(II). The rates of manganese(II) oxidation by live cultures and cell-free filtrates are substantially higher when the preparations are incubated in the presence of light. The rates of oxidation by washed cell extracts, however, are light independent. Thus, AzwK-3b invokes two Mn(II) oxidation mechanisms when it is incubated in the presence of light, in contrast to the predominantly direct enzymatic oxidation in the dark. In the presence of light, production of photochemically active metabolites is coupled with initial direct enzymatic Mn(II) oxidation, resulting in higher Mn(II) oxidation rates. Thus, Roseobacter-like bacteria may not only play a previously unrecognized role in Mn(II) oxidation and cycling in coastal surface waters but also induce a novel photooxidation pathway that provides an alternative means of Mn(II) oxidation in the photic zone. PMID:16672501

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

    PubMed

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

    2016-01-01

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

  5. Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6

    PubMed Central

    Zhang, Xiaoxin

    2016-01-01

    Aquabacterium parvum B6 is a potential nitrate-dependent Fe(II)-oxidizing bacterium. The genes related to its denitrifying mechanism and iron metabolisms were unknown. We present the draft genome of Aquabacterium parvum B6, which could provide further insight into the nitrate-dependent Fe(II)-oxidizing mechanism of strain B6. PMID:26823591

  6. Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6.

    PubMed

    Zhang, Xiaoxin; Ma, Fang; Szewzyk, Ulrich

    2016-01-01

    Aquabacterium parvum B6 is a potential nitrate-dependent Fe(II)-oxidizing bacterium. The genes related to its denitrifying mechanism and iron metabolisms were unknown. We present the draft genome of Aquabacterium parvum B6, which could provide further insight into the nitrate-dependent Fe(II)-oxidizing mechanism of strain B6. PMID:26823591

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

    PubMed Central

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

    2016-01-01

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

  8. Physiological and transcriptional responses of Nitrosomonas europaea to TiO2 and ZnO nanoparticles and their mixtures.

    PubMed

    Yu, Ran; Wu, Junkang; Liu, Meiting; Chen, Lianghui; Zhu, Guangcan; Lu, Huijie

    2016-07-01

    The short-term combined effects of two most extensively used nanoparticles (NPs) TiO2 NPs (n-TiO2) and ZnO NPs (n-ZnO) versus their individual cytotoxicities on a model ammonia-oxidizing bacterium, Nitrosomonas europaea, were investigated at both physiological and transcriptional levels. n-ZnO exerted more serious impairment effects on cell morphology, cell density, membrane integrity, and ammonia monooxygenase activity than n-TiO2. However, the co-existing n-TiO2 displayed a dose-dependent mitigation effect on n-ZnO cytotoxicity. Consistently, the n-TiO2 and n-ZnO mixture-impacted global transcriptional expression profile, obtained with the whole-genome microarray technique, was more comparable to the n-TiO2-impacted one than that impacted by n-ZnO. The expressions of numerous genes associated with heavy metal scavenging, DNA repair, and oxidative stress response were less up-regulated under the binary impacts of NP mixture than n-ZnO. Moreover, only n-ZnO alone stimulated the up-regulations of heavy metal resistance genes, which further implied the capacity of co-existing n-TiO2 to alleviate n-ZnO cytotoxicity. In addition, the damage of cell membrane structures and the suppression of cell membrane biogenesis-related gene expressions under the influence of either individual NPs or their combinations strongly suggested that the interruption of cell membranes and the associated metabolic activities would probably be one of NPs' critical cytotoxicity mechanisms. PMID:26996914

  9. Transcription of All amoC Copies Is Associated with Recovery ofNitrosomonas europaea from Ammonia Starvation

    SciTech Connect

    Berube, Paul M.; Samudrala, Ram; Stahl, David A.

    2007-09-21

    The chemolithotrophic ammonia-oxidizing bacteriumNitrosomonas europaea is known to be highly resistant to starvationconditions. The transcriptional response of N. europaea to ammoniaaddition following short- and long-term starvation was examined by primerextension and S1 nuclease protection analyses of genes encoding enzymesfor ammonia oxidation (amoCAB operons) and CO2 fixation (cbbLS), a third,lone copy of amoC (amoC3), and two representative housekeeping genes(glyA and rpsJ). Primer extension analysis of RNA isolated from growing,starved, and recovering cells revealed two differentially regulatedpromoters upstream of the two amoCAB operons. The distal sigma 70 typeamoCAB promoter was constitutively active in the presence of ammonia, butthe proximal promoter was only active when cells were recovering fromammonia starvation. The lone, divergent copy of amoC (amoC3) wasexpressed only during recovery. Both the proximal amoC1,2 promoter andthe amoC3 promoter are similar to gram-negative sigma E promoters, thusimplicating sigma E in the regulation of the recovery response. Althoughmodeling of subunit interactions suggested that a nonconservative prolinesubstitution in AmoC3 may modify the activity of the holoenzyme,characterization of a Delta amoC3 strain showed no significant differencein starvation recovery under conditions evaluated. In contrast to the amotranscripts, a delayed appearance of transcripts for a gene required forCO2 fixation (cbbL) suggested that its transcription is retarded untilsufficient energy is available. Overall, these data revealed a programmedexit from starvation likely involving regulation by sigma E and thecoordinated regulation of catabolic and anabolic genes.

  10. Initial reactions in anaerobic ethylbenzene oxidation by a denitrifying bacterium, strain EB1.

    PubMed Central

    Ball, H A; Johnson, H A; Reinhard, M; Spormann, A M

    1996-01-01

    Initial reactions in anaerobic oxidation of ethylbenzene were investigated in a denitrifying bacterium, strain EB1. Cells of strain EB1 mineralized ethylbenzene to CO2 under denitrifying conditions, as demonstrated by conversion of 69% of [14C]ethylbenzene to 14CO2. In anaerobic suspensions of strain EB1 cells metabolizing ethylbenzene, the transient formation and consumption of 1-phenylethanol, acetophenone, and an as yet unidentified compound were observed. On the basis of growth experiments and spectroscopic data, the unknown compound is proposed to be benzoyl acetate. Cell suspension experiments using H2(18)O demonstrated that the hydroxyl group of the first product of anoxic ethylbenzene oxidation, 1-phenylethanol, is derived from water. A tentative pathway for anaerobic ethylbenzene mineralization by strain EB1 is proposed. PMID:8824622

  11. Inhibition of ammonia monooxygenase in Nitrosomonas europaea by carbon disulfide.

    PubMed Central

    Hyman, M R; Kim, C Y; Arp, D J

    1990-01-01

    Carbon disulfide has long been recognized as a potent inhibitor of nitrification, and it is the likely active component in several nitrification inhibitors suitable for field use. The effects of this compound on Nitrosomonas europaea have been investigated, and the site of action has been determined. Low concentrations of CS2 (less than 400 microM) produced a time-dependent inhibition of ammonia-dependent O2 uptake but did not inhibit hydrazine-oxidizing activity. CS2 also produced distinct changes in difference spectra of whole cells. These results suggest that ammonia monooxygenase (AMO) is the site of action of CS2. Unlike the case for thiourea and acetylene, saturating concentrations of CS2 did not fully inhibit AMO, and the inhibition resulted in a low but significant rate of ammonia-dependent O2 uptake. The effects of CS2 were not competitive with respect to ammonia concentration, and the inhibition by CS2 did not require the turnover of AMO to take effect. The ability of CS2-treated cells to incorporate [14C]acetylene into the 28-kilodalton polypeptide of AMO was used to demonstrate that the effects of CS2 are compatible with a mode of action which involves a reduction of the rate of turnover of AMO without effects on the catalytic mechanism. It is proposed that CS2 may act on AMO by reversibly reacting with a suitable nucleophilic amino acid in close proximity to the active site copper. Images PMID:2118501

  12. Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers

    PubMed Central

    Bottomley, Peter J.

    2015-01-01

    Nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional N-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The N. winogradskyi genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626, nwiI) and a putative acyl-HSL autoinducer receptor (nwi0627, nwiR) with amino acid sequences 38 to 78% identical to those in Rhodopseudomonas palustris and other Rhizobiales. Expression of nwiI and nwiR correlated with acyl-HSL production during culture. N. winogradskyi produces two distinct acyl-HSLs, N-decanoyl-l-homoserine lactone (C10-HSL) and a monounsaturated acyl-HSL (C10:1-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C10:1-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS. PMID:26092466

  13. ["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum].

    PubMed

    Zhilina, T N; Zavarzina, D G; Kolganova, T V; Turova, T P; Zavarzin, G A

    2005-01-01

    From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum." PMID:16400991

  14. Distribution of Nitrosomonas europaea and Paracoccus denitrificans Immobilized in Tubular Polymeric Gel for Nitrogen Removal

    PubMed Central

    Uemoto, Hiroaki; Saiki, Hiroshi

    2000-01-01

    To improve the cooperative removal of nitrogen by Nitrosomonas europaea and Paracoccus denitrificans, we controlled their distribution in a tubular gel. When ethanol was supplied inside the tubular gel as an electron donor, their distributions overlapped in the external region of the gel. By changing the electron donor from ethanol to gaseous hydrogen, the distribution of P. denitrificans shifted to the inside of the tube and was separated from that of N. europaea. The separation resulted in an increase of the oxidation rate of ammonia by 25%. PMID:10653756

  15. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Valois, Frederica; Bollmann, Annette; Bottomley, Peter J; Klotz, Martin G; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Sayavedra-Soto, Luis; Woyke, Tanja; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Kyrpides, Nikos; Varghese, Neha; Mikhailova, Natalia; Markowitz, Victor; Palaniappan, Krishna; Ivanova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris

    2016-01-01

    Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments. PMID:27471578

  16. Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath.

    PubMed

    Poret-Peterson, Amisha T; Graham, James E; Gulledge, Jay; Klotz, Martin G

    2008-12-01

    Methylococcus capsulatus strain Bath, a methane-oxidizing bacterium, and ammonia-oxidizing bacteria (AOB) carry out the first step of nitrification, the oxidation of ammonia to nitrite, through the intermediate hydroxylamine. AOB use hydroxylamine oxidoreductase (HAO) to produce nitrite. M. capsulatus Bath was thought to oxidize hydroxylamine with cytochrome P460 (cytL), until the recent discovery of an hao gene in its genome. We used quantitative PCR analyses of cDNA from M. capsulatus Bath incubated with CH(4) or CH(4) plus 5 mM (NH(4))(2)SO(4) to determine whether cytL and hao transcript levels change in response to ammonia. While mRNA levels for cytL were not affected by ammonia, hao mRNA levels increased by 14.5- and 31-fold in duplicate samples when a promoter proximal region of the transcript was analyzed, and by sixfold when a region at the distal end of the transcript was analyzed. A conserved open reading frame, orf2, located 3' of hao in all known AOB genomes and in M. capsulatus Bath, was cotranscribed with hao and showed increased mRNA levels in the presence of ammonia. These data led to designating this gene pair as haoAB, with the role of haoB still undefined. We also determined mRNA levels for additional genes that encode proteins involved in N-oxide detoxification: cytochrome c'-beta (CytS) and nitric oxide (NO) reductase (NorCB). Whereas cytS mRNA levels increased in duplicate samples by 28.5- and 40-fold in response to ammonia, the cotranscribed norC-norB mRNA did not increase. Our results strongly suggest that M. capsulatus Bath possesses a functional, ammonia-responsive HAO involved in nitrification. PMID:18650926

  17. Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph

    SciTech Connect

    Daniel J. Arp

    2005-05-25

    Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression: The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression: N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression: Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and

  18. Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph

    SciTech Connect

    Daniel J Arp

    2005-06-15

    Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression. The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression. N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression. Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and

  19. Axenic cultures of Nitrosomonas europaea and Nitrobacter winogradskyi in autotrophic conditions: a new protocol for kinetic studies.

    PubMed

    Farges, B; Poughon, L; Roriz, D; Creuly, C; Dussap, C-G; Lasseur, C

    2012-07-01

    As a part of a natural biological N-cycle, nitrification is one of the steps included in the conception of artificial ecosystems designed for extraterrestrial life support systems (LSS) such as Micro-Ecological Life Support System Alternative (MELiSSA) project, which is the LSS project of the European Space Agency. Nitrification in aerobic environments is carried out by two groups of bacteria in a two-step process. The ammonia-oxidizing bacteria (Nitrosomonas europaea) realize the oxidation of ammonia to nitrite, and the nitrite-oxidizing bacteria (Nitrobacter winogradskyi), the oxidation of nitrite to nitrate. In both cases, the bacteria achieve these oxidations to obtain an energy and reductant source for their growth and maintenance. Furthermore, both groups also use CO₂ predominantly as their carbon source. They are typically found together in ecosystems, and consequently, nitrite accumulation is rare. Due to the necessity of modeling accurately conversion yields and transformation rates to achieve a complete modeling of MELiSSA, the present study focuses on the experimental determination of nitrogen to biomass conversion yields. Kinetic and mass balance studies for axenic cultures of Nitrosomonas europaea and Nitrobacter winogradskyi in autotrophic conditions are performed. The follow-up of these cultures is done using flow cytometry for assessing biomass concentrations and ionic chromatography for ammonium, nitrite, and nitrate concentrations. A linear correlation is observed between cell count and optical density (OD) measurement (within a 10 % accuracy) validating OD measurements for an on-line estimation of biomass quantity even at very low biomass concentrations. The conversion between cell count and biomass concentration has been determined: 7.1 × 10¹² cells g dry matter (DM)⁻¹ for Nitrobacter and 6.3 × 10¹² cells g DM⁻¹ for Nitrosomonas. Nitrogen substrates and products are assessed redundantly showing excellent agreement for mass

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

    PubMed Central

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

    2015-01-01

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

  1. Heterotrimeric NADH-Oxidizing Methylenetetrahydrofolate Reductase from the Acetogenic Bacterium Acetobacterium woodii

    PubMed Central

    Bertsch, Johannes; Öppinger, Christian; Hess, Verena; Langer, Julian D.

    2015-01-01

    ABSTRACT The methylenetetrahydrofolate reductase (MTHFR) of acetogenic bacteria catalyzes the reduction of methylene-THF, which is highly exergonic with NADH as the reductant. Therefore, the enzyme was suggested to be involved in energy conservation by reducing ferredoxin via electron bifurcation, followed by Na+ translocation by the Rnf complex. The enzyme was purified from Acetobacterium woodii and shown to have an unprecedented subunit composition containing the three subunits RnfC2, MetF, and MetV. The stable complex contained 2 flavin mononucleotides (FMN), 23.5 ± 1.2 Fe and 24.5 ± 1.5 S, which fits well to the predicted six [4Fe4S] clusters in MetV and RnfC2. The enzyme catalyzed NADH:methylviologen and NADH:ferricyanide oxidoreductase activity but also methylene-tetrahydrofolate (THF) reduction with NADH as the reductant. The NADH:methylene-THF reductase activity was high (248 U/mg) and not stimulated by ferredoxin. Furthermore, reduction of ferredoxin, alone or in the presence of methylene-THF and NADH, was never observed. MetF or MetVF was not able to catalyze the methylene-THF-dependent oxidation of NADH, but MetVF could reduce methylene-THF using methyl viologen as the electron donor. The purified MTHFR complex did not catalyze the reverse reaction, the endergonic oxidation of methyl-THF with NAD+ as the acceptor, and this reaction could not be driven by reduced ferredoxin. However, addition of protein fractions made the oxidation of methyl-THF to methylene-THF coupled to NAD+ reduction possible. Our data demonstrate that the MTHFR of A. woodii catalyzes methylene-THF reduction according to the following reaction: NADH + methylene-THF → methyl-THF + NAD+. The differences in the subunit compositions of MTHFRs of bacteria are discussed in the light of their different functions. IMPORTANCE Energy conservation in the acetogenic bacterium Acetobacterium woodii involves ferredoxin reduction followed by a chemiosmotic mechanism involving Na

  2. [Screening, denitrification characteristics, and anaerobic ammonium oxidation ability of denitrifying bacterium aHD7].

    PubMed

    Chu, Shu-Yi; Jiang, Hui-Xia; Xiao, Ji-Bo; Shan, Sheng-Dao

    2012-11-01

    A highly efficient denitrifying bacterium aHD7 was screened from activated sludge. After static culture at 30 degrees C for 3 days, the denitrification rate of the aHD7 reached 91.7%, and during denitrification, nitrite had lower accumulation, with its concentration basically maintained at 1.8 mg x L(-1). The microscopy observation demonstrated that the aHD7 was a gram-negative bacillus, with an average size of 0.5 microm x (1.5-2.5) microm. Based on its biochemical/morphological characteristics and homologic analysis of 16S rDNA sequence, the aHD7 was identified as Pseudomonas mendocina. The investigation on the factors affecting the denitrification capacity of aHD7 showed that at the initial concentration of nitrate nitrogen being less than 276.95 mg x L(-1), the denitrification rate was almost 100%, and when the initial concentration of nitrate nitrogen was as high as 553.59 mg x L(-1), the denitrification rate could reach 66.8%, with little nitrite accumulated. Ethanol was the most suitable carbon source. C/N ratio 6-8 and pH value 6-9 benefited the denitrification. The aHD7 had a good ability of anaerobic ammonium oxidation, and its average ammonium utilization rate reached 4.56 mg x L(-1) x d(-1). PMID:23431796

  3. [Isolation, identification and oxidizing characterization of an iron-sulfur oxidizing bacterium LY01 from acid mine drainage].

    PubMed

    Liu, Yu-jiao; Yang, Xin-ping; Wang, Shi-mei; Liang, Yin

    2013-05-01

    An acidophilic iron-sulfur oxidizing bacterium LY01 was isolated from acid mine drainage of coal in Guizhou Province, China. Strain LY01 was identified as Acidithiobacillusferrooxidans by morphological and physiological characteristics, and phylogenetic analysis of its 16S rRNA gene sequence. Strain LY01 was able to grow using ferrous ion (Fe2+), elemental sulfur (S0) and pyrite as sole energy source, respectively, but significant differences in oxidation efficiency and bacterial growth were observed when different energy source was used. When strain LY01 was cultured in 9K medium with 44.2 g x L(-1) FeSO4.7H2O as the substrate, the oxidation efficiency of Fe2+ was 100% in 30 h and the cell number of strain LY01 reached to 4.2 x 10(7) cell x mL(-1). When LY01 was cultured in 9K medium with 10 g x L(-1) S0 as the substrate, 6.7% S0 oxidation efficiency, 2001 mg x L(-1) SO4(2-) concentration and 8.9 x 10(7) cell x mL(-1) cell number were observed in 21 d respectively. When LY01 was cultured with 30 g x L(-1) pyrite as the substrate, the oxidation efficiency of pyrite, SO4(2-) concentration and cell number reached 10%, 4443 mg x L(-1) and 3.4 x 10(8) cell x mL(-1) respectively in 20 d. The effects of different heavy metals (Ni2+, Pb2+) on oxidation activity of strain LY01 cultured with pyrite were investigated. Results showed that the oxidation activity of strain LY01 was inhibited to a certain extent with the addition of Ni2+ at 10-100 mg x L(-1) to the medium, but the addition of 10-100 mg x L(-1) Pb2+ had no effect on LY01 activity. PMID:23914550

  4. Bacterium-Generated Nitric Oxide Hijacks Host Tumor Necrosis Factor Alpha Signaling and Modulates the Host Cell Cycle In Vitro

    PubMed Central

    Mocca, Brian

    2012-01-01

    In mammalian cells, nitric oxide (NO·) is an important signal molecule with concentration-dependent and often controversial functions of promoting cell survival and inducing cell death. An inducible nitric oxide synthase (iNOS) in various mammalian cells produces higher levels of NO· from l-arginine upon infections to eliminate pathogens. In this study, we reveal novel pathogenic roles of NO· generated by bacteria in bacterium-host cell cocultures using Moraxella catarrhalis, a respiratory tract disease-causing bacterium, as a biological producer of NO·. We recently demonstrated that M. catarrhalis cells that express the nitrite reductase (AniA protein) can produce NO· by reducing nitrite. Our study suggests that, in the presence of pathophysiological levels of nitrite, this opportunistic pathogen hijacks host cell signaling and modulates host gene expression through its ability to produce NO· from nitrite. Bacterium-generated NO· significantly increases the secretion of tumor necrosis factor alpha (TNF-α) and modulates the expression of apoptotic proteins, therefore triggering host cell programmed death partially through TNF-α signaling. Furthermore, our study reveals that bacterium-generated NO· stalls host cell division and directly results in the death of dividing cells by reducing the levels of an essential regulator of cell division. This study provides unique insight into why NO· may exert more severe cytotoxic effects on fast growing cells, providing an important molecular basis for NO·-mediated pathogenesis in infections and possible therapeutic applications of NO·-releasing molecules in tumorigenesis. This study strongly suggests that bacterium-generated NO· can play important pathogenic roles during infections. PMID:22636782

  5. Hydrogen isotope fractionation in lipids of the methane-oxidizing bacterium Methylococcus capsulatus

    NASA Astrophysics Data System (ADS)

    Sessions, Alex L.; Jahnke, Linda L.; Schimmelmann, Arndt; Hayes, John M.

    2002-11-01

    Hydrogen isotopic compositions of individual lipids from Methylococcus capsulatus, an aerobic, methane-oxidizing bacterium, were analyzed by hydrogen isotope-ratio-monitoring gas chromatography-mass spectrometry (GC-MS). The purposes of the study were to measure isotopic fractionation factors between methane, water, and lipids and to examine the biochemical processes that determine the hydrogen isotopic composition of lipids. M. capsulatus was grown in six replicate cultures in which the δD values of methane and water were varied independently. Measurement of concomitant changes in δD values of lipids allowed estimation of the proportion of hydrogen derived from each source and the isotopic fractionation associated with the utilization of each source. All lipids examined, including fatty acids, sterols, and hopanols, derived 31.4 ± 1.7% of their hydrogen from methane. This was apparently true whether the cultures were harvested during exponential or stationary phase. Examination of the relevant biochemical pathways indicates that no hydrogen is transferred directly (with C-H bonds intact) from methane to lipids. Accordingly, we hypothesize that all methane H is oxidized to H 2O, which then serves as the H source for all biosynthesis, and that a balance between diffusion of oxygen and water across cell membranes controls the concentration of methane-derived H 2O at 31%. Values for α l/ w, the isotopic fractionation between lipids and water, were 0.95 for fatty acids and 0.85 for isoprenoid lipids. These fractionations are significantly smaller than those measured in higher plants and algae. Values for α l/ m, the isotopic fractionation between lipids and methane, were 0.94 for fatty acids and 0.79 for isoprenoid lipids. Based on these results, we predict that methanotrophs living in seawater and consuming methane with typical δD values will produce fatty acids with δD between -50 and -170‰, and sterols and hopanols with δD between -150 and -270‰.

  6. Short-term effects of TiO2, CeO2, and ZnO nanoparticles on metabolic activities and gene expression of Nitrosomonas europaea.

    PubMed

    Yu, Ran; Fang, Xiaohua; Somasundaran, Ponisseril; Chandran, Kartik

    2015-06-01

    Nanosized TiO2 (n-TiO2), CeO2 (n-CeO2), and ZnO (n-ZnO) and bulk ZnO were chosen for a 4-h exposure study on a model ammonia oxidizing bacterium, Nitrosomonas europaea. n-ZnO displayed the most serious cytotoxicity while n-TiO2 was the least toxic one. The change of cell morphologies, the retardance of specific oxygen uptake rates and ammonia oxidation rates, and the depression of amoA gene expressions under NP stresses were generally observed when the cell densities and membrane integrities were not significantly impaired yet. The TEM imaging and the synchrotron X-ray fluorescence microscopy of the NPs impacted cells revealed the increase of the corresponding intracellular Ti, Ce or Zn contents and suggested the intracellular NP accumulation. The elevation of intracellular S contents accompanied with higher K contents implied the possible activation of thiol-containing glutathione and thioredoxin production for NP stress alleviation. The NP cytotoxicity was not always a function of NP concentration. The 200 mg L(-1) n-TiO2 or n-CeO2 impacted cells displayed the similar ammonia oxidation activities but higher amoA gene expression levels than the 20 mg L(-1) NPs impacted ones. Such phenomenon further indicated the possible establishment of an anti-toxicity mechanism in N. europaea at the genetic level to redeem the weakened AMO activities along with the NP aggregation effects. PMID:25710320

  7. Investigating Nitrosomonas europaea stress biomarkers in batch, continuous culture, and biofilm reactors.

    PubMed

    Radniecki, Tyler S; Lauchnor, Ellen G

    2011-01-01

    The understanding of nitrification inhibition in ammonia oxidizing bacteria (AOB) by priority pollutants and emerging contaminants is critical in managing the nitrogen cycle to preserve current water supplies, one of the National Academy of Engineers Grand Challenges in Engineering for the twenty-first century. Nitrosomonas europaea is an excellent model AOB for nitrification inhibition experimentation due to its well-defined NH(3) metabolism and the availability of a wide range of physiological and transcriptional tools that can characterize the mechanism of nitrification inhibition and probe N. europaea's response to the inhibitor. This chapter is a compilation of the physiological and transcriptional methods that have been used to characterize nitrification inhibition of N. europaea under a wide variety of growth conditions including batch, continuously cultured, and in biofilms. The protocols presented here can be applied to other AOB, and may be readily adapted for other autotrophic bacteria (e.g., nitrite oxidizing bacteria). PMID:21514466

  8. 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).

  9. 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).

  10. Biological reduction of uranium coupled with oxidation of ammonium by Acidimicrobiaceae bacterium A6 under iron reducing conditions.

    PubMed

    Gilson, Emily R; Huang, Shan; Jaffé, Peter R

    2015-11-01

    This study investigated the possibility of links between the biological immobilization of uranium (U) and ammonium oxidation under iron (Fe) reducing conditions. The recently-identified Acidimicrobiaceae bacterium A6 (ATCC, PTA-122488) derives energy from ammonium oxidation coupled with Fe reduction. This bacterium has been found in various soil and wetland environments, including U-contaminated wetland sediments. Incubations of Acidimicrobiaceae bacteria A6 with nontronite, an Fe(III)-rich clay, and approximately 10 µM U indicate that these bacteria can use U(VI) in addition to Fe(III) as an electron acceptor in the presence of ammonium. Measurements of Fe(II) production and ammonium oxidation support this interpretation. Concentrations of approximately 100 µM U were found to entirely inhibit Acidimicrobiaceae bacteria A6 activity. These results suggest that natural sites of active ammonium oxidation under Fe reducing conditions by Acidimicrobiaceae bacteria A6 could be hotspots of U immobilization by bioreduction. This is the first report of biological U reduction that is not coupled to carbon oxidation. PMID:26525893

  11. Manganese(III) binding to a pyoverdine siderophore produced by a manganese(II)-oxidizing bacterium

    NASA Astrophysics Data System (ADS)

    Parker, Dorothy L.; Sposito, Garrison; Tebo, Bradley M.

    2004-12-01

    The possible roles of siderophores (high affinity chelators of iron(III)) in the biogeochemistry of manganese remain unknown. Here we investigate the interaction of Mn(III) with a pyoverdine-type siderophore (PVD MnB1) produced by the model Mn(II)-oxidizing bacterium Pseudomonas putida strain MnB1. PVD MnB1 confirmed typical pyoverdine behavior with respect to: (a) its absorption spectrum at 350-600 nm, both in the absence and presence of Fe(III), (b) the quenching of its fluorescence by Fe(III), (c) the formation of a 1:1 complex with Fe(III), and (d) the thermodynamic stability constant of its Fe(III) complex. The Mn(III) complex of PVD MnB1 had a 1:1 Mn:pvd molar ratio, showed fluorescence quenching, and exhibited a light absorption spectrum (A max = 408-410 nm) different from that of either PVD MnB1-Fe(III) or uncomplexed PVD MnB1. Mn(III) competed strongly with Fe(III) for binding by PVD MnB1 in culture filtrates (pH 8, 4°C). Equilibration with citrate, a metal-binding ligand, did not detectably release Mn from its PVD MnB1 complex at a citrate/PVD MnB1 molar ratio of 830 (pH 8, 4°C), whereas pyrophosphate under the same conditions removed 55% of the Mn from its PVD MnB1 complex. Most of the PVD MnB1-complexed Mn was released by reaction with ascorbate, a reducing agent, or with EDTA, a ligand that is also oxidized by Mn(III). Data on the competition for binding to PVD MnB1 by Fe(III) vs. Mn(III) were used to determine a thermodynamic stability constant (nominally at 4°C) for the neutral species MnHPVD MnB1 (log K = 47.5 ± 0.5, infinite dilution reference state). This value was larger than that determined for FeHPVD MnB1 (log K = 44.6 ± 0.5). This result has important implications for the metabolism, solubility, speciation, and redox cycling of manganese, as well as for the biologic uptake of iron.

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  13. MELiSSA third compartment: Nitrosomonas europaea and Nitrobacter winogradskyi axenic cultures in bioreactors

    NASA Astrophysics Data System (ADS)

    Cruvellier, Nelly; Lasseur, Christophe; Poughon, Laurent; Creuly, Catherine; Dussap, Gilles

    Nitrogen is a key element for the life and its balance on Earth is regulated by the nitrogen cycle. This loop includes several steps among which nitrification that permits the transformation of the ammonium into nitrate. The MELiSSA loop is an artificial ecosystem designed for life support systems (LSS). It is based on the carbon and nitrogen cycles and the recycling of the non-edible part of the higher plants and the waste produced by the crew. In this order, all the wastes are collected in the first compartment to degrade them into organic acids and CO2. These compounds are joining the second compartment which is a photoheterotrophic compartment where at the outlet an organic-free medium containing ammonium is produced. This solution will be the substrate of the third compartment where nitrification is done. This compartment has to oxidize the ammonium into nitrate, and this biological reaction needs two steps. In the MELiSSA loop, the nitrification is carried out by two bacteria: Nitrosomonas europaea ATCC® 19718™ which is oxidizing ammonia into nitrite and Nitrobacter winogradskyi ATCC® 25391™ which is producing nitrate from nitrite in the third compartment. These two bacteria are growing in axenic conditions on a fixed bed bioreactor filled with Biostyr® beads. The nitrogen compounds are controlled by Ionic Chromatography and colorimetric titration for each sample. The work presented here deals with the culture of both bacteria in pure cultures and mixed cultures in stirred and aerated bioreactors of different volumes. The first aim of our work is the characterization of the bacteria growth in bioreactors and in the nitrifying fixed-bed column. The experimental results confirm that the growth is slow; the maximal growth rate in suspended cultures is 0.054h-1 for Nitrosomonas europaea and 0.022h-1 for Nitrobacter winogradskyi. Mixed cultures are difficult to control and operate but one could be done for more than 500 hours. The characterization of the

  14. Indirect Oxidation of Co(II) in the Presence of the Marine Mn(II)-Oxidizing Bacterium Bacillus Sp. Strain SG-1

    SciTech Connect

    Murray, K.J.; Webb, S.M.; Bargar, J.R.; Tebo, B.M.; /Scripps Inst. Oceanography /SLAC, SSRL /Oregon Health Sci. U.

    2009-04-29

    Cobalt(II) oxidation in aquatic environments has been shown to be linked to Mn(II) oxidation, a process primarily mediated by bacteria. This work examines the oxidation of Co(II) by the spore-forming marine Mn(II)-oxidizing bacterium Bacillus sp. strain SG-1, which enzymatically catalyzes the formation of reactive nanoparticulate Mn(IV) oxides. Preparations of these spores were incubated with radiotracers and various amounts of Co(II) and Mn(II), and the rates of Mn(II) and Co(II) oxidation were measured. Inhibition of Mn(II) oxidation by Co(II) and inhibition of Co(II) oxidation by Mn(II) were both found to be competitive. However, from both radiotracer experiments and X-ray spectroscopic measurements, no Co(II) oxidation occurred in the complete absence of Mn(II), suggesting that the Co(II) oxidation observed in these cultures is indirect and that a previous report of enzymatic Co(II) oxidation may have been due to very low levels of contaminating Mn. Our results indicate that the mechanism by which SG-1 oxidizes Co(II) is through the production of the reactive nanoparticulate Mn oxide.

  15. A New Chemolithoautotrophic Arsenite-Oxidizing Bacterium Isolated from a Gold Mine: Phylogenetic, Physiological, and Preliminary Biochemical Studies

    PubMed Central

    Santini, Joanne M.; Sly, Lindsay I.; Schnagl, Roger D.; Macy, Joan M.

    2000-01-01

    A previously unknown chemolithoautotrophic arsenite-oxidizing bacterium has been isolated from a gold mine in the Northern Territory of Australia. The organism, designated NT-26, was found to be a gram-negative motile rod with two subterminal flagella. In a minimal medium containing only arsenite as the electron donor (5 mM), oxygen as the electron acceptor, and carbon dioxide-bicarbonate as the carbon source, the doubling time for chemolithoautotrophic growth was 7.6 h. Arsenite oxidation was found to be catalyzed by a periplasmic arsenite oxidase (optimum pH, 5.5). Based upon 16S rDNA phylogenetic sequence analysis, NT-26 belongs to the Agrobacterium/Rhizobium branch of the α-Proteobacteria and may represent a new species. This recently discovered organism is the most rapidly growing chemolithoautotrophic arsenite oxidizer known. PMID:10618208

  16. 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

    2016-01-01

    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. PMID:26941148

  17. Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing Bacterium

    PubMed Central

    Regar, Raj Kumar; Gaur, Vivek Kumar; Mishra, Gayatri; Jadhao, Sudhir; Kamthan, Mohan

    2016-01-01

    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. PMID:26941148

  18. 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

  19. Draft Genome Sequence of Geobacillus subterraneus Strain K, a Hydrocarbon-Oxidizing Thermophilic Bacterium Isolated from a Petroleum Reservoir in Kazakhstan

    PubMed Central

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

    2016-01-01

    The draft genome sequence of Geobacillus subterraneus strain K, a thermophilic aerobic oil-oxidizing bacterium isolated from production water of the Uzen high-temperature oil field in Kazakhstan, is presented here. The genome is annotated for elucidation of the genomic and phenotypic diversity of thermophilic alkane-oxidizing bacteria. PMID:27491973

  20. Draft Genome Sequence of Geobacillus subterraneus Strain K, a Hydrocarbon-Oxidizing Thermophilic Bacterium Isolated from a Petroleum Reservoir in Kazakhstan.

    PubMed

    Poltaraus, Andrey B; Sokolova, Diyana S; Grouzdev, Denis S; Ivanov, Timophey M; Malakho, Sophia G; Korshunova, Alena V; Tourova, Tatiyana P; Nazina, Tamara N

    2016-01-01

    The draft genome sequence of Geobacillus subterraneus strain K, a thermophilic aerobic oil-oxidizing bacterium isolated from production water of the Uzen high-temperature oil field in Kazakhstan, is presented here. The genome is annotated for elucidation of the genomic and phenotypic diversity of thermophilic alkane-oxidizing bacteria. PMID:27491973

  1. Test Medium for the Growth of Nitrosomonas europaea

    PubMed Central

    Sato, Chikashi; Schnoor, Jerald L.; McDonald, Donald B.; Huey, Jon

    1985-01-01

    A mineral medium for studying the growth of Nitrosomonas europaea was developed and examined. The medium was defined in terms of chemical speciation by using chemical equilibrium computer models. The medium significantly increased the metabolic activity of the organisms compared with previously developed media, yielding a specific growth rate as high as 3.0 day−1 (generation time, 5.5 h). The specific growth rate was enhanced by increasing the inoculum and was linearly correlated with the inoculum-to-total-culture volume ratio on a semilog scale. A reproducible growth rate for N. europaea was obtained with this medium under controlled experimental conditions. PMID:16346783

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

    PubMed

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

    1998-01-01

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

  3. Influence of Mn oxides on the reduction of uranium(VI) by the metal-reducing bacterium Shewanella putrefaciens

    NASA Astrophysics Data System (ADS)

    Fredrickson, James K.; Zachara, John M.; Kennedy, David W.; Liu, Chongxuan; Duff, Martine C.; Hunter, Douglas B.; Dohnalkova, Alice

    2002-09-01

    The potential for Mn oxides to modify the biogeochemical behavior of U during reduction by the subsurface bacterium Shewanella putrefaciens strain CN32 was investigated using synthetic Mn(III/IV) oxides (pyrolusite [β-MnO 2], bixbyite [Mn 2O 3] and K +-birnessite [K 4Mn 14O 27 · 8H 2O]). In the absence of bacteria, pyrolusite and bixbyite oxidized biogenic uraninite (UO 2[s]) to soluble U(VI) species, with bixbyite being the most rapid oxidant. The Mn(III/IV) oxides lowered the bioreduction rate of U(VI) relative to rates in their absence or in the presence of gibbsite (Al[OH] 3) added as a non-redox-reactive surface. Evolved Mn(II) increased with increasing initial U(VI) concentration in the biotic experiments, indicating that valence cycling of U facilitated the reduction of Mn(III/IV). Despite an excess of the Mn oxide, 43 to 100% of the initial U was bioreduced after extended incubation. Analysis of thin sections of bacterial Mn oxide suspensions revealed that the reduced U resided in the periplasmic space of the bacterial cells. However, in the absence of Mn(III/IV) oxides, UO 2(s) accumulated as copious fine-grained particles external to the cell. These results indicate that the presence of Mn(III/IV) oxides may impede the biological reduction of U(VI) in subsoils and sediments. However, the accumulation of U(IV) in the cell periplasm may physically protect reduced U from oxidation, promoting at least a temporal state of redox disequilibria.

  4. Gene function analysis in extremophiles: the "nif" regulon of the strict iron oxidizing bacterium "Leptospirillum ferrooxidans"

    NASA Astrophysics Data System (ADS)

    Parro, Victor; Moreno-Paz, Mercedes

    2004-03-01

    In Centro de Astrobiologia it has been considered the Tinto river as a model ecosystem to study life based on iron. The final goal is to study the biological and metabolic diversity in microorganisms living there, following a genomic approach, to get insights to the mechanisms of adaptation to this environment. The Gram-negative bacterium Leptospirillum ferrooxidans is one of the most abundant microorganisms in the river, and it is one of the main responsible in maintenance of pH balance and, as a consequence, the physico-chemical properties of the exosystem. We have constructed a Shotgun DNA microarrays from this bacterium and we have used it to studied its genetic capacity for nitrogen fixation. With this approach we have identified most of the genes necessary for dinitrogen (N2) reduction, confirming the capacity of L. ferrooxidans as a free diazotrophic (nitrogen fixer) microorganism.

  5. Predicting Structure and Function for Novel Proteins of an Extremophilic Iron Oxidizing Bacterium

    NASA Astrophysics Data System (ADS)

    Wheeler, K.; Zemla, A.; Banfield, J.; Thelen, M.

    2007-12-01

    Proteins isolated from uncultivated microbial populations represent the functional components of microbial processes and contribute directly to community fitness under natural conditions. Investigations into proteins in the environment are hindered by the lack of genome data, or where available, the high proportion of proteins of unknown function. We have identified thousands of proteins from biofilms in the extremely acidic drainage outflow of an iron mine ecosystem (1). With an extensive genomic and proteomic foundation, we have focused directly on the problem of several hundred proteins of unknown function within this well-defined model system. Here we describe the geobiological insights gained by using a high throughput computational approach for predicting structure and function of 421 novel proteins from the biofilm community. We used a homology based modeling system to compare these proteins to those of known structure (AS2TS) (2). This approach has resulted in the assignment of structures to 360 proteins (85%) and provided functional information for up to 75% of the modeled proteins. Detailed examination of the modeling results enables confident, high-throughput prediction of the roles of many of the novel proteins within the microbial community. For instance, one prediction places a protein in the phosphoenolpyruvate/pyruvate domain superfamily as a carboxylase that fills in a gap in an otherwise complete carbon cycle. Particularly important for a community in such a metal rich environment is the evolution of over 25% of the novel proteins that contain a metal cofactor; of these, one third are likely Fe containing proteins. Two of the most abundant proteins in biofilm samples are unusual c-type cytochromes. Both of these proteins catalyze iron- oxidation, a key metabolic reaction supporting the energy requirements of this community. Structural models of these cytochromes verify our experimental results on heme binding and electron transfer reactivity, and

  6. Copper-containing protein from the membranes of methane oxidizing bacterium Methylococcus capsulatus (strain M) containing methane monooxygenase

    SciTech Connect

    Burbaev, D.Sh.; Moroz, I.A.; Gvozdev, R.I. |

    1994-12-31

    The goal of the present work was to study copper-containing center of the membrane of methane oxidizing bacterium, M. capsulatus, strain M, by ESR spectroscopy. The bacteria were grown and the membrane preparation particles, fraction O{sub 1} were isolated as described earlier. The results reveal that the fraction of particles mediating oxidation of CH{sub 4} includes a Cu-protein with a minimal molecular mass of 49 kD. This protein has the type 2 ESR signal characteristic of copper with nitrogen-containing ligands. Histidine residues are most probable ligands. The protein is likely to be incorporated into pMMO, although its function (electron transfer, activation of {sub 2}) is far for clear.

  7. Influence of Mn oxides on the reduction of U(VI) by the metal-reducing bacterium Shewanella putrefaciens

    SciTech Connect

    Fredrickson, Jim K.; Zachara, John M.; Kennedy, David W.; Liu, Chongxuan; Duff, Martine C.; Hunter, David; Dohnalkova, Alice

    2002-09-16

    Dissimilatory metal-reducing bacteria (DMRB) enzymatically reduce Fe(III), Mn(III/IV), U(VI), and other polyvalent metals during anaerobic respiration. Previous investigations of the bacterial reduction of U(VI) in the presence of goethite (a-FeOOH) found that, in spite of potential competition as an electron acceptor, goethite had little impact on the bacterial reduction of U(VI) to insoluble U(IV). Mn(III/IV) oxides are also electron acceptors for DMRB but are stronger oxidants than Fe(III) oxides. Differences in the solubility of oxidized Mn and U challenges predictions of their biogeochemical behavior during redox cycling. The potential for Mn oxides to modify the biogeochemical behavior of U during reduction by a subsurface bacterium Shewanella putrefaciens CN32 was investigated using synthetic Mn(III/IV) oxides [pyrolusite ({beta}-MnO{sub 2}), bixbyite (Mn{sub 2}O{sub 3}) and K{sup +}-birnessite (K{sub 4}Mn{sub 14}O{sub 27} {center_dot} 8H{sub 2}O)]. In the absence of bacteria, pyrolusite and bixbyite oxidized biogenic uraninite (UO{sub 2}(s)) to soluble U(VI) species, with bixbyite being the most rapid oxidant. The Mn(III/IV) oxides lowered the bioreduction rate of U(VI) relative to rates in their absence, or in the presence of gibbsite [Al(OH){sub 3}] added as a non-redox reactive surface. Evolved Mn(II) increased with increasing initial U(VI) concentration in the biotic experiments, indicating that valence cycling of U facilitated the reduction of Mn(III/IV). Despite an excess of the Mn oxide, 43-100% of the initial U was bioreduced after extended incubation. Analysis of thin sections of bacterial-Mn oxide suspensions revealed that the reduced U resided in the periplasmic space of the bacterial cells. In the absence of Mn(III/IV) oxides, UO{sub 2}(s) accumulated as copius fine-grained particles external to the cell. These results indicate that the presence of Mn(III/IV) oxides may impede the biological reduction of U(VI) in subsoils and sediments?.

  8. 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.

  9. MeLiSSA third compartment: a kinetic and stoichiometric study for Nitrosomonas europaea and Nitrobacter winogradskyi axenic cultures

    NASA Astrophysics Data System (ADS)

    Creuly, Catherine; Poughon, Laurent; Dussap, Claude-Gilles; Farges, Berangere

    2012-07-01

    As a part of a natural biological N-cycle, nitrification is one of the steps included in the conception of artificial ecosystems designed for extraterrestrial life support systems (LSS). In MELiSSA loop, which is based on carbon and nitrogen recycling, the non-edible part of the higher plants and the waste produced by the crew are collected in the liquefying compartment that degrades the chemically complex wastes into simpler building blocks (organic acids and CO2). The organic acids are eliminated in the second photoheterotrophic compartment letting an organic free medium mostly containing minerals and N-NH+4 nitrogen. The third compartment is in charge to re-oxidize N-NH+4 in order to make nitrogen usable by the following compartments. In MELiSSA, the constraint is to perform axenic cultures in order to fully control the genetic status of the culture and a thorough modelling for developing a control strategy of the compartment and of the loop, knowing that the reliability of the production of oxidized forms of nitrogen NO3- directly impacts the behaviour of the following compartments. Nitrification in aerobic environments is carried out by two groups of bacteria in co-cultures in a two-step process. The ammonia-oxidizing bacteria (Nitrosomonas europaea) realize the oxidation of ammonia to nitrite and the nitrite-oxidizing bacteria (Nitrobacter winogradskyi) the oxidation of nitrite to nitrate. In both cases, the bacteria achieve the oxidations to obtain an energy and reductant source for their growth and maintenance. Both groups use CO2 predominantly as their carbon source. They are typically found together in ecosystems and, consequently, nitrite accumulation is rare. This study concerns kinetic and mass balances studies of axenic cultures of Ns. europaea and Nb. winogradskyi in autotrophic conditions. The daily follow-up of these cultures is done using a new protocol involving flow cytometry and ionic chromatography. Nitrogen substrates and products are

  10. Toxic Effects of Linear Alkylbenzene Sulfonate on Metabolic Activity, Growth Rate, and Microcolony Formation of Nitrosomonas and Nitrosospira Strains

    PubMed Central

    Brandt, Kristian K.; Hesselso/e, Martin; Roslev, Peter; Henriksen, Kaj; So/rensen, Jan

    2001-01-01

    Strong inhibitory effects of the anionic surfactant linear alkylbenzene sulfonate (LAS) on four strains of autotrophic ammonia-oxidizing bacteria (AOB) are reported. Two Nitrosospira strains were considerably more sensitive to LAS than two Nitrosomonas strains were. Interestingly, the two Nitrosospira strains showed a weak capacity to remove LAS from the medium. This could not be attributed to adsorption or any other known physical or chemical process, suggesting that biodegradation of LAS took place. In each strain, the metabolic activity (50% effective concentration [EC50], 6 to 38 mg liter−1) was affected much less by LAS than the growth rate and viability (EC50, 3 to 14 mg liter−1) were. However, at LAS levels that inhibited growth, metabolic activity took place only for 1 to 5 days, after which metabolic activity also ceased. The potential for adaptation to LAS exposure was investigated with Nitrosomonas europaea grown at a sublethal LAS level (10 mg liter−1); compared to control cells, preexposed cells showed severely affected cell functions (cessation of growth, loss of viability, and reduced NH4+ oxidation activity), demonstrating that long-term incubation at sublethal LAS levels was also detrimental. Our data strongly suggest that AOB are more sensitive to LAS than most heterotrophic bacteria are, and we hypothesize that thermodynamic constraints make AOB more susceptible to surfactant-induced stress than heterotrophic bacteria are. We further suggest that AOB may comprise a sensitive indicator group which can be used to determine the impact of LAS on microbial communities. PMID:11375155

  11. Photoinhibition of Phaeocystis globosa resulting from oxidative stress induced by a marine algicidal bacterium Bacillus sp. LP-10

    PubMed Central

    Guan, Chengwei; Guo, Xiaoyun; Li, Yi; Zhang, Huajun; Lei, Xueqian; Cai, Guanjing; Guo, Jiajia; Yu, Zhiming; Zheng, Tianling

    2015-01-01

    Harmful algal blooms caused by Phaeocystis globosa have resulted in staggering losses to coastal countries because of their world-wide distribution. Bacteria have been studied for years to control the blooms of harmful alga, however, the action mechanism of them against harmful algal cells is still not well defined. Here, a previously isolated algicidal bacterium Bacillus sp. LP-10 was used to elucidate the potential mechanism involved in the dysfunction of P. globosa algal cells at physiological and molecular levels. Our results showed Bacillus sp. LP-10 induced an obvious rise of reactive oxygen species (ROS), which was supposed to be major reason for algal cell death. Meanwhile, the results revealed a significant decrease of photosynthetic physiological indexes and apparent down-regulated of photosynthesis-related genes (psbA and rbcS) and protein (PSII reaction center protein D1), after treated by Bacillus sp. LP-10 filtrates, suggesting photoinhibition occurred in the algal cells. Furthermore, our results indicated that light played important roles in the algal cell death. Our work demonstrated that the major lethal reason of P. globosa cells treated by the algicidal bacterium was the photoinhibition resulted from oxidative stress induced by Bacillus sp. LP-10. PMID:26601700

  12. Characterization of a novel thiosulfate dehydrogenase from a marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH.

    PubMed

    Sharmin, Sultana; Yoshino, Eriko; Kanao, Tadayoshi; Kamimura, Kazuo

    2016-01-01

    A marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH, was isolated to develop a bioleaching process for NaCl-containing sulfide minerals. Because the sulfur moiety of sulfide minerals is metabolized to sulfate via thiosulfate as an intermediate, we purified and characterized the thiosulfate dehydrogenase (TSD) from strain SH. The enzyme had an apparent molecular mass of 44 kDa and was purified 71-fold from the solubilized membrane fraction. Tetrathionate was the product of the TSD-oxidized thiosulfate and ferricyanide or ubiquinone was the electron acceptor. Maximum enzyme activity was observed at pH 4.0, 40 °C, and 200 mM NaCl. To our knowledge, this is the first report of NaCl-stimulated TSD activity. TSD was structurally different from the previously reported thiosulfate-oxidizing enzymes. In addition, TSD activity was strongly inhibited by 2-heptyl-4-hydroxy-quinoline N-oxide, suggesting that the TSD is a novel thiosulfate:quinone reductase. PMID:26393925

  13. Initial Reactions in Anaerobic Oxidation of m-Xylene by the Denitrifying Bacterium Azoarcus sp. Strain T

    PubMed Central

    Krieger, Cynthia J.; Beller, Harry R.; Reinhard, Martin; Spormann, Alfred M.

    1999-01-01

    The initial enzymatic steps in anaerobic m-xylene oxidation were studied in Azoarcus sp. strain T, a denitrifying bacterium capable of mineralizing m-xylene via 3-methylbenzoate. Permeabilized cells of m-xylene-grown Azoarcus sp. strain T catalyzed the addition of m-xylene to fumarate to form (3-methylbenzyl)succinate. In the presence of succinyl coenzyme A (CoA) and nitrate, (3-methylbenzyl)succinate was oxidized to E-(3-methylphenyl)itaconate (or a closely related isomer) and 3-methylbenzoate. Kinetic studies conducted with permeabilized cells and whole-cell suspensions of m-xylene-grown Azoarcus sp. strain T demonstrated that the specific rate of in vitro (3-methylbenzyl)succinate formation accounts for at least 15% of the specific rate of in vivo m-xylene consumption. Based on these findings, we propose that Azoarcus sp. strain T anaerobically oxidizes m-xylene to 3-methylbenzoate (or its CoA thioester) via (3-methylbenzyl)succinate and E-(3-methylphenyl)itaconate (or its CoA thioester) in a series of reactions that are analogous to those recently proposed for anaerobic toluene oxidation to benzoyl-CoA. A deuterium kinetic isotope effect was observed in the (3-methylbenzyl)succinate synthase reaction (and the benzylsuccinate synthase reaction), suggesting that a rate-determining step in this novel fumarate addition reaction involves breaking a C-H bond. PMID:10515931

  14. Purification and characterization of sulfide:quinone oxidoreductase from an acidophilic iron-oxidizing bacterium, Acidithiobacillus ferrooxidans.

    PubMed

    Wakai, Satoshi; Tsujita, Mizuho; Kikumoto, Mei; Manchur, Mohammed A; Kanao, Tadayoshi; Kamimura, Kazuo

    2007-11-01

    Sulfide:quinone oxidoreductase (SQR) was purified from membrane of acidophilic chemolithotrophic bacterium Acidithiobacillus ferrooxidans NASF-1 cells grown on sulfur medium. It was composed of a single polypeptide with an apparent molecular mass of 47 kDa. The apparent K(m) values for sulfide and ubiquinone were 42 and 14 muM respectively. The apparent optimum pH for the SQR activity was about 7.0. A gene encoding a putative SQR of A. ferrooxidans NASF-1 was cloned and sequenced. The gene was expressed in Escherichia coli as a thioredoxin-fusion protein in inclusion bodies in an inactive form. A polyclonal antibody prepared against the recombinant protein reacted immunologically with the purified SQR. Western blotting analysis using the antibody revealed an increased level of SQR synthesis in sulfur-grown A. ferrooxidans NASF-1 cells, implying the involvement of SQR in elemental sulfur oxidation in sulfur-grown A. ferrooxidans NASF-1 cells. PMID:17986789

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

    PubMed Central

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

    2016-01-01

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

  16. Electron microscopic investigation of the hydrogen-oxidizing acetate-forming anaerobic bacterium Acetobacterium woodii.

    PubMed

    Mayer, F; Lurz, R; Schoberth, S

    1977-11-18

    Acetobacterium woodii is a Gram-positive anaerobic nonsporeforming bacterium able to grow on H2 and CO2 as sole sources of energy. The product of fermentation is acetic acid. Fine structural analysis showed rod-shaped flagellated cells, and coccoid cells without flagella arranged predominantly in pairs and chains. The cell wall was found to be composed of three layers. The cell surface exhibited a periodic array of particles consisting of subunits. The cytoplasmic membrane showed particles either in random distribution or in a hexagonal pattern. Intracytoplasmic membranes were rarely observed, whereas inclusion bodies of varying shapes, predominantly in an uncommon disc-shape, could frequently be observed. Their content was dissolved in ultrathin sections indicating hydrophobic nature. PMID:596994

  17. Purification and some properties of ubiquinol oxidase from obligately chemolithotrophic iron-oxidizing bacterium, Thiobacillus ferrooxidans NASF-1.

    PubMed

    Kamimura, K; Fujii, S; Sugio, T

    2001-01-01

    Ubiquinol-oxidizing activity was detected in an acidophilic chemolithotrophic iron-oxidizing bacterium, T. ferrooxidans. The ubiquinol oxidase was purified 79-fold from plasma membranes of T. ferrooxidans NASF-1 cells. The purified oxidase is composed of two polypeptides with apparent molecular masses of 32,600 and 50,100 Da, as measured by gel electrophoresis in the presence of sodium dodecyl sulfate. The absorption spectrum of the reduced enzyme at room temperature showed big peaks at 530 and 563, and a small broad peak at 635 nm, indicating the involvement of cytochromes b and d. Characteristic peaks of cytochromes a and c were not observed in the spectrum at around 600 and 550 nm, respectively. This enzyme combined with CO, and its CO-reduced minus reduced difference spectrum showed peaks at 409 nm and 563 nm and a trough at 431 nm. These results indicated that the oxidase contained cytochrome b, but the involvement of cytochrome d was not clear. The enzyme catalyzed the oxidations of ubiquinol-2 and reduced N,N,N',N'-tetramethyl-p-phenylenediamine dihydrochloride. The ubiquinol oxidase activity was activated by the addition of albumin and lecithin to the reaction mixture and inhibited by the respiratory inhibitors KCN, HQNO, NaN3, and antimycin A1, although the enzyme was relatively resistant to KCN, and the divalent cation, Zn2+, compared with ubiquinol oxidases of E. coli. PMID:11272847

  18. 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

  19. 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. PMID:27297893

  20. Nitrogen isotopomer site preference of N2O produced by Nitrosomonas europaea and Methylococcus capsulatus Bath.

    PubMed

    Sutka, R L; Ostrom, N E; Ostrom, P H; Gandhi, H; Breznak, J A

    2003-01-01

    The relative importance of individual microbial pathways in nitrous oxide (N(2)O) production is not well known. The intramolecular distribution of (15)N in N(2)O provides a basis for distinguishing biological pathways. Concentrated cell suspensions of Methylococcus capsulatus Bath and Nitrosomonas europaea were used to investigate the site preference of N(2)O by microbial processes during nitrification. The average site preference of N(2)O formed during hydroxylamine oxidation by M. capsulatus Bath (5.5 +/- 3.5 per thousand) and N. europaea (-2.3 +/- 1.9 per thousand) and nitrite reduction by N. europaea (-8.3 +/- 3.6 per thousand) differed significantly (ANOVA, f((2,35)) = 247.9, p = 0). These results demonstrate that the mechanisms for hydroxylamine oxidation are distinct in M. capsulatus Bath and N. europaea. The average delta(18)O-N(2)O values of N(2)O formed during hydroxylamine oxidation for M. capsulatus Bath (53.1 +/- 2.9 per thousand) and N. europaea (-23.4 +/- 7.2 per thousand) and nitrite reduction by N. europaea (4.6 +/- 1.4 per thousand) were significantly different (ANOVA, f((2,35)) = 279.98, p = 0). Although the nitrogen isotope value of the substrate, hydroxylamine, was similar in both cultures, the observed fractionation (delta(15)N) associated with N(2)O production via hydroxylamine oxidation by M. capsulatus Bath and N. europaea (-2.3 and 26.0 per thousand, respectively) provided evidence that differences in isotopic fractionation were associated with these two organisms. The site preferences in this study are the first measured values for isolated microbial processes. The differences in site preference are significant and indicate that isotopomers provide a basis for apportioning biological processes producing N(2)O. PMID:12661029

  1. The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium

    PubMed Central

    Imlay, James A.

    2014-01-01

    Oxic environments are hazardous. Molecular oxygen adventitiously abstracts electrons from many redox enzymes, continuously forming intracellular superoxide and hydrogen peroxide. These species can destroy the activities of metalloenzymes and the integrity of DNA, which forces organisms to protect themselves with scavenging enzymes and repair systems. Nevertheless, elevated levels of oxidants quickly poison bacteria, and both microbial competitors and hostile eukaryotic hosts exploit this vulnerability by assaulting them with peroxides or superoxide-forming antibiotics. In response, bacteria activate elegant adaptive strategies. In this Review, I summarize our current knowledge of oxidative stress in Escherichia coli, the model organism for which our understanding of damage and defence is most well-developed. PMID:23712352

  2. Novel Essential Role of Ethanol Oxidation Genes at Low Temperature Revealed by Transcriptome Analysis in the Antarctic Bacterium Pseudomonas extremaustralis

    PubMed Central

    Tribelli, Paula M.; Solar Venero, Esmeralda C.; Ricardi, Martiniano M.; Gómez-Lozano, Maria; Raiger Iustman, Laura J.; Molin, Søren; López, Nancy I.

    2015-01-01

    Temperature is one of the most important factors for bacterial growth and development. Cold environments are widely distributed on earth, and psychrotolerant and psychrophilic microorganisms have developed different adaptation strategies to cope with the stress derived from low temperatures. Pseudomonas extremaustralis is an Antarctic bacterium able to grow under low temperatures and to produce high amounts of polyhydroxyalkanoates (PHAs). In this work, we analyzed the genome-wide transcriptome by RNA deep-sequencing technology of early exponential cultures of P. extremaustralis growing in LB (Luria Broth) supplemented with sodium octanoate to favor PHA accumulation at 8°C and 30°C. We found that genes involved in primary metabolism, including tricarboxylic acid cycle (TCA) related genes, as well as cytochromes and amino acid metabolism coding genes, were repressed at low temperature. Among up-regulated genes, those coding for transcriptional regulatory and signal transduction proteins were over-represented at cold conditions. Remarkably, we found that genes involved in ethanol oxidation, exaA, exaB and exaC, encoding a pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenase, the cytochrome c550 and an aldehyde dehydrogenase respectively, were up-regulated. Along with RNA-seq experiments, analysis of mutant strains for pqqB (PQQ biosynthesis protein B) and exaA were carried out. We found that the exaA and pqqB genes are essential for growth under low temperature in LB supplemented with sodium octanoate. Additionally, p-rosaniline assay measurements showed the presence of alcohol dehydrogenase activity at both 8°C and 30°C, while the activity was abolished in a pqqB mutant strain. These results together with the detection of ethanol by gas chromatography in P. extremaustralis cultures grown at 8°C support the conclusion that this pathway is important under cold conditions. The obtained results have led to the identification of novel components involved

  3. Novel Essential Role of Ethanol Oxidation Genes at Low Temperature Revealed by Transcriptome Analysis in the Antarctic Bacterium Pseudomonas extremaustralis.

    PubMed

    Tribelli, Paula M; Solar Venero, Esmeralda C; Ricardi, Martiniano M; Gómez-Lozano, Maria; Raiger Iustman, Laura J; Molin, Søren; López, Nancy I

    2015-01-01

    Temperature is one of the most important factors for bacterial growth and development. Cold environments are widely distributed on earth, and psychrotolerant and psychrophilic microorganisms have developed different adaptation strategies to cope with the stress derived from low temperatures. Pseudomonas extremaustralis is an Antarctic bacterium able to grow under low temperatures and to produce high amounts of polyhydroxyalkanoates (PHAs). In this work, we analyzed the genome-wide transcriptome by RNA deep-sequencing technology of early exponential cultures of P. extremaustralis growing in LB (Luria Broth) supplemented with sodium octanoate to favor PHA accumulation at 8°C and 30°C. We found that genes involved in primary metabolism, including tricarboxylic acid cycle (TCA) related genes, as well as cytochromes and amino acid metabolism coding genes, were repressed at low temperature. Among up-regulated genes, those coding for transcriptional regulatory and signal transduction proteins were over-represented at cold conditions. Remarkably, we found that genes involved in ethanol oxidation, exaA, exaB and exaC, encoding a pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenase, the cytochrome c550 and an aldehyde dehydrogenase respectively, were up-regulated. Along with RNA-seq experiments, analysis of mutant strains for pqqB (PQQ biosynthesis protein B) and exaA were carried out. We found that the exaA and pqqB genes are essential for growth under low temperature in LB supplemented with sodium octanoate. Additionally, p-rosaniline assay measurements showed the presence of alcohol dehydrogenase activity at both 8°C and 30°C, while the activity was abolished in a pqqB mutant strain. These results together with the detection of ethanol by gas chromatography in P. extremaustralis cultures grown at 8°C support the conclusion that this pathway is important under cold conditions. The obtained results have led to the identification of novel components involved

  4. Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium.

    PubMed

    Manzoor, Shahid; Müller, Bettina; Niazi, Adnan; Bongcam-Rudloff, Erik; Schnürer, Anna

    2013-01-01

    Clostridium ultunense strain Esp belongs to the functional group of syntrophic acetate-oxidizing bacteria (SAOB), which have been identified as key organisms for efficient biogas production from protein-rich materials. Genome analysis and comparative genomics might aid us to define physiological features that are essential for maintaining this particular syntrophic lifestyle. PMID:23538905

  5. Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium

    PubMed Central

    Manzoor, Shahid; Niazi, Adnan; Bongcam-Rudloff, Erik; Schnürer, Anna

    2013-01-01

    Clostridium ultunense strain Esp belongs to the functional group of syntrophic acetate-oxidizing bacteria (SAOB), which have been identified as key organisms for efficient biogas production from protein-rich materials. Genome analysis and comparative genomics might aid us to define physiological features that are essential for maintaining this particular syntrophic lifestyle. PMID:23538905

  6. First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.

    PubMed

    Manzoor, Shahid; Bongcam-Rudloff, Erik; Schnürer, Anna; Müller, Bettina

    2013-01-01

    Syntrophic acetate-oxidizing bacteria (SAOB) have been identified as key organisms for efficient biogas production from protein-rich materials. Tepidanaerobacter acetatoxydans is the first reported SAOB for which the genome has been sequenced. Genome analysis will aid us in understanding the mechanisms regulating syntrophy, particularly energy-conserving and electron transfer mechanisms. PMID:23469343

  7. First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1

    PubMed Central

    Manzoor, Shahid; Bongcam-Rudloff, Erik; Schnürer, Anna

    2013-01-01

    Syntrophic acetate-oxidizing bacteria (SAOB) have been identified as key organisms for efficient biogas production from protein-rich materials. Tepidanaerobacter acetatoxydans is the first reported SAOB for which the genome has been sequenced. Genome analysis will aid us in understanding the mechanisms regulating syntrophy, particularly energy-conserving and electron transfer mechanisms. PMID:23469343

  8. Draft Genome Sequence of the Methane-Oxidizing Bacterium Methylococcus capsulatus (Texas)

    PubMed Central

    Hult, Lene T. Olsen; Kuczkowska, Katarzyna; Jacobsen, Morten; Lea, Tor; Pope, Phillip B.

    2012-01-01

    Methanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic activities that enable the oxidation of one-carbon compounds, most notably methane. Here we describe the annotated draft genome sequence of the aerobic methanotroph Methylococcus capsulatus (Texas), a type strain originally isolated from sewer sludge. PMID:23144383

  9. Draft genome sequence of the methane-oxidizing bacterium Methylococcus capsulatus (Texas).

    PubMed

    Kleiveland, Charlotte R; Hult, Lene T Olsen; Kuczkowska, Katarzyna; Jacobsen, Morten; Lea, Tor; Pope, Phillip B

    2012-12-01

    Methanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic activities that enable the oxidation of one-carbon compounds, most notably methane. Here we describe the annotated draft genome sequence of the aerobic methanotroph Methylococcus capsulatus (Texas), a type strain originally isolated from sewer sludge. PMID:23144383

  10. Involvement of sulfide:quinone oxidoreductase in sulfur oxidation of an acidophilic iron-oxidizing bacterium, Acidithiobacillus ferrooxidans NASF-1.

    PubMed

    Wakai, Satoshi; Kikumoto, Mei; Kanao, Tadayoshi; Kamimura, Kazuo

    2004-12-01

    The effects of cyanide, azide, and 2-n-Heptyl-4-hydroxy-quinoline-N-oxide (HQNO) on the oxidation of ferrous ion or elemental sulfur with Acidithiobacillus ferrooxidans NASF-1 cells grown in iron- or sulfur-medium were examined. The iron oxidation of both iron- and sulfur-grown cells was strongly inhibited by cyanide and azide, but not by HQNO. Sulfur oxidation was relatively resistant to cyanide and azide, and inhibited by HQNO. Higher sulfide oxidation, ubiquinol dehydrogenase activity, and sulfide:quinone oxidoreductase (SQR) activity were observed in sulfur-grown cells more than in iron-grown cells. Sulfide oxidation in the presence of ubiquinone with the membrane fraction was inhibited by HQNO, but not by cyanide, azide, antimycin A, and myxothiazol. The transcription of three genes, encoding an aa(3)-type cytochrome c oxidase (coxB), a bd-type ubiquinol oxidase (cydA), and an sqr, were measured by real-time reverse transcription polymerase chain reaction. The transcriptional levels of coxB and cydA genes were similar in sulfur- and iron-grown cells, but that of sqr was 3-fold higher in sulfur-grown cells than in iron-grown cells. A model is proposed for the oxidation of reduced inorganic sulfur compounds in A. ferrooxidans NASF-1 cells. PMID:15618623

  11. Pyoverdine synthesis by the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1

    PubMed Central

    Parker, Dorothy L.; Lee, Sung-Woo; Geszvain, Kati; Davis, Richard E.; Gruffaz, Christelle; Meyer, Jean-Marie; Torpey, Justin W.; Tebo, Bradley M.

    2014-01-01

    When iron-starved, the Mn(II)-oxidizing bacteria Pseudomonas putida strains GB-1 and MnB1 produce pyoverdines (PVDGB-1 and PVDMnB1), siderophores that both influence iron uptake and inhibit manganese(II) oxidation by these strains. To explore the properties and genetics of a PVD that can affect manganese oxidation, LC-MS/MS, and various siderotyping techniques were used to identify the peptides of PVDGB-1 and PVDMnB1 as being (for both PVDs): chromophore-Asp-Lys-OHAsp-Ser-Gly-aThr-Lys-cOHOrn, resembling a structure previously reported for P. putida CFML 90-51, which does not oxidize Mn. All three strains also produced an azotobactin and a sulfonated PVD, each with the peptide sequence above, but with unknown regulatory or metabolic effects. Bioinformatic analysis of the sequenced genome of P. putida GB-1 suggested that a particular non-ribosomal peptide synthetase (NRPS), coded by the operon PputGB1_4083-4086, could produce the peptide backbone of PVDGB-1. To verify this prediction, plasmid integration disruption of PputGB1_4083 was performed and the resulting mutant failed to produce detectable PVD. In silico analysis of the modules in PputGB1_4083-4086 predicted a peptide sequence of Asp-Lys-Asp-Ser-Ala-Thr-Lsy-Orn, which closely matches the peptide determined by MS/MS. To extend these studies to other organisms, various Mn(II)-oxidizing and non-oxidizing isolates of P. putida, P. fluorescens, P. marincola, P. fluorescens-syringae group, P. mendocina-resinovorans group, and P. stutzerii group were screened for PVD synthesis. The PVD producers (12 out of 16 tested strains) were siderotyped and placed into four sets of differing PVD structures, some corresponding to previously characterized PVDs and some to novel PVDs. These results combined with previous studies suggested that the presence of OHAsp or the flexibility of the pyoverdine polypeptide may enable efficient binding of Mn(III). PMID:24847318

  12. Remediation of chromium(VI) by a methane-oxidizing bacterium.

    PubMed

    Al Hasin, Abubakr; Gurman, Stephen J; Murphy, Loretta M; Perry, Ashlee; Smith, Thomas J; Gardiner, Philip H E

    2010-01-01

    Methane-oxidizing bacteria are ubiquitous in the environment and are globally important in oxidizing the potent greenhouse gas methane. It is also well recognized that they have wide potential for bioremediation of organic and chlorinated organic pollutants, thanks to the wide substrate ranges of the methane monooxygenase enzymes that they produce. Here we have demonstrated that the well characterized model methanotroph Methylococcus capsulatus (Bath) is able to bioremediate chromium(VI) pollution over a wide range of concentrations (1.4-1000 mg L(-1) of Cr(6+)), thus extending the bioremediation potential of this major group of microorganisms to include an important heavy-metal pollutant. The chromium(VI) reduction reaction was dependent on the availability of reducing equivalents from the growth substrate methane and was partially inhibited by the metabolic poison sodium azide. X-ray spectroscopy showed that the cell-associated chromium was predominantly in the +3 oxidation state and associated with cell- or medium-derived moieties that were most likely phosphate groups. The genome sequence of Mc. capsulatus (Bath) suggests at least five candidate genes for the chromium(VI) reductase activity in this organism. PMID:20039753

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

    PubMed

    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

  14. 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

  15. Purification and some properties of sulfur reductase from the iron-oxidizing bacterium Thiobacillus ferrooxidans NASF-1.

    PubMed

    Ng, K Y; Sawada, R; Inoue, S; Kamimura, K; Sugio, T

    2000-01-01

    Thiobacillus ferrooxidans strain NASF-1 grown aerobically in an Fe2+ (3%)-medium produces hydrogen sulfide (H2S) from elemental sulfur under anaerobic conditions with argon gas at pH 7.5. Sulfur reductase, which catalyzes the reduction of elemental sulfur (S0) with NAD(P)H as an electron donor to produce hydrogen sulfide (H2S) under anaerobic conditions, was purified 69-fold after 35-65% ammonium sulfate precipitation and Q-Sepharose FF, Phenyl-Toyopearl 650 ML, and Blue Sepharose FF column chromatography, with a specific activity of 57.6 U (mg protein)(-1). The purified enzyme was quite labile under aerobic conditions, but comparatively stable in the presence of sodium hydrosulfite and under anaerobic conditions, especially under hydrogen gas conditions. The purified enzyme showed both sulfur reductase and hydrogenase activities. Both activities had an optimum pH of 9.0. Sulfur reductase has an apparent molecular weight of 120,000 Da, and is composed of three different subunits (M(r) 54,000 Da (alpha), 36,000 Da (beta), and 35,000 Da (gamma)), as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This is the first report on the purification of sulfur reductase from a mesophilic and obligate chemolithotrophic iron-oxidizing bacterium. PMID:16232842

  16. Isolation and preliminary characterization of new cytochrome c from autotrophic haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens.

    PubMed

    Antipov, Alexey N; Tishkov, Vladimir I

    2012-12-01

    New small cytochrome c (TniCYT) was purified from haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens. The protein was analyzed by mass spectrometry as well as using visible, CD and EPR spectroscopy. It was found that TniCYT is a monomer with a molecular mass of 9461 Da which contains two hemes per molecule. The data of CD and EPR spectroscopy showed that two hemes possess different optical activity and are in distinct, high and low spin states. TniCYT was also demonstrated to have unusual characteristics in the visible spectrum, namely, the splitting of characteristic peaks was observed in α- and β-bands of the heme spectrum when the reduced form of cytochrome was analyzed. The α-band has two peaks with maximum at 548 and 556 nm whereas the β-band showes ones at 520 and 528 nm. According to the MALDI finger-print analysis, the new cytochrome has a unique amino acid sequence. PMID:22809527

  17. 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.

  18. Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3

    PubMed Central

    Li, Chun-Yang; Chen, Xiu-Lan; Shao, Xuan; Wei, Tian-Di; Wang, Peng; Xie, Bin-Bin; Qin, Qi-Long; Zhang, Xi-Ying; Su, Hai-Nan; Song, Xiao-Yan; Shi, Mei; Zhou, Bai-Cheng

    2015-01-01

    ABSTRACT Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. TMAO can also be metabolized by marine bacteria into volatile methylated amines, the precursors of the greenhouse gas nitrous oxide. However, it was not known how TMAO is recognized and imported by bacteria. Ruegeria pomeroyi DSS-3, a marine Roseobacter, has an ATP-binding cassette transporter, TmoXWV, specific for TMAO. TmoX is the substrate-binding protein of the TmoXWV transporter. In this study, the substrate specificity of TmoX of R. pomeroyi DSS-3 was characterized. We further determined the structure of the TmoX/TMAO complex and studied the TMAO-binding mechanism of TmoX by biochemical, structural, and mutational analyses. A Ca2+ ion chelated by an extended loop in TmoX was shown to be important for maintaining the stability of TmoX. Molecular dynamics simulations indicate that TmoX can alternate between “open” and “closed” states for binding TMAO. In the substrate-binding pocket, four tryptophan residues interact with the quaternary amine of TMAO by cation-π interactions, and Glu131 forms a hydrogen bond with the polar oxygen atom of TMAO. The π-π stacking interactions between the side chains of Phe and Trp are also essential for TMAO binding. Sequence analysis suggests that the TMAO-binding mechanism of TmoX may have universal significance in marine bacteria, especially in the marine Roseobacter clade. This study sheds light on how marine microorganisms utilize TMAO. IMPORTANCE Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. The products of TMAO metabolized by bacteria are part of the precursors of the greenhouse gas nitrous oxide. It is unclear how TMAO is recognized and imported by bacteria. TmoX is the substrate-binding protein of a TMAO-specific transporter. Here, the substrate specificity of TmoX of Ruegeria pomeroyi DSS-3 was characterized. The TMAO-binding mechanism of TmoX was studied by biochemical, structural

  19. Hydrophobised sawdust as a carrier for immobilisation of the hydrocarbon-oxidizing bacterium Rhodococcus ruber.

    PubMed

    Podorozhko, Elena A; Lozinsky, Vladimir I; Ivshina, Irena B; Kuyukina, Maria S; Krivorutchko, Anastasiya B; Philp, Jim C; Cunningham, Colin J

    2008-04-01

    Pine sawdust treated by a series of hydrophobising agents (drying oil, organosilicon emulsion, n-hexadecane and paraffin) was examined as carrier for adsorption immobilisation of hydrocarbon-oxidizing bacterial cells Rhodococcus ruber. It was shown that hydrophobising agents based on drying oil turned out to be optimal (among the other modifiers examined) for the preparation of sawdust carriers suitable for the efficient immobilisation. The results obtained demonstrate promising possibilities in developing a wide range of available and cheap, biodegradable cellulose-containing carriers that possess varying surface hydrophobicity. PMID:17481891

  20. Uncovering a microbial enigma: isolation and characterization of the streamer-generating, iron-oxidizing, acidophilic bacterium "Ferrovum myxofaciens".

    PubMed

    Johnson, D Barrie; 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

  1. Thermithiobacillus plumbiphilus sp. nov., a sulfur-oxidizing bacterium isolated from lead sulfide.

    PubMed

    Watanabe, Tomohiro; Miura, Aya; Shinohara, Arisa; Kojima, Hisaya; Fukui, Manabu

    2016-05-01

    A novel sulfur oxidizer, strain wk12T, was isolated from an industrially synthesized lead (II) sulfide. The G+C content of the genomic DNA was around 58.5 mol%. The major components in the cellular fatty acid profile were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The strain oxidized lead sulfide, thiosulfate and tetrathionate as electron donors to support autotrophic growth. Cells of strain wk12T were motile, rod-shaped (0.5-1.0 × 0.7-2.2 μm), and Gram-stain-negative. For growth, the temperature range was 5-37 °C, and optimum growth was observed at 28-32 °C. The pH range for growth was 5.8-8.7, with optimum growth at pH 6.4-7.1. Optimum growth of the isolate was observed in medium without NaCl, and no growth was observed in the medium containing 0.5 M or more NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the class Acidithiobacillia. The closest relative with a validly published name was Thermithiobacillus tepidarius DSM 3134T, with a 16S rRNA gene sequence similarity of 96 %. On the basis of phylogenetic and phenotypic properties, strain wk12T represents a novel species of the genus Thermithiobacillus, for which the name Thermithiobacillus plumbiphilus sp. nov. is proposed. The type strain is wk12T ( = NBRC 111508T = DSM 101799T). PMID:26873326

  2. Synthesis of poly(3-hydroxybutyrate) by the autotrophic CO-oxidizing bacterium Seliberia carboxydohydrogena Z-1062.

    PubMed

    Volova, Tatiana; Zhila, Natalia; Shishatskaya, Ekaterina

    2015-10-01

    The present study addresses growth parameters and physiological and biochemical characteristics of the aerobic CO-oxidizing carboxydobacterium Seliberia carboxydohydrogena Z-1062. Poly(3-hydroxybutyrate) yields were investigated in experiments with limiting concentrations of mineral nutrients (nitrogen or sulfur or nitrogen and sulfur) in batch culture of S. carboxydohydrogena Z-1062 grown on gas mixtures consisting of CO(2), O(2), H(2), and CO. CO concentrations of 10, 20, and 30 % v/v did not affect polymer synthesis, whose content after 56-h cultivation under limiting concentrations of nitrogen and sulfur was 52.6-62.8 % of biomass weight at a productivity of 0.13-0.22 g/L h. The inhibitory effect of CO on cell concentration was revealed at CO concentration of 30 % v/v. That also caused a decrease in substrate (H(2) and O(2)) use efficiency. Thus, this carboxydobacterium can be regarded as a potential producer of polyhydroxyalkanoates from industrial hydrogenous sources. PMID:26254039

  3. Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust.

    PubMed

    Sylvan, Jason B; Hoffman, Colleen L; Momper, Lily M; Toner, Brandy M; Amend, Jan P; Edwards, Katrina J

    2015-06-01

    A facultatively anaerobic bacterium, designated strain 1MBB1T, was isolated from basaltic breccia collected from 341 m below the seafloor by seafloor drilling of Rigil Guyot during Integrated Ocean Drilling Program Expedition 330. The cells were straight rods, 0.5 μm wide and 1-3 μm long, that occurred singly and in chains. Strain 1MBB1T stained Gram-positive. Catalase and oxidase were produced. The isolate grew optimally at 30 °C and pH 7.5, and could grow with up to 12 % (w/v) NaCl. The DNA G+C content was 40.5 mol%. The major cellular fatty acids were C16:1ω11c (26.5 %), anteiso-C15:0 (19.5 %), C16:0 (18.7 %) and iso-C15:0 (10.4 %), and the cell-wall diamino acid was meso-diaminopimelic acid. Endospores of strain 1MBB1T oxidized Mn(II) to Mn(IV), and siderophore production by vegetative cells was positive. Phylogenetic analysis of the 16S rRNA gene indicated that strain 1MBB1T was a member of the family Bacillaceae, with Bacillus foraminis CV53T and Bacillus novalis LMG 21837T being the closest phylogenetic neighbours (96.5 and 96.2 % similarity, respectively). This is the first novel species described from deep subseafloor basaltic crust. On the basis of our polyphasic analysis, we conclude that strain 1MBB1T represents a novel species of the genus Bacillus, for which we propose the name Bacillus rigiliprofundi sp. nov. The type strain is 1MBB1T ( = NCMA B78T = LMG 28275T). PMID:25813363

  4. Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California, on the basis of 16S rRNA sequences.

    PubMed

    Ward, B B; Martino, D P; Diaz, M C; Joye, S B

    2000-07-01

    Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the beta subdivision of the division Proteobacteria (beta-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different beta-subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the gamma subdivision of the Proteobacteria, did not amplify target from any samples. PMID:10877781

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

    DOE PAGESBeta

    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.

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

    DOE PAGESBeta

    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.

  7. Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi).

    PubMed

    Thiel, Vera; Hamilton, Trinity L; Tomsho, Lynn P; Burhans, Richard; Gay, Scott E; Schuster, Stephan C; Ward, David M; Bryant, Donald A

    2014-01-01

    The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons. PMID:25189583

  8. Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi)

    PubMed Central

    Thiel, Vera; Hamilton, Trinity L.; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Schuster, Stephan C.; Ward, David M.

    2014-01-01

    The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons. PMID:25189583

  9. The Crystal Structure of Nitrosomonas europaea Sucrose Synthase Reveals Critical Conformational Changes and Insights into Sucrose Metabolism in Prokaryotes

    PubMed Central

    Wu, Rui; Asención Diez, Matías D.; Figueroa, Carlos M.; Machtey, Matías; Iglesias, Alberto A.; Ballicora, Miguel A.

    2015-01-01

    ABSTRACT In this paper we report the first crystal structure of a prokaryotic sucrose synthase from the nonphotosynthetic bacterium Nitrosomonas europaea. The obtained structure was in an open form, whereas the only other available structure, from the plant Arabidopsis thaliana, was in a closed conformation. Comparative structural analysis revealed a “hinge-latch” combination, which is critical to transition between the open and closed forms of the enzyme. The N. europaea sucrose synthase shares the same fold as the GT-B family of the retaining glycosyltransferases. In addition, a triad of conserved homologous catalytic residues in the family was shown to be functionally critical in the N. europaea sucrose synthase (Arg567, Lys572, and Glu663). This implies that sucrose synthase shares not only a common origin with the GT-B family but also a similar catalytic mechanism. The enzyme preferred transferring glucose from ADP-glucose rather than UDP-glucose like the eukaryotic counterparts. This predicts that these prokaryotic organisms have a different sucrose metabolic scenario from plants. Nucleotide preference determines where the glucose moiety is targeted after sucrose is degraded. IMPORTANCE We obtained biochemical and structural evidence of sucrose metabolism in nonphotosynthetic bacteria. Until now, only sucrose synthases from photosynthetic organisms have been characterized. Here, we provide the crystal structure of the sucrose synthase from the chemolithoautotroph N. europaea. The structure supported that the enzyme functions with an open/close induced fit mechanism. The enzyme prefers as the substrate adenine-based nucleotides rather than uridine-based like the eukaryotic counterparts, implying a strong connection between sucrose and glycogen metabolism in these bacteria. Mutagenesis data showed that the catalytic mechanism must be conserved not only in sucrose synthases but also in all other retaining GT-B glycosyltransferases. PMID:26013491

  10. Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1

    PubMed Central

    Liu, Juan; Wang, Zheming; Belchik, Sara M.; Edwards, Marcus J.; Liu, Chongxuan; Kennedy, David W.; Merkley, Eric D.; Lipton, Mary S.; Butt, Julea N.; Richardson, David J.; Zachara, John M.; Fredrickson, James K.; Rosso, Kevin M.; Shi, Liang

    2012-01-01

    The Gram-negative bacterium Sideroxydans lithotrophicus ES-1 (ES-1) grows on FeCO3 or FeS at oxic–anoxic interfaces at circumneutral pH, and the ES-1-mediated Fe(II) oxidation occurs extracellularly. However, the molecular mechanisms underlying ES-1’s ability to oxidize Fe(II) remain unknown. Survey of the ES-1 genome for candidate genes for microbial extracellular Fe(II) oxidation revealed that it contained a three-gene cluster encoding homologs of Shewanella oneidensis MR-1 (MR-1) MtrA, MtrB, and CymA that are involved in extracellular Fe(III) reduction. Homologs of MtrA and MtrB were also previously shown to be involved in extracellular Fe(II) oxidation by Rhodopseudomonas palustris TIE-1. To distinguish them from those found in MR-1, the identified homologs were named MtoAB and CymAES-1. Cloned mtoA partially complemented an MR-1 mutant without MtrA with regards to ferrihydrite reduction. Characterization of purified MtoA showed that it was a decaheme c-type cytochrome and oxidized soluble Fe(II). Oxidation of Fe(II) by MtoA was pH- and Fe(II)-complexing ligand-dependent. Under conditions tested, MtoA oxidized Fe(II) from pH 7 to pH 9 with the optimal rate at pH 9. MtoA oxidized Fe(II) complexed with different ligands at different rates. The reaction rates followed the order Fe(II)Cl2 >  Fe(II)–citrate > Fe(II)–NTA > Fe(II)–EDTA with the second-order rate constants ranging from 6.3 × 10−3 μM−1 s−1 for oxidation of Fe(II)Cl2 to 1.0 × 10−3 μM−1 s−1 for oxidation of Fe(II)–EDTA. Thermodynamic modeling showed that redox reaction rates for the different Fe(II)-complexes correlated with their respective estimated reaction-free energies. Collectively, these results demonstrate that MtoA is a functional Fe(II)-oxidizing protein that, by working in concert with MtoB and CymAES-1, may oxidize Fe(II) at the bacterial surface and transfer released electrons across the bacterial cell envelope to the quinone pool in the

  11. Evidence that anaerobic oxidation of toluene in the denitrifying bacterium Thauera aromatica is initiated by formation of benzylsuccinate from toluene and fumarate.

    PubMed

    Biegert, T; Fuchs, G; Heider, J

    1996-06-15

    Toluene is degraded anoxically to CO2 by the denitrifying bacterium Thauera aromatica. Toluene first becomes oxidized to benzoyl-CoA by O2-independent reactions. Benzoyl-CoA is then reduced to non-aromatic products by benzoyl-CoA reductase. We set out to study the reactions employed for the initial activation of toluene and its oxidation to the level of benzoate. Evidence is provided for a novel way of toluene degradation based on experiments with cell-free extracts and with whole toluene-grown cells: Cell-free extracts oxidized [14C]toluene to [14C]benzoyl-CoA via several radioactive intermediates. This reaction was strictly dependent on the presence of fumarate, coenzyme A and nitrate as electron acceptor; acetyl-CoA and ATP were not necessary for the reaction. The first product formed in vitro was benzylsuccinate; (2H8)toluene was converted to (2H7)benzylsuccinate. Formation of benzylsuccinate from toluene was independent of coenzyme A and nitrate, but it required the presence of fumarate. Other tricarboxylic acid cycle intermediates were converted to fumarate in cell extracts and therefore could partially substitute for fumarate. [14C]Benzylsuccinate was oxidized further to [14C]benzoyl-CoA and [14C]benzoate in cell extracts if coenzyme A and nitrate were present. No benzyl alcohol and benzaldehyde and no phenylpropionate could be detected as intermediates. In isotope trapping experiments with cell suspensions, two intermediates from [14C]toluene were detected, benzoate and benzylsuccinate. This corroborates the sequence of reactions deduced from in vitro experiments. A hypothetical degradation pathway for the anaerobic oxidation of toluene to benzoyl-CoA via an initial addition of fumarate to the methyl group of toluene and following beta-oxidation of the benzylsuccinate formed is suggested. PMID:8706665

  12. Microbial oxidative sulfur metabolism: biochemical evidence of the membrane-bound heterodisulfide reductase-like complex of the bacterium Aquifex aeolicus.

    PubMed

    Boughanemi, Souhela; Lyonnet, Jordan; Infossi, Pascale; Bauzan, Marielle; Kosta, Artémis; Lignon, Sabrina; Giudici-Orticoni, Marie-Thérèse; Guiral, Marianne

    2016-08-01

    The Hdr (heterodisulfide reductase)-like enzyme is predicted, from gene transcript profiling experiments previously published, to be essential in oxidative sulfur metabolism in a number of bacteria and archaea. Nevertheless, no biochemical and physicochemical data are available so far about this enzyme. Genes coding for it were identified in Aquifex aeolicus, a Gram-negative, hyperthermophilic, chemolithoautotrophic and microaerophilic bacterium that uses inorganic sulfur compounds as electron donor to grow. We provide biochemical evidence that this Hdr-like enzyme is present in this sulfur-oxidizing prokaryote (cultivated with thiosulfate or elemental sulfur). We demonstrate, by immunolocalization and cell fractionation, that Hdr-like enzyme is associated, presumably monotopically, with the membrane fraction. We show by co-immunoprecipitation assay or partial purification, that the Hdr proteins form a stable complex composed of at least five subunits, HdrA, HdrB1, HdrB2, HdrC1 and HdrC2, present in two forms of high molecular mass on native gel (∼240 and 450 kDa). These studies allow us to propose a revised model for dissimilatory sulfur oxidation pathways in A. aeolicus, with Hdr predicted to generate sulfite. PMID:27284018

  13. Characterizing the metabolic trade-off in Nitrosomonas europaea in response to changes in inorganic carbon supply.

    PubMed

    Jiang, D; Khunjar, W O; Wett, B; Murthy, S N; Chandran, K

    2015-02-17

    The link between the nitrogen and one-carbon cycles forms the metabolic basis for energy and biomass synthesis in autotrophic nitrifying organisms, which in turn are crucial players in engineered nitrogen removal processes. To understand how autotrophic nitrifying organisms respond to inorganic carbon (IC) conditions that could be encountered in engineered partially nitrifying systems, we investigated the response of one of the most extensively studied model ammonia oxidizing bacteria, Nitrosomonas europaea (ATCC19718), to three IC availability conditions: excess gaseous and excess ionic IC supply (40× stoichiometric requirement), excess gaseous IC supply (4× stoichiometric requirement in gaseous form only), and limiting IC supply (0.25× stoichiometric requirement). We found that, when switching from excess gaseous and excess ionic IC supply to excess gaseous IC supply, N. europaea chemostat cultures demonstrated an acclimation period that was characterized by transient decreases in the ammonia removal efficiency and transient peaks in the specific oxygen uptake rate. Limiting IC supply led to permanent reactor failures (characterized by biomass washout and failure of ammonia removal) that were preceded by similar decreases in the ammonia removal efficiency and peaks in the specific oxygen uptake rate. Notably, both excess gaseous IC supply and limiting IC supply elicited a previously undocumented increase in nitric and nitrous oxide emissions. Further, gene expression patterns suggested that excess gaseous IC supply and limiting IC supply led to consistent up-regulation of ammonia respiration genes and carbon assimilation genes. Under these conditions, interrogation of the N. europaea proteome revealed increased levels of carbon fixation and transport proteins and decreased levels of ammonia oxidation proteins (active in energy synthesis pathways). Together, the results indicated that N. europaea mobilized enhanced IC scavenging pathways for biosynthesis and

  14. Identification of Bacteria Responsible for Ammonia Oxidation in Freshwater Aquaria

    PubMed Central

    Burrell, Paul C.; Phalen, Carol M.; Hovanec, Timothy A.

    2001-01-01

    Culture enrichments and culture-independent molecular methods were employed to identify and confirm the presence of novel ammonia-oxidizing bacteria (AOB) in nitrifying freshwater aquaria. Reactors were seeded with biomass from freshwater nitrifying systems and enriched for AOB under various conditions of ammonia concentration. Surveys of cloned rRNA genes from the enrichments revealed four major strains of AOB which were phylogenetically related to the Nitrosomonas marina cluster, the Nitrosospira cluster, or the Nitrosomonas europaea-Nitrosococcus mobilis cluster of the β subdivision of the class Proteobacteria. Ammonia concentration in the reactors determined which AOB strain dominated in an enrichment. Oligonucleotide probes and PCR primer sets specific for the four AOB strains were developed and used to confirm the presence of the AOB strains in the enrichments. Enrichments of the AOB strains were added to newly established aquaria to determine their ability to accelerate the establishment of ammonia oxidation. Enrichments containing the Nitrosomonas marina-like AOB strain were most efficient at accelerating ammonia oxidation in newly established aquaria. Furthermore, if the Nitrosomonas marina-like AOB strain was present in the original enrichment, even one with other AOB, only the Nitrosomonas marina-like AOB strain was present in aquaria after nitrification was established. Nitrosomonas marina-like AOB were 2% or less of the cells detected by fluorescence in situ hybridization analysis in aquaria in which nitrification was well established. PMID:11722936

  15. Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions.

    PubMed

    Takeuchi, Mio; Yamagishi, Takao; Kamagata, Yoichi; Oshima, Kenshiro; Hattori, Masahira; Katayama, Taiki; Hanada, Satoshi; Tamaki, Hideyuki; Marumo, Katsumi; Maeda, Hiroto; Nedachi, Munetomo; Iwasaki, Wataru; Suwa, Yuichi; Sakata, Susumu

    2015-06-01

    A moderately thermophilic, aerobic, stalked bacterium (strain MA2T) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MA2T was most closely related to the genera Rhodobium,Parvibaculum, and Rhodoligotrophos (92-93 % similarity) within the class Alphaproteobacteria. Strain MA2T was a Gram-stain-negative and stalked dimorphic bacteria. The temperature range for growth was 16-48 °C (optimum growth at 42 °C). This strain required yeast extract and NaCl (>1 %, w/v) for growth, tolerated up to 11 % (w/v) NaCl, and was capable of utilizing various carbon sources. The major cellular fatty acid and major respiratory quinone were C18 : 1ω7c and ubiquinone-10, respectively. The DNA G+C content was 60.7 mol%. Strain MA2T performed denitrification and produced N2O from nitrate under strictly microaerobic conditions. Strain MA2T possessed periplasmic nitrate reductase (Nap) genes but not membrane-bound nitrate reductase (Nar) genes. On the basis of this morphological, physiological, biochemical and genetic information a novel genus and species, Tepidicaulis marinus gen. nov., sp. nov., are proposed, with MA2T ( = NBRC 109643T = DSM 27167T) as the type strain of the species. PMID:25740933

  16. D1FHS, the Type Strain of the Ammonia-Oxidizing Bacterium Nitrosococcus wardiae spec. nov.: Enrichment, Isolation, Phylogenetic, and Growth Physiological Characterization

    PubMed Central

    Wang, Lin; Lim, Chee Kent; Dang, Hongyue; Hanson, Thomas E.; Klotz, Martin G.

    2016-01-01

    An ammonia-oxidizing bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4T. The average nucleotide identity between the genomes of strain D1FHS and N. halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic ammonia-oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37°C in dark. Because pertinent conditions for other studied Nitrosococcus spp. are 100–200 mM ammonium and <700 mM NaCl at pH of 7.5 to 8.0 and at 28–32°C, D1FHS is physiologically distinct from other Nitrosococcus spp. in terms of substrate, salt, and thermal tolerance. PMID:27148201

  17. Identification and Characterization of MtoA: a Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-oxidizing Bacterium Sideroxydans lithotrophicus ES-1

    SciTech Connect

    Liu, Juan; Wang, Zheming; Belchik, Sara M.; Edwards, Marcus; Liu, Chongxuan; Kennedy, David W.; Merkley, Eric D.; Lipton, Mary S.; Butt, Julea N.; Richardson, David; Zachara, John M.; Fredrickson, Jim K.; Rosso, Kevin M.; Shi, Liang

    2012-02-08

    The Gram-negative bacterium Sideroxydans lithotrophicus ES-1 (ES-1) grows on FeCO{sub 3} or FeS at oxic-anoxic interfaces at circumneutral pH, and the ES-1-mediated Fe(II) oxidation occurs extracellularly. However, the molecular mechanisms underlying ES-1's ability to oxidize Fe(II) remain unknown. Survey of the ES-1 genome for the genes known for microbial extracellular Fe(II) oxidation revealed that it contained a three-gene cluster encoding an MtrA homologue, an MtrB homologue and a CymA homologue. The homologues of MtrA, MtrB and/or CymA were previously shown to be involved in extracellular Fe(II) oxidation by Rhodopseudomonas palustris TIE-1 and in extracellular Fe(III) reduction by Shewanella oneidensis MR-1 (MR-1). To distinguish them from those found in MR-1, the identified homologues were named MtoAB and CymA{sub ES-1}, respectively. The gene for MtoA was cloned, and cloned mtoA partially complemented an MR-1 mutant without MtrA in ferrihydrite reduction. Following overexpression in MR-1 cells, recombinant MtoA was purified. Characterization of purified MtoA showed that it was a decaheme c-type cytochrome and oxidized soluble Fe(II). Oxidation of Fe(II) by MtoA was pH- and Fe(II)-complexing ligand-dependent. Under conditions tested, MtoA oxidized Fe(II) at pH ranging from 7-9, and optimal oxidation occurred at pH 9, possibly because of the attendant net increase of [Fe(OH){sup +}] at higher pH. MtoA oxidized Fe(II) complexed with different ligands at different rates. The reaction rates followed the order Fe(II)Cl2 > Fe(II)-citrate > Fe(III)-NTA > Fe(II)-EDTA with the second-order rate constants ranging from 5.5 x 10{sup -3} {micro}M{sup -1}s{sup -1} for oxidation of Fe(II)Cl{sub 2} to 1.0 x 10{sup -3} {micro}M{sup -1}s{sup -1} for oxidation of Fe(II)-EDTA. Thermodynamic modeling shows that redox reaction rate differences for the different Fe(II)-complexes correlated with estimated reaction-free energies. Collectively, these results suggest that MtoA is a

  18. Effect of uncouplers on endogenous respiration and ferrous iron oxidation in a chemolithoautotrophic bacterium Acidithiobacillus (Thiobacillus) ferrooxidans.

    PubMed

    Chen, Yongqiang; Suzuki, Isamu

    2004-08-01

    Oxidation of ferrous iron (Fe2+) to ferric iron (Fe3+) with oxygen (O2) by Acidithiobacillus (Thiobacillus) ferrooxidans is considered to be inhibited by uncouplers. Oxidation of the endogenous substrates (presumably NADH) with O2 or Fe3+, on the other hand, was stimulated by uncouplers, 2,4-dinitrophenol (DNP) and carbonylcyanide-m-chlorophenyl-hydrazone (CCCP), as expected in respiratorily controlled mitochondria or heterotrophic bacteria. Amytal and rotenone were inhibitory. Fe3+ reduction by endogenous substrates was studied extensively and was found to be stimulated by a permeable anion, SCN- and weak acids, as well as the above uncouplers. Proton translocating properties of some of these stimulators were shown by following a pH change in the cell suspension. It was concluded that any compounds that destroy proton electrochemical gradient, Deltap, stimulated endogenous respiration. Stimulation of Fe2+ or ascorbate oxidation by lower concentrations of uncouplers was successfully demonstrated by shortening the reaction time, but only to a small extent. Uncouplers at concentrations stimulatory to endogenous respiration inhibited Fe2+ oxidation if present before Fe2+ addition. The inhibition by 10 microM CCCP was reversed by washing the cells in a buffer. Complex I inhibitors, atabrine, rotenone and amytal inhibited Fe2+ oxidation, more strongly in the presence of 0.1 mM DNP. It is proposed that Fe2+ oxidation required Deltap perhaps to climb an energetically uphill reaction or to reduce NAD+ to NADH by reversed electron flow for CO2 fixation. The latter interpretation implies some obligatory coupling between Fe2+ oxidation and NAD+ reduction. PMID:15268949

  19. Keep your Sox on: Community genomics-directed isolation and microscopic characterization of the dominant subsurface sulfur-oxidizing bacterium in a sediment aquifer

    NASA Astrophysics Data System (ADS)

    Mullin, S. W.; Wrighton, K. C.; Luef, B.; Wilkins, M. J.; Handley, K. M.; Williams, K. H.; Banfield, J. F.

    2012-12-01

    Community genomics and proteomics (proteogenomics) can be used to predict the metabolic potential of complex microbial communities and provide insight into microbial activity and nutrient cycling in situ. Inferences regarding the physiology of specific organisms then can guide isolation efforts, which, if successful, can yield strains that can be metabolically and structurally characterized to further test metagenomic predictions. Here we used proteogenomic data from an acetate-stimulated, sulfidic sediment column deployed in a groundwater well in Rifle, CO to direct laboratory amendment experiments to isolate a bacterial strain potentially involved in sulfur oxidation for physiological and microscopic characterization (Handley et al, submitted 2012). Field strains of Sulfurovum (genome r9c2) were predicted to be capable of CO2 fixation via the reverse TCA cycle and sulfur oxidation (Sox and SQR) coupled to either nitrate reduction (Nap, Nir, Nos) in anaerobic environments or oxygen reduction in microaerobic (cbb3 and bd oxidases) environments; however, key genes for sulfur oxidation (soxXAB) were not identified. Sulfidic groundwater and sediment from the Rifle site were used to inoculate cultures that contained various sulfur species, with and without nitrate and oxygen. We isolated a bacterium, Sulfurovum sp. OBA, whose 16S rRNA gene shares 99.8 % identity to the gene of the dominant genomically characterized strain (genome r9c2) in the Rifle sediment column. The 16S rRNA gene of the isolate most closely matches (95 % sequence identity) the gene of Sulfurovum sp. NBC37-1, a genome-sequenced deep-sea sulfur oxidizer. Strain OBA grew via polysulfide, colloidal sulfur, and tetrathionate oxidation coupled to nitrate reduction under autotrophic and mixotrophic conditions. Strain OBA also grew heterotrophically, oxidizing glucose, fructose, mannose, and maltose with nitrate as an electron acceptor. Over the range of oxygen concentrations tested, strain OBA was not

  20. DqsIR quorum sensing-mediated gene regulation of the extremophilic bacterium Deinococcus radiodurans in response to oxidative stress.

    PubMed

    Lin, Lin; Dai, Shang; Tian, Bing; Li, Tao; Yu, Jiangliu; Liu, Chengzhi; Wang, Liangyan; Xu, Hong; Zhao, Ye; Hua, Yuejin

    2016-05-01

    Here, we show that AHLs can be employed by Deinococcus radiodurans, which belongs to the unique phylum Deinococcus-Thermus and is known for its cellular resistance to environmental stresses. An AHL-mediated quorum-sensing system (DqsI/DqsR) was identified in D. radiodurans. We found that under non-stress conditions, the AHL level was "shielded" by quorum quenching enzymes, whereas AHLs accumulated when D. radiodurans was exposed to oxidative stress. Upon exposure to H2 O2 , AHL synthetic enzymes (DqsI) were immediately induced, while the expression of quorum-quenching enzymes began to increase approximately 30 min after exposure to H2 O2 , as shown by time-course analyses of gene expression. Both dqsI mutant (DMDqsI) and dqsR mutant (MDqsR) were more sensitive to oxidative stress compared with the wild-type strain. Exogenous AHLs (5 μM) could completely restore the survival fraction of DMDqsI under oxidative stress. RNA-seq analysis showed that a number of genes involved in stress-response, cellular cleansing, and DNA repair had altered transcriptional levels in MDqsR. The DqsR, acting as a regulator of quorum sensing, controls gene expression along with AHLs. Hence, the DqsIR-mediated quorum sensing that mediates gene regulation is an adaptive strategy for D. radiodurans in response to oxidative stresses and is conserved in the extremophilic Deinococcus bacteria. PMID:26789904

  1. Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum

    PubMed Central

    Islam, Tajul; Jensen, Sigmund; Reigstad, Laila Johanne; Larsen, Øivind; Birkeland, Nils-Kåre

    2008-01-01

    Methanotrophic bacteria constitute a ubiquitous group of microorganisms playing an important role in the biogeochemical carbon cycle and in control of global warming through natural reduction of methane emission. These bacteria share the unique ability of using methane as a sole carbon and energy source and have been found in a great variety of habitats. Phylogenetically, known methanotrophs constitute a rather limited group and have so far only been affiliated with the Proteobacteria. Here, we report the isolation and initial characterization of a nonproteobacterial obligately methanotrophic bacterium. The isolate, designated Kam1, was recovered from an acidic hot spring in Kamchatka, Russia, and is more thermoacidophilic than any other known methanotroph, with optimal growth at ≈55°C and pH 3.5. Kam1 is only distantly related to all previously known methanotrophs and belongs to the Verrucomicrobia lineage of evolution. Genes for methane monooxygenases, essential for initiation of methane oxidation, could not be detected by using standard primers in PCR amplification and Southern blot analysis, suggesting the presence of a different methane oxidation enzyme. Kam1 also lacks the well developed intracellular membrane systems typical for other methanotrophs. The isolate represents a previously unrecognized biological methane sink, and, due to its unusual phylogenetic affiliation, it will shed important light on the origin, evolution, and diversity of biological methane oxidation and on the adaptation of this process to extreme habitats. Furthermore, Kam1 will add to our knowledge of the metabolic traits and biogeochemical roles of the widespread but poorly understood Verrucomicrobia phylum. PMID:18172218

  2. Surface Mn(II) oxidation actuated by a multicopper oxidase in a soil bacterium leads to the formation of manganese oxide minerals

    PubMed Central

    Zhang, Zhen; Zhang, Zhongming; Chen, Hong; Liu, Jin; Liu, Chang; Ni, Hong; Zhao, Changsong; Ali, Muhammad; Liu, Fan; Li, Lin

    2015-01-01

    In this manuscript, we report that a bacterial multicopper oxidase (MCO266) catalyzes Mn(II) oxidation on the cell surface, resulting in the surface deposition of Mn(III) and Mn(IV) oxides and the gradual formation of bulky oxide aggregates. These aggregates serve as nucleation centers for the formation of Mn oxide micronodules and Mn-rich sediments. A soil-borne Escherichia coli with high Mn(II)-oxidizing activity formed Mn(III)/Mn(IV) oxide deposit layers and aggregates under laboratory culture conditions. We engineered MCO266 onto the cell surfaces of both an activity-negative recipient and wild-type strains. The results confirmed that MCO266 governs Mn(II) oxidation and initiates the formation of deposits and aggregates. By contrast, a cell-free substrate, heat-killed strains, and intracellularly expressed or purified MCO266 failed to catalyze Mn(II) oxidation. However, purified MCO266 exhibited Mn(II)-oxidizing activity when combined with cell outer membrane component (COMC) fractions in vitro. We demonstrated that Mn(II) oxidation and aggregate formation occurred through an oxygen-dependent biotic transformation process that requires a certain minimum Mn(II) concentration. We propose an approximate electron transfer pathway in which MCO266 transfers only one electron to convert Mn(II) to Mn(III) and then cooperates with other COMC electron transporters to transfer the other electron required to oxidize Mn(III) to Mn(IV). PMID:26039669

  3. Effects of inhibitors and NaCl on the oxidation of reduced inorganic sulfur compounds by a marine acidophilic, sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH.

    PubMed

    Kamimura, Kazuo; Higashino, Emi; Kanao, Tadayoshi; Sugio, Tsuyoshi

    2005-02-01

    The effect of NaCl and the pathways of the oxidation of reduced inorganic sulfur compounds were studied using resting cells and cell-free extracts of Acidithiobacillus thiooxidans strain SH. This isolate specifically requires NaCl for growth. The oxidation of sulfur and sulfite by resting cells was strongly inhibited by 2-heptyl-4-hydroxyquinoline-N-oxide. Carbonylcyanide m-chlorophenyl-hydrazone and monensin were also relatively strong inhibitors. Thiosulfate-oxidizing activity was not inhibited by these uncouplers. Valinomycin did not inhibit the oxidation of sulfur compounds. NaCl stimulated the sulfur- and sulfite-oxidizing activities in resting cells but not in cell-free extracts. The tetrathionate-oxidizing activity in resting cells was slightly stimulated by NaCl, whereas it did not influence the thiosulfate-oxidizing activity. Sulfide oxidation was biphasic, suggesting the formation of intermediate sulfur. The initial phase of sulfide oxidation was not affected by NaCl, whereas the subsequent oxidation of sulfur in the second phase was Na+-dependent. A model is proposed for the role of NaCl in the metabolism of reduced sulfur compounds in A. thiooxidans strain SH. PMID:15375674

  4. A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

    PubMed Central

    Weissgerber, Thomas; Sylvester, Marc; Kröninger, Lena

    2014-01-01

    In the present study, we compared the proteome response of Allochromatium vinosum when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (≥1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantified A. vinosum proteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (hyd; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515). PMID:24487535

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

    PubMed

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

    2016-05-01

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

  6. 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

  7. Novel Genes of the dsr Gene Cluster and Evidence for Close Interaction of Dsr Proteins during Sulfur Oxidation in the Phototrophic Sulfur Bacterium Allochromatium vinosum

    PubMed Central

    Dahl, Christiane; Engels, Sabine; Pott-Sperling, Andrea S.; Schulte, Andrea; Sander, Johannes; Lübbe, Yvonne; Deuster, Oliver; Brune, Daniel C.

    2005-01-01

    Seven new genes designated dsrLJOPNSR were identified immediately downstream of dsrABEFHCMK, completing the dsr gene cluster of the phototrophic sulfur bacterium Allochromatium vinosum D (DSM 180T). Interposon mutagenesis proved an essential role of the encoded proteins for the oxidation of intracellular sulfur, an obligate intermediate during the oxidation of sulfide and thiosulfate. While dsrR and dsrS encode cytoplasmic proteins of unknown function, the other genes encode a predicted NADPH:acceptor oxidoreductase (DsrL), a triheme c-type cytochrome (DsrJ), a periplasmic iron-sulfur protein (DsrO), and an integral membrane protein (DsrP). DsrN resembles cobyrinic acid a,c-diamide synthases and is probably involved in the biosynthesis of siro(heme)amide, the prosthetic group of the dsrAB-encoded sulfite reductase. The presence of most predicted Dsr proteins in A. vinosum was verified by Western blot analysis. With the exception of the constitutively present DsrC, the formation of Dsr gene products was greatly enhanced by sulfide. DsrEFH were purified from the soluble fraction and constitute a soluble α2β2γ2-structured 75-kDa holoprotein. DsrKJO were purified from membranes pointing at the presence of a transmembrane electron-transporting complex consisting of DsrKMJOP. In accordance with the suggestion that related complexes from dissimilatory sulfate reducers transfer electrons to sulfite reductase, the A. vinosum Dsr complex is copurified with sulfite reductase, DsrEFH, and DsrC. We therefore now have an ideal and unique possibility to study the interaction of sulfite reductase with other proteins and to clarify the long-standing problem of electron transport from and to sulfite reductase, not only in phototrophic bacteria but also in sulfate-reducing prokaryotes. PMID:15687204

  8. Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum.

    PubMed

    Dahl, Christiane; Engels, Sabine; Pott-Sperling, Andrea S; Schulte, Andrea; Sander, Johannes; Lübbe, Yvonne; Deuster, Oliver; Brune, Daniel C

    2005-02-01

    Seven new genes designated dsrLJOPNSR were identified immediately downstream of dsrABEFHCMK, completing the dsr gene cluster of the phototrophic sulfur bacterium Allochromatium vinosum D (DSM 180(T)). Interposon mutagenesis proved an essential role of the encoded proteins for the oxidation of intracellular sulfur, an obligate intermediate during the oxidation of sulfide and thiosulfate. While dsrR and dsrS encode cytoplasmic proteins of unknown function, the other genes encode a predicted NADPH:acceptor oxidoreductase (DsrL), a triheme c-type cytochrome (DsrJ), a periplasmic iron-sulfur protein (DsrO), and an integral membrane protein (DsrP). DsrN resembles cobyrinic acid a,c-diamide synthases and is probably involved in the biosynthesis of siro(heme)amide, the prosthetic group of the dsrAB-encoded sulfite reductase. The presence of most predicted Dsr proteins in A. vinosum was verified by Western blot analysis. With the exception of the constitutively present DsrC, the formation of Dsr gene products was greatly enhanced by sulfide. DsrEFH were purified from the soluble fraction and constitute a soluble alpha(2)beta(2)gamma(2)-structured 75-kDa holoprotein. DsrKJO were purified from membranes pointing at the presence of a transmembrane electron-transporting complex consisting of DsrKMJOP. In accordance with the suggestion that related complexes from dissimilatory sulfate reducers transfer electrons to sulfite reductase, the A. vinosum Dsr complex is copurified with sulfite reductase, DsrEFH, and DsrC. We therefore now have an ideal and unique possibility to study the interaction of sulfite reductase with other proteins and to clarify the long-standing problem of electron transport from and to sulfite reductase, not only in phototrophic bacteria but also in sulfate-reducing prokaryotes. PMID:15687204

  9. Clarifying the regulation of NO/N2O production in Nitrosomonas europaea during anoxic-oxic transition via flux balance analysis of a metabolic network model.

    PubMed

    Perez-Garcia, Octavio; Villas-Boas, Silas G; Swift, Simon; Chandran, Kartik; Singhal, Naresh

    2014-09-01

    The metabolic mechanism regulating the production of nitric and nitrous oxide (NO, N2O) in ammonia oxidizing bacteria (AOB) was characterized by flux balance analysis (FBA) of a stoichiometric metabolic network (SMN) model. The SMN model was created using 51 reactions and 44 metabolites of the energy metabolism in Nitrosomonas europaea, a widely studied AOB. FBA of model simulations provided estimates for reaction rates and yield ratios of intermediate metabolites, substrates, and products. These estimates matched well, deviating on average by 15% from values for 17 M yield ratios reported for non-limiting oxygen and ammonium concentrations. A sensitivity analysis indicated that the reactions catalysed by cytochromes aa3 and P460 principally regulate the pathways of NO and N2O production (hydroxylamine oxidoreductase mediated and nitrifier denitrification). FBA of simulated N. europaea exposure to oxic-anoxic-oxic transition indicated that NO and N2O production primarily resulted from an intracellular imbalance between the production and consumption of electron equivalents during NH3 oxidation, and that NO and N2O are emitted when the sum of their production rates is greater than half the rate of NO oxidation by cytochrome P460. PMID:24862955

  10. Potential application of aerobic denitrifying bacterium Pseudomonas aeruginosa PCN-2 in nitrogen oxides (NOx) removal from flue gas.

    PubMed

    Zheng, Maosheng; Li, Can; Liu, Shufeng; Gui, Mengyao; Ni, Jinren

    2016-11-15

    Conventional biological removal of nitrogen oxides (NOx) from flue gas has been severely restricted by the presence of oxygen. This paper presents an efficient alternative for NOx removal at varying oxygen levels using the newly isolated bacterial strain Pseudomonas aeruginosa PCN-2 which was capable of aerobic and anoxic denitrification. Interestingly, nitric oxide (NO), as the obligatory intermediate, was negligibly accumulated during nitrate and nitrite reduction. Moreover, normal nitrate reduction with decreasing NO accumulation was realized under O2 concentration ranging from 0 to 100%. Reverse transcription and real-time quantitative polymerase chain reaction (RT-qPCR) analysis revealed that high efficient NO removal was attributed to the coordinate regulation of gene expressions including napA (for periplasmic nitrate reductase), nirS (for cytochrome cd1 nitrite reductase) and cnorB (for NO reductase). Further batch experiments demonstrated the immobilized strain PCN-2 possessed high capability of removing NO and nitrogen dioxide (NO2) at O2 concentration of 0-10%. A biotrickling filter established with present strain achieved high NOx removal efficiencies of 91.94-96.74% at inlet NO concentration of 100-500ppm and O2 concentration of 0-10%, which implied promising potential applications in purifying NOx contaminated flue gas. PMID:27469045

  11. Biomineralization by a Newly-Isolated Stalk-Forming Fe-oxidizing Bacterium: Towards Interpretation of Putative Fe Microfossils

    NASA Astrophysics Data System (ADS)

    Krepski, S. T.; Chan, C. S.

    2010-12-01

    Diverse aerobic, lithotrophic Fe-oxidizing bacteria (FeOB) produce distinctive extracellular Fe-rich filaments, which resemble putative Fe microfossils dating from recent to 1.7 Ga (Slack et al., 2007, EPSL: 243). The filament morphology, texture, and composition are promising biosignatures for these FeOB; however, somewhat similar morphologies have been shown to result from chemical precipitates. In order to accurately identify and interpret such biosignatures, morphology must described in detail and be linked to physiological function and growth conditions in extant organisms. Towards this goal, we aimed to isolate a novel, stalk-forming microaerophilic FeOB, since there exist few isolates. We successfully obtained a pure strain (named R-1) from a circumneutral, freshwater Fe seep in Christiana Creek, Newark, DE. This strain produces a twisted stalk, similar to Gallionella and Mariprofundus in morphology and in mineralogy. Our work shows that R-1 is a neutrophilic obligate FeOB, unable to oxidize other organic or inorganic substrates. It is a Beta-Proteobacterium in the Gallionellaceae family but is phylogenetically distinct from previously isolated Gallionella sp. and Sideroxydans sp. The closest cultured relative is S. lithotrophicus (97% similar) and the closest environmental clone is 98% similar. We have begun growing R-1 and the marine stalk-forming FeOB Mariprofundus ferrooxydans in microslide cultures, which allow direct microscope observation without disturbing growth. We are monitoring oxygen concentration gradients and FeOB response to oxygen levels. In order to link morphology to biological function and growth conditions, we will observe stalk formation under various conditions and document various morphological and textural parameter (e.g. branching and orientation) to establish criteria for biogenicity. No organisms are known to make stalks under anaerobic conditions, so if these structures are detected in the rock record, they could be used as

  12. A PerR-like protein involved in response to oxidative stress in the extreme bacterium Deinococcus radiodurans

    SciTech Connect

    Liu, Chengzhi; Wang, Liangyan; Li, Tao; Lin, Lin; Dai, Shang; Tian, Bing Hua, Yuejin

    2014-07-18

    Highlights: • We report a novel PerR-like protein of Fur family in D. radiodurans that is not annotated in the current database. • drperR responses to H{sub 2}O{sub 2} and functions as a negative regulator of katE and dps. • We provided implications on how to utilize sequenced genome data and the importance of genome data mining. • This study adds knowledge to complicated regulatory network that responds to ROS stress in D. radiodurans. - Abstract: Response and defense systems against reactive oxygen species (ROS) contribute to the remarkable resistance of Deinococcus radiodurans to oxidative stress induced by oxidants or radiation. However, mechanisms involved in ROS response and defense systems of D. radiodurans are not well understood. Fur family proteins are important in ROS response. Only a single Fur homolog is predicted by sequence similarity in the current D. radiodurans genome database. Our bioinformatics analysis demonstrated an additional guanine nucleotide in the genome of D. radiodurans that is not in the database, leading to the discovery of another Fur homolog DrPerR. Gene disruption mutant of DrPerR showed enhanced resistance to hydrogen peroxide (H{sub 2}O{sub 2}) and increased catalase activity in cell extracts. Real-time PCR results indicated that DrPerR functions as a repressor of the catalase gene katE. Meanwhile, derepression of dps (DNA-binding proteins from starved cells) gene under H{sub 2}O{sub 2} stress by DrPerR point to its regulatory role in metal ions hemostasis. Thus, DrPerR might function as a Fur homolog protein which is involved in ROS response and defense. These results help clarify the complicated regulatory network that responds to ROS stress in D. radiodurans.

  13. Description of a novel indole-oxidizing bacterium Pseudomonas indoloxydans sp. nov., isolated from a pesticide-contaminated site.

    PubMed

    Manickam, Natesan; Ghosh, Anuradha; Jain, Rakesh K; Mayilraj, Shanmugam

    2008-06-01

    A Gram-negative, deep brown-pigmented Gammaproteobacteria, strain IPL-1(T), capable of oxidizing indole was isolated from a lindane-contaminated site and subjected to a polyphasic taxonomic study. Most of the physiological and biochemical properties, major fatty acids (C(18:1)omega7c, C(16:1)omega7c/iso C(15:0) 2OH and C(16:0)), estimated DNA G+C content (67.2mol%) and 16S rRNA gene sequence analysis showed that strain IPL-1(T) belonged to the genus Pseudomonas. Strain IPL-1(T) exhibited highest 16S rRNA gene sequence similarity with Pseudomonas pseudoalcaligenes (99.0%), followed by Pseudomonas alcaliphila (98.7%), Pseudomonas oleovorans (98.3%), Pseudomonas nitroreducens (98.0%), Pseudomonas mendocina (97.6%) and Pseudomonas stutzeri (97.4%). However, the DNA-DNA relatedness values between strain IPL-1(T) and the closely related taxa were between 22% and 61%. On the basis of differential phenotypic characteristics and genotypic distinctiveness, strain IPL-1(T) should be classified within the genus Pseudomonas as a novel species, for which the name Pseudomonas indoloxydans is proposed. The type strain is IPL-1(T) (=MTCC 8062(T)=JCM 14246(T)). PMID:18406094

  14. Isolation and characterization of a diazotrophic, oxalate-oxidizing bacterium from sour grass (Oxalis pes-caprae L.).

    PubMed

    Sahin, Nurettin

    2005-04-01

    A new type of nitrogen-fixing, oxalate-oxidizing Azospirillum sp. was isolated from the roots of Oxalis pes-caprae. Polyphasic taxonomy was performed, including auxanography using API galleries, physiological tests and 16S rRNA sequence comparison. Optimum growth occurred at 30 degrees C, pH 7.5. Growth was observed at 37 and 42 degrees C with oxalate and in the presence of 3-4% NaCl and 2% potassium oxalate. In liquid culture, the doubling time (t(d)) with oxalate was 9 h. Its closest phylogenetic neighbors, as deduced by 16S rDNA-based analysis, were Azospirillum brasilense, Azospirillum doebereinerae and Azospirillum lipoferum, with 99.5, 98.4 and 96.7% sequence similarity, respectively. The strain differed from A. brasilense by its ability to use N-acetylglucosamine, D-glucose and D-mannitol. It may be a variant strain of A. brasilense. Oxalotrophic, N2-fixing species of the genus Azospirillum may be important contributors to soil formation, soil fertility, and retention and/or cycling of elements necessary for plant growth. PMID:15808950

  15. The roles of bacterial biofilm and oxidizing enzymes in the biodegradation of plastic by the bacterium Rhodococcus ruber (C208)

    NASA Astrophysics Data System (ADS)

    Sivan, A.; Gilan, I.; Santo, M.

    2011-12-01

    novel method for isolating mutants impaired in their production of biofilms (but not in their growth performance) was developed and utilized to isolate such mutants. Indeed, combining the Crystal Violet staining with confocal microscopy we were able to show that such mutants, not only contains reduced amounts of biofilm but also alters biofilm architecture. The above characterization of wild type and mutant strains can be utilized to determine the role of biofilm on the biodegradation of polyethylene. C208 produces laccase (phenol oxidase). This is an oxidizing enzyme that requires copper for induction and activity. In the presence of copper the biodegradation of mineral oil and of polyethylene, by C208, increased by up to 25% and 100%, respectively. Treatment of polyethylene films with a cell free-extract of laccase resulted in an increase of more then 40% in the carbonyl peak (indicating oxidation) as measured by FTIR. Furthermore, during 2 weeks of incubation, with C208 laccase, the molecular weight of polyethylene was reduced by 25%. It seems that laccase alone could not account for all degrading activity and, presumably, more enzyme(s) capable of degrading olefins are yet to be discovered.

  16. Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath.

    PubMed

    Stolyar, S; Costello, A M; Peeples, T L; Lidstrom, M E

    1999-05-01

    Genes for the subunits of particulate methane monooxygenase, PmoABC, have been sequenced from the gamma-proteobacterial methanotroph Methylococcus capsulatus Bath. M. capsulatus Bath contains two complete copies of pmoCAB, as well as a third copy of pmoC. The two pmoCAB regions were almost identical at the nucleotide sequence level, differing in only 13 positions in 3183 bp. At the amino acid level, each translated gene product contained only one differing residue in each copy. However, the pmoC3 sequence was more divergent from the two other pmoC copies at both the far N-terminus and far C-terminus. Chromosomal insertion mutations were generated in all seven genes. Null mutants could not be obtained for pmoC3, suggesting that it may play an essential role in growth on methane. Null mutants were obtained for pmoC1, pmoC2, pmoA1, pmoA2, pmoB1 and pmoB2. All of these mutants grew on methane, demonstrating that both gene copies were functional. Copy 1 mutants showed about two-thirds of the wild-type whole-cell methane oxidation rate, while copy 2 mutants showed only about one-third of the wild-type rate, indicating that both gene copies were necessary for wild-type particulate methane monooxygenase activity. It was not possible to obtain double null mutants that were defective in both pmo copies, which may indicate that some expression of pMMO is important for growth. PMID:10376840

  17. Citreicella manganoxidans sp. nov., a novel manganese oxidizing bacterium isolated from a shallow water hydrothermal vent in Espalamaca (Azores).

    PubMed

    Rajasabapathy, Raju; Mohandass, Chellandi; Dastager, Syed Gulam; Liu, Qing; Li, Wen-Jun; Colaço, Ana

    2015-12-01

    A Gram-stain negative, non-motile, non-spore forming, aerobic and rod or narrow lemon-shaped bacterial strain, VSW210(T), was isolated from surface seawater in a shallow water hydrothermal vent region in Espalamaca (Azores). Strain VSW210(T) was found to grow optimally at 30 °C, at pH 7 and in the presence of 2-6 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain VSW210(T) clusters with the type strain Citreicella marina CK-I3-6(T) (sequence similarity value of 99.6 %), but DNA-DNA hybridization showed DNA-DNA relatedness between the strain VSW210(T) and C. marina CK-I3-6(T) to be 55.8 ± 3.2 %. The DNA G+C content of strain VSW210(T) was determined to be 67.4 mol%. The cellular fatty acid profiles of strain VSW210(T) was found to contain C18:1 ω7c (80.1 %) and C16:0 (9.2 %). The major polar lipids in strain VSW210(T) were identified as phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified phospholipid. Strain VSW210(T) was found to be able to oxidize soluble Mn(II) to insoluble MnO2, which was confirmed with LBB staining. Differential phenotypic properties and genetic uniqueness revealed that this strain VSW210(T) is distinguishable from other species of the genus Citreicella. On the basis of the data presented, strain VSW210(T) is considered to represent a novel species of the genus Citreicella, for which the name Citreicella manganoxidans sp. nov. is proposed. The type strain is VSW210(T) (=KCTC 32497(T) = MCC 2286(T)). PMID:26404429

  18. AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea

    PubMed Central

    Miyamoto, Tatsuki; Yokota, Akiko; Tsuneda, Satoshi; Noda, Naohiro

    2016-01-01

    Nitrosomonas europaea carries numerous toxin-antitoxin systems. However, despite the abundant representation in its chromosome, studies have not surveyed the underlying molecular functions in detail, and their biological roles remain enigmatic. In the present study, we found that a chromosomally-encoded MazF family member, predicted at the locus NE1181, is a functional toxin endoribonuclease, and constitutes a toxin-antitoxin system, together with its cognate antitoxin, MazE. Massive parallel sequencing provided strong evidence that this toxin endoribonuclease exhibits RNA cleavage activity, primarily against the AAU triplet. This sequence-specificity was supported by the results of fluorometric assays. Our results indicate that N. europaea alters the translation profile and regulates its growth using the MazF family of endoribonuclease under certain stressful conditions. PMID:27271670

  19. AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea.

    PubMed

    Miyamoto, Tatsuki; Yokota, Akiko; Tsuneda, Satoshi; Noda, Naohiro

    2016-01-01

    Nitrosomonas europaea carries numerous toxin-antitoxin systems. However, despite the abundant representation in its chromosome, studies have not surveyed the underlying molecular functions in detail, and their biological roles remain enigmatic. In the present study, we found that a chromosomally-encoded MazF family member, predicted at the locus NE1181, is a functional toxin endoribonuclease, and constitutes a toxin-antitoxin system, together with its cognate antitoxin, MazE. Massive parallel sequencing provided strong evidence that this toxin endoribonuclease exhibits RNA cleavage activity, primarily against the AAU triplet. This sequence-specificity was supported by the results of fluorometric assays. Our results indicate that N. europaea alters the translation profile and regulates its growth using the MazF family of endoribonuclease under certain stressful conditions. PMID:27271670

  20. Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi.

    PubMed

    Sorokin, Dimitry Y; Vejmelkova, Dana; Lücker, Sebastian; Streshinskaya, Galina M; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Kleerbezem, Robbert; van Loosdrecht, Mark; Muyzer, Gerard; Daims, Holger

    2014-06-01

    A novel nitrite-oxidizing bacterium (NOB), strain Lb(T), was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain Lb(T) was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8-7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C(18 : 1)ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain Lb(T) into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain Lb(T) represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is Lb(T) ( = DSM 23161(T) = UNIQEM U798(T)). PMID:24573161

  1. Silver nanoparticles temporarily retard NO2 - production without significantly affecting N2 O release by Nitrosomonas europaea.

    PubMed

    Michels, Camila; Yang, Yu; Moreira Soares, Hugo; Alvarez, Pedro J J

    2015-10-01

    Nitrifying bacteria are highly susceptible to silver nanoparticles (AgNPs). However, the effect of sublethal exposure to AgNPs after their release of nitrogenous compounds of environmental concern (e.g., the greenhouse gas nitrous oxide [N2 O] and the common water pollutant nitrite [NO2 -]) has not been systematically investigated. The present study reports the effect of AgNPs (and potentially released silver ions [Ag(+) ]) on NO2 - and N2 O production by Nitrosomonas europaea, and on the transcription of the associated genes. The release of NO2 - was more negatively affected than the production of N2 O. For example, exposure to AgNPs at 0.075 mg/L temporarily enhanced N2 O production (by 12%) without affecting nitrite release, whereas higher AgNP concentrations (>0.25 mg/L) inhibited NO2 - release (by >12%) but not N2 O production. Transcriptomic analyses corroborated these trends; AgNPs at 0.075 mg/L increased the expression of the nitric oxide reductase gene (norQ) associated with N2 O production (by 5.3-fold to 12.8-fold), whereas both 0.075 mg/L of Ag(+) and 0.75 mg/L of AgNPs down-regulated the ammonia monooxygenase gene (amoA2; by 0.08-fold to 0.15-fold and 0.32-fold to 0.64-fold, respectively), the nitrite reductase gene (nirK; by 0.01-fold to 0.02-fold and 0.22-fold to 0.44-fold, respectively), and norQ (by 0.11-fold to 0.15-fold and 0.32-fold to 0.57-fold, respectively). These results suggest that AgNP release to sewage treatment plants and land application of AgNP-containing biosolids should be minimized because of their potential temporary stimulation of N2 O release and interference with nitrification. Environ Toxicol Chem 2015;34:2231-2235. © 2015 SETAC. PMID:26010547

  2. Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed.

    PubMed

    An, Thuy T; Picardal, Flynn W

    2014-08-01

    A novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBM(T), was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBM(T) were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBM(T) was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16-37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBM(T), but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBM(T) grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5 mol%. The major cellular fatty acids were anteiso-C(15 : 0) and C(18 : 1)ω7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBM(T) into a distinct lineage within the class Deltaproteobacteria. The closest, cultivated phylogenetic relative of strain SCBM(T) was Desulfarculus baarsii DSM 2075(T), with only 91.7% 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBM(T) represents a novel genus and species of sulfate

  3. 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. PMID:26908287

  4. Structure of Nitrosocystis oceanus and Comparison with Nitrosomonas and Nitrobacter1

    PubMed Central

    Murray, R. G. E.; Watson, S. W.

    1965-01-01

    Murray, R. G. E. (University of Western Ontario, London, Ont., Canada), and S. W. Watson. Structure of Nitrosocystis oceanus and comparison with Nitrosomonas and Nitrobacter. J. Bacteriol. 89:1594–1609. 1965.—Nitrosocystis oceanus has distinctive features: the cell wall (overall thickness, 250 A) has an inner triplet structure and a dense enveloping layer; between these lie the “cell-wall organelles” (two or more per cell; plaques about 0.5 μ in diameter and 0.1 μ thick) of unknown function and genesis. The plasma membrane (ca. 80 A) shows rare intrusions that form irregular peripheral vesicles, which appear to form the component lamellae of the “membranous organelle” and probably detach from the periphery. The membranous organelles consist of about 20 vesicles so flattened that the lumen is only 100 A thick. The outer surfaces are in contact and form a triplet structure with an accentuated center line; these lamellae almost traverse the cell, displace the cytoplasm and the nucleoplasms, and form the prominent, seemingly permanent, feature of the cell. Division is constrictive without trace of a septum, and the act of division divides the membranous organelle. No mesosomes appear to be formed. Nitrosomonas europaea shows no sign of a cell-wall organelle or of the outer enveloping layer of wall. The cytoplasm contains intrusive paired lamellae, which might or might not remain connected to the periphery, and they do not fuse or form regular associations. These are thought to be the equivalent of the vesicles in Nitrosocystis but remaining almost parallel and close to the plasma membrane. Nitrobacter agilis has a unique plasma membrane with a (50 A) dense layer applied to the inside of the usual unit membrane. All of the components are represented in the intrusions, which are arranged over and shape the poles of the cells, with close and regular spacing. Each nitrifier was distinctive; in common they have membrane systems which, it is considered, must

  5. 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.

  6. Characterization of the c-type cytochromes of Nitrosomonas europaea with the aid of fluorescent gels

    PubMed Central

    Miller, David J.; Wood, Paul M.

    1982-01-01

    When a total soluble extract of Nitrosomonas europaea was denatured with dodecyl sulphate, subjected to dodecyl sulphate/polyacrylamide-gel electrophoresis and illuminated with near-u.v. light, eight bands of protein fluorescence were observed. All but one of these bands were red in colour, a property characteristic of c-type cytochromes. Standard techniques were used to purify soluble c-type cytochromes from this organism, and it was then possible to assign all but two very minor bands to specific c-type cytochromes, namely hydroxylamine oxidase, cytochrome c-554, cytochrome c-552 and a cytochrome c-550 not previously described. The eight band had fluorescence peaking in the green region of the spectrum, probably caused by covalently bound flavin, and co-purified with hydroxylamine oxidase. The following physical properties were determined for these components: isoelectric point, molecular weights according to gel filtration and mobility on dodecyl sulphate/polyacrylamide gels, and α-band spectra at room temperature and 77K. Redox potentials were measured as follows: cytochrome c-554, Em,7 = +20mV; cytochrome c-552, Em,7 = +230mV; cytochrome c-550, Em,7 = +140mV. When washed membranes were applied to dodecyl sulphate/polyacrylamide gels in the same way, a number of fluorescent bands were observed that could be matched by soluble proteins. In addition, there was one band that could not be detected in supernatants, migrating with an apparent molecular weight of 24000. This species is probably coincident with a c-type cytochrome having Em,7 = +170mV found in redox titration of these membranes. In future studies, gel fluorescence should form a useful complement to spectroscopy for analysis of cytochrome composition in active cell-free preparations or semi-purified material. PMID:6299271

  7. [Nitrous oxide fluxes of constructed wetlands to treat sewage wastewater].

    PubMed

    Wu, Juan; Zhang, Jian; Jia, Wen-Lin; Xie, Hui-Jun; Roy, R Gu

    2009-11-01

    The nitrous oxide fluxes and ammonia-oxidizing bacterium in two typical constructed wetlands, i.e. subsurface flow (SF) and free water surface (FWS) were studied by the method of static chamber-gas chromatography. The results showed that the mean N2O fluxes were 296.5 microg x (m2 x h)(-1) and 28.2 microg x (m2 x h)(-1) respectively, and two typical wetlands were all the sources of atmosphere nitrous oxide as a whole. SF wetland exhibited a higher risk of N2O emissions, and the mean N2O flux in this system was higher than the values reported in the literature for ecosystems, e.g. farmland, forest, grassland and marsh. The nitrous oxide fluxes in test wetlands presented obvious seasonal and diurnal variation, and the highest N2O emission flux was in July. The highest flux was (762.9 +/- 239.3) microg x (m2 x h)(-1) and (91.9 +/- 20.3) microg x (m2 x h)(-1) in SF and FWS wetlands, respectively. The peak flux mostly occurred around midday, whereas the minimum flux likely occurred in the early morning. The results indicated that the growth of Phragmites australis and temperature were the key factors controlling the variation of N2O fluxes. The average N2O emission from the microsites above the inflow zones was higher than that above the outflow microsites. High influent strength promoted nitrification and denitrification, and high fluxes were obtained. The clone results showed that Nitrosomonas and Nitrosospira were the main ammonia-oxidizing microorganisms contributing to N2O production in constructed wetlands. PMID:20063721

  8. 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.

  9. Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment.

    PubMed

    Hiorns, W D; Hastings, R C; Head, I M; McCarthy, A J; Saunders, J R; Pickup, R W; Hall, G H

    1995-11-01

    Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as specific PCR amplification primers and probes. The specificities of primer pairs for eubacterial, Nitrosospira and Nitrosomonas rRNA genes were established with sequence databases, and the primer pairs were used to amplify DNA from laboratory cultures and environmental samples. Eubacterial rRNA genes amplified from samples of soil and activated sludge hybridized with an oligonucleotide probe specific for Nitrosospira spp., but not with a Nitrosomonas-specific probe. Lakewater and sediment samples were analysed using a nested PCR technique in which eubacterial rRNA genes were subjected to a secondary amplification with Nitrosomonas or Nitrosospira specific primers. Again, the presence of Nitrosospira DNA, but not Nitrosomonas DNA, was detected and this was confirmed by hybridization of the amplified DNA with an internal oligonucleotide probe. Enrichments of lakewater and sediment samples, incubated for two weeks in the presence of ammonium, produced nitrite and were found to contain DNA from both Nitrosospira and Nitrosomonas as determined by nested PCR amplification and probing of 16S rRNA genes. This demonstrates that Nitrosospira spp. are widespread in the environment. The implications of the detection of Nitrosomonas DNA only after enrichment culture are discussed. PMID:8535507

  10. Hydroxylamine addition impact to Nitrosomonas europaea activity in the presence of monochloramine

    EPA Science Inventory

    In drinking water, monochloramine may promote ammonia–oxidizing bacteria (AOB) growth because of concurrent ammonia presence. AOB use (i) ammonia monooxygenase for biological ammonia oxidation to hydroxylamine and (ii) hydroxylamine oxidoreductase for hydroxylamine oxidation to ...

  11. Selective inhibition of ammonium oxidation and nitrification-linked N2O formation by methyl fluoride and dimethyl ether

    USGS Publications Warehouse

    Miller, L.G.; Coutlakis, M.D.; Oremland, R.S.; Ward, B.B.

    1993-01-01

    Methyl fluoride (CH3F) and dimethyl ether (DME) inhibited nitrification in washed-cell suspensions of Nitrosomonas europaea and in a variety of oxygenated soils and sediments. Headspace additions of CH3F (10% [vol/vol]) and DME (25% [vol/vol]) fully inhibited NO2- and N2O production from NH4+ in incubations of N. europaea, while lower concentrations of these gases resulted in partial inhibition. Oxidation of hydroxylamine (NH2OH) by N. europaea and oxidation of NO2- by a Nitrobacter sp. were unaffected by CH3F or DME. In nitrifying soils, CH3F and DME inhibited N2O production. In field experiments with surface flux chambers and intact cores, CH3F reduced the release of N2O from soils to the atmosphere by 20- to 30-fold. Inhibition by CH3F also resulted in decreased NO3- + NO2- levels and increased NH4+ levels in soils. CH3F did not affect patterns of dissimilatory nitrate reduction to ammonia in cell suspensions of a nitrate- respiring bacterium, nor did it affect N2O metabolism in denitrifying soils. CH3F and DME will be useful in discriminating N2O production via nitrification and denitrification when both processes occur and in decoupling these processes by blocking NO2- and NO3- production.

  12. The nitrate-ammonifying and nosZ-carrying bacterium Bacillus vireti is a potent source and sink for nitric and nitrous oxide under high nitrate conditions.

    PubMed

    Mania, Daniel; Heylen, Kim; van Spanning, Rob J M; Frostegård, Asa

    2014-10-01

    Several Gram-positive bacteria carry genes for anaerobic reduction of NO3(-) via NO2(-) to NH4(+) or gaseous nitrogen compounds, but the processes are understudied for these organisms. Here, we present results from a whole-genome analysis of the soil bacterium Bacillus vireti and a phenotypic characterization of intermediate and end-products, formed under anoxic conditions in the presence of NO3(-). Bacillus vireti has a versatile metabolism. It produces acetate, formate, succinate and lactate from fermentation and performs dissimilatory nitrate reduction via NO2(-) to ammonium (DNRA) using NrfA, while NirB may detoxify NO2(-) in the cytoplasm. Moreover, it produces NO from an unknown source and reduces it via N2O to N2 using two enzymes connected to denitrification: an unusual NO reductase, qCuA Nor encoded by cbaA, and a z-type N2O reductase, encoded by nosZ. In batch cultures, B. vireti reduced all NO3(-) to NO2(-) before the NO2(-) was reduced further. The quantities of all products varied with the initial NO3(-) concentration. With 5 mM NO3(-) , 90% was reduced to NH4 (+) while with ≥ 20 mM NO3(-), 50% was reduced to NO, N2O and N2. This organism is thus an aggressive NO2(-) accumulator and may act as a net source and sink of NO and N2O. PMID:24708037

  13. Draft Genome Sequence of Comamonas thiooxydans Strain S23T (DSM 17888T), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India

    PubMed Central

    Narayan, Kunwar Digvijay; Badhai, Jhasketan; Whitman, William B.

    2016-01-01

    The genus Comamonas contains species isolated from various environments, such as termite guts, wetlands, activated sludge, soil, humans, and fresh water. Here, we report the draft genome sequence of Comamonas thiooxydans strain S23T capable of oxidizing thiosulfate under mixotrophic growth conditions. Based upon draft genome sequencing, the genome is 5.3 Mb and encodes 4,767 proteins. The Comamonas thiooxydans whole-genome sequence will help understand the metabolic diversity in sulfur oxidation pathways. PMID:27516520

  14. Draft Genome Sequence of Comamonas thiooxydans Strain S23T (DSM 17888T), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India.

    PubMed

    Narayan, Kunwar Digvijay; Badhai, Jhasketan; Whitman, William B; Das, Subrata K

    2016-01-01

    The genus Comamonas contains species isolated from various environments, such as termite guts, wetlands, activated sludge, soil, humans, and fresh water. Here, we report the draft genome sequence of Comamonas thiooxydans strain S23(T) capable of oxidizing thiosulfate under mixotrophic growth conditions. Based upon draft genome sequencing, the genome is 5.3 Mb and encodes 4,767 proteins. The Comamonas thiooxydans whole-genome sequence will help understand the metabolic diversity in sulfur oxidation pathways. PMID:27516520

  15. Humic substance-mediated reduction of iron(III) oxides and degradation of 2,4-D by an alkaliphilic bacterium, Corynebacterium humireducens MFC-5.

    PubMed

    Wu, Chun-yuan; Zhuang, Li; Zhou, Shun-gui; Yuan, Yong; Yuan, Tian; Li, Fang-bai

    2013-03-01

    With the use of an alkaliphilic bacterium, Corynebacterium humireducens MFC-5, this study investigated the reduction of goethite (α-FeOOH) and degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) mediated by different humic substances (humics) and quinones in alkaline conditions (pH of 9.0). The results indicated that (i) using sucrose as the electron donor, the strain MFC-5 was capable of reducing anthraquinone-2,6-disulfonic acid (AQDS), anthraquinone-2-disulfonic acid (AQS), anthraquinone-2-carboxylic acid (AQC), humic acid (HA) and fulvic acid (FA), and its reducing capability ranked as AQC > AQS > AQDS > FA > HA; (ii) the anaerobic reduction of α-FeOOH and 2,4-D by the strain was insignificant, while the reductions were greatly enhanced by the addition of quinones/humics serving as redox mediators; (iii) the Fe(III) reduction rate was positively related to the content of quinone functional groups and the electron-accepting capacities (EAC) of quinones/humics based on fourier-transform infrared spectroscopy (FT-IR) and electrochemical analyses; however, such a relationship was not found in 2,4-D degradation probably because quinone reduction was not the rate-limiting step of quinone-mediated reduction of 2,4-D. Using the example of α-FeOOH and 2,4-D, this study well demonstrated the important role of humics reduction on the Fe(III)/Fe(II) biogeochemical cycle and chlorinated organic compounds degradation in alkaline reducing environments. PMID:23217085

  16. Humic substance-mediated reduction of iron(III) oxides and degradation of 2,4-D by an alkaliphilic bacterium, Corynebacterium humireducens MFC-5

    PubMed Central

    Wu, Chun-yuan; Zhuang, Li; Zhou, Shun-gui; Yuan, Yong; Yuan, Tian; Li, Fang-bai

    2013-01-01

    With the use of an alkaliphilic bacterium, Corynebacterium humireducens MFC-5, this study investigated the reduction of goethite (α-FeOOH) and degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) mediated by different humic substances (humics) and quinones in alkaline conditions (pH of 9.0). The results indicated that (i) using sucrose as the electron donor, the strain MFC-5 was capable of reducing anthraquinone-2,6-disulfonic acid (AQDS), anthraquinone-2-disulfonic acid (AQS), anthraquinone-2-carboxylic acid (AQC), humic acid (HA) and fulvic acid (FA), and its reducing capability ranked as AQC > AQS > AQDS > FA > HA; (ii) the anaerobic reduction of α-FeOOH and 2,4-D by the strain was insignificant, while the reductions were greatly enhanced by the addition of quinones/humics serving as redox mediators; (iii) the Fe(III) reduction rate was positively related to the content of quinone functional groups and the electron-accepting capacities (EAC) of quinones/humics based on fourier-transform infrared spectroscopy (FT-IR) and electrochemical analyses; however, such a relationship was not found in 2,4-D degradation probably because quinone reduction was not the rate-limiting step of quinone-mediated reduction of 2,4-D. Using the example of α-FeOOH and 2,4-D, this study well demonstrated the important role of humics reduction on the Fe(III)/Fe(II) biogeochemical cycle and chlorinated organic compounds degradation in alkaline reducing environments. Funding Information This study was supported by the National Natural Science Foundation of China (Nos 41101211, 31070460, 41101477), and The Project Sponsored by the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry. PMID:23217085

  17. Improvement of biological nitrogen removal with nitrate-dependent Fe(II) oxidation bacterium Aquabacterium parvum B6 in an up-flow bioreactor for wastewater treatment.

    PubMed

    Zhang, Xiaoxin; Li, Ang; Szewzyk, Ulrich; Ma, Fang

    2016-11-01

    Aquabacterium parvum strain B6 exhibited efficient nitrate-dependent Fe(II) oxidation ability using nitrate as an electron acceptor. A continuous up-flow bioreactor that included an aerobic and an anoxic section was constructed, and strain B6 was added to the bioreactor as inocula to explore the application of microbial nitrate-dependent Fe(II) oxidizing (NDFO) efficiency in wastewater treatment. The maximum NRE (anoxic section) and TNRE of 46.9% and 79.7%, respectively, could be obtained at a C/N ratio of 5.3:1 in the influent with HRT of 17. Meanwhile, the taxonomy composition of the reactor was assessed, as well. The NDFO metabolism of strain B6 could be expected because of its relatively dominant position in the anoxic section, whereas potential heterotrophic nitrification and aerobic denitrification developed into the prevailing status in the aerobic section after 50days of continuous operation. PMID:27544912

  18. Draft genome of iron-oxidizing bacterium Leptospirillum sp. YQP-1 isolated from a volcanic lake in the Wudalianchi volcano, China.

    PubMed

    Yan, Lei; Zhang, Shuang; Yu, Gaobo; Ni, Yongqing; Wang, Weidong; Hu, Huixin; Chen, Peng

    2015-12-01

    Leptospirillum sp. YQP-1, a member of iron-oxidizing bacteria was isolated from volcanic lake in northeast China. Here, we report the draft genome sequence of the strain YQP-1 with a total genome size of 3,103,789 bp from 85 scaffolds (104 contigs) with 58.64% G + C content. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LIEB00000000. PMID:26697362

  19. Draft genome of iron-oxidizing bacterium Leptospirillum sp. YQP-1 isolated from a volcanic lake in the Wudalianchi volcano, China

    PubMed Central

    Yan, Lei; Zhang, Shuang; Yu, Gaobo; Ni, Yongqing; Wang, Weidong; Hu, Huixin; Chen, Peng

    2015-01-01

    Leptospirillum sp. YQP-1, a member of iron-oxidizing bacteria was isolated from volcanic lake in northeast China. Here, we report the draft genome sequence of the strain YQP-1 with a total genome size of 3,103,789 bp from 85 scaffolds (104 contigs) with 58.64% G + C content. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LIEB00000000. PMID:26697362

  20. Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens.

    PubMed

    Flood, Beverly E; Jones, Daniel S; Bailey, Jake V

    2015-08-01

    A marine facultative anaerobe, strain SIP-G1T, was isolated from salt marsh sediments, Falmouth, MA, USA. Phylogenetic analysis of its 16S rRNA gene sequence indicated that it belongs to an unclassified clade of Gammaproteobacteria that includes numerous sulfur-oxidizing bacteria that are endosymbionts of marine invertebrates endemic to sulfidic habitats. Strain SIP-G1T is a member of the genus Sedimenticola, of which there is one previously described isolate, Sedimenticola selenatireducens AK4OH1T. S. selenatireducens AK4OH1T was obtained for further characterization and comparison with strain SIP-G1T. The two strains were capable of coupling the oxidation of thiosulfate, tetrathionate, elemental sulfur and sulfide to autotrophic growth and they produced sulfur inclusions as metabolic intermediates. They showed varying degrees of O2 sensitivity, but when provided amino acids or peptides as a source of energy, they appeared more tolerant of O2 and exhibited concomitant production of elemental sulfur inclusions. The organic substrate preferences and limitations of these two organisms suggest that they possess an oxygen-sensitive carbon fixation pathway(s). Organic acids may be used to produce NADPH through the TCA cycle and are used in the formation of polyhydroxyalkanoates. Cell-wall-deficient morphotypes appeared when organic compounds (especially acetate) were present in excess and reduced sulfur was absent. Levels of DNA-DNA hybridization (∼47%) and phenotypic characterization indicate that strain SIP-G1T represents a separate species within the genus Sedimenticola, for which the name Sedimenticola thiotaurini sp. nov. is proposed. The type strain is SIP-G1T ( = ATCC BAA-2640T = DSM 28581T). The results also justify emended descriptions of the genus Sedimenticola and of S. selenatireducens. PMID:25944805

  1. Comparative Proteomic Analysis of Methanothermobacter themautotrophicus ΔH in Pure Culture and in Co-Culture with a Butyrate-Oxidizing Bacterium

    PubMed Central

    Enoki, Miho; Shinzato, Naoya; Sato, Hiroaki; Nakamura, Kohei; Kamagata, Yoichi

    2011-01-01

    To understand the physiological basis of methanogenic archaea living on interspecies H2 transfer, the protein expression of a hydrogenotrophic methanogen, Methanothermobacter thermautotrophicus strain ΔH, was investigated in both pure culture and syntrophic coculture with an anaerobic butyrate oxidizer Syntrophothermus lipocalidus strain TGB-C1 as an H2 supplier. Comparative proteomic analysis showed that global protein expression of methanogen cells in the model coculture was substantially different from that of pure cultured cells. In brief, in syntrophic coculture, although methanogenesis-driven energy generation appeared to be maintained by shifting the pathway to the alternative methyl coenzyme M reductase isozyme I and cofactor F420-dependent process, the machinery proteins involved in carbon fixation, amino acid synthesis, and RNA/DNA metabolisms tended to be down-regulated, indicating restrained cell growth rather than vigorous proliferation. In addition, our proteome analysis revealed that α subunits of proteasome were differentially acetylated between the two culture conditions. Since the relevant modification has been suspected to regulate proteolytic activity of the proteasome, the global protein turnover rate could be controlled under syntrophic growth conditions. To our knowledge, the present study is the first report on N-acetylation of proteasome subunits in methanogenic archaea. These results clearly indicated that physiological adaptation of hydrogenotrophic methanogens to syntrophic growth is more complicated than that of hitherto proposed. PMID:21904627

  2. Protein-mediated adhesion of the dissimilatory Fe(III)-reducing bacterium Shewanella alga BrY to hydrous ferric oxide

    SciTech Connect

    Caccavo, F. Jr.

    1999-11-01

    The rate and extent of bacterial Fe(III) mineral reduction are governed by molecular-scale interactions between the bacterial cell surface and the mineral surface. These interactions are poorly understood. This study examined the role of surface proteins in the adhesion of Shewanella alga BrY to hydrous ferric oxide (HFO). Enzymatic degradation of cell surface polysaccharides had no effect on cell adhesion to HFO. The proteolytic enzymes Streptomyces griseus protease and chymotrypsin inhibited the adhesion of S. alga BrY cells to HFO through catalytic degradation of surface proteins. Trypsin inhibited S. alga BrY adhesion solely through surface-coating effects. Protease and chymotrypsin also mediated desorption of adhered S. alga BrY cells from HFO while trypsin did not mediate cell desorption. Protease removed a single peptide band that represented a protein with an apparent molecular mass of 50 kDa. Chymotrypsin removed two peptide bands that represented proteins with apparent molecular masses of 60 and 31 kDa. These proteins represent putative HGO adhesion molecules. A. alga BrY adhesion was inhibited by up to 46% when cells were cultured at sub-MICs of chloramphenicol, suggesting that protein synthesis is necessary for adhesion. Proteins extracted from the surface of S. alga BrY cells inhibited adhesion to HFO by up to 41%. A number of these proteins bound specifically to HFO, suggesting that a complex system of surface proteins mediates S. alga BrY adhesion to HFO.

  3. Labeling of the pathogenic bacterium Staphylococcus aureus with gold or ferric oxide-core nanoparticles highlights new capabilities for investigation of host-pathogen interactions.

    PubMed

    Depke, Maren; Surmann, Kristin; Hildebrandt, Petra; Jehmlich, Nico; Michalik, Stephan; Stanca, Sarmiza E; Fritzsche, Wolfgang; Völker, Uwe; Schmidt, Frank

    2014-02-01

    Throughout the world, infections caused by bacteria such as Staphylococcus aureus are a major cause of morbidity and mortality. In order to gain some understanding of the complicated physiological link between host and pathogen, modern techniques such as confocal microscopy and sophisticated OMICs technologies are suitable. However, labeling of pathogens such as S. aureus with green fluorescent protein, for example, or the generation of a reliable antibody, which are prerequisites for the application of reproducible isolation techniques, does not always succeed. Here, we present a universal approach for monitoring pathogen traffic after internalization into host cells by fluorescence microscopy and for isolation of bacteria from host-pathogen interaction assays using gold or ferric oxide-core, poly(vinyl alcohol) coated, and fluorescence-labeled nanoparticles (NP). The incubation of S. aureus HG001 with those NP had only minor effects on the bacterial growth in vitro. Quantitative proteome analysis after 24 h of NP incubation revealed that presence of NP provoked only marginal changes in the proteome pattern. The method presented enabled us to investigate the behavior of S. aureus HG001 during infection of S9 human epithelial cells by means of fluorescence microscopy and proteomics using magnetic separation or cell sorting. PMID:24347542

  4. Life in an Arsenic-Containing Gold Mine: Genome and Physiology of the Autotrophic Arsenite-Oxidizing Bacterium Rhizobium sp. NT-26

    PubMed Central

    Andres, Jérémy; Arsène-Ploetze, Florence; Barbe, Valérie; Brochier-Armanet, Céline; Cleiss-Arnold, Jessica; Coppée, Jean-Yves; Dillies, Marie-Agnès; Geist, Lucie; Joublin, Aurélie; Koechler, Sandrine; Lassalle, Florent; Marchal, Marie; Médigue, Claudine; Muller, Daniel; Nesme, Xavier; Plewniak, Frédéric; Proux, Caroline; Ramírez-Bahena, Martha Helena; Schenowitz, Chantal; Sismeiro, Odile; Vallenet, David; Santini, Joanne M.; Bertin, Philippe N.

    2013-01-01

    Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions. PMID:23589360

  5. Xuhuaishuia manganoxidans gen. nov., sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediments from the Pacific Polymetallic Nodule Province.

    PubMed

    Wang, Long; Liu, Yan; Shi, Xiaochong; Wang, Yanan; Zheng, Yanfen; Dai, Xiaofeng; Zhang, Xiao-Hua

    2016-03-01

    A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY6-4T, was isolated from the surface sediment of the Pacific Clarion-Clipperton Fracture Zone. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain DY6-4T formed a lineage within the family Rhodobacteraceae and was distinct from the most closely related genera Sulfitobacter, Aliiroseovarius and Loktanella (94.0-96.0 %, 93.4-96.0 % and 91.9-95.9 % 16S rRNA gene sequence similarity, repectively). Optimal growth occurred in the presence of 1 % (w/v) NaCl, at pH 7.0 and at 28 °C. Strain DY6-4T contained ubiquinone-10 (Q-10) as the major ubiquinone, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and one unidentified aminolipid as the predominant polar lipids, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the main fatty acids (>10 % of the total). The DNA G+C content of strain DY6-4T was 66.6 mol%. On the basis of the polyphasic analyses, strain DY6-4T is considered to represent a novel species of a novel genus in the Roseobacter clade of the family Rhodobacteraceae, for which the name Xuhuaishuia manganoxidans gen. nov., sp. nov. is proposed. The type strain is DY6-4T ( = KCTC 42421T = MCCC 1K00502T). PMID:26800670

  6. Induction of nitric oxide production by polyosides from the cell walls of Streptococcus mutans OMZ 175, a gram-positive bacterium, in the rat aorta.

    PubMed Central

    Martin, V; Kleschyov, A L; Klein, J P; Beretz, A

    1997-01-01

    The cardiovascular dysfunctions associated with septic shock induced by gram-negative or gram-positive bacteria (gram-positive or gram-negative septic shock) are comparable. In gram-negative septic shock, lipopolysaccharide (LPS) induces nitric oxide (NO) synthase, which contributes to the vascular hypotension and hyporeactivity to vasoconstrictors. The role of NO in gram-positive septic shock and the nature of the bacterial wall components responsible for the vascular effects of gram-positive bacteria are not well known. This study investigated the vascular effects of cell wall serotype polyosides, rhamnose glucose polymers (RGPs), from Streptococcus mutans, in comparison with lipoteichoic acid (LTA) from Staphylococcus aureus, on the induction of NO synthase activity in the rat aorta. We show that 10 microg of both RGPs and LTA per ml induced hyporeactivity to noradrenaline, L-arginine-induced relaxation, increases of 2.2- and 7.8-fold, respectively, of cyclic GMP production, and increases of 7- and 12-fold in nitrite release. All of these effects appeared after several hours of incubation and were inhibited by N(omega)-nitro-L-arginine methyl ester (L-NAME), an inhibitor of NO synthase. Electron paramagnetic resonance spin trapping experiments demonstrated directly that RGPs and LTA induced NO overproduction (four- to eightfold, respectively) in rat aortic rings; this production was inhibited by L-NAME and prevented by dexamethasone. These results demonstrate directly the induction of NO production in vascular tissue by LTA and show that another, chemically different component of gram-positive bacteria can also have these properties. This result suggests that different components of the gram-positive bacterial wall could be implicated in the genesis of cardiovascular dysfunctions observed in gram-positive septic shock. PMID:9169734

  7. Media effects on Nitrosomonas Europaea Monochloramine Disinfection Kinetics using Propidium Monoazide Quantitative Real-time PCR

    EPA Science Inventory

    Monochloramine use as a secondary disinfectant in the United States is predicted to increase to 57% of all surface and 7% of all ground water systems. With monochloramine addition, there is a risk of nitrification in the distribution system by ammonia-oxidizing bacteria (AOB). Ba...

  8. Media Effects on Nitrosomonas Europaea Monochloramine Disinfection Kinetics Using Propidium Monoazide Quantitative Real-time PCR

    EPA Science Inventory

    Monochloramine use as a secondary disinfectant in the United States is predicted to increase to 57% of all surface and 7% of all ground water systems. With monochloramine addition, there is a risk of nitrification in the distribution system by ammonia-oxidizing bacteria (AOB). Ba...

  9. Media Effects on Nitrosomonas Europaea Monochloramine Disinfection Kinetics Using Propidium Monoazide Quantitative Real-time PCR

    EPA Science Inventory

    Monochloramine use as a secondary disinfectant in the United States is predicted to increase to 57% of all surface and 7% of all ground water systems. With monochloramine addition, there is a risk of nitrification in the distribution system by ammonia-oxidizing bacteria (AOB). Ni...

  10. OXIDATION OF METHYL FLUORIDE AND DIMETHYL ETHER BY AMMONIA MONOOXYGENASE IN NITROSOMONAS EUROPAEA. (R825689C009)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  11. Inhibitory Effects of C2 to C10 1-Alkynes on Ammonia Oxidation in Two Nitrososphaera Species

    PubMed Central

    Taylor, K.; Tennigkeit, B.; Palatinszky, M.; Stieglmeier, M.; Myrold, D. D.; Schleper, C.; Wagner, M.; Bottomley, P. J.

    2015-01-01

    A previous study showed that ammonia oxidation by the Thaumarchaeota Nitrosopumilus maritimus (group 1.1a) was resistant to concentrations of the C8 1-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. In this study, the inhibitory effects of octyne and other C2 to C10 1-alkynes were evaluated on the nitrite production activity of two pure culture isolates from Thaumarchaeota group 1.1b, Nitrososphaera viennensis strain EN76 and Nitrososphaera gargensis. Both N. viennensis and N. gargensis were insensitive to concentrations of octyne that cause complete and irreversible inactivation of nitrite production by ammonia-oxidizing bacteria. However, octyne concentrations (≥20 μM) that did not inhibit N. maritimus partially inhibited nitrite production in N. viennensis and N. gargensis in a manner that did not show the characteristics of irreversible inactivation. In contrast to previous studies with an ammonia-oxidizing bacterium, Nitrosomonas europaea, octyne inhibition of N. viennensis was: (i) fully and immediately reversible, (ii) not competitive with NH4+, and (iii) without effect on the competitive interaction between NH4+ and acetylene. Both N. viennensis and N. gargensis demonstrated the same overall trend in regard to 1-alkyne inhibition as previously observed for N. maritimus, being highly sensitive to ≤C5 alkynes and more resistant to longer-chain length alkynes. Reproducible differences were observed among N. maritimus, N. viennensis, and N. gargensis in regard to the extent of their resistance/sensitivity to C6 and C7 1-alkynes, which may indicate differences in the ammonia monooxygenase binding and catalytic site(s) among the Thaumarchaeota. PMID:25576608

  12. Further studies on a human intestinal bacterium Ruminococcus sp. END-1 for transformation of plant lignans to mammalian lignans.

    PubMed

    Jin, Jong-Sik; Hattori, Masao

    2009-08-26

    A human intestinal bacterium Ruminococcus (R.) sp. END-1 capable of oxidizing (-)-enterodiol to (-)-enterolactone, enantioselectively, was further investigated from the perspective of transformation of plant lignans to mammalian lignans; A cell-free extract of the bacterium transformed (-)-enterodiol to (-)-enterolactone through an intermediate, enterolactol. The bacterium showed not only oxidation but also demethylation and deglucosylation activities for plant lignans. Arctiin and secoisolariciresinol diglucoside were converted to (-)-dihydroxyenterolactone and (+)-dihydroxyenterodiol, respectively. Moreover, by coincubation with Eggerthella sp. SDG-2, the bacterium transformed arctiin and secoisolariciresinol diglucoside to (-)-enterolactone and (+)-enterodiol, respectively. PMID:19630415

  13. Detection and analysis of two serotypes of ammonia-oxidizing bacteria in sewage plants by flow cytometry.

    PubMed Central

    Völsch, A; Nader, W F; Geiss, H K; Nebe, G; Birr, C

    1990-01-01

    Two different serotypes of the genus Nitrosomonas were isolated from samples of the sewage plant Heidelberg. These nitrifiers were enumerated in activated sludge of various other sewage plants after immunofluorescent labeling and staining with propidium iodide by flow cytometry. The concentrations of these serotypes of Nitrosomonas spp. were in the range of 0.1 to 2%. Also, a test for the determination of the activity of ammonia-oxidizing bacteria was developed. Nitrite-oxidizing bacteria were specifically inhibited with sodium chlorate, and the activity of ammonia-oxidizing bacteria could be calculated from the increase of nitrite. Concentrations and activities of ammonia oxidizers were measured for a period of 6 months in the sewage plant Heidelberg. With one exception, activities and concentrations of ammonia-oxidizing bacteria decreased and increased in parallel. PMID:2403253

  14. 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.

  15. Determination of the Effects of Medium Composition on the Monochloramine Disinfection Kinetics of Nitrosomonas europaea by the Propidium Monoazide Quantitative PCR and Live/Dead BacLight Methods

    EPA Science Inventory

    Various media compositions (phosphate 1-50 mM; ionic strength 2.8-150 meq/L) significantly affected Nitrosomonas europaea monochloramine disinfection kinetics determined by Live/Dead BacLight (LD) and propidium monoazide quantitative PCR (PMA-qPCR) methods (lag coefficient 37-490...

  16. 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. PMID:27480511

  17. Comparison of the community structures of ammonia-oxidizing bacteria and archaea in rhizoplanes of floating aquatic macrophytes.

    PubMed

    Wei, Bo; Yu, Xin; Zhang, Shuting; Gu, Li

    2011-09-20

    Some common floating aquatic macrophytes could remove nutrients, such as nitrogen, from eutrophic water. However, the relationship between these macrophytes and the ammonia-oxidizing microorganisms on their rhizoplanes is still unknown. In this study, we examined communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) on the rhizoplanes of common floating aquatic macrophytes (Eichhornia crassipes, Pistia stratiotes and Ipomoea aquatic) in a eutrophic reservoir.The results show that AOB were the predominant ammonia-oxidizer on the three rhizoplanes. The principal AOB were Nitrosomonas europaea and Nitrosomonas ureae clades. The principal group of AOA was most similar to the clone from activated sludge. The ratio of AOB amoA gene copies to AOA varied from 1.36 (on E. crassipes) to 41.90 (on P. stratiotes). Diversity of AOA was much lower than that of AOB in most samples, with the exception of P. stratiotes. PMID:21239153

  18. Intracellular iron minerals in a dissimilatory iron-reducing bacterium.

    PubMed

    Glasauer, Susan; Langley, Sean; Beveridge, Terry J

    2002-01-01

    Among prokaryotes, there are few examples of controlled mineral formation; the formation of crystalline iron oxides and sulfides [magnetite (Fe3O4) or greigite (Fe3S4)] by magnetotactic bacteria is an exception. Shewanella putrefaciens CN32, a Gram-negative, facultative anaerobic bacterium that is capable of dissimilatory iron reduction, produced microscopic intracellular grains of iron oxide minerals during growth on two-line ferrihydrite in a hydrogen-argon atmosphere. The minerals, formed at iron concentrations found in the soil and sedimentary environments where these bacteria are active, could represent an unexplored pathway for the cycling of iron by bacteria. PMID:11778045

  19. Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.

    PubMed

    Sauder, Laura A; Ross, Ashley A; Neufeld, Josh D

    2016-04-01

    Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representativeNitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway. PMID:26946536

  20. Acclimatization of communities of ammonia oxidizing bacteria to seasonal changes in optimal conditions in a coke wastewater treatment plant.

    PubMed

    Kim, Young Mo

    2013-11-01

    The goal of this study was to investigate the correlation between optimal conditions of ammonia oxidation rates (AORs) and communities of ammonia oxidizing bacteria (AOB) adapting to seasonal changes in a full-scale wastewater treatment plant (WWTP). The optimal temperature and pH of specific AORs reflected seasonal variation patterns, showing the lowest values during the cold season, while the highest values in the warm season. Throughout the study period, Nitrosomonas europaea/eutropha and Nitrosomonas nitrosa remained the dominant AOB, indicating resistance to the influences of a changing environment. These results show that the optimal conditions for AOR can be adjusted to accommodate changing environmental conditions, relying on the acclimatization of a stable AOB community to given conditions, without any visible shift in the AOB community. PMID:24001689

  1. Polyclonal Antibodies Recognizing the AmoB Protein of Ammonia Oxidizers of the β-Subclass of the Class Proteobacteria

    PubMed Central

    Pinck, Claudia; Coeur, Caroline; Potier, Patrick; Bock, Eberhard

    2001-01-01

    A 41-kDa protein of Nitrosomonas eutropha was purified, and the N-terminal amino acid sequence was found to be nearly identical with the sequence of AmoB, a subunit of ammonia monooxygenase. This protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the β-subclass of Proteobacteria (Nitrosomonas, including Nitrosococcus mobilis, which belongs phylogenetically to Nitrosomonas; Nitrosospira; Nitrosolobus; and Nitrosovibrio). In contrast, the antibodies did not react with ammonia oxidizers affiliated with the γ-subclass of Proteobacteria (Nitrosococcus oceani and Nitrosococcus halophilus). Moreover, methane oxidizers (Methylococcus capsulatus, Methylocystis parvus, and Methylomonas methanica) containing the related particulate methane monooxygenase were not detected. Quantitative immunoblot analysis revealed that total cell protein of N. eutropha consisted of approximately 6% AmoB, when cells were grown using standard conditions (mineral medium containing 10 mM ammonium). This AmoB amount was shown to depend on the ammonium concentration in the medium. About 14% AmoB of total protein was found when N. eutropha was grown with 1 mM ammonium, whereas 4% AmoB was detected when 100 mM ammonium were used. In addition, the cellular amount of AmoB was influenced by the absence of the substrate. Cells starved for more than 2 months contained nearly twice as much AmoB as actively growing cells, although these cells possessed low ammonia-oxidizing activity. AmoB was always present and could even be detected in cells of Nitrosomonas after 1 year of ammonia starvation. PMID:11133435

  2. The 1.3-Å resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins

    PubMed Central

    Lupo, Domenico; Li, Xiao-Dan; Durand, Anne; Tomizaki, Takashi; Cherif-Zahar, Baya; Matassi, Giorgio; Merrick, Mike; Winkler, Fritz K.

    2007-01-01

    The Rhesus (Rh) proteins are a family of integral membrane proteins found throughout the animal kingdom that also occur in a number of lower eukaryotes. The significance of Rh proteins derives from their presence in the human red blood cell membrane, where they constitute the second most important group of antigens used in transfusion medicine after the ABO group. Rh proteins are related to the ammonium transport (Amt) protein family and there is considerable evidence that, like Amt proteins, they function as ammonia channels. We have now solved the structure of a rare bacterial homologue (from Nitrosomonas europaea) of human Rh50 proteins at a resolution of 1.3 Å. The protein is a trimer, and analysis of its subunit interface strongly argues that all Rh proteins are likely to be homotrimers and that the human erythrocyte proteins RhAG and RhCE/D are unlikely to form heterooligomers as previously proposed. When compared with structures of bacterial Amt proteins, NeRh50 shows several distinctive features of the substrate conduction pathway that support the concept that Rh proteins have much lower ammonium affinities than Amt proteins and might potentially function bidirectionally. PMID:18032606

  3. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    PubMed Central

    Ramsay, Bradley D.; Hwang, Chiachi; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; Peters, Lin; Chertkov, Olga; Held, Brittany; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren J.; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mikhailova, Natalia; Pagani, Ioanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy

    2015-01-01

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction. PMID:25767232

  4. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    DOE PAGESBeta

    Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; et al

    2015-03-12

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

  5. Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten wastewater treatment systems.

    PubMed

    Gao, Jingfeng; Luo, Xin; Wu, Guixia; Li, Ting; Peng, Yongzhen

    2014-04-01

    The abundance and diversity of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in ten wastewater treatment systems (WTSs) by polymerase chain reaction (PCR), cloning, sequencing, and quantitative real-time PCR (qPCR). The ten WTSs included four full-scale municipal WTSs, three full-scale industrial WTSs, and three lab-scale WTSs. AOB were present in all the WTSs, whereas AOA were detected in nine WTSs. QPCR data showed that AOB amoA genes (4.625 × 10(4)-9.99 × 10(9) copies g(-1) sludge) outnumbered AOA amoA genes (oxidization in WTSs. Interestingly, it was found that AOA and AOB coexisted with anaerobic ammonia oxidation (anammox) bacteria in three anammox WTSs with relatively higher abundance. In a full-scale industrial WTS where effluent ammonia was higher than influent ammonia, both AOA and AOB showed higher abundance. The phylogenetic analysis of AOB amoA genes showed that genera Nitrosomonas was the most dominant species in the ten WTSs; Nitrosomonas europaea cluster was the dominant major cluster, followed by Nitrosomonas-like cluster and Nitrosomonas oligotropha cluster; and AOB species showed higher diversity than AOA species. AOA were found to be affiliated with two major clusters: Nitrososphaera cluster and Nitrosopumilus cluster. Nitrososphaera cluster was the most dominant species in different samples and distributed worldwide. PMID:24318009

  6. 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. PMID:25336721

  7. Influence of organics and silica on Fe(II) oxidation rates and cell-mineral aggregate formation by the green-sulfur Fe(II)-oxidizing bacterium Chlorobium ferrooxidans KoFox - Implications for Fe(II) oxidation in ancient oceans

    NASA Astrophysics Data System (ADS)

    Gauger, Tina; Byrne, James M.; Konhauser, Kurt O.; Obst, Martin; Crowe, Sean; Kappler, Andreas

    2016-06-01

    Most studies on microbial phototrophic Fe(II) oxidation (photoferrotrophy) have focused on purple bacteria, but recent evidence points to the importance of green-sulfur bacteria (GSB). Their recovery from modern ferruginous environments suggests that these photoferrotrophs can offer insights into how their ancient counterparts grew in Archean oceans at the time of banded iron formation (BIF) deposition. It is unknown, however, how Fe(II) oxidation rates, cell-mineral aggregate formation, and Fe-mineralogy vary under environmental conditions reminiscent of the geological past. To address this, we studied the Fe(II)-oxidizer Chlorobium ferrooxidans KoFox, a GSB living in co-culture with the heterotrophic Geospirillum strain KoFum. We investigated the mineralogy of Fe(III) metabolic products at low/high light intensity, and in the presence of dissolved silica and/or fumarate. Silica and fumarate influenced the crystallinity and particle size of the produced Fe(III) minerals. The presence of silica also enhanced Fe(II) oxidation rates, especially at high light intensities, potentially by lowering Fe(II)-toxicity to the cells. Electron microscopic imaging showed no encrustation of either KoFox or KoFum cells with Fe(III)-minerals, though weak associations were observed suggesting co-sedimentation of Fe(III) with at least some biomass via these aggregates, which could support diagenetic Fe(III)-reduction. Given that GSB are presumably one of the most ancient photosynthetic organisms, and pre-date cyanobacteria, our findings, on the one hand, strengthen arguments for photoferrotrophic activity as a likely mechanism for BIF deposition on a predominantly anoxic early Earth, but, on the other hand, also suggest that preservation of remnants of Fe(II)-oxidizing GSB as microfossils in the rock record is unlikely.

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

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

  9. Anaerobic degradation of toluene by a denitrifying bacterium.

    PubMed Central

    Evans, P J; Mang, D T; Kim, K S; Young, L Y

    1991-01-01

    A denitrifying bacterium, designated strain T1, that grew with toluene as the sole source of carbon under anaerobic conditions was isolated. The type of agar used in solid media and the toxicity of toluene were determinative factors in the successful isolation of strain T1. Greater than 50% of the toluene carbon was oxidized to CO2, and 29% was assimilated into biomass. The oxidation of toluene to CO2 was stoichiometrically coupled to nitrate reduction and denitrification. Strain T1 was tolerant of and grew on 3 mM toluene after a lag phase. The rate of toluene degradation was 1.8 mumol min-1 liter-1 (56 nmol min-1 mg of protein-1) in a cell suspension. Strain T1 was distinct from other bacteria that oxidize toluene anaerobically, but it may utilize a similar biochemical pathway of oxidation. In addition, o-xylene was transformed to a metabolite in the presence of toluene but did not serve as the sole source of carbon for growth of strain T1. This transformation was dependent on the degradation of toluene. Images PMID:2059037

  10. Maintenance Energy Demand and Starvation Recovery Dynamics of Nitrosomonas europaea and Nitrobacter winogradskyi Cultivated in a Retentostat with Complete Biomass Retention

    PubMed Central

    Tappe, W.; Laverman, A.; Bohland, M.; Braster, M.; Rittershaus, S.; Groeneweg, J.; van Verseveld, H. W.

    1999-01-01

    Nitrosomonas europaea and Nitrobacter winogradskyi (strain “Engel”) were grown in ammonia-limited and nitrite-limited conditions, respectively, in a retentostat with complete biomass retention at 25°C and pH 8. Fitting the retentostat biomass and oxygen consumption data of N. europaea and N. winogradskyi to the linear equation for substrate utilization resulted in up to eight-times-lower maintenance requirements compared to the maintenance energy demand (m) calculated from chemostat experiments. Independent of the growth rate at different stages of such a retention culture, the maximum specific oxygen consumption rate measured by mass spectrometric analysis of inlet and outlet gas oxygen content always amounted to approximately 45 μmol of O2 mg−1 of biomass-C · h−1 for both N. europaea and N. winogradskyi. When bacteria were starved for different time periods (up to 3 months), the spontaneous respiratory activity after an ammonia or nitrite pulse decreased with increasing duration of the previous starvation time period, but the observed decrease was many times faster for N. winogradskyi than for N. europaea. Likewise, the velocity of resuscitation decreased with extended time periods of starvation. The increase in oxygen consumption rates during resuscitation referred to the reviving population only, since in parallel no significant increase in the cell concentrations was detectable. N. europaea more readily recovers from starvation than N. winogradskyi, explaining the occasionally observed nitrite accumulation in the environment after ammonia becomes available. From chloramphenicol (100 μg · ml−1) inhibition experiments with N. winogradskyi, it has been concluded that energy-starved cells must have a lower protein turnover rate than nonstarved cells. As pointed out by Stein and Arp (L. Y. Stein and D. J. Arp, Appl. Environ. Microbiol. 64:1514–1521, 1998), nitrifying bacteria in soil have to cope with extremely low nutrient concentrations

  11. The capacity of phototrophic sulfur bacterium Thiocapsa roseopersicina for chemosynthesis.

    PubMed

    Kondratieva, E N; Zhukov, V G; Ivanovsky, R N; Petushkova, U P; Monosov, E Z

    1976-07-01

    Purple sulfur bacterium Thiocapsa roseopersicina strain BBS requiring vitamin B12 may grow in the dark in media containing no other organic compounds. Under such conditions the cells oxidize sulfide and thiosulfate with the use of O2 and assimilate carbon dioxide. After 10--30s assimilation of NaH14CO3 about 60% of radioactivity is found in phosphorylated compounds characteristic for the reductive pentose phosphate cycle. The possibility of the function of this cycle in the dark in the presence of O2 is confirmed by the capacity of cells grown under such conditions to synthesize ribulose-1,5-diphosphate carboxylase. All this evidence suggests the ability of T. roseopersicina to change from phototrophy to aerobic chemolithoautotrophy. PMID:942280

  12. 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

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

    PubMed

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

    2015-12-01

    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

  14. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant.

    PubMed

    Wu, Yi-Ju; Whang, Liang-Ming; Fukushima, Toshikazu; Chang, Shao-Hsiung

    2013-04-01

    The diversity and abundance of ammonia-oxidizing Betaproteobacteria and archaea were investigated in a full-scale municipal wastewater treatment plant where the wastewater conductivity level varied considerably (due to seawater salinity intrusion) during this study between 2004 and 2007. Based on the quantitative polymerase chain reaction of ammonia monooxygenase subunit A (amoA) genes, an increase in the ammonia oxidizing bacteria amoA gene copies occurred with a decrease in the wastewater salinity level. A corresponding decrease in the average ammonia-oxidizing archaea to bacteria ratio, from 1.22 (2004 and 2005), 0.17 (2006), and then to 0.07 (2007), was observed. Phylogenetic analyses on amoA gene sequences indicated that Nitrosomonas marina-like ammonia oxidizing bacteria and Thaumarcheota Ⅰ.1a (marina group) ammonia-oxidizing archaea were dominant when the wastewater salinity level fluctuated at high values with an average of 4.83 practical salinity unit (psu), while Nitrosomonas urea-like ammonia oxidizing bacteria and Thaumarcheota Ⅰ.1b (soil group) ammonia-oxidizing archaea became dominant when the wastewater salinity decreased to a more stable lower level with an average of 1.93 psu. Based on the amoA gene-based terminal restriction fragment length polymorphism analyses, results from this study demonstrated that the observed shift in ammonia oxidizing bacteria and archaea populations is likely caused by a change of the wastewater salinity level. PMID:23232030

  15. Regulation of caffeate respiration in the acetogenic bacterium Acetobacterium woodii.

    PubMed

    Dilling, Sabrina; Imkamp, Frank; Schmidt, Silke; Müller, Volker

    2007-06-01

    The anaerobic acetogenic bacterium Acetobacterium woodii can conserve energy by oxidation of various substrates coupled to either carbonate or caffeate respiration. We used a cell suspension system to study the regulation and kinetics of induction of caffeate respiration. After addition of caffeate to suspensions of fructose-grown cells, there was a lag phase of about 90 min before caffeate reduction commenced. However, in the presence of tetracycline caffeate was not reduced, indicating that de novo protein synthesis is required for the ability to respire caffeate. Induction also took place in the presence of CO(2), and once a culture was induced, caffeate and CO(2) were used simultaneously as electron acceptors. Induction of caffeate reduction was also observed with H(2) plus CO(2) as the substrate, but the lag phase was much longer. Again, caffeate and CO(2) were used simultaneously as electron acceptors. In contrast, during oxidation of methyl groups derived from methanol or betaine, acetogenesis was the preferred energy-conserving pathway, and caffeate reduction started only after acetogenesis was completed. The differential flow of reductants was also observed with suspensions of resting cells in which caffeate reduction was induced prior to harvest of the cells. These cell suspensions utilized caffeate and CO(2) simultaneously with fructose or hydrogen as electron donors, but CO(2) was preferred over caffeate during methyl group oxidation. Caffeate-induced resting cells could reduce caffeate and also p-coumarate or ferulate with hydrogen as the electron donor. p-Coumarate or ferulate also served as an inducer for caffeate reduction. Interestingly, caffeate-induced cells reduced ferulate in the absence of an external reductant, indicating that caffeate also induces the enzymes required for oxidation of the methyl group of ferulate. PMID:17416687

  16. pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China.

    PubMed

    Li, Hu; Weng, Bo-Sen; Huang, Fu-Yi; Su, Jian-Qiang; Yang, Xiao-Ru

    2015-07-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity. PMID:25744648

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

    PubMed

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

    2006-10-01

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

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

    PubMed

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

    1980-12-19

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

  19. Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans.

    PubMed

    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

    2009-10-20

    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 Au(0). 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

  20. P450 enzymes from the bacterium Novosphingobium aromaticivorans.

    PubMed

    Bell, Stephen G; Wong, Luet-Lok

    2007-08-31

    Twelve of the fifteen potential P450 enzymes from the bacterium Novosphingobium aromaticivorans, which is known to degrade a wide range of aromatic hydrocarbons, have been produced via heterologous expression in Escherichia coli. The enzymes were tested for their ability to bind a range of substrates including polyaromatic hydrocarbons. While two of the enzymes were found to bind aromatic compounds (CYP108D1 and CYP203A2), the others show binding with a variety of compounds including linear alkanes (CYP153C1) and mono- and sesqui-terpenoid compounds (CYP101B1, CYP101C1, CYP101D1, CYP101D2, CYP111A1, and CYP219A1). A 2Fe-2S ferredoxin (Arx-A), which is associated with CYP101D2, was also produced. The activity of five of the P450 enzymes (CYP101B1, CYP101C1, CYP101D1, CYP101D2, and CYP111A2) was reconstituted with Arx-A and putidaredoxin reductase (of the P450cam system from Pseudomonas putida) in a Class I type electron transfer system. Preliminary characterisation of the majority of the substrate oxidation products is reported. PMID:17618912

  1. P450 enzymes from the bacterium Novosphingobium aromaticivorans

    SciTech Connect

    Bell, Stephen G. . E-mail: stephen.bell@chem.ox.ac.uk; Wong, Luet-Lok

    2007-08-31

    Twelve of the fifteen potential P450 enzymes from the bacterium Novosphingobium aromaticivorans, which is known to degrade a wide range of aromatic hydrocarbons, have been produced via heterologous expression in Escherichia coli. The enzymes were tested for their ability to bind a range of substrates including polyaromatic hydrocarbons. While two of the enzymes were found to bind aromatic compounds (CYP108D1 and CYP203A2), the others show binding with a variety of compounds including linear alkanes (CYP153C1) and mono- and sesqui-terpenoid compounds (CYP101B1, CYP101C1, CYP101D1, CYP101D2, CYP111A1, and CYP219A1). A 2Fe-2S ferredoxin (Arx-A), which is associated with CYP101D2, was also produced. The activity of five of the P450 enzymes (CYP101B1, CYP101C1, CYP101D1, CYP101D2, and CYP111A2) was reconstituted with Arx-A and putidaredoxin reductase (of the P450cam system from Pseudomonas putida) in a Class I type electron transfer system. Preliminary characterisation of the majority of the substrate oxidation products is reported.

  2. 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

  3. 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

  4. 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.

  5. The chemical formula of a magnetotactic bacterium.

    PubMed

    Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

    2012-05-01

    Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life. PMID:22170293

  6. INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium.

    PubMed

    Araujo Granda, Pablo; Gras, Anna; Ginovart, Marta; Moulton, Vincent

    2016-08-21

    We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans. The individuals in the model represent microbes and the individual-based model INDISIM gives the behavior-rules that they use for their nutrient uptake and reproduction cycle. Three previously described metabolic pathways for P. denitrificans were selected and translated into balanced chemical equations using a thermodynamic model. These stoichiometric reactions are an intracellular model for the individual behavior-rules for metabolic maintenance and biomass synthesis and result in the release of different nitrogen oxides to the medium. The model was implemented using the NetLogo platform and it provides an interactive tool to investigate the different steps of denitrification carried out by a denitrifying bacterium. The simulator can be obtained from the authors on request. PMID:27179457

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

    PubMed

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

    1997-09-01

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

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

    PubMed Central

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

    1997-01-01

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

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

    PubMed

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

    2016-12-01

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

  10. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

    DOE PAGESBeta

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

    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.

  11. A novel strategy for acetonitrile wastewater treatment by using a recombinant bacterium with biofilm-forming and nitrile-degrading capability.

    PubMed

    Li, Chunyan; Yue, Zhenlei; Feng, Fengzhao; Xi, Chuanwu; Zang, Hailian; An, Xuejiao; Liu, Keran

    2016-10-01

    There is a great need for efficient acetonitrile removal technology in wastewater treatment to reduce the discharge of this pollutant in untreated wastewater. In this study, a nitrilase gene (nit) isolated from a nitrile-degrading bacterium (Rhodococcus rhodochrous BX2) was cloned and transformed into a biofilm-forming bacterium (Bacillus subtilis N4) that expressed the recombinant protein upon isopropylthio-β-galactoside (IPTG) induction. The recombinant bacterium (B. subtilis N4-pHT01-nit) formed strong biofilms and had nitrile-degrading capability. Further testing demonstrated that biofilms formed by B. subtilis N4-pHT01-nit were highly resistant to loading shock from acetonitrile and almost completely degraded the initial concentration of acetonitrile (800 mg L(-1)) within 24 h in a moving bed biofilm reactor (MBBR) after operation for 35 d. The bacterial composition of the biofilm, identified by high-throughput sequencing, in a reactor in which the B. subtilis N4-pHT01-nit bacterium was introduced indicated that the engineered bacterium was successfully immobilized in the reactor and became dominant genus. This work demonstrates that an engineered bacterium with nitrile-degrading and biofilm-forming capacity can improve the degradation of contaminants in wastewater. This approach offers a novel strategy for enhancing the biological oxidation of toxic pollutants in wastewater. PMID:27434252

  12. An Experiment in Autotrophic Fermentation: Microbial Oxidation of Hydrogen Sulfide.

    ERIC Educational Resources Information Center

    Sublette, Kerry L.

    1989-01-01

    Described is an experiment which uses an autotrophic bacterium to anaerobically oxidize hydrogen sulfide to sulfate in a batch-stirred tank reactor. Discusses background information, experimental procedure, and sample results of this activity. (CW)

  13. A static and dynamical Mössbauer study of photochemical biological switch of valence states in the respiratory pigments of rhodospirillum rubrum bacterium

    NASA Astrophysics Data System (ADS)

    Rao, K. R. P. M.; Iyengar, P. K.

    1986-04-01

    We have carried out a dynamical Mössbauer spectroscopy study of photochemical reversible biological switching of oxidation-reduction processes in iron atoms present in the respiratory pigments of Rhodospirillum rubrum bacterium. The experimental technique utilised enabled us to determine an upper limit to the reaction time of about 25 ms.

  14. Effects of dissolved oxygen and pH on nitrous oxide production rates in autotrophic partial nitrification granules.

    PubMed

    Rathnayake, Rathnayake M L D; Oshiki, Mamoru; Ishii, Satoshi; Segawa, Takahiro; Satoh, Hisashi; Okabe, Satoshi

    2015-12-01

    The effects of dissolved oxygen (DO) and pH on nitrous oxide (N2O) production rates and pathways in autotrophic partial nitrification (PN) granules were investigated at the granular level. N2O was primarily produced by betaproteobacterial ammonia-oxidizing bacteria, mainly Nitrosomonas europaea, in the oxic surface layer (<200μm) of the autotrophic PN granules. N2O production increased with increasing bulk DO concentration owing to activation of the ammonia (i.e., hydroxylamine) oxidation in this layer. The highest N2O emissions were observed at pH 7.5, although the ammonia oxidation rate was unchanged between pH 6.5 and 8.5. Overall, the results of this study suggest that in situ analyses of PN granules are essential to gaining insight into N2O emission mechanisms in a granule. PMID:26318242

  15. Epiphyton as a Niche for Ammonia-Oxidizing Bacteria: Detailed Comparison with Benthic and Pelagic Compartments in Shallow Freshwater Lakes▿

    PubMed Central

    Coci, M.; Bodelier, P. L. E.; Laanbroek, H. J.

    2008-01-01

    Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated. PMID:18263748

  16. 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.

  17. Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711.

    PubMed

    Shoemaker, William R; Muscarella, Mario E; Lennon, Jay T

    2015-01-01

    We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments. PMID:26089434

  18. Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711

    PubMed Central

    Shoemaker, William R.; Muscarella, Mario E.

    2015-01-01

    We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments. PMID:26089434

  19. 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. PMID:25133457

  20. 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.

  1. Enrichment and physiological characterization of a novel Nitrospira-like bacterium obtained from a marine sponge.

    PubMed

    Off, Sandra; Alawi, Mashal; Spieck, Eva

    2010-07-01

    Members of the nitrite-oxidizing genus Nitrospira are most likely responsible for the second step of nitrification, the conversion of nitrite (NO(2)(-)) to nitrate (NO(3)(-)), within various sponges. We succeeded in obtaining an enrichment culture of Nitrospira derived from the mesohyl of the marine sponge Aplysina aerophoba using a traditional cultivation approach. Electron microscopy gave first evidence of the shape and ultrastructure of this novel marine Nitrospira-like bacterium (culture Aa01). We characterized these bacteria physiologically with regard to optimal incubation conditions, especially the temperature and substrate range in comparison to other Nitrospira cultures. Best growth was obtained at temperatures between 28 degrees C and 30 degrees C in mineral medium with 70% North Sea water and a substrate concentration of 0.5 mM nitrite under microaerophilic conditions. The Nitrospira culture Aa01 is very sensitive against nitrite, because concentrations higher than 1.5 mM resulted in a complete inhibition of growth. Sequence analyses of the 16S rRNA gene revealed that the novel Nitrospira-like bacterium is separated from the sponge-specific subcluster and falls together with an environmental clone from Mediterranean sediments (98.6% similarity). The next taxonomically described species Nitrospira marina is only distantly related, with 94.6% sequence similarity, and therefore the culture Aa01 represents a novel species of nitrite-oxidizing bacteria. PMID:20511427

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

    USGS Publications Warehouse

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

    1996-01-01

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

  3. 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

  4. Pangenome Evolution in the Marine Bacterium Alteromonas.

    PubMed

    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

  5. Strain IMB-1, a novel bacterium for the removal of methyl bromide in fumigated agricultural soils

    USGS Publications Warehouse

    Connell, Hancock T.L.; Costello, A.M.; Lidstrom, M.E.; Oremland, R.S.

    1998-01-01

    A facultatively methylotrophic bacterium, strain IMB-1, that has been isolated from agricultural soil grows on methyl bromide (MeBr), methyl iodide, methyl chloride, and methylated amines, as well as on glucose, pyruvate, or acetate. Phylogenetic analysis of its 16S rRNA gene sequence indicates that strain IMB-1 classes in the alpha subgroup of the class Proteobacteria and is closely related to members of the genus Rhizobium. The ability of strain IMB-1 to oxidize MeBr to CO2 is constitutive in cells regardless of the growth substrate. Addition of cell suspensions of strain IMB-1 to soils greatly accelerates the oxidation of MeBr, as does pretreatment of soils with low concentrations of methyl iodide. These results suggest that soil treatment strategies can be devised whereby bacteria can effectively consume MeBr during field fumigations, which would diminish or eliminate the outward flux of MeBr to the atmosphere.

  6. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond

    PubMed Central

    Lu, Shimin; Liu, Xingguo; Ma, Zhuojun; Liu, Qigen; Wu, Zongfan; Zeng, Xianlei; Shi, Xu; Gu, Zhaojun

    2016-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster. PMID:26834709

  7. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond.

    PubMed

    Lu, Shimin; Liu, Xingguo; Ma, Zhuojun; Liu, Qigen; Wu, Zongfan; Zeng, Xianlei; Shi, Xu; Gu, Zhaojun

    2015-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0-50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0-10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0-2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10-15 and 20-25 cm depths) were grouped into the Nitrosopumilus cluster. PMID:26834709

  8. 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.

  9. Effects of substrates on N2O emissions in an anaerobic ammonium oxidation (anammox) reactor.

    PubMed

    Jin, Yue; Wang, Dunqiu; Zhang, Wenjie

    2016-01-01

    N2O emission in the anaerobic ammonium oxidation (anammox) process is of growing concern. In this study, effects of substrate concentrations on N2O emissions were investigated in an anammox reactor. Extremely high N2O emissions of 1.67 % were led by high NH4-N concentrations. Results showed that N2O emissions have a positive correlation with NH4-N concentrations in the anammox reactor. Reducing NH4-N concentrations by recycling pump resulted in decreasing N2O emissions. In addition, further studies were performed to identify a key biological process that is contributed to N2O emissions from the anammox reactor. Based on the results obtained, Nitrosomonas, which can oxidize ammonia to nitrite, was deemed as the main sources of N2O emissions. PMID:27376009

  10. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria.

    PubMed

    Kozlowski, Jessica A; Kits, K Dimitri; Stein, Lisa Y

    2016-01-01

    Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity. PMID:27462312

  11. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria

    PubMed Central

    Kozlowski, Jessica A.; Kits, K. Dimitri; Stein, Lisa Y.

    2016-01-01

    Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity. PMID:27462312

  12. 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

  13. 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. PMID:26048926

  14. Ammonia-oxidizer communities in an agricultural soil treated with contrasting nitrogen sources

    PubMed Central

    Habteselassie, Mussie Y.; Xu, Li; Norton, Jeanette M.

    2013-01-01

    The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for six seasons with contrasting nitrogen (N) sources. Molecular tools based on the genes encoding ammonia monooxygenase were used to characterize the ammonia oxidizer (AO) communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control), dairy waste compost, liquid dairy waste (LW), and ammonium sulfate (AS) treatments at approximately 100 and 200 kg available N ha-1 over 6 years. The N treatment affected the quantity of AO based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 107, 2.5 × 107, and 2.1 × 107copies g-1 soil, respectively) than in the control (8.1 × 106 copies g-1 soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 107 copies g-1 soil, average). The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of 6 years of contrasting nitrogen sources applications caused changes in AO abundance while the community composition remained relatively stable for both AOB and AOA. PMID:24223575

  15. Using Pure Cultures to Define the Site Preference of Nitrous Oxide Produced by Microbial Nitrification and Denitrification

    NASA Astrophysics Data System (ADS)

    Sutka, R. L.; Breznak, J. A.; Ostrom, N. E.; Ostrom, P. H.; Gandhi, H.

    2004-12-01

    Defining the site preference of nitrous oxide (N2O) produced in pure culture studies is crucial to interpreting field data. We have previously demonstrated that the intramolecular distribution of nitrogen isotopes (isotopomers) can be used to differentiate N2O produced by nitrifier denitrification and nitrification in cultures of Nitrosomonas europaea. Here, we have expanded on our initial results and evaluated the isotopomeric composition of N2O produced during nitrification and nitrifier denitrification with cultures of Nitrosospira multiformis. In addition, we have analyzed N2O produced during methanotrophic nitrification, denitrification, and fungal denitrification. To evaluate N2O production during nitrification and nitrifier denitrification, we compared the site preference of N2O formed as a result of nitrite reduction and hydroxylamine oxidation with Nitrosomonas europaea and Nitrosospira multiformis. The average site preference of N2O produced by hydroxylamine oxidation was similar for Nitrosomonas europaea (33.0 ± 3.5 ‰ ) and Nitrosospira multiformis (33.1 ± 4.2 ‰ ). Nitrous oxide produced by nitrifier-denitrification by Nitrosomonas europaea and Nitrosospira multiformis had a similar site preference of - 1.4 ± 4.4 ‰ and - 1.1 ± 2.6 ‰ respectively. The results indicate that it is possible to differentiate between N2O produced by nitrite reduction and hydroxylamine oxidation by ammonia oxidizing bacteria. Methanotrophic nitrification was evaluated by analyzing the N2O produced during hydroxylamine oxidation in concentrated cell suspensions of two methane oxidizing bacteria. The site preference of N2O produced by the two methane oxidizers, Methylococcus capsulatus Bath and Methylosinus trichosporium was 31.8 ± 4.7 ‰ and 33.0 ± 4.5 ‰ respectively. The results indicate that a site preference of 33 ‰ is applicable for nitrification regardless of whether a methane oxidizer or ammonia oxidizer is involved in the reaction. To determine the site

  16. 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

    2015-01-01

    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

  17. 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

  18. Endophytic Bacterium-Triggered Reactive Oxygen Species Directly Increase Oxygenous Sesquiterpenoid Content and Diversity in Atractylodes lancea.

    PubMed

    Zhou, Jia-Yu; Yuan, Jie; Li, Xia; Ning, Yi-Fan; Dai, Chuan-Chao

    2016-03-01

    Oxygenous terpenoids are active components of many medicinal plants. However, current studies that have focused on enzymatic oxidation reactions cannot comprehensively clarify the mechanisms of oxygenous terpenoid synthesis and diversity. This study shows that an endophytic bacterium can trigger the generation of reactive oxygen species (ROS) that directly increase oxygenous sesquiterpenoid content and diversity in Atractylodes lancea. A. lancea is a famous but endangered Chinese medicinal plant that contains abundant oxygenous sesquiterpenoids. Geo-authentic A. lancea produces a wider range and a greater abundance of oxygenous sesquiterpenoids than the cultivated herb. Our previous studies have shown the mechanisms behind endophytic promotion of the production of sesquiterpenoid hydrocarbon scaffolds; however, how endophytes promote the formation of oxygenous sesquiterpenoids and their diversity is unclear. After colonization by Pseudomonas fluorescens ALEB7B, oxidative burst and oxygenous sesquiterpenoid accumulation in A. lancea occur synchronously. Treatment with exogenous hydrogen peroxide (H2O2) or singlet oxygen induces oxidative burst and promotes oxygenous sesquiterpenoid accumulation in planta. Conversely, pretreatment of plantlets with the ROS scavenger ascorbic acid significantly inhibits the oxidative burst and oxygenous sesquiterpenoid accumulation induced by P. fluorescens ALEB7B. Further in vitro oxidation experiments show that several oxygenous sesquiterpenoids can be obtained from direct oxidation caused by H2O2 or singlet oxygen. In summary, this study demonstrates that endophytic bacterium-triggered ROS can directly oxidize oxygen-free sesquiterpenoids and increase the oxygenous sesquiterpenoid content and diversity in A. lancea, providing a novel explanation of the mechanisms of oxygenous terpenoid synthesis in planta and an essential complementarity to enzymatic oxidation reactions. PMID:26712554

  19. Endophytic Bacterium-Triggered Reactive Oxygen Species Directly Increase Oxygenous Sesquiterpenoid Content and Diversity in Atractylodes lancea

    PubMed Central

    Zhou, Jia-Yu; Yuan, Jie; Li, Xia; Ning, Yi-Fan

    2015-01-01

    Oxygenous terpenoids are active components of many medicinal plants. However, current studies that have focused on enzymatic oxidation reactions cannot comprehensively clarify the mechanisms of oxygenous terpenoid synthesis and diversity. This study shows that an endophytic bacterium can trigger the generation of reactive oxygen species (ROS) that directly increase oxygenous sesquiterpenoid content and diversity in Atractylodes lancea. A. lancea is a famous but endangered Chinese medicinal plant that contains abundant oxygenous sesquiterpenoids. Geo-authentic A. lancea produces a wider range and a greater abundance of oxygenous sesquiterpenoids than the cultivated herb. Our previous studies have shown the mechanisms behind endophytic promotion of the production of sesquiterpenoid hydrocarbon scaffolds; however, how endophytes promote the formation of oxygenous sesquiterpenoids and their diversity is unclear. After colonization by Pseudomonas fluorescens ALEB7B, oxidative burst and oxygenous sesquiterpenoid accumulation in A. lancea occur synchronously. Treatment with exogenous hydrogen peroxide (H2O2) or singlet oxygen induces oxidative burst and promotes oxygenous sesquiterpenoid accumulation in planta. Conversely, pretreatment of plantlets with the ROS scavenger ascorbic acid significantly inhibits the oxidative burst and oxygenous sesquiterpenoid accumulation induced by P. fluorescens ALEB7B. Further in vitro oxidation experiments show that several oxygenous sesquiterpenoids can be obtained from direct oxidation caused by H2O2 or singlet oxygen. In summary, this study demonstrates that endophytic bacterium-triggered ROS can directly oxidize oxygen-free sesquiterpenoids and increase the oxygenous sesquiterpenoid content and diversity in A. lancea, providing a novel explanation of the mechanisms of oxygenous terpenoid synthesis in planta and an essential complementarity to enzymatic oxidation reactions. PMID:26712554

  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. 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.

  2. Microcalorimetric Measurements of Glucose Metabolism by Marine Bacterium Vibrio alginolyticus

    PubMed Central

    Gordon, Andrew S.; Millero, Frank J.; Gerchakov, Sol M.

    1982-01-01

    Microcalorimetric measurements of heat production from glucose by Vibrio alginolyticus were made to assess the viability of calorimetry as a technique for studying the metabolism of marine bacteria at organic nutrient concentrations found in marine waters. The results show that the metabolism of glucose by this bacterium can be measured by calorimetry at submicromolar concentrations. A linear correlation between glucose concentration and total heat production was observed over a concentration range of 8 mM to 0.35 μM. It is suggested that these data indicate a constant efficiency of metabolism for this bacterium over the wide range of glucose concentrations studied. PMID:16346131

  3. Nitrification resilience and community dynamics of ammonia-oxidizing bacteria with respect to ammonia loading shock in a nitrification reactor treating steel wastewater.

    PubMed

    Cho, Kyungjin; Shin, Seung Gu; Lee, Joonyeob; Koo, Taewoan; Kim, Woong; Hwang, Seokhwan

    2016-08-01

    The aim of this study was to investigate the nitrification resilience pattern and examine the key ammonia-oxidizing bacteria (AOB) with respect to ammonia loading shocks (ALSs) in a nitrification bioreactor treating steel wastewater. The perturbation experiments were conducted in a 4-L bioreactor operated in continuous mode with a hydraulic retention time of 10 d. Three sequential ALSs were given to the bioreactor (120, 180 and 180 mg total ammonia nitrogen (TAN)/L. When the first shock was given, the nitrification process completely recovered after 14 d of further operation. However, the resilience duration was significantly reduced to ∼1 d after the second and third ALSs. In the bioreactor, Nitrosomonas aestuarii dominated the other AOB species, Nitrosomonas europaea and N. nitrosa, throughout the process. In addition, the population of N. aestuarii increased with ammonia utilization following each ALS; i.e., this species responded to acute ammonia overloadings by contributing to ammonia oxidation. This finding suggests that N. aestuarii could be exploited to achieve stable nitrification in industrial wastewaters that contain high concentrations of ammonia. PMID:26896313

  4. Distribution and Abundance of Archaeal and Bacterial Ammonia Oxidizers in the Sediments of the Dongjiang River, a Drinking Water Supply for Hong Kong

    PubMed Central

    Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Wang, Aijie; Sun, Guoping

    2013-01-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b-and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg−1 sediment, NH4+-N >144 mg kg−1 sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg−1 sediment, NH4+-N <93 mg kg−1 sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem. PMID:24256973

  5. Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in mediterranean urban stream biofilms.

    PubMed

    Merbt, Stephanie N; Auguet, Jean-Christophe; Blesa, Alba; Martí, Eugènia; Casamayor, Emilio O

    2015-01-01

    Streams affected by wastewater treatment plant (WWTP) effluents are hotspots of nitrification. We analyzed the influence of WWTP inputs on the abundance, distribution, and composition of epilithic ammonia-oxidizing (AO) assemblages in five Mediterranean urban streams by qPCR and amoA gene cloning and sequencing of both archaea (AOA) and bacteria (AOB). The effluents significantly modified stream chemical parameters, and changes in longitudinal profiles of both NH(4)(+) and NO(3)(-) indicated stimulated nitrification activity. WWTP effluents were an allocthonous source of both AOA, essentially from the Nitrosotalea cluster, and mostly of AOB, mainly Nitrosomonas oligotropha, Nitrosomonas communis, and Nitrosospira spp. changing the relative abundance and the natural composition of AO assemblages. Under natural conditions, Nitrososphaera and Nitrosopumilus AOA dominated AO assemblages, and AOB were barely detected. After the WWTP perturbation, epilithic AOB increased by orders of magnitude whereas AOA did not show quantitative changes but a shift in population composition to dominance of Nitrosotalea spp. The foraneous AOB successfully settled in downstream biofilms and probably carried out most of the nitrification activity. Nitrosotalea were only observed downstream and only in biofilms exposed to either darkness or low irradiance. In addition to other potential environmental limitations for AOA distribution, this result suggests in situ photosensitivity as previously reported for Nitrosotalea under laboratory conditions. PMID:25062836

  6. Biodegradation of Ethylene Glycol by a Salt-Requiring Bacterium1

    PubMed Central

    Gonzalez, Carlos F.; Taber, Willard A.; Zeitoun, M. A.

    1972-01-01

    A gram-negative nonmotile rod which was capable of using 1,2-14C-ethylene glycol as a sole carbon source for growth was isolated from a brine pond, Great Salt Lake, Utah. The bacterium (ATCC 27042) required at least 0.85% NaCl for growth and, although the chloride ion was replaceable by sulfate ion, the sodium ion was not replaceable by potassium ion. The maximal concentration of salt tolerated for growth was approximately 12%. The bacterium was oxidase-negative when N,N-dimethyl-p-phenylenediamine was used and weakly positive when N,N,N′,N′-tetramethyl-p-phenylenediamine was used. It grows on many sugars but does not ferment them, it does not have an exogenous vitamin requirement, and it possesses a guanine plus cytosine ratio of 64.3%. Incorporation of ethylene glycol carbon into cell and respired CO2 was quantitated by use of radioactive ethylene glycol and a force-aerated fermentor. Glucose suppressed ethylene glycol metabolism. Cells grown on ethylene and propylene glycol respired ethylene glycol in a Warburg respirometer more rapidly than cells grown on glucose. Spectrophotometric evidence was obtained for oxidation of glycolate to glyoxylate by a dialyzed cell extract. PMID:4568254

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

    PubMed

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

    2016-01-01

    Thermosulfurimonas dismutans S95(T), 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

  8. Microfabrication of patterns of adherent marine bacterium Phaeobacter inhibens using soft lithography and scanning probe lithography.

    PubMed

    Zhao, Chuan; Burchardt, Malte; Brinkhoff, Thorsten; Beardsley, Christine; Simon, Meinhard; Wittstock, Gunther

    2010-06-01

    Two lithographic approaches have been explored for the microfabrication of cellular patterns based on the attachment of marine bacterium Phaeobacter inhibens strain T5. Strain T5 produces a new antibiotic that makes this bacterium potentially interesting for the pharmaceutical market and as a probiotic organism in aquacultures and in controlling biofouling. The microcontact printing (microCP) method is based on the micropatterning of self-assembled monolayers (SAMs) terminated with adhesive end groups such as CH(3) and COOH and nonadhesive groups (e.g., short oligomers of ethylene glycol (OEG)) to form micropatterned substrates for the adhesion of strain T5. The scanning probe lithographic method is based on the surface modification of OEG SAM by using a microelectrode, the probe of a scanning electrochemical microscope (SECM). Oxidizing agents (e.g., Br(2)) were electrogenerated in situ at the microelectrodes from Br(-) in aqueous solution to remove OEG SAMs locally, which allows the subsequent adsorption of bacteria. Various micropatterns of bacteria could be formed in situ on the substrate without a prefabricated template. The fabricated cellular patterns may be applied to a variety of marine biological studies that require the analysis of biofilm formation, cell-cell and cell-surface interactions, and cell-based biosensors and bioelectronics. PMID:20397716

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

    PubMed

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

    2009-09-01

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

  10. Determinants of spontaneous mutation in the bacterium Escherichia coli as revealed by whole-genome sequencing

    PubMed Central

    Foster, Patricia L.; Lee, Heewook; Popodi, Ellen; Townes, Jesse P.; Tang, Haixu

    2015-01-01

    A complete understanding of evolutionary processes requires that factors determining spontaneous mutation rates and spectra be identified and characterized. Using mutation accumulation followed by whole-genome sequencing, we found that the mutation rates of three widely diverged commensal Escherichia coli strains differ only by about 50%, suggesting that a rate of 1–2 × 10−3 mutations per generation per genome is common for this bacterium. Four major forces are postulated to contribute to spontaneous mutations: intrinsic DNA polymerase errors, endogenously induced DNA damage, DNA damage caused by exogenous agents, and the activities of error-prone polymerases. To determine the relative importance of these factors, we studied 11 strains, each defective for a major DNA repair pathway. The striking result was that only loss of the ability to prevent or repair oxidative DNA damage significantly impacted mutation rates or spectra. These results suggest that, with the exception of oxidative damage, endogenously induced DNA damage does not perturb the overall accuracy of DNA replication in normally growing cells and that repair pathways may exist primarily to defend against exogenously induced DNA damage. The thousands of mutations caused by oxidative damage recovered across the entire genome revealed strong local-sequence biases of these mutations. Specifically, we found that the identity of the 3′ base can affect the mutability of a purine by oxidative damage by as much as eightfold. PMID:26460006

  11. 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.

  12. 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...

  13. Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140.

    PubMed

    Escano, Jerome; Deng, Peng; Lu, Shi-En; Smith, Lief

    2016-01-01

    Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin 1140, and the strain has been genetically engineered to combat dental caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome provides new insights into the strain's superior colonization properties and its utility in replacement therapy. PMID:27257196

  14. Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140

    PubMed Central

    Escano, Jerome; Deng, Peng; Lu, Shi-En

    2016-01-01

    Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin 1140, and the strain has been genetically engineered to combat dental caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome provides new insights into the strain’s superior colonization properties and its utility in replacement therapy. PMID:27257196

  15. Genomic Analysis of Melioribacter roseus, Facultatively Anaerobic Organotrophic Bacterium Representing a Novel Deep Lineage within Bacteriodetes/Chlorobi Group

    PubMed Central

    Kadnikov, Vitaly V.; Mardanov, Andrey V.; Podosokorskaya, Olga A.; Gavrilov, Sergey N.; Kublanov, Ilya V.; Beletsky, Alexey V.; Bonch-Osmolovskaya, Elizaveta A.; Ravin, Nikolai V.

    2013-01-01

    Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi. PMID:23301019

  16. Identification of an anaerobic bacterium which reduces perchlorate and chlorate as Wolinella succinogenes

    SciTech Connect

    Wallace, W.; Attaway, H. |

    1995-12-31

    Perchlorate and chlorate salts are widely used by the chemical, aerospace and defense industries as oxidizers in propellant, explosives and pyrotechnics. The authors have isolated a anaerobic bacterium which is capable of the dissimilatory reduction of both perchlorate and chlorate for energy and growth. Strain HAP-1 is a gram negative, thin rod, non-sporeforming, highly motile strict anaerobe. Antibiotic resistance profiles, utilization of carbon substrates and electron acceptors demonstrated similar physiological characteristics to Wolinella succinogenes. Pairwise comparisons of 16S RNA sequences showed only a 0.75% divergence between strain HAP-1 and W. succinogenes. Physiological, morphological and 16S RRNA sequence data indicate strain HAP-1 is a subspecies of W. succinogenes that can utilize perchlorate and chlorate as terminal electron acceptors.

  17. Cytochrome P450 enzymes from the metabolically diverse bacterium Rhodopseudomonas palustris

    SciTech Connect

    Bell, Stephen G. . E-mail: stephen.bell@chem.ox.ac.uk; Hoskins, Nicola; Xu Feng; Caprotti, Domenico; Rao Zihe; Wong, L.-L. . E-mail: luet.wong@chem.ox.ac.uk

    2006-03-31

    Four (CYP195A2, CYP199A2, CYP203A1, and CYP153A5) of the seven P450 enzymes, and palustrisredoxin A, a ferredoxin associated with CYP199A2, from the metabolically diverse bacterium Rhodopseudomonas palustris have been expressed and purified. A range of substituted benzenes, phenols, benzaldehydes, and benzoic acids was shown to bind to the four P450 enzymes. Monooxygenase activity of CYP199A2 was reconstituted with palustrisredoxin A and putidaredoxin reductase of the P450cam system from Pseudomonas putida. We found that 4-ethylbenzoate and 4-methoxybenzoate were oxidized to single products, and 4-methoxybenzoate was demethylated to form 4-hydroxybenzoate. Crystals of substrate-free CYP199A2 which diffracted to {approx}2.0 A have been obtained.

  18. Uncoupling effect of fatty acids in halo- and alkalotolerant bacterium Bacillus pseudofirmus FTU.

    PubMed

    Popova, I V; Bodrova, M E; Mokhova, E N; Muntyan, M S

    2004-10-01

    Natural uncouplers of oxidative phosphorylation, long-chain non-esterified fatty acids, cause uncoupling in the alkalo- and halotolerant bacterium Bacillus pseudofirmus FTU. The uncoupling effect in the bacterial cells was manifested as decrease of membrane potential and increase of respiratory activity. The membrane potential decrease was detected only in bacterial cells exhausted by their endogenous substrates. In proteoliposomes containing reconstituted bacterial cytochrome c oxidase, fatty acids caused a "mild" uncoupling effect by reducing membrane potential only at low rate of membrane potential generation. "Free respiration" induced by the "mild" uncouplers, the fatty acids, can be considered as possible mechanism responsible for adaptation of the bacteria to a constantly changed environment. PMID:15527418

  19. Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system.

    PubMed

    Brown, Monisha N; Briones, Aurelio; Diana, James; Raskin, Lutgarde

    2013-01-01

    This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system (RAS) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia-oxidizing populations were examined by targeting 16S rRNA and amoA genes of ammonia-oxidizing bacteria (AOB) and archaea (AOA). The nitrite-oxidizing bacteria (NOB) were investigated by targeting the 16S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to Nitrosomonas marina and Nitrosopumilus maritimus. The NOB detected were related to Nitrospira marina and Nitrospira moscoviensis, and Nitrospira marina-type NOB were more abundant than N. moscoviensis-type NOB. Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira marina-over N. moscoviensis-type NOB. PMID:22775980

  20. Biochemistry of Ammonia Monoxygenase from Nitrosomonas

    SciTech Connect

    Alan Hooper

    2009-07-15

    Major results. 1. CytochromecM552, a protein in the electron transfer chain to ammonia monooxygenase. Purification, modeling of protein structure based on primary structure, characterization of 4 hemes by magnetic spectroscopy, potentiometry, ligand binding and turnover. Kim, H. J., ,Zatsman, et al. 2008). 2. Characterization of proteins which thought to be involved in the AMO reaction or to protect AMO from toxic nitrogenous intermediates such as NO. Nitrosocyanin is a protein present only in bacteria which catalyze the ammonia monoxygenase reaction (1). Cytochrome c P460 beta and cytochrome c’ beta.

  1. 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).

  2. 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.

  3. 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.

  4. Delta8(14)-steroids in the bacterium Methylococcus capsulatus.

    PubMed Central

    Bouvier, P; Rohmer, M; Benveniste, P; Ourisson, G

    1976-01-01

    The 4,4-dimethyl and 4alpha-methyl sterols of the bacterium Methylococcus capsulatus were identified as 4,4-dimethyl- and 4alpha-methyl-5alpha-cholest-8(14)-en-3beta-ol and 4,4-dimethyl- and 4alpha-methyl-5alpha-cholesta-8(14),24-dien-3beta-ol. Sterol biosynthesis is blocked at the level of 4alpha-methyl delta8(14)-sterols. PMID:999649

  5. 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

  6. An on-bacterium flow cytometric immunoassay for protein quantification.

    PubMed

    Lan, Wen-Jun; Lan, Wei; Wang, Hai-Yan; Yan, Lei; Wang, Zhe-Li

    2013-09-01

    The polystyrene bead-based flow cytometric immunoassay has been widely reported. However, the preparation of functional polystyrene bead is still inconvenient. This study describes a simple and easy on-bacterium flow cytometric immunoassay for protein quantification, in which Staphylococcus aureus (SAC) is used as an antibody-antigen carrier to replace the polystyrene bead. The SAC beads were prepared by carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling, paraformaldehyde fixation and antibody binding. Carcinoembryonic antigen (CEA) and cytokeratin-19 fragment (CYFRA 21-1) proteins were used as models in the test system. Using prepared SAC beads, biotinylated proteins, and streptavidin-phycoerythrin (SA-PE), the on-bacterium flow cytometric immunoassay was validated by quantifying CEA and CYFRA 21-1 in sample. Obtained data demonstrated a concordant result between the logarithm of the protein concentration and the logarithm of the PE mean fluorescence intensity (MFI). The limit of detection (LOD) in this immunoassay was at least 0.25 ng/ml. Precision and accuracy assessments appeared that either the relative standard deviation (R.S.D.) or the relative error (R.E.) was <10%. The comparison between this immunoassay and a polystyrene bead-based flow cytometric immunoassay showed a correlation coefficient of 0.998 for serum CEA or 0.996 for serum CYFRA 21-1. In conclusion, the on-bacterium flow cytometric immunoassay may be of use in the quantification of serum protein. PMID:23739299

  7. Active Autotrophic Ammonia-Oxidizing Bacteria in Biofilm Enrichments from Simulated Creek Ecosystems at Two Ammonium Concentrations Respond to Temperature Manipulation▿†

    PubMed Central

    Avrahami, Sharon; Jia, Zhongjun; Neufeld, Josh D.; Murrell, J. Colin; Conrad, Ralf; Küsel, Kirsten

    2011-01-01

    The first step of nitrification, the oxidation of ammonia to nitrite, is important for reducing eutrophication in freshwater environments when coupled with anammox (anaerobic ammonium oxidation) or denitrification. We analyzed active formerly biofilm-associated aerobic ammonia-oxidizing communities originating from Ammerbach (AS) and Leutra South (LS) stream water (683 ± 550 [mean ± standard deviation] and 16 ± 7 μM NH4+, respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using 13CO2, we found that members of the Bacteria and not Archaea were the functionally dominant autotrophic ammonia oxidizers at all temperatures under relatively high ammonium loads. The copy numbers of bacterial amoA genes in 13C-labeled DNA were lower at 30°C than at 13°C in both stream enrichment cultures. However, the community composition of the ammonia-oxidizing bacteria (AOB) in the 13C-labeled DNA responded differently to temperature manipulation at two ammonium concentrations. In LS enrichments incubated at the in situ temperature (13°C), Nitrosomonas oligotropha-like sequences were retrieved with sequences from Nitrosospira AmoA cluster 4, while the proportion of Nitrosospira sequences increased at higher temperatures. In AS enrichments incubated at 13°C and 20°C, AmoA cluster 4 sequences were dominant; Nitrosomonas nitrosa-like sequences dominated at 30°C. Biofilm-associated AOB communities were affected differentially by temperature at two relatively high ammonium concentrations, implicating them in a potential role in governing contaminated freshwater AOB distributions. PMID:21890674

  8. [Distribution and Diversity of Ammonium-oxidizing Archaea and Ammonium-oxidizing Bacteria in Surface Sediments of Oujiang River].

    PubMed

    Li, Hu; Huang, Fu-yi; Su, Jian-qiang; Hong, You-wei; Yu, Shen

    2015-12-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in the biogeochemical nitrogen cycle. Rivers are important ecosystems containing a large number of functional microbes in nitrogen cycle. In this study, denaturing gradient gel electrophoresis (DGGE ) and real-time quantitative PCR (qPCR) technology were used to analyze the distribution and diversity of AOA and AOB in sediments from Oujiang. The results showed that the AOA community structure was similar among various sites, while the AOB community structure was significantly different, in which all detected AOB sequences were classified into Nitrosospira and Nitrosomonas, and 90% affiliated to Nitrosospira. The community composition of AOA was influenced by NH₄⁺ and TS, in addition, the AOB composition was affected by NH₄⁺, EC, pH, NO₃⁻, TC and TN. Total sulfur (TS) and electrical conductivity (EC) were the major factors influencing the diversity of AOA and AOB, respectively. AOA abundance was significantly higher than that of AOB. EC, NH₄⁺-N and NO₃⁻-N were the main environmental factors affecting the abundance of AOA and AOB. This study indicated that the community composition and diversity of AOA and AOB were significantly influenced by environmental factors, and AOA might be dominant drivers in the ammonia oxidation process in Oujiang surface sediment. PMID:27012006

  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. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    PubMed Central

    Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

    2010-01-01

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

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

    PubMed Central

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

    1996-01-01

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

  12. Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.

    PubMed

    Marusenko, Yevgeniy; Garcia-Pichel, Ferran; Hall, Sharon J

    2015-02-01

    In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability. PMID:25764551

  13. Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen

    PubMed Central

    Fitzgerald, Colin M.; Camejo, Pamela; Oshlag, J. Zachary; Noguera, Daniel R.

    2015-01-01

    Ammonia-oxidizing microbial communities involved in ammonia oxidation under low dissolved oxygen (DO) conditions (<0.3 mg/L) were investigated using chemostat reactors. One lab-scale reactor (NS_LowDO) was seeded with sludge from a full-scale wastewater treatment plant (WWTP) not adapted to low-DO nitrification, while a second reactor (JP_LowDO) was seeded with sludge from a full-scale WWTP already achieving low-DO nitrifiaction. The experimental evidence from quantitative PCR, rDNA tag pyrosequencing, and fluorescence in situ hybridization (FISH) suggested that ammonia-oxidizing bacteria (AOB) in the Nitrosomonas genus were responsible for low-DO nitrification in the NS_LowDO reactor, whereas in the JP_LowDO reactor nitrification was not associated with any known ammonia-oxidizing prokaryote. Neither reactor had a significant population of ammonia-oxidizing archaea (AOA) or anaerobic ammonium oxidation (anammox) organisms. Organisms isolated from JP_LowDO were capable of autotrophic and heterotrophic ammonia utilization, albeit without stoichiometric accumulation of nitrite or nitrate. Based on the experimental evidence we propose that Pseudomonas, Xanthomonadaceae, Rhodococcus, and Sphingomonas are involved in nitrification under low-DO conditions. PMID:25506762

  14. Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoeflea sp. 2WW, Isolated from Arsenic-Contaminated Groundwater

    PubMed Central

    Cavalca, Lucia; Corsini, Anna; Andreoni, Vincenza

    2013-01-01

    Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp. strain 2WW, which consists of a 4.15-Mb chromosome and contains different genes that are involved in arsenic transformations. PMID:24356838

  15. Crystal structures of complexes of NAD{sup +}-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    SciTech Connect

    Filippova, E. V. Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-07-15

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI{sub 2} with the coupled reduction of nicotinamide adenine dinucleotide (NAD{sup +}). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD{sup +}-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 A resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.

  16. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

    PubMed

    Behrendt, Undine; Kämpfer, Peter; Glaeser, Stefanie P; Augustin, Jürgen; Ulrich, Andreas

    2016-06-01

    In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed. PMID:27030972

  17. Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment

    USGS Publications Warehouse

    Finster, K.; Coates, J.D.; Liesack, W.; Pfennig, N.

    1997-01-01

    A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27(T), was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27(T) is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27(T) belongs to the Desulfuromonas cluster in the recently proposed family 'Geobacteraceae' in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27(T) represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publications, is the name proposed for strain NZ27(T) in this paper.

  18. Characterization of recombinant glutathione reductase from the psychrophilic Antarctic bacterium Colwellia psychrerythraea.

    PubMed

    Ji, Mikyoung; Barnwell, Callie V; Grunden, Amy M

    2015-07-01

    Glutathione reductases catalyze the reduction of oxidized glutathione (glutathione disulfide, GSSG) using NADPH as the substrate to produce reduced glutathione (GSH), which is an important antioxidant molecule that helps maintain the proper reducing environment of the cell. A recombinant form of glutathione reductase from Colwellia psychrerythraea, a marine psychrophilic bacterium, has been biochemically characterized to determine its molecular and enzymatic properties. C. psychrerythraea glutathione reductase was shown to be a homodimer with a molecular weight of 48.7 kDa using SDS-PAGE, MALDI-TOF mass spectrometry and gel filtration. The C. psychrerythraea glutathione reductase sequence shows significant homology to that of Escherichia coli glutathione reductase (66 % identity), and it possesses the FAD and NADPH binding motifs, as well as absorption spectrum features which are characteristic of flavoenzymes such as glutathione reductase. The psychrophilic C. psychrerythraea glutathione reductase exhibits higher k cat and k cat/K m at lower temperatures (4 °C) compared to mesophilic Baker's yeast glutathione reductase. However, C. psychrerythraea glutathione reductase was able to complement an E. coli glutathione reductase deletion strain in oxidative stress growth assays, demonstrating the functionality of C. psychrerythraea glutathione reductase over a broad temperature range, which suggests its potential utility as an antioxidant enzyme in heterologous systems. PMID:26101017

  19. Influence of plaque-forming bacterium, Rhodobacteraceae sp. on the growth of Chlorella vulgaris.

    PubMed

    Chen, Zhangran; Zhang, Jingyan; Lei, Xueqian; Zhang, Bangzhou; Cai, Guanjing; Zhang, Huajun; Li, Yi; Zheng, Wei; Tian, Yun; Xu, Hong; Zheng, Tianling

    2014-10-01

    Experiments were conducted to find out the molecular features, infection process of a special alga plaque-forming microorganism and its potential influence on the biomass of Chlorella vulgaris during the infection process. Direct contact between the algal cell and the bacterium may be the primary steps needed for the bacterium to lyse the alga. Addition of C. vulgaris cells into f/2 medium allowed us obtain the object bacterium. The 16S rRNA gene sequence comparisons results showed that the plaque-forming bacterium kept the closest relationship with Labrenzia aggregata IAM 12614(T) at 98.90%. The existence of the bacterium could influence both the dry weight and lipid content of C. vulgaris. This study demonstrated that direct cell wall disruption of C. vulgaris by the bacterium would be a potentially effective method to utilize the biomass of microalgae. PMID:25086475

  20. Response of performance and ammonia oxidizing bacteria community to high salinity stress in membrane bioreactor with elevated ammonia loading.

    PubMed

    Wang, Zhu; Luo, Gan; Li, Jun; Chen, Shi-Yu; Li, Yan; Li, Wen-Tao; Li, Ai-Min

    2016-09-01

    Effect of elevated ammonia loading rate (ALR) and increasing salinity on the operation of membrane bioreactor (MBR) and the response of microbial community were investigated. Results showed that MBR started up with 1% NaCl stress achieved amazing nitrification performance at high salinity up to 4% when treating wastewater containing 1000mg/L NH(+)4-N. Further increasing salinity to 7% led to failure of MBR unrecoverably. Steep decline of sludge activity contributed to the extremely worse performance. High-throughput sequencing analysis showed that both ALR and salinity had selective effects on the microbial community structure. In genus level, Methyloversatilis and Maribacter were enriched during the operation. Survival of salt-resistant microbes contributed to the rising of richness and diversity at 2% and 4% NaCl stress. Analysis of amoA-gene-based cloning revealed Nitrosomonas marina are chiefly responsible for catalyzing ammonia oxidation in high ALR at high salinity stress. PMID:27290667

  1. Fast Neutron Irradiation of the Highly Radioresistant Bacterium Deinococcus Radiodurans

    NASA Astrophysics Data System (ADS)

    Case, Diane Louise

    Fast neutron dose survival curves were generated for the bacterium Deinococcus radiodurans, which is renowned for its unusually high resistance to gamma, x-ray, and ultraviolet radiation, but for which fast neutron response was unknown. The fast neutrons were produced by the University of Massachusetts Lowell 5.5-MV, type CN Van de Graaff accelerator through the ^7Li(p,n)^7 Be reaction by bombarding a thick metallic lithium target with a 4-MeV proton beam. The bacteria were uniformly distributed on 150-mm agar plates and were exposed to the fast neutron beam under conditions of charged particle equilibrium. The plates were subdivided into concentric rings of increasing diameter from the center to the periphery of the plate, within which the average neutron dose was calculated as the product of the precisely known neutron fluence at the average radius of the ring and the neutron energy dependent kerma factor. The neutron fluence and dose ranged from approximately 3 times 1013 n cm^ {-2} to 1 times 1012 n cm^ {-2}, and 200 kilorad to 5 kilorad, respectively, from the center to the periphery of the plate. Percent survival for Deinococcus radiodurans as a function of fast neutron dose was derived from the ability of the irradiated cells to produce visible colonies within each ring compared to that of a nonirradiated control population. The bacterium Escherichia coli B/r (CSH) was irradiated under identical conditions for comparative purposes. The survival response of Deinococcus radiodurans as a result of cumulative fast neutron exposures was also investigated. The quantification of the ability of Deinococcus radiodurans to survive cellular insult from secondary charged particles, which are produced by fast neutron interactions in biological materials, will provide valuable information about damage and repair mechanisms under extreme cellular stress, and may provide new insight into the origin of this bacterium's unprecedented radiation resistance.

  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. The terminal oxidase in the marine bacterium Pseudomonas nautica 617.

    PubMed

    Simpson, H; Denis, M; Malatesta, F

    1997-06-01

    The molecular properties of a novel membrane quinol oxidase from the marine bacterium Pseudomonas nautica 617 are presented. The protein contains 2b hemes/mole which may be distinguished by EPR spectroscopy but not by optical spectroscopy and electrochemistry. Respiration, though being cyanide insensitive, is not inhibited by carbon monoxide and oxygen reduction is carried out only half-way with production of hydrogen peroxide. The terminal oxidase represents, therefore, a unique example in the large family of terminal oxidases known up to date. PMID:9337488

  4. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    SciTech Connect

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

    1984-10-01

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

  5. Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

    PubMed

    Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

    2016-04-21

    Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain. PMID:26972517

  6. Chemolithotrophic growth of the aerobic hyperthermophilic bacterium Thermocrinis ruber OC 14/7/2 on monothioarsenate and arsenite.

    PubMed

    Härtig, Cornelia; Lohmayer, Regina; Kolb, Steffen; Horn, Marcus A; Inskeep, William P; Planer-Friedrich, Britta

    2014-12-01

    Novel insights are provided regarding aerobic chemolithotrophic growth of Thermocrinis ruber OC14/7/2 on the electron donors arsenite and monothioarsenate. Thermocrinis ruber is a hyperthermophilic bacterium that thrives in pH-neutral to alkaline hot springs and grows on hydrogen, elemental sulfur, and thiosulfate. Our study showed that T. ruber can also utilize arsenite as sole electron donor producing arsenate. Growth rates of 0.024 h(-1) were lower than for oxidation of thiosulfate to sulfate (μ = 0.247 h(-1)). Fast growth was observed on monothioarsenate (μ = 0.359 h(-1)), comprising different abiotic and biotic redox interactions. The initial dominant process was abiotic transformation of monothioarsenate to arsenate and elemental sulfur, followed by microbial oxidation of sulfur to sulfate. Elevated microbial activity during stationary growth of T. ruber might be explained by microbial oxidation of thiosulfate and arsenite, both also products of abiotic monothioarsenate transformation. However, the observed rapid decrease of monothioarsenate, exceeding concentrations in equilibrium with its products, also indicates direct microbial oxidation of arsenic-bond S(-II) to sulfate. Free sulfide was oxidized abiotically too fast to play a role as electron donor for T. ruber. Our present laboratory and previous field studies suggest that thioarsenates can either indirectly or directly be used by (hyper)thermophiles in arsenic-sulfidic environments. PMID:25251939

  7. Optimized inhibition assays reveal different inhibitory responses of hydroxylamine oxidoreductases from beta- and gamma-proteobacterial ammonium-oxidizing bacteria.

    PubMed

    Nishigaya, Yuki; Fujimoto, Zui; Yamazaki, Toshimasa

    2016-07-29

    Ammonia-oxidizing bacteria (AOB), ubiquitous chemoautotrophic bacteria, convert ammonia (NH3) to nitrite (NO2(-)) via hydroxylamine as energy source. Excessive growth of AOB, enhanced by applying large amounts of ammonium-fertilizer to the farmland, leads to nitrogen leaching and nitrous oxide gas emission. To suppress these unfavorable phenomena, nitrification inhibitors, AOB specific bactericides, are widely used in fertilized farmland. However, new nitrification inhibitors are desired because of toxicity and weak-effects of currently used inhibitors. Toward development of novel nitrification inhibitors that target hydroxylamine oxidoreductase (HAO), a key enzyme of nitrification in AOB, we established inhibitor evaluation systems that include simplified HAO purification procedure and high-throughput HAO activity assays for the purified enzymes and for the live AOB cells. The new assay systems allowed us to observe distinct inhibitory responses of HAOs from beta-proteobacterial AOB (βAOB) Nitrosomonas europaea (NeHAO) and gamma-proteobacterial AOB (γAOB) Nitrosococcus oceani (NoHAO) against phenylhydrazine, a well-known suicide inhibitor for NeHAO. Consistently, the live cells of N. europaea, Nitrosomonas sp. JPCCT2 and Nitrosospira multiformis of βAOB displayed higher responses to phenylhydrazine than those of γAOB N. oceani. Our homology modeling studies suggest that different inhibitory responses of βAOB and γAOB are originated from different local environments around the substrate-binding sites of HAOs in these two classes of bacteria due to substitutions of two residues. The results reported herein strongly recommend inhibitor screenings against both NeHAO of βAOB and NoHAO of γAOB to develop HAO-targeting nitrification inhibitors with wide anti-AOB spectra. PMID:27173879

  8. Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

    PubMed Central

    Wang, Baozhan; Zhao, Jun; Guo, Zhiying; Ma, Jing; Xu, Hua; Jia, Zhongjun

    2015-01-01

    Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO3−-N g−1 dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in 13C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of 13CO2 by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the 13C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The 13C-NOB was overwhelmingly

  9. Impact of TiO₂ and ZnO nanoparticles at predicted environmentally relevant concentrations on ammonia-oxidizing bacteria cultures under ammonia oxidation.

    PubMed

    Luo, Zhuanxi; Qiu, Zhaozheng; Chen, Zheng; Du Laing, Gijs; Liu, Aifen; Yan, Changzhou

    2015-02-01

    Increased application of titanium dioxide and zinc oxide nanoparticles (nano-TiO2 and nano-ZnO) raises concerns related to their environmental impacts. The effects that such nanoparticles have on environmental processes and the bacteria that carry them out are largely unknown. In this study, ammonia-oxidizing bacteria (AOB) enrichment cultures, grown from surface sediments taken from an estuary wetland in Fujian Province, China, were spiked with nano-TiO2 and nano-ZnO (with an average size of 32 and 43 nm, respectively) at predicted environmentally relevant concentrations (≤2 mg L(-1)) to determine their impacts on ammonia oxidation and the mechanisms involved. Results showed that higher nano-TiO2 concentrations significantly inhibited ammonia oxidation in enrichment cultures. It is noteworthy that the average ammonia oxidation rate was significantly correlated to the Shannon index, the Simpson's index, and AOB abundance. This suggested that ammonia oxidation inhibition primarily resulted from a reduction of AOB biodiversity and abundance. However, AOB biodiversity and abundance as well as the average ammonia oxidation rate were not inhibited by nano-ZnO at predicted environmentally relevant concentrations. Accordingly, an insignificant correlation was established between biodiversity and abundance of the AOB amoA gene and the average ammonia oxidation rate under nano-ZnO treatments. AOB present in samples belonged to the β-Proteobacteria class with an affinity close to Nitrosospira and Nitrosomonas genera. This suggested that identified impacts of nano-TiO2 and nano-ZnO on ammonia oxidation processes can be extrapolated to some extent to natural aquatic environments. Complex impacts on AOB may result from different nanomaterials present in aquatic environments at various ambient conditions. Further investigation on how and to what extent different nanomaterials influence AOB diversity and abundance and their subsequent ammonia oxidation processes is therefore

  10. 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

  11. Molybdate reduction to molybdenum blue by an Antarctic bacterium.

    PubMed

    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

  12. Biological Control of Meloidogyne hapla Using an Antagonistic Bacterium

    PubMed Central

    Park, Jiyeong; Seo, Yunhee; Kim, Young Ho

    2014-01-01

    We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN) Meloidogyne hapla in carrot (Daucus carota subsp. sativus) and tomato (Solanum lycopersicum). Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla. PMID:25289015

  13. Radiation response mechanisms of the extremely radioresistant bacterium Deinococcus radiodurans.

    PubMed

    Kobayashi, Yasuhiko; Narumi, Issay; Satoh, Katsuya; Funayama, Tomoo; Kikuchi, Masahiro; Kitayama, Shigeru; Watanabe, Hiroshi

    2004-11-01

    Effect of microgravity on recovery of bacterial cells from radiation damage was examined in IML-2, S/MM-4 and S/MM-9 experiments using the extremely radioresistant bacterium Deinococcus radiodurans. The cells were irradiated with gamma rays before the space flight and incubated on board the Space Shuttle. The survival of the wild type cells incubated in space increased compared with the ground controls, suggesting that the recovery of this bacterium from radiation damage was enhanced under the space environment. No difference was observed between the survivals of radiosensitive mutant rec30 cells incubated in space and on the ground. The amount of DNA-repair related RecA protein induced under microgravity was similar to those of ground controls, however, induction of PprA protein, product of a unique radiation-inducible gene (designated pprA) responsible for loss of radiation resistance in repair-deficient mutant, KH311, was enhanced under microgravity compared with ground controls. Recent investigation in vitro showed that PprA preferentially bound to double-stranded DNA carrying strand breaks, inhibited Escherichia coli exonuclease III activity, and stimulated the DNA end-joining reaction catalyzed by DNA ligases. These results suggest that D. radiodurans has a radiation-induced non-homologous end-joining (NHEJ) repair mechanism in which PprA plays a critical role. PMID:15858357

  14. 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. PMID:27263016

  15. Metabolism of threo-beta-methylmalate by a soil bacterium.

    PubMed

    Suzuki, S; Takeuchi, Y; Sasaki, K; Katsuki, H

    1976-10-01

    Studies on threo-beta-methylmalate metabolism in a soil bacterium of the genus Bacillus which can utilize threo-beta-methylmalate as a sole carbon source were carried out. When DL-threo-beta-methylmalate was incubated with a cell-free extract of the bacterium, citramalate was found to be formed. Similarly, formation of threo-beta-methylmalate from DL-citramalate was confirmed. These dicarbosylic acids were identified by gas chromatography-mass spectrometry. Examination of inducibility, substrate specificity, and cofactor requirement of the enzymes involved in the reactions showed the existence of two interconversion reactions between the threo-beta-methylmalate and citramalate. One was an interconversion reaction between L-threo-beta-methylmalate and L-citramalate via mesaconate and the other was an interconversion reaction between D-threo-beta-methylmalate and D-citramalate via citraconate. These reactions were both reversible and were catalyzed by distinct and inducible enzymes. It is suggested that the two reactions participate in the catabolism of threo-beta-methylmalate. PMID:1010849

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

    PubMed

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

    2015-11-01

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

  17. Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus▿ †

    PubMed Central

    van de Werken, Harmen J. G.; Verhaart, Marcel R. A.; VanFossen, Amy L.; Willquist, Karin; Lewis, Derrick L.; Nichols, Jason D.; Goorissen, Heleen P.; Mongodin, Emmanuel F.; Nelson, Karen E.; van Niel, Ed W. J.; Stams, Alfons J. M.; Ward, Donald E.; de Vos, Willem M.; van der Oost, John; Kelly, Robert M.; Kengen, Servé W. M.

    2008-01-01

    Caldicellulosiruptor saccharolyticus is an extremely thermophilic, gram-positive anaerobe which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO2, and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to coutilize glucose and xylose make this bacterium an attractive candidate for microbial bioenergy production. Here, the complete genome sequence of C. saccharolyticus, consisting of a 2,970,275-bp circular chromosome encoding 2,679 predicted proteins, is described. Analysis of the genome revealed that C. saccharolyticus has an extensive polysaccharide-hydrolyzing capacity for cellulose, hemicellulose, pectin, and starch, coupled to a large number of ABC transporters for monomeric and oligomeric sugar uptake. The components of the Embden-Meyerhof and nonoxidative pentose phosphate pathways are all present; however, there is no evidence that an Entner-Doudoroff pathway is present. Catabolic pathways for a range of sugars, including rhamnose, fucose, arabinose, glucuronate, fructose, and galactose, were identified. These pathways lead to the production of NADH and reduced ferredoxin. NADH and reduced ferredoxin are subsequently used by two distinct hydrogenases to generate hydrogen. Whole-genome transcriptome analysis revealed that there is significant upregulation of the glycolytic pathway and an ABC-type sugar transporter during growth on glucose and xylose, indicating that C. saccharolyticus coferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks is a highly desirable feature of this lignocellulose-utilizing, biofuel-producing bacterium. PMID:18776029

  18. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE PAGESBeta

    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

  19. Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring.

    PubMed

    Slobodkin, A; Reysenbach, A L; Strutz, N; Dreier, M; Wiegel, J

    1997-04-01

    A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7T; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 microns, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74 degrees C with an optimum at 65 degrees C. The pH range for growth at 65 degrees C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO2, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H2 was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO2, nitrate, sulfate, sulfite, or elemental sulfur. The G + C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type-positive Bacillus-Clostridium subphylum. PMID:9103646

  20. New Functional Sulfide Oxidase-Oxygen Reductase Supercomplex in the Membrane of the Hyperthermophilic Bacterium Aquifex aeolicus*

    PubMed Central

    Prunetti, Laurence; Infossi, Pascale; Brugna, Myriam; Ebel, Christine; Giudici-Orticoni, Marie-Thérèse; Guiral, Marianne

    2010-01-01

    Aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. It was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (H2S) to molecular oxygen. H2S is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. We have purified and characterized a novel membrane-bound multienzyme supercomplex that brings together all the molecular components involved in this bioenergetic chain. Our results indicate that this purified structure consists of one dimeric bc1 complex (complex III), one cytochrome c oxidase (complex IV), and one or two sulfide quinone reductases as well as traces of the monoheme cytochrome c555 and quinone molecules. In addition, this work strongly suggests that the cytochrome c oxidase in the supercomplex is a ba3-type enzyme. The supercomplex has a molecular mass of about 350 kDa and is enzymatically functional, reducing O2 in the presence of the electron donor, H2S. This is the first demonstration of the existence of such a respirasome carrying a sulfide oxidase-oxygen reductase activity. Moreover, the kinetic properties of the sulfide quinone reductase change slightly when integrated in the supercomplex, compared with the free enzyme. We previously purified a complete respirasome involved in hydrogen oxidation and sulfur reduction from Aquifex aeolicus. Thus, two different bioenergetic pathways (sulfur reduction and sulfur oxidation) are organized in this bacterium as supramolecular structures in the membrane. A model for the energetic sulfur metabolism of Aquifex aeolicus is proposed. PMID:20971847

  1. Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring

    SciTech Connect

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

    1997-04-01

    A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7{sup T}; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 {mu}m, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74{degrees}C with an optimum at 65{degrees}C. The pH range for growth at 65{degrees}C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO{sub 2}, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H{sub 2} was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO{sub 2}, nitrate, sulfate, sulfite, or elemental sulfur. The G+C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type positive Bacillus-Clostridium subphylum.

  2. amoA Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

    PubMed Central

    Li, Jialin; Nedwell, David B.; Beddow, Jessica; Dumbrell, Alex J.; McKew, Boyd A.; Thorpe, Emma L.

    2014-01-01

    Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw]−1 day−1 in June, increasing to 37.4 μmol N gdw−1 day−1 in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw−1 day−1 in June, increasing to 11.7 μmol N gdw−1 day−1 in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification. PMID:25326303

  3. amoA Gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not Archaea dominate N cycling in the Colne Estuary, United Kingdom.

    PubMed

    Li, Jialin; Nedwell, David B; Beddow, Jessica; Dumbrell, Alex J; McKew, Boyd A; Thorpe, Emma L; Whitby, Corinne

    2015-01-01

    Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw](-1) day(-1) in June, increasing to 37.4 μmol N gdw(-1) day(-1) in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw(-1) day(-1) in June, increasing to 11.7 μmol N gdw(-1) day(-1) in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification. PMID:25326303

  4. Biomass Yield Efficiency of the Marine Anammox Bacterium, “Candidatus Scalindua sp.,” is Affected by Salinity

    PubMed Central

    Awata, Takanori; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2015-01-01

    The growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. Among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium “Candidatus Scalindua sp.” is still lower than those of other anammox bacteria enriched from freshwater environments. The activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity and organic compounds. Therefore, in the present study, the effects of salinity and volatile fatty acids (VFAs) on the anammox activity, inorganic carbon uptake, and biomass yield efficiency of “Ca. Scalindua sp.” enriched from the marine sediments of Hiroshima Bay, Japan, were investigated in batch experiments. Differences in VFA concentrations (0–10 mM) were observed under varying salinities (0.5%–4%). Anammox activity was high at 0.5%–3.5% salinity, but was 30% lower at 4% salinity. In addition, carbon uptake was higher at 1.5%–3.5% salinity. The results of the present study clearly demonstrated that the biomass yield efficiency of the marine anammox bacterium “Ca. Scalindua sp.” was significantly affected by salinity. On the other hand, the presence of VFAs up to 10 mM did not affect anammox activity, carbon uptake, or biomass yield efficiency. PMID:25740428

  5. 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.

  6. 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

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

    PubMed

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

    2016-01-01

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

  8. 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.

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

    DOE PAGESBeta

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; Klingeman, Dawn Marie; Keller, Martin; Xu, Jian; Reddy, Harish Kumar; Borovok, Ilya; Grinberg, Inna Rozman; Lamed, Raphael; et al

    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.

  10. FEEDING EXPERIMENTS WITH BACTERIUM PULLORUM. THE TOXICITY OF INFECTED EGGS.

    PubMed

    Rettger, L F; Hull, T G; Sturges, W S

    1916-04-01

    The problem of eradicating ovarian infection in the domestic fowl assumes still greater importance than heretofore, in the light of data recently acquired. Not only is it of great significance to eliminate the permanent carriers of Bacterium pullorum from all flocks of fowls from the standpoint of successful poultry breeding, but also because they constitute a possible source of danger to man. Eggs which harbor Bacterium pullorum in the yolk in large numbers may produce abnormal conditions, when fed, not only in young chicks, but in adult fowls, young rabbits, guinea pigs, and kittens. The toxicity for young rabbits is most pronounced, the infection usually resulting in the death of the animals. In kittens the most prominent symptoms are those of severe food-poisoning with members of the paratyphoid group of bacteria. The possibility of infected eggs causing serious disturbances in young children and in the sick and convalescent of all ages must therefore receive serious consideration. Ovarian infection of fowls is very common throughout this country. Hence, a large proportion of the marketed eggs are infected with Bacterium pullorum. When such eggs are allowed to remain in nests under broody hens, or in warm storage places, for comparatively few hours, they contain large numbers of the organism. Soft boiling, coddling, and frying on one side only do not necessarily render the yolks free from viable bacteria; therefore, eggs which have gone through these processes may, like raw eggs, be the cause of serious disturbances in persons who are particularly susceptible to such influences, and especially to infants. That no well authenticated instances of egg-poisoning of this kind are on record does not warrant the assumption that there have been no cases. The etiology of infantile stomach and intestinal disturbances is as yet too little understood; in fact, it may be said that many of these disorders have no known cause, and almost as much may be said regarding gastro

  11. Characterization of monofunctional catalase KatA from radioresistant bacterium Deinococcus radiodurans.

    PubMed

    Kobayashi, Issei; Tamura, Takashi; Sghaier, Haitham; Narumi, Issay; Yamaguchi, Shotaro; Umeda, Koichi; Inagaki, Kenji

    2006-04-01

    Catalase plays a key role in protecting cells against toxic reactive oxygen species. Here we report on the cloning, purification and characterization of a catalase (KatA, DR1998) from the extremely radioresistant bacterium Deinococcus radiodurans. The size of purified D. radiodurans KatA monomer was 65 kDa while gel filtration revealed that the size of the enzyme was 240 kDa, suggesting that KatA formed a homotetramer in solution. Purified KatA displayed a final specific activity of 68,800 U/mg of protein. The catalase activity of KatA was inhibited by sodium azide, sodium cyanide and 3-amino-1,2,4-triazole. The absorption spectrum of KatA exhibited a Soret band at 408 nm. The position of the spectral peak remained unchanged following reduction of KatA with dithionite. No peroxidase activity was found for KatA. These results demonstrate that D. radiodurans KatA is a typical monofunctional heme-containing catalase. The stability of KatA with respect to H2O2 stress was superior to that of commercially available Aspergillus niger and bovine liver catalases. The relative abundance of KatA in cells in addition to the H2O2 resistance property may play a role in the survival strategy of D. radiodurans against oxidative damage. PMID:16716939

  12. Aerobic and anaerobic degradation of a range of alkyl sulfides by a denitrifying marine bacterium

    USGS Publications Warehouse

    Visscher, P.T.; Taylor, B.F.

    1993-01-01

    A pure culture of a bacterium was obtained from a marine microbial mat by using an anoxic medium containing dimethyl sulfide (DMS) and nitrate. The isolate grew aerobically or anaerobically as a denitrifier on alkyl sulfides, including DMS, dimethyl disulfide, diethyl sulfide (DES), ethyl methyl sulfide, dipropyl sulfide, dibutyl sulfide, and dibutyl disulfide. Cells grown on an alkyl sulfide or disulfide also oxidized the corresponding thiols, namely, methanethiol, ethanethiol, propanethiol, or butanethiol. Alkyl sulfides were metabolized by induced or derepressed cells with oxygen, nitrate, or nitrite as electron acceptor. Cells grown on DMS immediately metabolized DMS, but there was a lag before DES was consumed; with DES-grown cells, DES was immediately used but DMS was used only after a lag. Chloramphenicol prevented the eventual use of DES by DMS-grown cells and DMS use by DES-grown cells, respectively, indicating separate enzymes for the metabolism of methyl and ethyl groups. Growth was rapid on formate, acetate, propionate, and butyrate but slow on methanol. The organism also grew chemolithotrophically on thiosulfate with a decrease in pH; growth required carbonate in the medium. Growth on sulfide was also carbonate dependent but slow. The isolate was identified as a Thiobacillus sp. and designated strain ASN-1. It may have utility for removing alkyl sulfides, and also nitrate, nitrite, and sulfide, from wastewaters.

  13. Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium

    SciTech Connect

    Wada, M.; Fukunaga, N.; Sasaki, S. )

    1989-08-01

    Biosynthesis of palmitic, palmitoleic, and cis-vaccenic acids in Pseudomonas sp. strain E-3 was investigated with in vitro and in vivo systems. (1-{sup 14}C)palmitic acid was aerobically converted to palmitoleate and cis-vaccenate, and the radioactivities on their carboxyl carbons were 100 and 43%, respectively, of the total radioactivity in the fatty acids. Palmitoyl coenzyme A desaturase activity was found in the membrane fraction. (1-{sup 14}C)stearic acid was converted to octadecenoate and C16 fatty acids. The octadecenoate contained oleate and cis-vaccenate, but only oleate was produced in the presence of cerulenin. (1-{sup 14}C)lauric acid was aerobically converted to palmitate, palmitoleate, and cis-vaccenate. Under anaerobic conditions, palmitate (62%), palmitoleate (4%), and cis-vaccenate (34%) were produced from (1-{sup 14}C)acetic acid, while they amounted to 48, 39, and 14%, respectively, under aerobic conditions. In these incorporation experiments, 3 to 19% of the added radioactivity was detected in released {sup 14}CO{sub 2}, indicating that part of the added fatty acids were oxidatively decomposed. Partially purified fatty acid synthetase produced saturated and unsaturated fatty acids with chain lengths of C10 to C18. These results indicated that both aerobic and anaerobic mechanisms for the synthesis of unsaturated fatty acid are operating in this bacterium.

  14. Sodium-driven energy conversion for flagellar rotation of the earliest divergent hyperthermophilic bacterium

    PubMed Central

    Takekawa, Norihiro; Nishiyama, Masayoshi; Kaneseki, Tsuyoshi; Kanai, Tamotsu; Atomi, Haruyuki; Kojima, Seiji; Homma, Michio

    2015-01-01

    Aquifex aeolicus is a hyperthermophilic, hydrogen-oxidizing and carbon-fixing bacterium that can grow at temperatures up to 95 °C. A. aeolicus has an almost complete set of flagellar genes that are conserved in bacteria. Here we observed that A. aeolicus has polar flagellum and can swim with a speed of 90 μm s−1 at 85 °C. We expressed the A. aeolicus mot genes (motA and motB), which encode the torque generating stator proteins of the flagellar motor, in a corresponding mot nonmotile mutant of Escherichia coli. Its motility was slightly recovered by expression of A. aeolicus MotA and chimeric MotB whose periplasmic region was replaced with that of E. coli. A point mutation in the A. aeolicus MotA cytoplasmic region remarkably enhanced the motility. Using this system in E. coli, we demonstrate that the A. aeolicus motor is driven by Na+. As motor proteins from hyperthermophilic bacteria represent the earliest motor proteins in evolution, this study strongly suggests that ancient bacteria used Na+ for energy coupling of the flagellar motor. The Na+-driven flagellar genes might have been laterally transferred from early-branched bacteria into late-branched bacteria and the interaction surfaces of the stator and rotor seem not to change in evolution. PMID:26244427

  15. Sodium-driven energy conversion for flagellar rotation of the earliest divergent hyperthermophilic bacterium.

    PubMed

    Takekawa, Norihiro; Nishiyama, Masayoshi; Kaneseki, Tsuyoshi; Kanai, Tamotsu; Atomi, Haruyuki; Kojima, Seiji; Homma, Michio

    2015-01-01

    Aquifex aeolicus is a hyperthermophilic, hydrogen-oxidizing and carbon-fixing bacterium that can grow at temperatures up to 95 °C. A. aeolicus has an almost complete set of flagellar genes that are conserved in bacteria. Here we observed that A. aeolicus has polar flagellum and can swim with a speed of 90 μm s(-1) at 85 °C. We expressed the A. aeolicus mot genes (motA and motB), which encode the torque generating stator proteins of the flagellar motor, in a corresponding mot nonmotile mutant of Escherichia coli. Its motility was slightly recovered by expression of A. aeolicus MotA and chimeric MotB whose periplasmic region was replaced with that of E. coli. A point mutation in the A. aeolicus MotA cytoplasmic region remarkably enhanced the motility. Using this system in E. coli, we demonstrate that the A. aeolicus motor is driven by Na(+). As motor proteins from hyperthermophilic bacteria represent the earliest motor proteins in evolution, this study strongly suggests that ancient bacteria used Na(+) for energy coupling of the flagellar motor. The Na(+)-driven flagellar genes might have been laterally transferred from early-branched bacteria into late-branched bacteria and the interaction surfaces of the stator and rotor seem not to change in evolution. PMID:26244427

  16. Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

    PubMed Central

    Banderas, Alvaro; Guiliani, Nicolas

    2013-01-01

    The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS) cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS), we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME) to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase) might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process. PMID:23959118

  17. Bioinformatic prediction of gene functions regulated by quorum sensing in the bioleaching bacterium Acidithiobacillus ferrooxidans.

    PubMed

    Banderas, Alvaro; Guiliani, Nicolas

    2013-01-01

    The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS) cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS), we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME) to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase) might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process. PMID:23959118

  18. Remediation of contaminated subsurface materials by a metal-reducing bacterium

    SciTech Connect

    Gorby, Y.A.; Amonette, J.E.; Fruchter, J.S.

    1994-11-01

    A biotic approach for remediating subsurface sediments and groundwater contaminated with carbon tetrachloride (CT) and chromium was evaluated. Cells of the Fe(iii)-reducing bacterium strain BrY were added to sealed, anoxic flasks containing Hanford groundwater, natural subsurface sediments, and either carbon tetrachloride, CT, or oxidized chromium, Cr(VI). With lactate as the electron donor, BrY transformed CT to chloroform (CF), which accumulated to about 1 0 % of the initial concentration of CT. The remainder of the CT was transformed to unidentified, nonvolatile compounds. Transformation of CT by BrY was an indirect process Cells reduced solid phase Fe(ill) to chemically reactive FE(II) that chemically transformed the chlorinated contaminant. Cr(VI), in contrast, was reduced by a direct enzymatic reaction in the presence or absence of Fe(III)-bearing sediments. These results demonstrate that Fe(ill)-reducing bacteria provide potential for transforming CT and for reducing CR(VI) to less toxic Cr(III). Technologies for stimulating indigenous populations of metal-reducing bacteria or for introducing specific metal-reducing bacteria to the subsurface are being investigated.

  19. Aerobic and anaerobic degradation of a range of alkyl sulfides by a denitrifying marine bacterium.

    PubMed Central

    Visscher, P T; Taylor, B F

    1993-01-01

    A pure culture of a bacterium was obtained from a marine microbial mat by using an anoxic medium containing dimethyl sulfide (DMS) and nitrate. The isolate grew aerobically or anaerobically as a denitrifier on alkyl sulfides, including DMS, dimethyl disulfide, diethyl sulfide (DES), ethyl methyl sulfide, dipropyl sulfide, dibutyl sulfide, and dibutyl disulfide. Cells grown on an alkyl sulfide or disulfide also oxidized the corresponding thiols, namely, methanethiol, ethanethiol, propanethiol, or butanethiol. Alkyl sulfides were metabolized by induced or derepressed cells with oxygen, nitrate, or nitrite as electron acceptor. Cells grown on DMS immediately metabolized DMS, but there was a lag before DES was consumed; with DES-grown cells, DES was immediately used but DMS was used only after a lag. Chloramphenicol prevented the eventual use of DES by DMS-grown cells and DMS use by DES-grown cells, respectively, indicating separate enzymes for the metabolism of methyl and ethyl groups. Growth was rapid on formate, acetate, propionate, and butyrate but slow on methanol. The organism also grew chemolithotrophically on thiosulfate with a decrease in pH; growth required carbonate in the medium. Growth on sulfide was also carbonate dependent but slow. The isolate was identified as a Thiobacillus sp. and designated strain ASN-1. It may have utility for removing alkyl sulfides, and also nitrate, nitrite, and sulfide, from wastewaters. PMID:8285707

  20. Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae

    PubMed Central

    Trias, Rosalia; García-Lledó, Arantzazu; Sánchez, Noemí; López-Jurado, José Luis; Hallin, Sara

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for O. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions. PMID:22081571

  1. Abundance and diversity of ammonia-oxidizing microorganisms in the sediments of Jinshan Lake.

    PubMed

    Liu, Biao; Li, Yimin; Zhang, Jinping; Zhou, Xiaohong; Wu, Chundu

    2014-11-01

    Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH4-N, NO3-N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment. PMID:25008777

  2. Fungal lysis by a soil bacterium fermenting cellulose.

    PubMed

    Tolonen, Andrew C; Cerisy, Tristan; El-Sayyed, Hafez; Boutard, Magali; Salanoubat, Marcel; Church, George M

    2015-08-01

    Recycling of plant biomass by a community of bacteria and fungi is fundamental to carbon flow in terrestrial ecosystems. Here we report how the plant fermenting, soil bacterium Clostridium phytofermentans enhances growth on cellulose by simultaneously lysing and consuming model fungi from soil. We investigate the mechanism of fungal lysis to show that among the dozens of different glycoside hydrolases C. phytofermentans secretes on cellulose, the most highly expressed enzymes degrade fungi rather than plant substrates. These enzymes, the GH18 Cphy1799 and Cphy1800, synergize to hydrolyse chitin, a main component of the fungal cell wall. Purified enzymes inhibit fungal growth and mutants lacking either GH18 grow normally on cellulose and other plant substrates, but have a reduced ability to hydrolyse chitinous substrates and fungal hyphae. Thus, C. phytofermentans boosts growth on cellulose by lysing fungi with its most highly expressed hydrolases, highlighting the importance of fungal interactions to the ecology of cellulolytic bacteria. PMID:24798076

  3. 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

    2015-07-01

    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. PMID:26048701

  4. 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.

  5. 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. PMID:26965627

  6. 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.

  7. The domestication of the probiotic bacterium Lactobacillus acidophilus

    PubMed Central

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

    2014-01-01

    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. PMID:25425319

  8. Metabolic characterisation of a novel vanillylmandelate-degrading bacterium.

    PubMed

    Turner, J E; Allison, N; Fewson, C A

    1996-10-01

    A newly isolated gram-negative bacterium, possibly Brevundimonas diminuta, utilised D,L-vanillylmandelate (D,L-VMA) as a sole carbon and energy source. The organism converted D,L-VMA to vanillylglyoxylate using a soluble NAD-dependent dehydrogenase specific for D-VMA and a dye-linked, membrane-associated L-VMA dehydrogenase. Vanillylglyoxylate was further metabolised by decarboxylation, dehydrogenation and demethylation to protocatechuate. A 4,5-dioxygenase cleaved protocatechuate to 2-hydroxy-4-carboxymuconic semialdehyde. Partially purified d-VMA dehydrogenase exhibited optimal activity at 30 degrees C and pH 9.5 and had an apparent Km for D-VMA of 470 microM. Although induced by several substituted mandelates, the enzyme had a narrow substrate specificity range with virtually no activity towards D-mandelate. Such properties render the enzyme of potential use in both diagnostic and biosynthetic applications. PMID:8824148

  9. 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.

  10. Ability of a haloalkaliphilic bacterium isolated from Soap Lake, Washington to generate electricity at pH 11.0 and 7% salinity.

    PubMed

    Paul, Varun G; Minteer, Shelley D; Treu, Becky L; Mormile, Melanie R

    2014-01-01

    A variety of anaerobic bacteria have been shown to transfer electrons obtained from organic compound oxidation to the surface of electrodes in microbial fuel cells (MFCs) to produce current. Initial enrichments for iron (III) reducing bacteria were set up with sediments from the haloalkaline environment of Soap Lake, Washington, in batch cultures and subsequent transfers resulted in a culture that grew optimally at 7.0% salinity and pH 11.0. The culture was used to inoculate the anode chamber of a MFC with formate as the electron source. Current densities up to 12.5 mA/m2 were achieved by this bacterium. Cyclic voltammetry experiments demonstrated that an electron mediator, methylene blue, was required to transfer electrons to the anode. Scanning electron microscopic imaging of the electrode surface did not reveal heavy colonization of bacteria, providing evidence that the bacterium may be using an indirect mode of electron transfer to generate current. Molecular characterization of the 16S rRNA gene and restriction fragment length profiles (RFLP) analysis showed that the MFC enriched for a single bacterial species with a 99% similarity to the 16S rRNA gene of Halanaerobium hydrogeniformans. Though modest, electricity production was achieved by a haloalkaliphilic bacterium at pH 11.0 and 7.0% salinity. PMID:24645484

  11. Metabolism of 2-Methylpropene (Isobutylene) by the Aerobic Bacterium Mycobacterium sp. Strain ELW1

    PubMed Central

    Kottegoda, Samanthi; Waligora, Elizabeth

    2015-01-01

    An aerobic bacterium (Mycobacterium sp. strain ELW1) that utilizes 2-methylpropene (isobutylene) as a sole source of carbon and energy was isolated and characterized. Strain ELW1 grew on 2-methylpropene (growth rate = 0.05 h−1) with a yield of 0.38 mg (dry weight) mg 2-methylpropene−1. Strain ELW1 also grew more slowly on both cis- and trans-2-butene but did not grow on any other C2 to C5 straight-chain, branched, or chlorinated alkenes tested. Resting 2-methylpropene-grown cells consumed ethene, propene, and 1-butene without a lag phase. Epoxyethane accumulated as the only detected product of ethene oxidation. Both alkene consumption and epoxyethane production were fully inhibited in cells exposed to 1-octyne, suggesting that alkene oxidation is initiated by an alkyne-sensitive, epoxide-generating monooxygenase. Kinetic analyses indicated that 1,2-epoxy-2-methylpropane is rapidly consumed during 2-methylpropene degradation, while 2-methyl-2-propen-1-ol is not a significant metabolite of 2-methylpropene catabolism. Degradation of 1,2-epoxy-2-methylpropane by 2-methylpropene-grown cells led to the accumulation and further degradation of 2-methyl-1,2-propanediol and 2-hydroxyisobutyrate, two sequential metabolites previously identified in the aerobic microbial metabolism of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA). Growth of strain ELW1 on 2-methylpropene, 1,2-epoxy-2-methylpropane, 2-methyl-1,2-propanediol, and 2-hydroxyisobutyrate was fully inhibited when cobalt ions were omitted from the growth medium, while growth on 3-hydroxybutyrate and other substrates was unaffected by the absence of added cobalt ions. Our results suggest that, like aerobic MTBE- and TBA-metabolizing bacteria, strain ELW1 utilizes a cobalt/cobalamin-dependent mutase to transform 2-hydroxyisobutyrate. Our results have been interpreted in terms of their impact on our understanding of the microbial metabolism of alkenes and ether oxygenates. PMID:25576605

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

    PubMed

    Sipka, Gábor; Maróti, Péter

    2016-01-01

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

  13. Immobilization of Rhodococcus rhodochrous BX2 (an acetonitrile-degrading bacterium) with biofilm-forming bacteria for wastewater treatment.

    PubMed

    Li, Chunyan; Li, Yue; Cheng, Xiaosong; Feng, Liping; Xi, Chuanwu; Zhang, Ying

    2013-03-01

    In this study, a unique biofilm consisting of three bacterial strains with high biofilm-forming capability (Bacillus subtilis E2, E3, and N4) and an acetonitrile-degrading bacterium (Rhodococcus rhodochrous BX2) was established for acetonitrile-containing wastewater treatment. The results indicated that this biofilm exhibited strong resistance to acetonitrile loading shock and displayed a typical spatial and structural heterogeneity and completely depleted the initial concentration of acetonitrile (800mgL(-1)) within 24h in a moving-bed-biofilm reactor (MBBR) after operation for 30days. The immobilization of BX2 cells in the biofilm was confirmed by PCR-DGGE. It has been demonstrated that biofilm-forming bacteria can promote the immobilization of contaminant-degrading bacteria in the biofilms and can subsequently improve the degradation of contaminants in wastewater. This approach offers a novel strategy for enhancing biological oxidation of toxic pollutants in wastewater. PMID:23376196

  14. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    SciTech Connect

    Taghavi, S.; van der Lelie, D.; Hoffman, A.; Zhang, Y.-B.; Walla, M. D.; Vangronsveld, J.; Newman, L.; Monchy, S.

    2010-05-13

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa x deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  15. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

    PubMed Central

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J.

    2015-01-01

    Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

  16. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China.

    PubMed

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J

    2015-01-01

    Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

  17. 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

  18. Enrichment of denitrifying anaerobic methane oxidizing microorganisms.

    PubMed

    Hu, Shihu; Zeng, Raymond J; Burow, Luke C; Lant, Paul; Keller, Jurg; Yuan, Zhiguo

    2009-10-01

    The microorganisms responsible for anaerobic oxidation of methane (AOM) coupled to denitrification have not been clearly elucidated. Three recent publications suggested it can be achieved by a denitrifying bacterium with or without the involvement of anaerobic methanotrophic archaea. A key factor limiting the progress in this research field is the shortage of enrichment cultures performing denitrifying anaerobic methane oxidation (DAMO). In this study, DAMO cultures were enriched from mixed inoculum including sediment from a freshwater lake, anaerobic digester sludge and return activated sludge from a sewage treatment plant. Two reactors, operated at 35°C and at 22°C, respectively, showed simultaneous methane oxidation and nitrate reduction after several months of operation. Analysis of 16S rRNA gene clone libraries from the 35°C enrichment showed the presence of an archaeon closely related to other DAMO archaea and a dominated bacterium belonging to the yet uncultivated NC10 phylum. This culture preferred nitrite to nitrate as the electron acceptor. The present study suggests that the archaea are rather methanotrophs than methanogens. The highest denitrification rate achieved was 2.35 mmol NO3 (-) -N gVSS(-1)  day(-1) . The culture enriched at 22°C contained the same NC10 bacterium observed in the culture enriched at 35°C but no archaea. PMID:23765890

  19. 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. PMID:24637606

  20. Ultrasonic Treatment Enhanced Ammonia-Oxidizing Bacterial (AOB) Activity for Nitritation Process.

    PubMed

    Zheng, Min; Liu, Yan-Chen; Xin, Jia; Zuo, Hao; Wang, Cheng-Wen; Wu, Wei-Min

    2016-01-19

    Oxidation of ammonia to nitrite rather than nitrate is critical for nitritation process for wastewater treatment. We proposed a promising approach by using controlled ultrasonic treatment to enhance the activity of ammonia-oxidizing bacteria (AOB) and suppress that of nitrite-oxidizing bacteria (NOB). Batch activity assays indicated that when ultrasound was applied, AOB activity reached a peak level and then declined but NOB activity deteriorated continuously as the power intensity of ultrasound increased. Kinetic analysis of relative microbial activity versus ultrasonic energy density was performed to investigate the effect of operational factors (power, sludge concentration, and aeration) on AOB and NOB activities and the test parameters were selected for reactor tests. Laboratory sequential batch reactor (SBR) was further used to test the ultrasonic stimulus with 8 h per day operational cycle and synthetic waste urine as influent. With specific ultrasonic energy density of 0.09 kJ/mg VSS and continuously fed influent containing above 200 mg NH3-N/L, high AOB reproductive activity was achieved and nearly complete conversion of ammonia-N to nitrite was maintained. Microbial structure analysis confirmed that the treatment changed community of AOB, NOB, and heterotrophs. Known AOB Nitrosomonas genus remained at similar level in the biomass while typical NOB Nitrospira genus disappeared in the SBR under ultrasonic treatment and after the treatment was off for 30 days. PMID:26678011

  1. The abundance and diversity of ammonia-oxidizing bacteria in activated sludge under autotrophic domestication.

    PubMed

    Li, Qiang; Ma, Chao; Sun, Shifang; Xie, Hui; Zhang, Wei; Feng, Jun; Song, Cunjiang

    2013-04-01

    Ammonia-oxidizing bacteria (AOB) play a key role in nitrogen-removal wastewater treatment plants (WWTPs) as they can transform ammonia into nitrite. AOB can be enriched in activated sludge through autotrophic domestication although they are difficult to be isolated. In this study, autotrophic domestication was carried out in a lab-scale sequencing-batch-reactor (SBR) system with two activated sludge samples. The ammonia removal capacity of the sludge samples increased during the domestication, and pH exhibited a negative correlation with the ammonia removal amount, which indicated that it was one important factor of microbial ammonia oxidation. The count of AOB, measured by the most probable number (MPN) method, increased significantly during autotrophic domestication as ammonia oxidation efficiency was enhanced. We investigated the changes in the community structure of AOB before and after domestication by amoA clone library and T-RFLP profile. It showed that AOB had been successfully enriched and the community structure significantly shifted during the domestication. Two groups of AOB were found in sludge samples: Nitrosomonas-like group remained predominant all the time and Nitrosospira-like group changed obviously. Simultaneously, the total heterotrophic bacteria were investigated by MPN and Biolog assay. The metabolic diversity of heterotrophs had changed minutely, although the count of them decreased significantly and lost superiority of microbial communities in the sludge. PMID:24620598

  2. Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest.

    PubMed

    Zhang, Li-Mei; Wang, Mu; Prosser, James I; Zheng, Yuan-Ming; He, Ji-Zheng

    2009-11-01

    To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000-6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800-6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amoA abundance was greater than bacterial amoA abundance in lower altitude soils (or=5700 m a.s.l.). Both archaeal and bacterial amoA abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amoA cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amoA sequences fell within soil and sediment clusters, and the proportions of the major archaeal amoA clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils. PMID:19780828

  3. Thiobacillus thiophilus sp. nov., a chemolithoautotrophic, thiosulfate-oxidizing bacterium isolated from contaminated aquifer sediments.

    PubMed

    Kellermann, Claudia; Griebler, Christian

    2009-03-01

    Strain D24TN(T) was enriched and isolated from sediment collected from a tar oil-contaminated aquifer at a former gasworks site located in Duesseldorf-Flingern, Germany. Cells of strain D24TN(T) were rod-shaped, non-spore-forming and stained Gram-negative. Thiosulfate was used as an electron donor. The organism was obligately chemolithoautotrophic and facultatively anaerobic, and grew with either oxygen or nitrate as electron acceptor. Growth was observed at pH values between 6.3 and 8.7 and at temperatures of -2 to 30 degrees C; optimum growth occurred at pH 7.5-8.3 and 25-30 degrees C. The DNA G+C content was 61.5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain D24TN(T) clustered in the Betaproteobacteria and was most closely related to Thiobacillus denitrificans (97.6 %) and Thiobacillus thioparus (97.5 %). Based on the phenotypic, chemotaxonomic and phylogenetic data, strain D24TN(T) represents a novel species of the genus Thiobacillus, for which the name Thiobacillus thiophilus sp. nov. is proposed. The type strain is D24TN(T) (=DSM 19892(T)=JCM 15047(T)). PMID:19244446

  4. Production of hydrogen sulfide from tetrathionate by the iron-oxidizing bacterium Thiobacillus ferrooxidans NASF-1.

    PubMed

    Ng, K Y; Kamimura, K; Sugio, T

    2000-01-01

    When incubated under anaerobic conditions, five strains of Thiobacillus ferrooxidans tested produced hydrogen sulfide (H2S) from elemental sulfur at pH 1.5. However, among the strains, T. ferrooxidans NASF-1 and AP19-3 were able to use both elemental sulfur and tetrathionate as electron acceptors for H2S production at pH 1.5. The mechanism of H2S production from tetrathionate was studied with intact cells of strain NASF-1. Strain NASF-1 was unable to use dithionate, trithionate, or pentathionate as an electron acceptor. After 12 h of incubation under anaerobic conditions at 30 degrees C, 1.3 micromol of tetrathionate in the reaction mixture was decomposed, and 0.78 micromol of H2S and 0.6 micromol of trithionate were produced. Thiosulfate and sulfite were not detected in the reaction mixture. From these results, we propose that H2S is produced at pH 1.5 from tetrathionate by T. ferrooxidans NASF-1, via the following two-step reaction, in which AH2 represents an unknown electron donor in NASF-1 cells. Namely, tetrathionate is decomposed by tetrathionate-decomposing enzyme to give trithionate and elemental sulfur (S4O6(2-)-->S3O6(2-) + S(o), Eq. 1), and the elemental sulfur thus produced is reduced by sulfur reductase using electrons from AH2 to give H2S (S(o) + AH2-->H2S + A, Eq. 2). The optimum pH and temperature for H2S production from tetrathionate under argon gas were 1.5 and 30 degrees C, respectively. Under argon gas, the H2S production from tetrathionate stopped after 1 d of incubation, producing a total of 2.5 micromol of H2S/5 mg protein. In contrast, under H2 conditions, H2S production continued for 6 d, producing a total of 10.0 micromol of H2S/5 mg protein. These results suggest that electrons from H2 were used to reduce elemental sulfur produced as an intermediate to give H2S. Potassium cyanide at 0.5 mM slightly inhibited H2S production from tetrathionate, but increased that from elemental sulfur 3-fold. 2,4-Dinitrophenol at 0.05 mM, carbonylcyanide-m-chlorophenyl- hydrazone at 0.01 mM, mercury chloride at 0.05 mM, and sodium selenate at 1.0 mM almost completely inhibited H2S production from tetrathionate, but not from elemental sulfur. PMID:16232841

  5. Existence of Two Kinds of Sulfur-reducing Systems in Iron-oxidizing Bacterium Thiobacillus ferrooxidans.

    PubMed

    Ng, K Y; Inoue, S; Fujioka, A; Kamimura, K; Sugio, T

    1999-01-01

    Intact cells of Thiobacillus ferrooxidans NASF-1 incubated under anaerobic conditions in a reaction mixture containing 0.5% colloidal sulfur produced hydrogen sulfide (H2S) extracellularly. The amount of H2S produced by cells increased corresponding to the cell amounts and colloidal sulfur. Two activity peaks of H2S production were observed at pH 1.5 and 7.5. We tentatively called the enzyme activities pH 1.5- and pH 7.5-sulfur reducing systems, respectively. Seven strains of T. ferrooxidans tested had both the activities of pH 1.5- and pH 7.5-sulfur reducing systems, but at different levels. T. ferrooxidans NASF-1 showed the highest activity of the pH 1.5-sulfur reducing system and strain 13598 from ATCC showed the highest activity of the pH 7.5-sulfur reducing system. Further characteristics of H2S production were studied with intact cells of NASF-1. The optimum temperatures for pH 1.5- and pH 7.5-sulfur reducing systems of NASF-1 were 40°C. Hydrogen sulfide production continued for 8 days and total amounts of H2S produced at pH 7.5 and 1.5 were 832 and 620 nmol/mg protein, respectively. The pH 7.5-sulfur reducing system used only colloidal sulfur as the electron acceptor. However, the pH 1.5-sulfur reducing system used both colloidal sulfur and tetrathionate. Thiosulfate, dithionate, and sulfite could not be used as the electron acceptor for both of the sulfur reducing systems. Potassium cyanide activated by 3- fold the pH 1.5-sulfur reducing system activity at 0.5 mM but did not affect the activity of the pH 7.5-sulfur reducing system. An inhibitor of sulfite reductase, p-chloromercuribenzene sulfonic acid, did not affect either enzyme activity. Sodium molybdate and monoiodoacetic acid strongly inhibited the activity of the pH 1.5-sulfur reducing system at 1.0 mM, but not the activity of pH 7.5-sulfur reducing system. PMID:27385566

  6. The amino acid sequence of cytochrome c-555 from the methane-oxidizing bacterium Methylococcus capsulatus.

    PubMed Central

    Ambler, R P; Dalton, H; Meyer, T E; Bartsch, R G; Kamen, M D

    1986-01-01

    The amino acid sequence of the cytochrome c-555 from the obligate methanotroph Methylococcus capsulatus strain Bath (N.C.I.B. 11132) was determined. It is a single polypeptide chain of 96 residues, binding a haem group through the cysteine residues at positions 19 and 22, and the only methionine residue is a position 59. The sequence does not closely resemble that of any other cytochrome c that has yet been characterized. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50131 (12 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment. PMID:3006666

  7. Denitrification by a marine bacterium Pseudomonas nautica strain 617.

    PubMed

    Bonin, P; Gilewicz, M; Bertrand, J C

    1987-01-01

    A bacterial strain was isolated from a marine sediment highly contaminated by hydrocarbons. From taxonomic tests, it was identified as Pseudomonas nautica. This marine strain was able to grow on nitrate, nitrite and nitrous oxide as an electron acceptor. The terminal product from the denitrification was dinitrogen. Thus, P. nautica was a denitrifier. The kinetics of each step of denitrification was examined in resting cell suspensions. The relative rates of nitrate and nitrite reduction and of nitrite reduction and nitrous oxide production explain, respectively, the presence of accumulated nitrite and that of compound intermediate between nitrite and nitrous oxide. PMID:3620203

  8. 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

  9. Denitrification characteristics of a marine origin psychrophilic aerobic denitrifying bacterium.

    PubMed

    Zheng, Haiyan; Liu, Ying; Sun, Guangdong; Gao, Xiyan; Zhang, Qingling; Liu, Zhipei

    2011-01-01

    A psychrophilic aerobic denitrifying bacterium, strain S1-1, was isolated from a biological aerated filter conducted for treatment of recirculating water in a marine aquaculture system. Strain S1-1 was preliminarily identified as Psychrobacter sp. based on the analysis of its 16S rRNA gene sequence, which showed 100% sequence similarity to that of Psychrobacter sp. TSBY-70. Strain S1-1 grew well either in high nitrate or high nitrite conditions with a removal of 100% nitrate or 63.50% nitrite, and the total nitrogen removal rates could reach to 46.48% and 31.89%, respectively. The results indicated that nitrate was mainly reduced in its logarithmic growth phase with a very low level accumulation of nitrite, suggesting that the aerobic denitrification process of strain S1-1 occurred mainly in this phase. The GC-MS results showed that N2O was formed as the major intermediate during the aerobic denitrifying process of strain S1-1. Finally, factors affecting the growth of strain S1-1 and its aerobic denitrifying ability were also investigated. Results showed that the optimum aerobic denitrification conditions for strain S1-1 were sodium succinate as carbon source, C/N ratio15, salinity 10 g/L NaCl, incubation temperature 20 degrees C and initial pH 6.5. PMID:22432315

  10. 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

  11. 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.

  12. Novel Rickettsiella Bacterium in the Leafhopper Orosius albicinctus (Hemiptera: Cicadellidae)

    PubMed Central

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

    2013-01-01

    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. PMID:23645190

  13. Bacterium organizes hierarchical amorphous structure in microbial cellulose

    NASA Astrophysics Data System (ADS)

    Koizumi, S.; Yue, Z.; Tomita, Y.; Kondo, T.; Iwase, H.; Yamaguchi, D.; Hashimoto, T.

    2008-05-01

    A pellicle, a gel film of microbial cellulose, is a supermolecular system containing 99% of water by weight, which is closely related to an amorphous structure in it. Using ultra-small-angle neutron scattering, in order to cover over a wide range of length scales from nm to 10μm, we examined the hierarchical amorphous structure in the microbial cellulose, which is synthesized by a bacterium (Acetobacter xylinum). The microbial cellulose swollen by water shows small-angle scattering that obeys a power law q -behavior according to q-α as a function of the magnitude of the scattering vector q . The power law, determined by scattering, is attributed to a mass fractal due to the distribution of the center of mass for the crystallite (microfibril) in amorphous cellulose swollen by water. As q increases, α takes the values of 2.5, 1, and 2.35, corresponding, respectively, to a gel network composed of bundles, a bundle composed of cellulose ribbons, and concentration fluctuations in a bundle. From the mass fractal q -behavior and its length scale limits, we evaluated a volume fraction of crystallite in microbial cellulose. It was found that 90% of the cellulose bundle is occupied by amorphous cellulose containing water.

  14. Fitness correlates with the extent of cheating in a bacterium.

    PubMed

    Jiricny, N; Diggle, S P; West, S A; Evans, B A; Ballantyne, G; Ross-Gillespie, A; Griffin, A S

    2010-04-01

    There is growing awareness of the importance of cooperative behaviours in microbial communities. Empirical support for this insight comes from experiments using mutant strains, termed 'cheats', which exploit the cooperative behaviour of wild-type strains. However, little detailed work has gone into characterising the competitive dynamics of cooperative and cheating strains. We test three specific predictions about the fitness consequences of cheating to different extents by examining the production of the iron-scavenging siderophore molecule, pyoverdin, in the bacterium Pseudomonas aeruginosa. We create a collection of mutants that differ in the amount of pyoverdin that they produce (from 1% to 96% of the production of paired wild types) and demonstrate that these production levels correlate with both gene activity and the ability to bind iron. Across these mutants, we found that (1) when grown in a mixed culture with a cooperative wild-type strain, the relative fitness of a mutant is negatively correlated with the amount of pyoverdin that it produces; (2) the absolute and relative fitness of the wild-type strain in the mixed culture is positively correlated with the amount of pyoverdin that the mutant produces; and (3) when grown in a monoculture, the absolute fitness of the mutant is positively correlated with the amount of pyoverdin that it produces. Overall, we demonstrate that cooperative pyoverdin production is exploitable and illustrate how variation in a social behaviour determines fitness differently, depending on the social environment. PMID:20210835

  15. 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

  16. A serine sensor for multicellularity in a bacterium

    PubMed Central

    Subramaniam, Arvind R; DeLoughery, Aaron; Bradshaw, Niels; Chen, Yun; O’Shea, Erin; Losick, Richard; Chai, Yunrong

    2013-01-01

    We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase. DOI: http://dx.doi.org/10.7554/eLife.01501.001 PMID:24347549

  17. The acetylproteome of Gram-positive model bacterium Bacillus subtilis.

    PubMed

    Kim, Dooil; Yu, Byung Jo; Kim, Jung Ae; Lee, Yong-Jik; Choi, Soo-Geun; Kang, Sunghyun; Pan, Jae-Gu

    2013-05-01

    N(ε) -lysine acetylation, a reversible and highly regulated PTM, has been shown to occur in the model Gram-negative bacteria Escherichia coli and Salmonella enterica. Here, we extend this acetylproteome analysis to Bacillus subtilis, a model Gram-positive bacterium. Through anti-acetyllysine antibody-based immunoseparation of acetylpeptides followed by nano-HPLC/MS/MS analysis, we identified 332 unique lysine-acetylated sites on 185 proteins. These proteins are mainly involved in cellular housekeeping functions such as central metabolism and protein synthesis. Fifity-nine of the lysine-acetylated proteins showed homology with lysine-acetylated proteins previously identified in E. coli, suggesting that acetylated proteins are more conserved. Notably, acetylation was found at or near the active sites predicted by Prosite signature, including SdhA, RocA, Kbl, YwjH, and YfmT, indicating that lysine acetylation may affect their activities. In 2-amino-3-ketobutyrate CoA ligase Kbl, a class II aminotransferase, a lysine residue involved in pyridoxal phosphate attachment was found to be acetylated. This data set provides evidence for the generality of lysine acetylation in eubacteria and opens opportunities to explore the consequences of acetylation modification on the molecular physiology of B. subtilis. PMID:23468065

  18. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7.

    PubMed

    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

  19. Molecular study on cloned endoglucanase gene from rumen bacterium.

    PubMed

    Ozkose, Emin; Akyol, Ismail; Ekinci, Mehmet Sait

    2004-01-01

    An endoglucanase gene was subcloned from anaerobic rumen bacterium Ruminococcus flavefaciens strain 17. To express endoglucanase gene in Escherichia coli and Streptococcus bovis JB1, an endoglucanase gene fragment was inserted into pVA838-based shuttle vectors. Removal of endoglucanase gene promoter and expression of endoglucanase by promoter of S. bovis JB1 alpha-amylase gene (pACMCS) was also achieved. Survival of constructs pVACMCI, pTACMC and pACMCS, which carry endoglucanase gene, and stability of endoglucanase gene in S. bovis JB1, were observed. Maximal endoglucanase activities from S. bovis JB1/pVACMCI were 2- to 3-fold higher than from E. coli/pVACMCI. Specific cell activity of E. coli/pACMCS was found to be approximately 2- to -3 fold higher than the both E. coli/pVACMCI and E. coli/pTACMC. Specific cell activity of S. bovis JB1/pACMCS was also found to be approximately 2-fold higher than the both S. bovis/pVACMCI and S. bovis JB1/pTACMC. PMID:15925902

  20. 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

    2016-01-01

    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

  1. Mutation of bacterium Vibrio gazogenes for selective preparation of colorants.

    PubMed

    Alihosseini, Farzaneh; Lango, Jozsef; Ju, Kou-San; Hammock, Bruce D; Sun, Gang

    2010-01-01

    A novel marine bacterium strain effectively produced prodiginine type pigments. These colorants could dye wool, silk and synthetic fabrics such as polyester and polyacrylic and also show antibacterial properties against Escherichia coli and Staphylococcus aureus bacteria on the dyed products. Methyl nitrosoguanidine was used as a mutation agent to increase the genetic diversity and the production yield of the bacteria of the family of Vibrio gazogenes. The analysis of the mutated samples showed that two new main colorants as well as three previously found ones were produced. Liquid chromatography electro spray ionization mass spectrometry (LC-ESI-MS) and nuclear magnetic resonance (NMR) spectroscopic techniques were used to elucidate the structures of the newly produced colorants. Mass measurements revealed that the colorants C1, C2, C3, C4 have molecular masses of 321, 323, 351, and 295 Da. One unstable colorant C5 with molecular mass of 309 Da was detected as well. The mutated bacteria strains increased the yield of pigment production by about 81% and produced prodigiosin in 97% purity. The antibiotic activities of pure colorants are discussed as well. Based on their bio-activity and excellent dyeing capabilities, these colorants could be employed in cosmetic and textile industries. PMID:19902486

  2. 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

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

    PubMed

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

    2016-09-01

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

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

    DOE PAGESBeta

    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 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

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

    PubMed

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

    2001-01-01

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

  6. 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...

  7. Characterization of a Neochlamydia-like bacterium associated with epitheliocystis in cultured Arctic charr 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, conventiona...

  8. Extracellular electron transfer of a highly adhesive and metabolically versatile bacterium.

    PubMed

    Liu, Huan; Ishikawa, Masahito; Matsuda, Shoichi; Kimoto, Yuki; Hori, Katsutoshi; Hashimoto, Kazuhito; Nakanishi, Shuji

    2013-08-01

    Bacterial adhesion to a solid plays a predominant role in mediating the extracellular electron transfer for genus Acinetobactor, a metabolically versatile bacterium that can couple toluene degradation and electricity generation. PMID:23813865

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

    PubMed Central

    Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J.

    2014-01-01

    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. PMID:25477416

  10. 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...

  11. 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...

  12. Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium

    PubMed Central

    Yaakop, Amira Suriaty; Chan, Chia Sing; Kahar, Ummirul Mukminin; Ee, Robson

    2015-01-01

    Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium. PMID:25977433

  13. Desulfuromonas carbonis sp. nov., an Fe(III)-, S0- and Mn(IV)-reducing bacterium isolated from an active coalbed methane gas well.

    PubMed

    An, Thuy T; Picardal, Flynn W

    2015-05-01

    A novel, mesophilic, obligately anaerobic, acetate-oxidizing, dissimilatory iron-, sulfur-, and manganese-reducing bacterium, designated strain ICBM(T), was obtained from an active, coalbed methane gas well in Indiana, USA. Strain ICBM(T) was a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium that was rich in c-type cytochromes and formed red colonies in solid medium. Strain ICBM(T) conserved energy to support growth from the oxidation of acetate, propionate, pyruvate, malate, fumarate, succinate and dl-lactate, concomitant with dissimilatory iron reduction. Strain ICBM(T) fermented fumarate yielding succinate and acetate. Strain ICBM(T) was able to grow in the temperature range of 10 °C to 37 °C, NaCl concentration range of 0 to 1.2 M, and pH range of 6.5 to 8.0. The physiological characteristics of strain ICBM(T) indicated that it belongs to the Desulfuromonas cluster. The G+C content of its genomic DNA was 61.2 mol%. The predominant cellular fatty acids were C16 : 0 (39.3%), C16 : 1ω7c and/or iso-C15 : 0 2-OH (36.6%). The closest cultured phylogenetic relative of strain ICBM(T) was Desulfuromonas michiganensis BB1(T) with only 95% 16S rRNA gene sequence similarity. This confirmed that strain ICBM(T) is affiliated with the genus Desulfuromonas . On the basis of phenotypic and genotypic differences between strain ICBM(T) and other taxa of the genus Desulfuromonas , strain ICBM(T) represents a novel species for which the name Desulfuromonas carbonis sp. nov. is proposed (type strain ICBM(T) = DSM 29759(T) = JCM 30471(T)). Strain ICBM(T) is the first Fe(III)-, S(0)-, and Mn(IV)-reducing bacterium that was isolated from a coal bed. PMID:25736408

  14. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NASA Astrophysics Data System (ADS)

    Zheng, Y.; Huang, R.; Wang, B. Z.; Bodelier, P. L. E.; Jia, Z. J.

    2014-06-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and functional genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity 6-fold during a 19-day incubation period, while ammonia oxidation activity was significantly suppressed in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like MOB, and nitrifying communities appeared to be partially inhibited by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to an equal increase in Methylosarcina and Methylobacter-related type Ia MOB, indicating the differential growth requirements of representatives of these genera. An increase in 13C assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition partially inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, as well as growth of nitrite-oxidizing bacteria. These

  15. Draft Genome Sequence of DLB, a Dyella-Like Bacterium from the Planthopper Hyalesthes obsoletus

    PubMed Central

    Lahav, Tamar; Zchori-Fein, Einat; Naor, Vered; Freilich, Shiri

    2016-01-01

    We report here the draft genome sequence of a Dyella-like bacterium (DLB) isolated from Hyalesthes obsoletus, the insect vector of the uncultivable mollicute bacterium “Candidatus Phytoplasma.” This isolate inhibits Spiroplasma melliferum, a cultivable mollicute. The draft genome of DLB consists of 4,196,214 bp, with a 68.6% G+C content, and 3,757 genes were predicted. PMID:27445378

  16. Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium.

    PubMed

    Cui, Changzheng; Li, Zhijie; Qian, Jiangchao; Shi, Jie; Huang, Ling; Tang, Hongzhi; Chen, Xin; Lin, Kuangfei; Xu, Ping; Liu, Yongdi

    2016-05-10

    Martelella sp. strain AD-3, a moderate halophilic bacterium, was isolated from a petroleum-contaminated soil with high salinity in China. Here, we report the complete genome of strain AD-3, which contains one circular chromosome and two circular plasmids. An array of genes related to metabolism of polycyclic aromatic hydrocarbons and halophilic mechanism in this bacterium was identified by the whole genome analysis. PMID:26988395

  17. 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

  18. Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens

    PubMed Central

    Dalla Vecchia, Elena; Shao, Paul P.; Suvorova, Elena; Chiappe, Diego; Hamelin, Romain; Bernier-Latmani, Rizlan

    2014-01-01

    Desulfotomaculum reducens strain MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing Fe(III). Metal reduction in Gram-positive bacteria is poorly understood. Here, we investigated Fe(III) reduction with lactate, a non-fermentable substrate, as the electron donor. Lactate consumption is concomitant to Fe(III) reduction, but does not support significant growth, suggesting that little energy can be conserved from this process and that it may occur fortuitously. D. reducens can reduce both soluble [Fe(III)-citrate] and insoluble (hydrous ferric oxide, HFO) Fe(III). Because physically inaccessible HFO was not reduced, we concluded that reduction requires direct contact under these experimental conditions. This implies the presence of a surface exposed reductase capable of transferring electrons from the cell to the extracellular electron acceptor. With the goal of characterizing the role of surface proteins in D. reducens and of identifying candidate Fe(III) reductases, we carried out an investigation of the surface proteome (surfaceome) of D. reducens. Cell surface exposed proteins were extracted by trypsin cell shaving or by lysozyme treatment, and analyzed by liquid chromatography-tandem mass spectrometry. This investigation revealed that the surfaceome fulfills many functions, including solute transport, protein export, maturation and hydrolysis, peptidoglycan synthesis and modification, and chemotaxis. Furthermore, a few redox-active proteins were identified. Among these, three are putatively involved in Fe(III) reduction, i.e., a membrane-bound hydrogenase 4Fe-4S cluster subunit (Dred_0462), a heterodisulfide reductase subunit A (Dred_0143) and a protein annotated as alkyl hydroperoxide reductase but likely functioning as a thiol-disulfide oxidoreductase (Dred_1533). PMID:25191310

  19. Thermoanaerobacter siderophilus sp. nov., a novel dissimilatory Fe(III)-reducing, anaerobic, thermophilic bacterium.

    PubMed

    Slobodkin, A I; Tourova, T P; Kuznetsov, B B; Kostrikina, N A; Chernyh, N A; Bonch-Osmolovskaya, E A

    1999-10-01

    A thermophilic, anaerobic, spore-forming, dissimilatory Fe(III)-reducing bacterium, designated strain SR4T, was isolated from sediment of newly formed hydrothermal vents in the area of the eruption of Karymsky volcano on the Kamchatka peninsula. Cells of strain SR4T were straight-to-curved, peritrichous rods, 0.4-0.6 micron in diameter and 3.5-9.0 microns in length, and exhibited a slight tumbling motility. Strain SR4T formed round, refractile, heat-resistant endospores in terminally swollen sporangia. The temperature range for growth was 39-78 degrees C, with an optimum at 69-71 degrees C. The pH range for growth was 4.8-8.2, with an optimum at 6.3-6.5. Strain SR4T grew anaerobically with peptone as carbon source. Amorphous iron(III) oxide present in the medium stimulated the growth of strain SR4T; cell numbers increased with the concomitant accumulation of Fe(II). In the presence of Fe(III), strain SR4T grew on H2/CO2 and utilized molecular hydrogen. Strain SR4T reduced 9,10-anthraquinone-2,6-disulfonic acid, sulfite, thiosulfate, elemental sulfur and MnO2. Strain SR4T did not reduce nitrate or sulfate and was not capable of growth with O2. The fermentation products from glucose were ethanol, lactate, H2 and CO2. The G + C content of DNA was 32 mol%. 16S rDNA sequence analysis placed the organism in the genus Thermoanaerobacter. On the basis of physiological properties and phylogenetic analysis, it is proposed that strain SR4T (= DSM 12299T) should be assigned to a new species, Thermoanaerobacter siderophilus sp. nov. PMID:10555328

  20. Purification and characterization of the oxidase from the marine bacterium Pseudomonas nautica 617.

    PubMed

    Arnaud, S; Malatesta, F; Guigliarelli, B; Gayda, J P; Bertrand, P; Miraglio, R; Denis, M

    1991-06-01

    The aerobic respiratory system of the hydrocarbonoclastic marine bacterium Pseudomonas nautica 617 ends with a single terminal oxidase. It is a heme-containing membranous protein which has been demonstrated only to reduce molecular oxygen to hydrogen peroxide [Denis, M., Arnaud S. & Malatesta, F. (1989) FEBS Lett. 247, 475-479]. The purification of this oxidase was achieved in a single step through by DEAE-Trisacryl chromatography. SDS/PAGE showed the presence of four subunits. The pI was found to be 4.45 and a Mr of 130,000 was determined by gel filtration. The amino acid composition of the purified terminal oxidase has been determined. About 52% of the residues are hydrophobic, strengthening the membranous nature of this bacterial oxidase. Room temperature optical spectra are typical of heme b with a 560-nm band for the reduced form in the alpha range. The prosthetic group is made of two hemes b, one high-spin (S = 5/2, gl = 5.9, g parallel approximately 2.0), the other low-spin (S = 1/2, gz = 2.94, gy = 2.27). No other metal centre was detected by EPR. The two hemes remained unresolved in optical spectra, even at low temperature, and throughout redox titration. They behaved potentiometrically like a one-electron, single redox couple, with Em = 87 +/- 10 mV at pH 7.2 and 293 K. The purified oxidase did not oxidize ferrocytochrome c, but displayed quinol oxidase activity both with the native quinone (2419 nmol O2.min-1.mg protein-1 and commercially available coenzyme (101.74 nmol O2.min-1.mg protein-1). Exposure of the reduced enzyme to CO induced the collapse of alpha and beta bands as occurred during reoxidation. In contrast, NaCN and NaN3 fully inhibited the oxidase activity. Results are discussed with respect to other purified quinol oxidases. PMID:1645655

  1. Comprehensive insights into the response of Alexandrium tamarense to algicidal component secreted by a marine bacterium

    PubMed Central

    Lei, Xueqian; Li, Dong; Li, Yi; Chen, Zhangran; Chen, Yao; Cai, Guanjing; Yang, Xujun; Zheng, Wei; Zheng, Tianling

    2015-01-01

    Harmful algal blooms occur throughout the world, threatening human health, and destroying marine ecosystems. Alexandrium tamarense is a globally distributed and notoriously toxic dinoflagellate that is responsible for most paralytic shellfish poisoning incidents. The culture supernatant of the marine algicidal bacterium BS02 showed potent algicidal effects on A. tamarense ATGD98-006. In this study, we investigated the effects of this supernatant on A. tamarense at physiological and biochemical levels to elucidate the mechanism involved in the inhibition of algal growth by the supernatant of the strain BS02. Reactive oxygen species (ROS) levels increased following exposure to the BS02 supernatant, indicating that the algal cells had suffered from oxidative damage. The levels of cellular pigments, including chlorophyll a and carotenoids, were significantly decreased, which indicated that the accumulation of ROS destroyed pigment synthesis. The decline of the maximum photochemical quantum yield (Fv/Fm) and relative electron transport rate (rETR) suggested that the photosynthesis systems of algal cells were attacked by the BS02 supernatant. To eliminate the ROS, the activities of antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT), increased significantly within a short period of time. Real-time PCR revealed changes in the transcript abundances of two target photosynthesis-related genes (psbA and psbD) and two target respiration-related genes (cob and cox). The transcription of the respiration-related genes was significantly inhibited by the treatments, which indicated that the respiratory system was disturbed. Our results demonstrate that the BS02 supernatant can affect the photosynthesis process and might block the PS II electron transport chain, leading to the production of excessive ROS. The increased ROS can further destroy membrane integrity and pigments, ultimately inducing algal cell death. PMID:25667582

  2. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.

    PubMed

    Wang, Xiaoyu; Chen, Meili; Xiao, Jingfa; Hao, Lirui; Crowley, David E; Zhang, Zhewen; Yu, Jun; Huang, Ning; Huo, Mingxin; Wu, Jiayan

    2015-01-01

    Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals. PMID:26301592

  3. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

    PubMed Central

    Xiao, Jingfa; Hao, Lirui; Crowley, David E.; Zhang, Zhewen; Yu, Jun; Huang, Ning; Huo, Mingxin; Wu, Jiayan

    2015-01-01

    Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals. PMID:26301592

  4. Characterization of a prokaryotic haemerythrin from the methanotrophic bacterium Methylococcus capsulatus (Bath).

    PubMed

    Karlsen, Odd A; Ramsevik, Linda; Bruseth, Live J; Larsen, Øivind; Brenner, Annette; Berven, Frode S; Jensen, Harald B; Lillehaug, Johan R

    2005-05-01

    For a long time, the haemerythrin family of proteins was considered to be restricted to only a few phyla of marine invertebrates. When analysing differential protein expression in the methane-oxidizing bacterium, Methylococcus capsulatus (Bath), grown at a high and low copper-to-biomass ratio, respectively, we identified a putative prokaryotic haemerythrin expressed in high-copper cultures. Haemerythrins are recognized by a conserved sequence motif that provides five histidines and two carboxylate ligands which coordinate two iron atoms. The diiron site is located in a hydrophobic pocket and is capable of binding O(2). We cloned the M. capsulatus haemerythrin gene and expressed it in Escherichia coli as a fusion protein with NusA. The haemerythrin protein was purified to homogeneity cleaved from its fusion partner. Recombinant M. capsulatus haemerythrin (McHr) was found to fold into a stable protein. Sequence similarity analysis identified all the candidate residues involved in the binding of diiron (His22, His58, Glu62, His77, His81, His117, Asp122) and the amino acids forming the hydrophobic pocket in which O(2) may bind (Ile25, Phe59, Trp113, Leu114, Ile118). We were also able to model a three-dimensional structure of McHr maintaining the correct positioning of these residues. Furthermore, UV/vis spectrophotometric analysis demonstrated the presence of conjugated diiron atoms in McHr. A comprehensive genomic database search revealed 21 different prokaryotes containing the haemerythrin signature (PROSITE 00550), indicating that these putative haemerythrins may be a conserved prokaryotic subfamily. PMID:15885093

  5. Transverse and lateral distribution of phospholipids and glycolipids in the membrane of the bacterium Micrococcus luteus

    SciTech Connect

    de Bony, J.; Lopez, A.; Gilleron, M.; Welby, M.; Laneelle, G.; Rousseau, B.; Beaucourt, J.P.; Tocanne, J.F. )

    1989-05-02

    The photodimerization of anthracene was used to investigate the transverse and lateral distribution of lipids in the membrane of the Gram-positive bacterium Micrococcus luteus. 9-(2-Anthryl)nonanoic acid (9-AN) is incorporated at a high rate into various membrane lipids of M. luteus. On irradiation of intact bacteria at 360 nm, anthracene-labeled lipids form stable photodimers which can be extracted and separated by thin-layer chromatography. We present here the results of a study on the distribution of two major lipids, phosphatidylglycerol (PG) and dimannosyldiacylglycerol (DMDG), within each leaflet of the membrane lipid bilayer. After metabolic incorporation of a tritiated derivative of 9-AN in M. luteus, the radioactivity associated with the photodimers issued from PG and DMDG was counted. In the bacterial membrane, the ratio of PG-DMDG heterodimer with respect to PG-PG and DMDG-DMDG homodimers is around half of what should be obtained for a homogeneous mixture of the two lipids. In order to find out whether this was due to an asymmetric distribution of the two lipids between the two membrane leaflets or a heterogeneous distribution of the two lipids within the same membrane leaflet, the transverse distribution of PG and DMDG was also investigated. This was carried out by following the kinetics of oxidation of the two lipids by periodic acid in the membrane of M. luteus protoplasts. PG predominated slightly in the outer layer (60%), while DMDG was found to be symmetrically distributed between the two leaflets. By itself, this lipid asymmetry cannot account for the lipid distribution determined from the photodimerization experiments. This indicates that PG and DMDG are not homogeneously distributed in the plane of the bacterial membrane.

  6. A Novel Electrophototrophic Bacterium Rhodopseudomonas palustris Strain RP2, Exhibits Hydrocarbonoclastic Potential in Anaerobic Environments

    PubMed Central

    Venkidusamy, Krishnaveni; Megharaj, Mallavarapu

    2016-01-01

    An electrophototrophic, hydrocarbonoclastic bacterium Rhodopseudomonas palustris stain RP2 was isolated from the anodic biofilms of hydrocarbon fed microbial electrochemical remediation systems (MERS). Salient properties of the strain RP2 were direct electrode respiration, dissimilatory metal oxide reduction, spore formation, anaerobic nitrate reduction, free living diazotrophy and the ability to degrade n-alkane components of petroleum hydrocarbons (PH) in anoxic, photic environments. In acetate fed microbial electrochemical cells, a maximum current density of 305 ± 10 mA/m2 (1000Ω) was generated (power density 131.65 ± 10 mW/m2) by strain RP2 with a coulombic efficiency of 46.7 ± 1.3%. Cyclic voltammetry studies showed that anaerobically grown cells of strain RP2 is electrochemically active and likely to transfer electrons extracellularly to solid electron acceptors through membrane bound compounds, however, aerobically grown cells lacked the electrochemical activity. The ability of strain RP2 to produce current (maximum current density 21 ± 3 mA/m2; power density 720 ± 7 μW/m2, 1000 Ω) using PH as a sole energy source was also examined using an initial concentration of 800 mg l-1 of diesel range hydrocarbons (C9-C36) with a concomitant removal of 47.4 ± 2.7% hydrocarbons in MERS. Here, we also report the first study that shows an initial evidence for the existence of a hydrocarbonoclastic behavior in the strain RP2 when grown in different electron accepting and illuminated conditions (anaerobic and MERS degradation). Such observations reveal the importance of photoorganotrophic growth in the utilization of hydrocarbons from contaminated environments. Identification of such novel petrochemical hydrocarbon degrading electricigens, not only expands the knowledge on the range of bacteria known for the hydrocarbon bioremediation but also shows a biotechnological potential that goes well beyond its applications to MERS. PMID:27462307

  7. A Novel Electrophototrophic Bacterium Rhodopseudomonas palustris Strain RP2, Exhibits Hydrocarbonoclastic Potential in Anaerobic Environments.

    PubMed

    Venkidusamy, Krishnaveni; Megharaj, Mallavarapu

    2016-01-01

    An electrophototrophic, hydrocarbonoclastic bacterium Rhodopseudomonas palustris stain RP2 was isolated from the anodic biofilms of hydrocarbon fed microbial electrochemical remediation systems (MERS). Salient properties of the strain RP2 were direct electrode respiration, dissimilatory metal oxide reduction, spore formation, anaerobic nitrate reduction, free living diazotrophy and the ability to degrade n-alkane components of petroleum hydrocarbons (PH) in anoxic, photic environments. In acetate fed microbial electrochemical cells, a maximum current density of 305 ± 10 mA/m(2) (1000Ω) was generated (power density 131.65 ± 10 mW/m(2)) by strain RP2 with a coulombic efficiency of 46.7 ± 1.3%. Cyclic voltammetry studies showed that anaerobically grown cells of strain RP2 is electrochemically active and likely to transfer electrons extracellularly to solid electron acceptors through membrane bound compounds, however, aerobically grown cells lacked the electrochemical activity. The ability of strain RP2 to produce current (maximum current density 21 ± 3 mA/m(2); power density 720 ± 7 μW/m(2), 1000 Ω) using PH as a sole energy source was also examined using an initial concentration of 800 mg l(-1) of diesel range hydrocarbons (C9-C36) with a concomitant removal of 47.4 ± 2.7% hydrocarbons in MERS. Here, we also report the first study that shows an initial evidence for the existence of a hydrocarbonoclastic behavior in the strain RP2 when grown in different electron accepting and illuminated conditions (anaerobic and MERS degradation). Such observations reveal the importance of photoorganotrophic growth in the utilization of hydrocarbons from contaminated environments. Identification of such novel petrochemical hydrocarbon degrading electricigens, not only expands the knowledge on the range of bacteria known for the hydrocarbon bioremediation but also shows a biotechnological potential that goes well beyond its applications to MERS. PMID:27462307

  8. Response of the bacterium Cupriavidus metallidurans CH34 to space flight conditions.

    NASA Astrophysics Data System (ADS)

    Leys, N.; Wattiez, R.; Rosier, C.; de Boever, P.; Baatout, S.; Mergeay, M.

    Background When man goes to space inevitably microbes hitchhike along some needed others unwanted Knowledge is required to understand the behaviour of bacteria in spaceflight conditions Aim The aim of this work was to investigate the physiological and metabolic response and adaptation of the environmental model bacterium Cupriavidus metallidurans CH34 to space flight conditions The strain was grown in the International Space Station ISS during 2 separated Soyuz missions MESSAGE 1 2 experiments and in the Rotating Wall Vessel RWV mimicking microgravity on ground Results It was clear that pre- in- and post-flight incubation conditions are critical in spaceflight experiments and should be controlled monitored and taken into account as much as possible when comparing space flight with ground grown cells Distinct changes in physiology and metabolism were observed in the cell cultures grown in space flight when compared to correct ground control cultures A total of 12 proteins over-produced in space conditions were identified and divided in functional groups One group are proteins that protect the cell against physical damage such as heat-shock GrpE UspA and oxidative agents AhpC TrxB DpsA Another group of proteins is probably involved in a metabolic pathway to produce the energy-rich Acetyl-CoA Ald ExaC LpsJ CaiA with the help of a de carboxylase AcxABC Higher concentrations of this group of proteins were also detected in cells grown with acetone or 2-propanol as

  9. Comprehensive insights into the response of Alexandrium tamarense to algicidal component secreted by a marine bacterium.

    PubMed

    Lei, Xueqian; Li, Dong; Li, Yi; Chen, Zhangran; Chen, Yao; Cai, Guanjing; Yang, Xujun; Zheng, Wei; Zheng, Tianling

    2015-01-01

    Harmful algal blooms occur throughout the world, threatening human health, and destroying marine ecosystems. Alexandrium tamarense is a globally distributed and notoriously toxic dinoflagellate that is responsible for most paralytic shellfish poisoning incidents. The culture supernatant of the marine algicidal bacterium BS02 showed potent algicidal effects on A. tamarense ATGD98-006. In this study, we investigated the effects of this supernatant on A. tamarense at physiological and biochemical levels to elucidate the mechanism involved in the inhibition of algal growth by the supernatant of the strain BS02. Reactive oxygen species (ROS) levels increased following exposure to the BS02 supernatant, indicating that the algal cells had suffered from oxidative damage. The levels of cellular pigments, including chlorophyll a and carotenoids, were significantly decreased, which indicated that the accumulation of ROS destroyed pigment synthesis. The decline of the maximum photochemical quantum yield (Fv/Fm) and relative electron transport rate (rETR) suggested that the photosynthesis systems of algal cells were attacked by the BS02 supernatant. To eliminate the ROS, the activities of antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT), increased significantly within a short period of time. Real-time PCR revealed changes in the transcript abundances of two target photosynthesis-related genes (psbA and psbD) and two target respiration-related genes (cob and cox). The transcription of the respiration-related genes was significantly inhibited by the treatments, which indicated that the respiratory system was disturbed. Our results demonstrate that the BS02 supernatant can affect the photosynthesis process and might block the PS II electron transport chain, leading to the production of excessive ROS. The increased ROS can further destroy membrane integrity and pigments, ultimately inducing algal cell death. PMID:25667582

  10. Molecular Stress Responses to Nano-Sized Zero-Valent Iron (nZVI) Particles in the Soil Bacterium Pseudomonas stutzeri

    PubMed Central

    Saccà, Maria Ludovica; Fajardo, Carmen; Martinez-Gomariz, Montserrat; Costa, Gonzalo; Nande, Mar; Martin, Margarita

    2014-01-01

    Nanotoxicological studies were performed in vitro using the common soil bacterium Pseudomonas stutzeri to assess the potentially toxic impact of commercial nano-sized zero-valent iron (nZVI) particles, which are currently used for environmental remediation projects. The phenotypic response of P. stutzeri to nZVI toxicity includes an initial insult to the cell wall, as evidenced by TEM micrographs. Transcriptional analyses using genes of particular relevance in cellular activity revealed that no significant changes occurred among the relative expression ratios of narG, nirS, pykA or gyrA following nZVI exposure; however, a significant increase in katB expression was indicative of nZVI-induced oxidative stress in P. stutzeri. A proteomic approach identified two major defence mechanisms that occurred in response to nZVI exposure: a downregulation of membrane proteins and an upregulation of proteins involved in reducing intracellular oxidative stress. These biomarkers served as early indicators of nZVI response in this soil bacterium, and may provide relevant information for environmental hazard assessment. PMID:24586957

  11. Carboxydothermus siderophilus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic, dissimilatory Fe(III)-reducing bacterium from a Kamchatka hot spring.

    PubMed

    Slepova, Tatiana V; Sokolova, Tatyana G; Kolganova, Tatyana V; Tourova, Tatyana P; Bonch-Osmolovskaya, Elizaveta A

    2009-02-01

    A novel anaerobic, thermophilic, Fe(III)-reducing, CO-utilizing bacterium, strain 1315(T), was isolated from a hot spring of Geyser Valley on the Kamchatka Peninsula. Cells of the new isolate were Gram-positive, short rods. Growth was observed at 52-70 degrees C, with an optimum at 65 degrees C, and at pH 5.5-8.5, with an optimum at pH 6.5-7.2. In the presence of Fe(III) or 9,10-anthraquinone 2,6-disulfonate (AQDS), the bacterium was capable of growth with CO and yeast extract (0.2 g l(-1)); during growth under these conditions, strain 1315(T) produced H(2) and CO(2) and Fe(II) or AQDSH(2), respectively. Strain 1315(T) also grew by oxidation of yeast extract, glucose, xylose or lactate under a N(2) atmosphere, reducing Fe(III) or AQDS. Yeast extract (0.2 g l(-1)) was required for growth. Isolate 1315(T) grew exclusively with Fe(III) or AQDS as an electron acceptor. The generation time under optimal conditions with CO as growth substrate was 9.3 h. The G+C content of the DNA was 41.5+/-0.5 mol%. 16S rRNA gene sequence analysis placed the organism in the genus Carboxydothermus (97.8 % similarity with the closest relative). On the basis of physiological features and phylogenetic analysis, it is proposed that strain 1315(T) should be assigned to a novel species, Carboxydothermus siderophilus sp. nov., with the type strain 1315(T) (=VKPM 9905B(T) =VKM B-2474(T) =DSM 21278(T)). PMID:19196756

  12. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor

    NASA Technical Reports Server (NTRS)

    Myers, Charles R.; Nealson, Kenneth H.

    1988-01-01

    Microbes that couple growth to the reduction of manganese could play an important role in the biogeochemistry of certain anaerobic environments. Such a bacterium, Alteromonas putrefaciens MR-1, couples its growth to the reduction of manganese oxides only under anaerobic conditions. The characteristics of this reduction are consistent with a biological, and not an indirect chemical, reduction of manganese, which suggest that this bacterium uses manganic oxide as a terminal electron acceptor. It can also utilize a large number of other compounds as terminal electron acceptors; this versatility could provide a distinct advantage in environments where electron-acceptor concentrations may vary.

  13. 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

  14. Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium.

    PubMed

    Rivas, Raúl; Mateos, Pedro F; Martínez-Molina, Eustoquio; Velázquez, Encarna

    2005-01-01

    During a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99.3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA-DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C(15 : 0) and C(16 : 0). The DNA G+C content of strain XIL14T was 50.5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and beta-galactosidase. DNA-DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43.3 and 36.3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T). PMID:15653909

  15. 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. PMID:24516572

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

    PubMed

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

    2013-03-01

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

  17. Characterization of a rhodanese from the cyanogenic bacterium Pseudomonas aeruginosa.

    PubMed

    Cipollone, Rita; Bigotti, Maria Giulia; Frangipani, Emanuela; Ascenzi, Paolo; Visca, Paolo

    2004-12-01

    Pseudomonas aeruginosa, the rRNA group I type species of genus Pseudomonas, is a Gram-negative, aerobic bacterium responsible for serious infection in humans. P. aeruginosa pathogenicity has been associated with the production of several virulence factors, including cyanide. Here, the biochemical characterization of recombinant P. aeruginosa rhodanese (Pa RhdA), catalyzing the sulfur transfer from thiosulfate to a thiophilic acceptor, e.g., cyanide, is reported. Sequence homology analysis of Pa RhdA predicts the sulfur-transfer reaction to occur through persulfuration of the conserved catalytic Cys230 residue. Accordingly, the titration of active Pa RhdA with cyanide indicates the presence of one extra sulfur bound to the Cys230 Sgamma atom per active enzyme molecule. Values of K(m) for thiosulfate binding to Pa RhdA are 1.0 and 7.4mM at pH 7.3 and 8.6, respectively, and 25 degrees C. However, the value of K(m) for cyanide binding to Pa RhdA (=14 mM, at 25 degrees C) and the value of V(max) (=750 micromol min(-1)mg(-1), at 25 degrees C) for the Pa RhdA-catalyzed sulfur-transfer reaction are essentially pH- and substrate-independent. Therefore, the thiosulfate-dependent Pa RhdA persulfuration is favored at pH 7.3 (i.e., the cytosolic pH of the bacterial cell) rather than pH 8.6 (i.e., the standard pH for rhodanese activity assay). Within this pH range, conformational change(s) occur at the Pa RhdA active site during the catalytic cycle. As a whole, rhodanese may participate in multiple detoxification mechanisms protecting P. aeruginosa from endogenous and environmental cyanide. PMID:15522204

  18. 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.

  19. Bacterium-Mimicking Nanoparticle Surface Functionalization with Targeting Motifs

    PubMed Central

    Lai, Mei-Hsiu; Clay, Nicholas E.; Kim, Dong Hyun; Kong, Hyunjoon

    2015-01-01

    In recent years, surface modification of nanocarriers with targeting motifs has been explored to modulate delivery of various diagnostic, sensing and therapeutic molecular cargos to desired sites of interest in in vitro bioengineering platforms and in vivo pathologic tissue. However, most surface functionalization approaches are often plagued by complex chemical modifications and effortful purifications. To resolve such challenges, this study demonstrates a unique method to immobilize antibodies that can act as targeting motifs on the surfaces of nanocarriers, inspired by a process that bacteria use for immobilization of the host’s antibodies. We hypothesized that alkylated Staphylococcus aureus protein A (SpA) would self-assemble with micelles and subsequently induce stable coupling of antibodies to the micelles. We examined this hypothesis by using poly(2-hydroxyethyl-co-octadecyl aspartamide) (PHEA-g-C18) as a model polymer to form micelles. The self-assembly between micelles and alkylated SpA became more thermodynamically favorable by increasing the degree of substitution of octadecyl chains to PHEA-g-C18, due to a positive entropy change. Lastly, the simple mixing of SpA-PA-coupled micelles with antibodies resulted in the micelles coated by antibodies, as confirmed with a fluorescence resonance energy transfer (FRET) assay. The micelles coated by antibodies to VCAM-1 or integrin αv displayed higher binding affinity to a substrate coated by VCAM-1 and integrin αvβ3, respectively, than other controls, as evaluated with surface plasmon resonance (SPR) spectroscopy and a circulation-simulating flow chamber. We envisage this bacterium-inspired protein immobilization approach will be useful to improving the quality of targeted delivery of nanoparticles, and can be extended to modify the surface of a wide array of nanocarriers. PMID:25804130

  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. Diversity, Abundance, and Spatial Distribution of Sediment Ammonia-Oxidizing Betaproteobacteria in Response to Environmental Gradients and Coastal Eutrophication in Jiaozhou Bay, China▿ †

    PubMed Central

    Dang, Hongyue; Li, Jing; Chen, Ruipeng; Wang, Lin; Guo, Lizhong; Zhang, Zhinan; Klotz, Martin G.

    2010-01-01

    Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments. PMID:20511433

  2. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NASA Astrophysics Data System (ADS)

    Zheng, Y.; Huang, R.; Wang, B. Z.; Bodelier, P. L. E.; Jia, Z. J.

    2014-03-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and pmoA genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity by 6-fold during a 19 day incubation period, while ammonia oxidation activity was significantly inhibited in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like type Ia MOB, and nitrifying communities appeared to be suppressed by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to equal increase in Methylosarcina and Methylobacter-related MOB, indicating the differential growth requirements of representatives of these genera. Strikingly, type Ib MOB did not respond to methane nor to urea. Increase in 13C-assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, in addition of nitrite-oxidizing

  3. Release of Arsenic from Soil by a Novel Dissimilatory Arsenate-Reducing Bacterium, Anaeromyxobacter sp. Strain PSR-1

    PubMed Central

    Kudo, Keitaro; Yamaguchi, Noriko; Makino, Tomoyuki; Ohtsuka, Toshihiko; Kimura, Kenta; Dong, Dian Tao

    2013-01-01

    A novel arsenate-reducing bacterium, designated strain PSR-1, was isolated from arsenic-contaminated soil. Strain PSR-1 was phylogenetically closely related to Anaeromyxobacter dehalogenans 2CP-1T with 16S rRNA gene similarity of 99.7% and coupled the oxidation of acetate with the reduction of arsenate. Arsenate reduction was inhibited almost completely by respiratory inhibitors such as dicumarol and 2-heptyl-4-hydroxyquinoline N-oxide. Strain PSR-1 also utilized soluble Fe(III), ferrihydrite, nitrate, oxygen, and fumarate as electron acceptors. Strain PSR-1 catalyzed the release of arsenic from arsenate-adsorbed ferrihydrite. In addition, inoculation of washed cells of strain PSR-1 into sterilized soil successfully reproduced arsenic release. Arsenic K-edge X-ray absorption near-edge structure (XANES) analysis revealed that the proportion of arsenite in the soil solid phase actually increased from 20% to 50% during incubation with washed cells of strain PSR-1. These results suggest that strain PSR-1 is capable of reducing not only dissolved arsenate but also arsenate adsorbed on the soil mineral phase. Arsenate reduction by strain PSR-1 expands the metabolic versatility of Anaeromyxobacter dehalogenans. Considering its distribution throughout diverse soils and anoxic sediments, Anaeromyxobacter dehalogenans may play a role in arsenic release from these environments. PMID:23709511

  4. Systems biology defines the biological significance of redox-active proteins during cellulose degradation in an aerobic bacterium.

    PubMed

    Gardner, Jeffrey G; Crouch, Lucy; Labourel, Aurore; Forsberg, Zarah; Bukhman, Yury V; Vaaje-Kolstad, Gustav; Gilbert, Harry J; Keating, David H

    2014-10-01

    Microbial depolymerization of plant cell walls contributes to global carbon balance and is a critical component of renewable energy. The genomes of lignocellulose degrading microorganisms encode diverse classes of carbohydrate modifying enzymes, although currently there is a paucity of knowledge on the role of these proteins in vivo. We report the comprehensive analysis of the cellulose degradation system in the saprophytic bacterium Cellvibrio japonicus. Gene expression profiling of C. japonicus demonstrated that three of the 12 predicted β-1,4 endoglucanases (cel5A, cel5B, and cel45A) and the sole predicted cellobiohydrolase (cel6A) showed elevated expression during growth on cellulose. Targeted gene disruptions of all 13 predicted cellulase genes showed that only cel5B and cel6A were required for optimal growth on cellulose. Our analysis also identified three additional genes required for cellulose degradation: lpmo10B encodes a lytic polysaccharide monooxygenase (LPMO), while cbp2D and cbp2E encode proteins containing carbohydrate binding modules and predicted cytochrome domains for electron transfer. CjLPMO10B oxidized cellulose and Cbp2D demonstrated spectral properties consistent with redox function. Collectively, this report provides insight into the biological role of LPMOs and redox proteins in cellulose utilization and suggests that C. japonicus utilizes a combination of hydrolytic and oxidative cleavage mechanisms to degrade cellulose. PMID:25294408

  5. Community structure of ammonia-oxidizing microorganisms in the Grand Canal, Zhenjiang, of Jiangsu Province, China.

    PubMed

    Liu, Biao; Wu, Chundu; Zhou, Xiaohong

    2014-01-01

    In this study, we simultaneously investigated the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the Grand Canal (the Zhenjiang section). Both clone library and qPCR (quantitative polymerase chain reaction) indicated that the abundance and diversity of AOB were higher than AOA in the Grand Canal for all four seasons. Among the 109 archaeal amoA sequences retrieved, 62.39 and 37.61% fell within the Nitrosopumilus and Nitrososphaera clusters, respectively. The 128 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 81.25 and 18.75% of the AOB group, respectively. The AOA abundance was significantly and positively correlated with the NH4-N. The AOB abundance did not show significant correlations with the measured parameters. Obvious differences were observed for the AOA community compositions obtained from different seasons. The community structure of AOB changed slightly. It indicated that AOB seemed to play a more important role for the nitrification process than AOA in this environment, and was more adapted to this environment. PMID:25259486

  6. Competitive PCR for Quantitation of a Cytophaga-Flexibacter-Bacteroides Phylum Bacterium Associated with the Tuber borchii Vittad. Mycelium

    PubMed Central

    Barbieri, Elena; Riccioni, Giulia; Pisano, Anna; Sisti, Davide; Zeppa, Sabrina; Agostini, Deborah; Stocchi, Vilberto

    2002-01-01

    An uncultured bacterium associated with the ectomycorrhizal fungus Tuber borchii Vittad. was identified as a novel member of the Cytophaga-Flexibacter-Bacteroides group. Utilizing a quantitative PCR targeting the 16S rRNA gene, we relatively quantified this bacterium in the host. The estimated number of bacteria was found to be approximately 106 cells per 30-day-old T. borchii mycelium culture. This represents the first molecular attempt to enumerate an uncultured bacterium associated with a mycorrhizal fungus. PMID:12450871

  7. 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

  8. Photoactive yellow protein from the halophilic bacterium Salinibacter ruber.

    PubMed

    Memmi, Samy; Kyndt, John; Meyer, Terry; Devreese, Bart; Cusanovich, Michael; Van Beeumen, Jozef

    2008-02-19

    A gene for photoactive yellow protein (PYP) was identified from the genome sequence of the extremely halophilic aerobic bacterium Salinibacter ruber (Sr). The sequence is distantly related to the prototypic PYP from Halorhodospira halophila (Hh) (37% identity) and contains most of the amino acid residues identified as necessary for function. However, the Sr pyp gene is not flanked by its two biosynthetic genes as in other species. To determine as to whether the Sr pyp gene encodes a functional protein, we cloned and expressed it in Escherichia coli, along with the genes for chromophore biosynthesis from Rhodobacter capsulatus. The Sr PYP has a 31-residue N-terminal extension as compared to other PYPs that appears to be important for dimerization; however, truncation of these extra residues did not change the spectral and photokinetic properties. Sr PYP has an absorption maximum at 431 nm, which is at shorter wavelengths than the prototypical Hh PYP (at 446 nm). It is also photoactive, being reversibly bleached by either blue or white light. The kinetics of dark recovery is slower than any of the PYPs reported to date (4.27 x 10(-4) s(-1) at pH 7.5). Sr PYP appears to have a normal photocycle with the I1 and I2 intermediates. The presence of the I2' intermediate is also inferred on the basis of the effects of temperature and alchohol on recovery. Sr PYP has an intermediate spectral form in equilibrium with the 431 nm form, similar to R. capsulatus PYP and the Y42F mutant of Hh PYP. Increasing ionic strength stabilizes the 431 nm form at the expense of the intermediate spectral form, and the kinetics of recovery is accelerated 6.4-fold between 0 and 3.5 M salt. This is observed with ions from both the chaotropic and the kosmotropic series. Ionic strength also stabilizes PYP against thermal denaturation, as the melting temperature is increased from 74 degrees C in buffer alone to 92 degrees C in 2 M KCl. Sr accumulates KCl in the cytoplasm, like Halobacterium, to

  9. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

    PubMed Central

    Reis, Mariana P.; Ávila, Marcelo P.; Keijzer, Rosalinde M.; Barbosa, Francisco A. R.; Chartone-Souza, Edmar; Nascimento, Andréa M. A.; Laanbroek, Hendrikus J.

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  10. Nitritation versus full nitrification of ammonium-rich wastewater: comparison in terms of nitrous and nitric oxides emissions.

    PubMed

    Rodriguez-Caballero, A; Ribera, A; Balcázar, J L; Pijuan, M

    2013-07-01

    The processes of nitritation and full nitrification of synthetic reject wastewater were compared in terms of N2O and NO emissions. Two lab-scale sequencing batch reactors (SBR1 and SBR2) were enriched with Nitrosomonas (ammonia-oxidizing bacteria) and Nitrobacter (nitrite-oxidizing bacteria), as shown by fluorescence in situ hybridization (FISH) and high-resolution 16S rRNA tag pyrosequencing. Stable conversion of ammonium to nitrite and nitrite to nitrate was achieved in SBR1 and SBR2 respectively. Biomass from SBR2 was added in SBR1 in order to achieve full nitrification. Under nitritation, 1.22% of the converted-N was emitted as N2O, and 0.066% as NO. During the transition from nitritation to full nitrification, effluent nitrite concentrations decreased but nitrogen oxides were emitted at levels similar to the nitritation period. Gas emissions decreased sharply under full nitrification conditions (0.54% N2O-N/converted-N; 0.021% NO-N/converted-N), probably as a result of the combined effect of lower nitrite and ammonium concentrations in the bioreactor. PMID:23665516

  11. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

    PubMed

    Reis, Mariana P; Ávila, Marcelo P; Keijzer, Rosalinde M; Barbosa, Francisco A R; Chartone-Souza, Edmar; Nascimento, Andréa M A; Laanbroek, Hendrikus J

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  12. Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater ▿

    PubMed Central

    Reed, David W.; Smith, Jason M.; Francis, Christopher A.; Fujita, Yoshiko

    2010-01-01

    To evaluate the potential for organic nitrogen addition to stimulate the in situ growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA amoA genes outnumbering AOB amoA genes in all of the samples. Following urea addition, nitrate levels rose and bacterial amoA copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial amoA diversity was limited to two Nitrosomonas phylotypes, whereas archaeal amoA analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis. PMID:20190081

  13. 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.

  14. Thermodynamic characterization of a tetrahaem cytochrome isolated from a facultative aerobic bacterium, Shewanella frigidimarina: a putative redox model for flavocytochrome c3.

    PubMed Central

    Pessanha, Miguel; Louro, Ricardo O; Correia, Ilídio J; Rothery, Emma L; Pankhurst, Kate L; Reid, Graeme A; Chapman, Stephen K; Turner, David L; Salgueiro, Carlos A

    2003-01-01

    The facultative aerobic bacterium Shewanella frigidimarina produces a small c-type tetrahaem cytochrome (86 residues) under anaerobic growth conditions. This protein is involved in the respiration of iron and shares 42% sequence identity with the N-terminal domain of a soluble flavocytochrome, isolated from the periplasm of the same bacterium, which also contains four c -type haem groups. The thermodynamic properties of the redox centres and of an ionizable centre in the tetrahaem cytochrome were determined using NMR and visible spectroscopy techniques. This is the first detailed thermodynamic study performed on a tetrahaem cytochrome isolated from a facultative aerobic bacterium and reveals that this protein presents unique features. The redox centres have negative and different redox potentials, which are modulated by redox interactions between the four haems (covering a range of 8-56 mV) and by redox-Bohr interactions between the haems and an ionizable centre (-4 to -36 mV) located in close proximity to haem III. All of the interactions between the five centres are clearly dominated by electrostatic effects and the microscopic reduction potential of haem III is the one most affected by the oxidation of the other haems and by the protonation state of the molecule. Altogether, this study indicates that the tetrahaem cytochrome isolated from S. frigidimarina (Sfc) has the thermodynamic properties to work as an electron wire between its redox partners. Considering the high degree of sequence identity between Sfc and the cytochrome domain of flavocytochrome c(3), the structural similarities of the haem core, and that the macroscopic potentials are also identical, the results obtained in this work are rationalized in order to put forward a putative redox model for flavocytochrome c(3). PMID:12413396

  15. Sulfite Oxidation in Chlorobaculum Tepidum

    PubMed Central

    Rodriguez, Jesse; Hiras, Jennifer; Hanson, Thomas E.

    2011-01-01

    The green sulfur bacterium Chlorobaculum tepidum is proposed to oxidize sulfide and elemental sulfur via sulfite as an obligate intermediate. The sulfite pool is predicted to be contained in the cytoplasm and be oxidized by the concerted action of ApsBA, which directly oxidizes sulfite, and QmoABC, which transfers electrons from ApsBA to the quinone pool. Like other green sulfur bacteria, C. tepidum was unable to use exogenously provided sulfite as the sole electron donor. However, exogenous sulfite significantly stimulated the growth yield of sulfide limited batch cultures. The growth of C. tepidum mutant strains, CT0867/qmoB::TnOGm and CT0868/qmoC::TnOGm, was not increased by sulfite. Furthermore, these strains accumulated sulfite and displayed a growth yield decrease when grown on sulfide as the sole electron donor. These results support an obligate, cytoplasmic sulfite intermediate as part of the canonical sulfur oxidation pathway in C. tepidum that requires the Qmo complex for oxidation. PMID:21747809

  16. Metabolic energy from arsenite oxidation in Alcaligenes faecalis

    NASA Astrophysics Data System (ADS)

    Anderson, G. L.; Love, M.; Zeider, B. K.

    2003-05-01

    The aerobic soil bacterium, Alcaligenes faecalis, survives in cultures containing greater than 10 g/L of aqueous arsenic. Toleration of arsenite occurs by the enzymatic oxidation of arsenite (As^III), to the less toxic arsenate (As^V). In defined media, the bacterium grows faster in the presence of arsenite than in its absence. This suggests that the bacterium uses the redox potential of arsenite oxidation as metabolic energy. The oxidation occurs via periplasmic arsenite oxidase, azurin, and cytochrome c [11] which presumably pass electron equivalents through an electron transport chain involving cytochrome c oxidase aud oxygen as the terminal electron acceptor. The associated proton translocation would allow synthesis of ATP and provide a useful means of harnessing the redox potential of arsenite oxidation. Arsenite and arsenate assays of the media during bacterial growth indicate that arsenite is depleted during the exponential growth phase and occurs concomitantly with the expression of arsenite oxidase. These results suggest that arsenite is detoxified to arsenate during bacterial growth and are inconsistent with previous reported interpretations of growth data. Alcaligenes faecalis is dependent on organic carbon sources and is therefore not chemolithoautotrophic. The relationship between succinate and arsenite utilisation provides evidence for the use of arsenite as a supplemental energy source. Because Alcaligenes faecalis not only tolerates, but thrives, in very high concentrations of arsenic has important implications in bioremediation of environments contaminated by aqueous arsenic.

  17. 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

  18. 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.

  19. 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.

  20. A novel marine nitrite-oxidizing Nitrospira species from Dutch coastal North Sea water

    PubMed Central

    Haaijer, Suzanne C. M.; Ji, Ke; van Niftrik, Laura; Hoischen, Alexander; Speth, Daan; Jetten, Mike S. M.; Damsté, Jaap S. Sinninghe; Op den Camp, Huub J. M.

    2013-01-01

    Marine microorganisms are important for the global nitrogen cycle, but marine nitrifiers, especially aerobic nitrite oxidizers, remain largely unexplored. To increase the number of cultured representatives of marine nitrite-oxidizing bacteria (NOB), a bioreactor cultivation approach was adopted to first enrich nitrifiers and ultimately nitrite oxidizers from Dutch coastal North Sea water. With solely ammonia as the substrate an active nitrifying community consisting of novel marine Nitrosomonas aerobic ammonia oxidizers (ammonia-oxidizing bacteria) and Nitrospina and Nitrospira NOB was obtained which converted a maximum of 2 mmol of ammonia per liter per day. Switching the feed of the culture to nitrite as a sole substrate resulted in a Nitrospira NOB dominated community (approximately 80% of the total microbial community based on fluorescence in situ hybridization and metagenomic data) converting a maximum of 3 mmol of nitrite per liter per day. Phylogenetic analyses based on the 16S rRNA gene indicated that the Nitrospira enriched from the North Sea is a novel Nitrospira species with Nitrospira marina as the next taxonomically described relative (94% 16S rRNA sequence identity). Transmission electron microscopy analysis revealed a cell plan typical for Nitrospira species. The cytoplasm contained electron light particles that might represent glycogen storage. A large periplasmic space was present which was filled with electron dense particles. Nitrospira-targeted polymerase chain reaction analyses demonstrated the presence of the enriched Nitrospira species in a time series of North Sea genomic DNA samples. The availability of this new Nitrospira species enrichment culture facilitates further in-depth studies such as determination of physiological constraints, and comparison to other NOB species. PMID:23515432

  1. Effects of Agronomic Treatments on Structure and Function of Ammonia-Oxidizing Communities

    PubMed Central

    Phillips, Carol J.; Harris, Dave; Dollhopf, Sherry L.; Gross, Katherine L.; Prosser, James I.; Paul, Eldor A.

    2000-01-01

    The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the β subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 μg of NH4+-N ml−1, to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function. PMID:11097922

  2. Selective isolation of ammonia-oxidizing bacteria from autotrophic nitrifying granules by applying cell-sorting and sub-culturing of microcolonies

    PubMed Central

    Fujitani, Hirotsugu; Kumagai, Asami; Ushiki, Norisuke; Momiuchi, Kengo; Tsuneda, Satoshi

    2015-01-01

    Nitrification is a key process in the biogeochemical nitrogen cycle and biological wastewater treatment that consists of two stepwise reactions, ammonia oxidation by ammonia-oxidizing bacteria (AOB) or archaea followed by nitrite oxidation by nitrite-oxidizing bacteria. One of the representatives of the AOB group is Nitrosomonas mobilis species. Although a few pure strains of this species have been isolated so far, approaches to their preservation in pure culture have not been established. Here, we report isolation of novel members of the N. mobilis species from autotrophic nitrifying granules used for ammonia-rich wastewater treatment. We developed an isolation method focusing on microcolonies formation of nitrifying bacteria. Two kinds of distinctive light scattering signatures in a cell-sorting system enabled to separate microcolonies from single cells and heterogeneous aggregates within granule samples. Inoculation of a pure microcolony into 96-well microtiter plates led to successful sub-culturing and increased probability of isolation. Obtained strain Ms1 is cultivated in the liquid culture with relatively high ammonia or nitrite concentration, not extremely slow growing. Considering environmental clones that were closely related to N. mobilis and detected in various environments, the availability of this novel strain would facilitate to reveal this member’s ecophysiology in a variety of habitats. PMID:26528282

  3. 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.

  4. Ammonificins C and D, Hydroxyethylamine Chromene Derivatives from a Cultured Marine Hydrothermal Vent Bacterium, Thermovibrio ammonificans

    PubMed Central

    Andrianasolo, Eric H.; Haramaty, Liti; Rosario-Passapera, Richard; Vetriani, Costantino; Falkowski, Paul; White, Eileen; Lutz, Richard

    2012-01-01

    Chemical and biological investigation of the cultured marine hydrothermal vent bacterium, Thermovibrio ammonifican led to the isolation of two hydroxyethylamine chromene derivatives, ammonificins C and D. Their structures were elucidated using combination of NMR and mass spectrometry. Absolute stereochemistry was ascertained by comparison of experimental and calculated CD spectra. Biological evaluation and assessment were determined using the patented ApopScreen cell-based screen for apoptosis-induction. Ammonificins C and D induce apoptosis in micromolar concentrations. To our knowledge, this finding is the first report of chemical compounds that induce apoptosis from the cultured deep-sea marine organism, hydrothermal vent bacterium, Thermovibrio ammonificans. PMID:23170085

  5. From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus Subtilis

    PubMed Central

    Crawshaw, Samuel G.; Wipat, Anil

    2001-01-01

    Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression of Bacillus genes in situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere. PMID:18628943

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

    USGS Publications Warehouse

    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.

  7. Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  8. Halobacterium denitrificans sp. nov. - An extremely halophilic denitrifying bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  9. Carbon monoxide metabolism by the photosynthetic bacterium Rhodospirillum rubrum

    SciTech Connect

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

    1991-01-01

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

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

    PubMed

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

    2012-08-01

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

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

    PubMed

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

    2016-03-01

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

  12. 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

  13. 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

  14. 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

  15. Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

    PubMed Central

    Gkorezis, Panagiotis; Bottos, Eric M.; Van Hamme, Jonathan D.; Thijs, Sofie; Rineau, Francois; Balseiro-Romero, Maria; Weyens, Nele

    2015-01-01

    We report here the 4.7-Mb draft genome of Arthrobacter sp. SPG23, a hydrocarbonoclastic Gram-positive bacterium belonging to the Actinobacteria, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:26701084

  16. Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria

    NASA Astrophysics Data System (ADS)

    Hu, Haiyan; Lin, Hui; Zheng, Wang; Tomanicek, Stephen J.; Johs, Alexander; Feng, Xinbin; Elias, Dwayne A.; Liang, Liyuan; Gu, Baohua

    2013-09-01

    Methylmercury is a neurotoxin that poses significant health risks to humans. Some anaerobic sulphate- and iron-reducing bacteria can methylate oxidized forms of mercury, generating methylmercury. One strain of sulphate-reducing bacteria (Desulfovibrio desulphuricans ND132) can also methylate elemental mercury. The prevalence of this trait among different bacterial strains and species remains unclear, however. Here, we compare the ability of two strains of the sulphate-reducing bacterium Desulfovibrio and one strain of the iron-reducing bacterium Geobacter to oxidize and methylate elemental mercury in a series of laboratory incubations. Experiments were carried out under dark, anaerobic conditions, in the presence of environmentally relevant concentrations of elemental mercury. We report differences in the ability of these organisms to oxidize and methylate elemental mercury. In line with recent findings, we show that D.desulphuricans ND132 can both oxidize and methylate elemental mercury. We find that the rate of methylation of elemental mercury is about one-third the rate of methylation of oxidized mercury. We also show that Desulfovibrio alaskensis G20 can oxidize, but not methylate, elemental mercury. Geobacter sulphurreducens PCA is able to oxidize and methylate elemental mercury in the presence of cysteine. We suggest that the activity of methylating and non-methylating bacteria may together enhance the formation of methylmercury in anaerobic environments.

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

    SciTech Connect

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

    2008-06-30

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

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

    PubMed Central

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

    1986-01-01

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

  19. Reduction of carbon monoxide to formaldehyde by the terminal oxidase of the marine bacterium Pseudomonas nautica strain 617.

    PubMed

    Arnaud, S; Malatesta, F; Denis, M

    1992-01-27

    When exposed to CO, the aerobic respiratory system of the marine bacterium Pseudomonas nautica strain 617, previously reduced with dithionite, undergoes reoxidation. When dealing with the purified oxidase (dithionite reduced) exposure of the enzyme to CO induces its reoxidation (collapse of its alpha band). Under our experimental conditions, this form of the oxidase could not be reduced again by dithionite. Addition of formaldehyde to the native oxidized enzyme resulted in full inhibition of the oxidase reduction by dithionite, presumably due to complex formation. We hypothesized a reduction of CO into formaldehyde and a locking of the active site by the reaction product. By using flash photolysis, it was possible to turn over the enzyme, accumulate the reaction product and identify it as formaldehyde. When using the membrane-bound enzyme, formaldehyde accumulated without the help of flash photolysis. This unusual reduction of CO to formaldehyde could be related to the previously reported uncommon features of the P. nautica oxidase, in particular O2 reduction into H2O2 as end product [(1989) FEBS Lett. 247, 475-479]. PMID:1537399

  20. Anaerobic n-Alkane Metabolism by a Sulfate-Reducing Bacterium, Desulfatibacillum aliphaticivorans Strain CV2803T

    PubMed Central

    Cravo-Laureau, Cristiana; Grossi, Vincent; Raphel, Danielle; Matheron, Robert; Hirschler-Réa, Agnès

    2005-01-01

    The alkane-degrading, sulfate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803T, recently isolated from marine sediments, was investigated for n-alkane metabolism. The total cellular fatty acids of this strain had predominantly odd numbers of carbon atoms (C odd) when the strain was grown on a C-odd alkane (pentadecane) and even numbers of carbon atoms (C even) when it was grown on a C-even alkane (hexadecane). Detailed analyses of those fatty acids by gas chromatography/mass spectrometry allowed us to identify saturated 2-, 4-, 6-, and 8-methyl- and monounsaturated 6-methyl-branched fatty acids, with chain lengths that specifically correlated with those of the alkane. Growth of D. aliphaticivorans on perdeuterated hexadecane demonstrated that those methyl-branched fatty acids were directly derived from the substrate. In addition, cultures on pentadecane and hexadecane produced (1-methyltetradecyl)succinate and (1-methylpentadecyl)succinate, respectively. These results indicate that D. aliphaticivorans strain CV2803T oxidizes n-alkanes into fatty acids anaerobically, via the addition of fumarate at C-2. Based on our observations and on literature data, a pathway for anaerobic n-alkane metabolism by D. aliphaticivorans is proposed. This involves the transformation of the initial alkylsuccinate into a 4-methyl-branched fatty acid which, in addition to catabolic reactions, can alternatively undergo chain elongation and desaturation to form storage fatty acids. PMID:16000749

  1. Effect of oxide formation mechanisms on lead adsorption by biogenic manganese (hydr)oxides, iron (hydr)oxides, and their mixtures.

    PubMed

    Nelson, Yarrow M; Lion, Leonard W; Shuler, Michael L; Ghiorse, William C

    2002-02-01

    The effects of iron and manganese (hydr)oxide formation processes on the trace metal adsorption properties of these metal (hydr)oxides and their mixtures was investigated by measuring lead adsorption by iron and manganese (hydr)oxides prepared by a variety of methods. Amorphous iron (hydr)oxide formed by fast precipitation at pH 7.5 exhibited greater Pb adsorption (gamma(max) = 50 mmol of Pb/mol of Fe at pH 6.0) than iron (hydr)oxide formed by slow, diffusion-controlled oxidation of Fe(II) at pH 4.5-7.0 or goethite. Biogenic manganese(III/IV) (hydr)oxide prepared by enzymatic oxidation of Mn(II) by the bacterium Leptothrix discophora SS-1 adsorbed five times more Pb (per mole of Mn) than an abiotic manganese (hydr)oxide prepared by oxidation of Mn(II) with permanganate, and 500-5000 times more Pb than pyrolusite oxides (betaMnO2). X-ray crystallography indicated that biogenic manganese (hydr)oxide and iron (hydr)oxide were predominantly amorphous or poorly crystalline and their X-ray diffraction patterns were not significantly affected by the presence of the other (hydr)oxide during formation. When iron and manganese (hydr)oxides were mixed after formation, or for Mn biologically oxidized with iron(III) (hydr)oxide present, observed Pb adsorption was similar to that expected for the mixture based on Langmuir parameters for the individual (hydr)oxides. These results indicate that interactions in iron/manganese (hydr)oxide mixtures related to the formation process and sequence of formation such as site masking, alterations in specific surface area, or changes in crystalline structure either did not occur or had a negligible effect on Pb adsorption by the mixtures. PMID:11871557

  2. [Achievement of Sulfate-Reducing Anaerobic Ammonium Oxidation Reactor Started with Nitrate-Reducting Anaerobic Ammonium Oxidation].

    PubMed

    Liu, Zheng-chuan; Yuan, Lin-jiang; Zhou, Guo-biao; Li, Jing

    2015-09-01

    The transformation of nitrite-reducing anaerobic ammonium oxidation to sulfate-reducing anaerobic ammonium oxidation in an UASB was performed and the changes in microbial community were studied. The result showed that the sulfate reducing anaerobic ammonium oxidation process was successfully accomplished after 177 days' operation. The removal rate of ammonium nitrogen and sulfate were up to 58. 9% and 15. 7%, the removing load of ammonium nitrogen and sulfate were 74. 3 mg.(L.d)-1 and 77. 5 mg.(L.d)-1 while concentration of ammonium nitrogen and sulfate of influent were 130 mg.(L.d)-1 and 500 mg.(L.d)-1, respectively. The lost nitrogen and sulphur was around 2 in molar ratio. The pH value of the effluent was lower than that of the influent. Instead of Candidatus brocadia in nitrite reducing anaerobic ammonium oxidation granular sludge, Bacillus benzoevorans became the dominant species in sulfate reducing anaerobic ammonium oxidation sludge. The dominant bacterium in the two kinds of anaerobic ammonium oxidation process is different. Our results imply that the two anaerobic ammonium oxidation processes are carried out by different kind of bacterium. PMID:26717697

  3. Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile.

    PubMed

    Hernández, Marcela; Dumont, Marc G; Calabi, Marcela; Basualto, Daniel; Conrad, Ralf

    2014-02-01

    Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification. PMID:24596264

  4. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay.

    PubMed

    Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Zheng, Wei; Wen, Donghui

    2016-07-01

    The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge. PMID:26960319

  5. 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.

  6. 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. PMID:26853478

  7. 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

  8. Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1

    PubMed Central

    Lanois, Anne; Ogier, Jean-Claude; Gouzy, Jérome; Laroui, Christine; Rouy, Zoé; Givaudan, Alain

    2013-01-01

    We report the 4.3-Mb genome sequence of Xenorhabdus nematophila strain F1, a Gram-negative bacterium that is a symbiont of the entomopathogenic nematode Steinernema carpocapsae and pathogenic by direct injection for a wide variety of insects. PMID:23788541

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

    PubMed

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

    2016-01-01

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

  10. 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

  11. Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential

    PubMed Central

    Zhang, Xiaobo; Zhao, Chungui; Hong, Xuan

    2016-01-01

    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. PMID:27151789

  12. Aerobic mineralization of vinyl chlorides by a bacterium of the order Actinomycetales

    SciTech Connect

    Phelps, T.J.; Malachowsky, K.; Schram, R.M. ); White, D.C. Oak Ridge National Lab., TN )

    1991-04-01

    A gram-positive branched bacterium isolated from a trichloroethylene-degrading consortium mineralized vinyl chloride in growing cultures and cell suspensions. Greater than 67% of the (1,2-{sup 14}C)vinyl chloride was mineralized to carbon dioxide, with approximately 10% of the radioactivity appearing in {sup 14}C-aqueous-phase products.

  13. 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

  14. 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. PMID:27540159

  15. Complete Genome Sequence of Lysinibacillus sphaericus B1-CDA, a Bacterium That Accumulates Arsenic

    PubMed Central

    Rahman, Aminur; Nahar, Noor; Jass, Jana; Olsson, Björn

    2016-01-01

    Here, we report the genomic sequence and genetic composition of an arsenic-resistant bacterium, Lysinibacillus sphaericus B1-CDA. Assembly of the sequencing reads revealed that the genome size is ~4.5 Mb, encompassing ~80% of the chromosomal DNA. PMID:26798084

  16. Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1

    PubMed Central

    Trubitsyn, Denis; Geurink, Corey; Pikuta, Elena; Lefèvre, Christopher T.; McShan, W. Michael; Gillaspy, Allison F.

    2014-01-01

    Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate reduction, was isolated from Mono Lake, California. Here we report the 3.92-Mb draft genome sequence comprising 34 contigs and some results of its automated annotation. These data will improve our knowledge of mechanisms by which bacteria withstand extreme environments. PMID:25081260

  17. 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

  18. 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

  19. Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008

    PubMed Central

    Joshi, M. N.; Pandit, A. S.; Sharma, A.; Pandya, R. V.; Saxena, A. K.

    2013-01-01

    The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production. PMID:23469348

  20. Draft genome sequence of Pontibacter sp. nov. BAB1700, a halotolerant, industrially important bacterium.

    PubMed

    Joshi, M N; Sharma, A C; Pandya, R V; Patel, R P; Saiyed, Z M; Saxena, A K; Bagatharia, S B

    2012-11-01

    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

  1. Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008.

    PubMed

    Joshi, M N; Pandit, A S; Sharma, A; Pandya, R V; Saxena, A K; Bagatharia, S B

    2013-01-01

    The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production. PMID:23469348

  2. 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. PMID:26808869

  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

    2016-01-01

    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. PMID:27151789

  4. Genome Sequence of the Spinosyns-Producing Bacterium Saccharopolyspora spinosa NRRL 18395 ▿

    PubMed Central

    Pan, Yuanlong; Yang, Xi; Li, Jing; Zhang, Ruifen; Hu, Yongfei; Zhou, Yuguang; Wang, Jun; Zhu, Baoli

    2011-01-01

    Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological profile. Here, we present the first draft genome sequence of the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22 scaffolds. PMID:21478350

  5. Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.

    PubMed

    Ho, Ying-Ning; Huang, Chieh-Chen

    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

  6. Draft Genome Sequence and Gene Annotation of the Uropathogenic Bacterium Proteus mirabilis Pr2921

    PubMed Central

    Giorello, F. M.; Romero, V.; Farias, J.; Scavone, P.; Umpiérrez, A.; Zunino, P.

    2016-01-01

    Here, we report the genome sequence of Proteus mirabilis Pr2921, a uropathogenic bacterium that can cause severe complicated urinary tract infections. After gene annotation, we identified two additional copies of ucaA, one of the most studied fimbrial protein genes, and other fimbriae related-proteins that are not present in P. mirabilis HI4320. PMID:27340058

  7. 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.

  8. 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...

  9. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome.

    PubMed

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E; Gómez-Silva, Benito; 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

  10. 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.

  11. Draft Genome Sequence of “Candidatus Phytoplasma pruni” Strain CX, a Plant-Pathogenic Bacterium

    PubMed Central

    Shao, J.; Bottner-Parker, K. D.; Gundersen-Rindal, D. E.; Zhao, Y.; Davis, R. E.

    2015-01-01

    “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, which consists of 598,508 bases, with a G+C content of 27.21 mol%. PMID:26472824

  12. 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. PMID:25521138

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

    PubMed Central

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

    2012-01-01

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

  14. Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

    DOE PAGESBeta

    Thiel, Vera; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Schuster, Stephan C.; Ward, David M.; Bryant, Donald A.

    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.

  15. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower.

    PubMed

    Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; de Souza, Rocheli; Tadra-Sfeir, Michele; Faoro, Helisson; Alvarenga, Samuel M; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M P

    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

  16. 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

  17. Draft Genome Sequence of the Syntrophic Lactate-Degrading Bacterium Tepidanaerobacter syntrophicus JLT

    PubMed Central

    Matsuura, Norihisa; Ohashi, Akiko; Tourlousse, Dieter M.

    2016-01-01

    We report here a high-quality draft genome sequence of the type strain (JL) of Tepidanaerobacter syntrophicus, an obligately anaerobic and moderately thermophilic bacterium, which is able to perform syntrophic lactate degradation with hydrogenotrophic methanogens. The genome comprises 2.43 Mb in 9 scaffolds, with a G+C content of 38.6%. PMID:26868399

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

    PubMed Central

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

    2013-01-01

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

  19. First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T.

    PubMed

    Poehlein, Anja; Friedrich, Ines; Krüger, Larissa; Daniel, Rolf

    2016-01-01

    The moderately thermophilic bacterium Clostridium tepidiprofundi is Gram-positive and belongs to clostridial cluster I. It was isolated from a hydrothermal vent chimney. Substrates utilized by C. tepidiprofundi include casein, peptone, tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome consists of one replicon (3.06 Mb). PMID:27174286

  20. 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...