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Sample records for oxidizing bacterium nitrosomonas

  1. Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia.

    PubMed

    Suwa, Yuichi; Yuichi, Suwa; Norton, Jeanette M; Bollmann, Annette; Klotz, Martin G; Stein, Lisa Y; Laanbroek, Hendrikus J; Arp, Daniel J; Goodwin, Lynne A; Chertkov, Olga; Held, Brittany; Bruce, David; Detter, J Chris; Detter, Janine C; Tapia, Roxanne; Han, Cliff S

    2011-09-01

    Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower K(m)), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide.

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

    PubMed Central

    Kozlowski, Jessica A.; Kits, K. Dimitri

    2016-01-01

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

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

    PubMed

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

    2017-03-16

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed Central

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

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006. PMID:24019993

  6. 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.

  7. 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.

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  10. Effects of Soil and Water Content on Methyl Bromide Oxidation by the Ammonia-Oxidizing Bacterium Nitrosomonas europaea†

    PubMed Central

    Duddleston, Khrystyne N.; Bottomley, Peter J.; Porter, Angela; Arp, Daniel J.

    2000-01-01

    Little information exists on the potential of NH3-oxidizing bacteria to cooxidize halogenated hydrocarbons in soil. A study was conducted to examine the cooxidation of methyl bromide (MeBr) by an NH3-oxidizing bacterium, Nitrosomonas europaea, under soil conditions. Soil and its water content modified the availability of NH4+ and MeBr and influenced the relative rates of substrate (NH3) and cosubstrate (MeBr) oxidations. These observations highlight the complexity associated with characterizing soil cooxidative activities when soil and water interact to differentially affect substrate and cosubstrate availabilities. PMID:10831449

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

    PubMed Central

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

    2016-01-01

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

  12. 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

  13. Effects of selected pharmaceutically active compounds on the ammonia oxidizing bacterium Nitrosomonas europaea.

    PubMed

    Wang, Shuyi; Gunsch, Claudia K

    2011-01-01

    Pharmaceutically active compounds (PhACs) are commonly found in wastewater influent. However, little research has focused on determining their impact on fundamental processes in wastewater treatment such as nitrogen removal. In this study, focus was placed on 4 commonly occurring PhACs (ketoprofen, naproxen, carbamazepine and gemfibrozil). Their effect was ascertained in the ammonia oxidizing bacterium (AOB), Nitrosomonas europaea in terms of membrane integrity and nitrite production. These PhACs were shown to inhibit nitrite production at concentrations of 1 and 10 μM while no effect was observed at 0.1 μM. The maximum observed nitrification inhibition was 25%, 29%, 22% and 26% for ketoprofen, naproxen, carbamazepine and gemfibrozil, respectively. A decrease in the live/dead ratio ranging from 10% to 16% suggests that these PhACs affect membrane integrity in N.europaea. The difference in nitrite production between PhACs treated cells and non PhAC treated controls was still significant following washing suggesting that inhibition is irreversible. Finally, nitrite production when adjusted to the live fraction of cells was also found to decrease suggesting that PhACs inhibited the activity of surviving cells. These results suggest that the presence of PhACs may affect AOB activity and may impact nitrogen removal, a key function in wastewater treatment. Follow up studies with additional AOB and in mixed culture are needed to further confirm these results.

  14. Oxidation of nitrapyrin to 6-chloropicolinic acid by the ammonia-oxidizing bacterium nitrosomonas europaea

    SciTech Connect

    Vannelli, T.; Hooper, A.B.

    1992-07-01

    Suspensions of Nitrosomonas europaea catalyzed the oxidation of the commercial nitrification inhibitor nitrapyrin (2-chloro-6-(trichloromethyl)-pyridine). Rapid oxidation of nitrapyrin (at a concentration of 10 microM) required the concomitant oxidation of ammonia, hydroxylamine, or hydrazine. The turnover rate was highest in the presence of 10 mM ammonia (0.8 nmol of nitrapyrin per min/mg of protein). The product of the reaction was 6-chloropicolinic acid. By the use of (18)O2, it was shown that one of the oxygens in 6-chloropicolinic acid came from diatomic oxygen and that the other came from water. Approximately 13% of the radioactivity of (2,6-(14)C) nitrapyrin was shown to bind to cells. Most (94%) of the latter was bound indiscriminately to membrane proteins. The nitrapyrin bound to membrane proteins may account for the observed inactivation of ammonia oxidation. (Copyright (c) 1992, American Society for Microbiology.)

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

    PubMed

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

    2003-05-01

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

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

    PubMed Central

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

    2003-01-01

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

  17. Degradation of halogenated aliphatic compounds by the ammonia-oxidizing bacterium nitrosomonas europaea

    SciTech Connect

    Vannelli, T.; Logan, M.; Arciero, D.M.; Hooper, A.B. )

    1990-04-01

    Suspensions of Nitrosomonas europaea catalyzed the ammonia-stimulated aerobic transformation of the halogenated aliphatic compounds dichloromethane, dibromomethane, trichloromethane (chloroform), bromoethane, 1,2-dibromoethane (ethylene dibromide), 1,1,2-trichloroethane, 1,1,1-trichloroethane, monochloroethylene (vinyl chloride), gem-dichloroethylene, cis- and trans-dichloroethylene, cis-dibromoethylene, trichloroethylene, and 1,2,3-trichloropropane. Tetrachloromethane (carbon tetrachloride), tetrachloroethylene (perchloroethylene), and trans-dibromoethylene were not degraded.

  18. Degradation of halogenated aliphatic compounds by the ammonia-oxidizing bacterium Nitrosomonas europaea

    SciTech Connect

    Vannelli, T.; Logan, M.; Arciero, D.M.; Hooper, A.B.

    1990-01-01

    Suspensions of Nitrosomonas europaea catalyzed the ammonia-stimulated aerobic transformation of the halogenated aliphatic compounds dichloromethane, dibromomethane, trichloromethane (chloroform), bromoethane, 1,2-dibromoethane (ethylene dibromide), 1,1,2-trichloroethane, 1,1,1-trichloroethane, monochloroethylene (vinyl chloride), gem-dichloroethylene, cis- and trans-dichloroethylene, cis-dibromoethylene, trichloroethylene, and 1,2,3-trichloropropane. Tetrachloromethane (carbon tetrachloride), tetrachloroethylene (perchloroethylene), and trans-dibromoethylene were not degraded.

  19. Evolution and functional characterization of the RH50 gene from the ammonia-oxidizing bacterium Nitrosomonas europaea.

    PubMed

    Cherif-Zahar, Baya; Durand, Anne; Schmidt, Ingo; Hamdaoui, Nabila; Matic, Ivan; Merrick, Mike; Matassi, Giorgio

    2007-12-01

    The family of ammonia and ammonium channel proteins comprises the Amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous Rh proteins (Rh50 and Rh30) that have been described thus far only in eukaryotes. The existence of an RH50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium Nitrosomonas europaea. Here we have used a phylogenetic approach to study the evolution of the N. europaea RH50 gene, and we show that this gene, probably as a component of an integron cassette, has been transferred to the N. europaea genome by horizontal gene transfer. In addition, by functionally characterizing the Rh50(Ne) protein and the corresponding knockout mutant, we determined that NeRh50 can mediate ammonium uptake. The RH50(Ne) gene may thus have replaced functionally the AMT gene, which is missing in the genome of N. europaea and may be regarded as a case of nonorthologous gene displacement.

  20. 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.

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

    PubMed

    Stein, Lisa Y; Arp, Daniel J; Berube, Paul M; Chain, Patrick S G; Hauser, Loren; Jetten, Mike S M; Klotz, Martin G; Larimer, Frank W; Norton, Jeanette M; Op den Camp, Huub J M; Shin, Maria; 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 O(2) 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.

  2. The influence of Corexit 9500A and weathering on Alaska North Slope crude oil toxicity to the ammonia oxidizing bacterium, Nitrosomonas europaea.

    PubMed

    Radniecki, Tyler S; Schneider, Margaret C; Semprini, Lewis

    2013-03-15

    The toxicity of the water associated fraction (WAF) of Alaska North Slope Crude oil (ANSC), Corexit 9500A and the dispersant enhanced WAF (DEWAF) of ANSC:Corexit 9500A mixtures were examined on the model ammonia oxidizing bacterium, Nitrosomonas europaea. Corexit 9500A was not toxic at environmentally relevant concentrations. Corexit 9500A greatly increased the toxicity of ANSC by increasing the chemical oxygen demand (COD) of the DEWAF. However, a majority of the DEWAF compounds were not toxic to N. europaea. Weathered WAF and DEWAF were not toxic to N. europaea even though their COD did not change compared to non-weathered controls, suggesting that toxicity was due to a small volatile fraction of the ANSC. The over-expression of the NE1545 gene, a marker for aromatic hydrocarbon exposure, in N. europaea cells exposed to WAF and DEWAF suggests that aromatic hydrocarbons are bioavailable to the cells and may play a role in the observed toxicity.

  3. 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.

  4. Revision of N2O-Producing Pathways in the Ammonia-Oxidizing Bacterium Nitrosomonas europaea ATCC 19718

    PubMed Central

    Kozlowski, Jessica A.; Price, Jennifer

    2014-01-01

    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

  5. 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.

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

    PubMed Central

    Wahman, David G.; Kirisits, Mary Jo; Katz, Lynn E.; Speitel, Gerald E.

    2011-01-01

    Ammonia-oxidizing bacteria (AOB) in nitrifying biofilters degrading four regulated trihalomethanes—trichloromethane, bromodichloromethane, dibromochloromethane, and tribromomethane—were related to Nitrosomonas oligotropha. N. oligotropha is associated with chloraminated drinking water systems, and its presence in the biofilters might indicate that trihalomethane tolerance is another reason that this bacterium is dominant in chloraminated systems. PMID:21278264

  7. 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

  8. 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.

  9. Identification of the sources of nitrous oxide produced by oxidative and reductive processes in Nitrosomonas europaea

    PubMed Central

    Ritchie, G. A. F.; Nicholas, D. J. D.

    1972-01-01

    1. Cells of Nitrosomonas europaea produced N2O during the oxidation of ammonia and hydroxylamine. 2. The end-product of ammonia oxidation, nitrite, was the predominant source of N2O in cells. 3. Cells also produced N2O, but not N2 gas, by the reduction of nitrite under anaerobic conditions. 4. Hydroxylamine was oxidized by cell-free extracts to yield nitrite and N2O aerobically, but to yield N2O and NO anaerobically. 5. Cell extracts reduced nitrite both aerobically and anaerobically to NO and N2O with hydroxylamine as an electron donor. 6. The relative amounts of NO and N2O produced during hydroxylamine oxidation and/or nitrite reduction are dependent on the type of artificial electron acceptor utilized. 7. Partially purified hydroxylamine oxidase retained nitrite reductase activity but cytochrome oxidase was absent. 8. There is a close association of hydroxylamine oxidase and nitrite reductase activities in purified preparations. PMID:5073730

  10. Construction of recombinant Nitrosomonas europaea expressing green fluorescent protein in response to co-oxidation of chloroform.

    PubMed

    Gvakharia, Barbara O; Bottomley, Peter J; Arp, Daniel J; Sayavedra-Soto, Luis A

    2009-04-01

    Transcriptional fusions with gfp driven by the promoter region of mbla (NE2571) in pPRO/mbla4 and clpB (NE2402) in pPRO/clpb7 were used to transform the ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718). The two genes were chosen because their transcript levels were found at much higher levels in N. europaea in response to oxidation of chloroform and chloromethane. In N. europaea transformed with pPRO/mbla4, green fluorescent protein (GFP)-dependent fluorescence increased from 3- to 18-fold above control levels in response to increasing chloroform concentrations (7 to 28 microM), and from 8- to 10-fold in response to increasing hydrogen peroxide concentrations (2.5-7.5 mM). The GFP-dependent fluorescence of N. europaea transformed with pPRO/clpb7 also showed an increase of 6- to 10-fold in response to chloroform (28-100 microM) but did not respond to H(2)O(2). Our data provide proof of concept that biosensors can be fabricated in ammonia-oxidizing bacteria using "sentinel" genes that up-regulate in response to stress caused either by co-oxidation of chlorinated solvents or by the presence of H(2)O(2). The fabricated biosensors had a consistent concentration-dependent response to chloroform; however, these did not respond to other chlorinated compounds that cause similar cellular stress.

  11. Inhibition of phenol on the rates of ammonia oxidation by Nitrosomonas europaea grown under batch, continuous fed, and biofilm conditions.

    PubMed

    Lauchnor, Ellen G; Semprini, Lewis

    2013-09-01

    Ammonia oxidation by Nitrosomonas europaea, an ammonia oxidizing bacterium prevalent in wastewater treatment, is inhibited in the presence of phenol, due to interaction of the phenol with the ammonia monooxygenase enzyme. Suspended cells of N. europaea were cultured in batch reactors and continuous flow reactors at dilution rates of 0.01-0.2 d(-1). The rate of ammonia oxidation in the continuous cultures correlated to the dilution rate in the reactor. The batch and continuous cultures were exposed to 20 μM phenol and ammonia oxidation activity was measured by specific oxygen uptake rates (SOURs). Inhibition of NH3 oxidation by 20 μM phenol ranged from a 77% reduction of SOUR observed with suspended cells harvested during exponential growth, to 26% in biofilms. The extent of inhibition was correlated with ammonia oxidation rates in both suspended and biofilm cells, with greater percent inhibition observed with higher initial rates of NH3 oxidation. In biofilm grown cells, an increase in activity and phenol inhibition were both observed upon dispersing the biofilm cells into fresh, liquid medium. Under higher oxygen tension, an increase in the NO2(-) production of the biofilms was observed and biofilms were more susceptible to phenol inhibition. Dissolved oxygen microsensor measurements showed oxygen limited conditions existed in the biofilms. The ammonia oxidation rate was much lower in biofilms, which were less inhibited during phenol exposure. The results clearly indicate in both suspended and attached cells of N. europaea that a higher extent of phenol inhibition is positively correlated with a higher rate of NH3 oxidation (enzyme turnover).

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

    PubMed

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

    2011-04-01

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

  13. Methane oxidation by Nitrosococcus oceanus and Nitrosomonas europaea

    SciTech Connect

    Jones, R.D.; Morita, R.Y.

    1983-02-01

    Chemolithotrophic ammonium-oxidizing bacteria were examined as to their ability to oxidize methane in the absence of ammonium or nitrite. The addition of ammonium stimulated both CO/sub 2/ production and cellular incorporation of methane-carbon by N. oceanus and N. europaea. Less than 0.1 mM CH/sub 4/ in solution inhibited the oxidation of ammonium by N. oceanus by 87% but had no inhibitory effects on N. europaea. In the absence of NH/sub 4/-N, N. oceanus achieved a maximum methane oxidation rate of 2.20 x 10/sup -2/ ..mu..mol of CH/sub 4/ h/sup -1/ mg (dry weight) of cells/sup -1/, which remained constant as the methane concentration was increased. In the presence of NH/sub 4/-N (10 ppm (10 ..mu..g/ml)), its maximum rate was 26.4 x 10/sup -2/ ..mu..mol of CH/sub 4/ h/sup -1/ mg (dry weight) of cells/sup -1/ at a methane concentration of 1.19 x 10/sup -1/ mM. Increasing the methane concentrations above this level decreased CO/sub 2/ production, whereas cellular incorporation of methane-carbon continued to increase. N. europaea showed a linear response throughout the test range, with an activity of 196.0 x 10/sup -2/ ..mu..mol of CH/sub 4/ h/sup -1/ mg (dry weight) of cells/sup -1/ at a methane concentration of 1.38 x 10/sup -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. (JMT)

  14. Respiration-dependent proton translocation in Nitrosomonas europaea and its apparent absence in Nitrobacter agilis during inorganic oxidations.

    PubMed Central

    Hollocher, T C; Kumar, S; Nicholas, D J

    1982-01-01

    Oxygen pulse experiments were carried out with the nitrifying bacteria Nitrosomonas europaea and Nitrobacter agilis and with spheroplasts and everted vesicles prepared from Nitrobacter agilis. In addition to thiocyanate, the salting-in anions perchlorate and trichloroacetate proved to be permeant and effective in allowing respiration-dependent proton translocation with Nitrosomonas europaea. Valinomycin-K+, however, was generally ineffective in this respect with Nitrosomonas europaea. The observed leads to H+/O ratio for ammonium ion oxidation by Nitrosomonas europaea was 3.4; that for hydroxylamine and hydrazine cation oxidation was 4.4. These values, when corrected for production of stoichiometric protons and for the fact that the first step in ammonium ion oxidation (hydroxylamine production) is mediated by a monooxygenase, give effective leads to H+/O ratios of about 4 for these three substrates. This value compares favorably with those obtained with other aerobes. No convincing evidence was obtained for operation of a respiratory proton pump in Nitrobacter agilis during nitrite oxidation. Implications of this unexpected result are discussed. PMID:6277846

  15. Nitrosomonas europaea cytochrome P460 is a direct link between nitrification and nitrous oxide emission.

    PubMed

    Caranto, Jonathan D; Vilbert, Avery C; Lancaster, Kyle M

    2016-12-20

    Ammonia oxidizing bacteria (AOB) are major contributors to the emission of nitrous oxide (N2O). It has been proposed that N2O is produced by reduction of NO. Here, we report that the enzyme cytochrome (cyt) P460 from the AOB Nitrosomonas europaea converts hydroxylamine (NH2OH) quantitatively to N2O under anaerobic conditions. Previous literature reported that this enzyme oxidizes NH2OH to nitrite ([Formula: see text]) under aerobic conditions. Although we observe [Formula: see text] formation under aerobic conditions, its concentration is not stoichiometric with the NH2OH concentration. By contrast, under anaerobic conditions, the enzyme uses 4 oxidizing equivalents (eq) to convert 2 eq of NH2OH to N2O. Enzyme kinetics coupled to UV/visible absorption and electron paramagnetic resonance (EPR) spectroscopies support a mechanism in which an Fe(III)-NH2OH adduct of cyt P460 is oxidized to an {FeNO}(6) unit. This species subsequently undergoes nucleophilic attack by a second equivalent of NH2OH, forming the N-N bond of N2O during a bimolecular, rate-determining step. We propose that [Formula: see text] results when nitric oxide (NO) dissociates from the {FeNO}(6) intermediate and reacts with dioxygen. Thus, [Formula: see text] is not a direct product of cyt P460 activity. We hypothesize that the cyt P460 oxidation of NH2OH contributes to NO and N2O emissions from nitrifying microorganisms.

  16. Transformations of aromatic compounds by nitrosomonas europaea

    SciTech Connect

    Keener, W.K.; Arp, D.J.

    1994-06-01

    The soil bacterium Nitrosomonas europaea is an obligate autotroph which uses O2 as an electron acceptor and ammonia as its sole natural energy source. The ubiquity of nitrifying bacteria may facilitate their use in bioremediation applications, but such applications will require a thorough knowledge of the substrate range of Ammonia monooxygenase (AMO) (catalyzing the oxidation of ammonia). This study extends the know substrate range of N. europaea to include alkylbenzenes, halobenzenes, and various N- and O-containing aromatics. Evidence is also presented that oxidation of p-cresol and ring-substituted benzylic alcohols to corresponding aldehydes joccures even in the absence of AMO activity. 33 refs., 7 figs.

  17. Role of nitrite reductase in the ammonia-oxidizing pathway of Nitrosomonas europaea.

    PubMed

    Cantera, J Jason L; Stein, Lisa Y

    2007-10-01

    Metabolism of ammonia (NH(3)) and hydroxylamine (NH(2)OH) by wild-type and a nitrite reductase (nirK) deficient mutant of Nitrosomonas europaea was investigated to clarify the role of NirK in the NH(3) oxidation pathway. NirK-deficient N. europaea grew more slowly, consumed less NH(3), had a lower rate of nitrite (NO(2) (-)) production, and a significantly higher rate of nitrous oxide (N(2)O) production than the wild-type when incubated with NH(3) under high O(2) tension. In incubations with NH(3) under low O(2) tension, NirK-deficient N. europaea grew more slowly, but had only modest differences in NH(3) oxidation and product formation rates relative to the wild-type. In contrast, the nirK mutant oxidized NH(2)OH to NO(2) (-) at consistently slower rates than the wild-type, especially under low O(2) tension, and lost a significant pool of NH(2)OH-N to products other than NO(2) (-) and N(2)O. The rate of N(2)O production by the nirK mutant was ca. three times higher than the wild-type during hydrazine-dependent NO(2) (-) reduction under both high and low O(2) tension. Together, the results indicate that NirK activity supports growth of N. europaea by supporting the oxidation of NH(3) to NO(2) (-) via NH(2)OH, and stimulation of hydrazine-dependent NO(2) (-) reduction by NirK-deficient N. europaea indicated the presence of an alternative, enzymatic pathway for N(2)O production.

  18. Effect of Low-Density Static Magnetic Field on the Oxidation of Ammonium by Nitrosomonas europaea and by Activated Sludge in Municipal Wastewater.

    PubMed

    Filipič, Jasmina; Kraigher, Barbara; Tepuš, Brigita; Kokol, Vanja; Mandić-Mulec, Ines

    2015-06-01

    Ammonium removal is a key step in biological wastewater treatment and novel approaches that improve this process are in great demand. The aim of this study is to test the hypothesis that ammonium removal from wastewater can be stimulated by static magnetic fields. This was achieved by analysis of the effects of static magnetic field (SMF) on the growth and activity of Nitrosomonas europaea, a key ammonia-oxidising bacterium, where increased growth and increased ammonia oxidation rate were detected when bacteria were exposed to SMF at 17 mT. Additionally, the effect of SMF on mixed cultures of ammonia oxidisers in activated sludge, incubated in sequencing batch bioreactors simulating wastewater treatment process, was assessed. SMFs of 30 and 50 mT, but not of 10 mT, increased ammonium oxidation rate in municipal wastewater by up to 77% and stimulated ammonia oxidiser growth. The results demonstrate the potential for use of static magnetic fields in increasing ammonium removal rates in biological wastewater treatment plants.

  19. 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...

  20. Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea

    PubMed Central

    Giguere, Andrew; Chaplen, Frank; Bottomley, Peter J.

    2016-01-01

    ABSTRACT Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2) and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2. IC-limited cultures oxidized 25 to 58% of available NH3 to nitrite, depending on the dilution rate and Na2CO3 concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH3-limited cultures. Rates of N2O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH3-N that was transformed to N2O-N from 0.5% (replete) up to 4.4% (0.2 mM Na2CO3). Transcriptome analysis showed differential expression (P ≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C1 metabolism, including the genes for RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N2O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH3 oxidation from growth and increased N2O production. IMPORTANCE Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent

  1. Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment.

    PubMed

    Urakawa, Hidetoshi; Garcia, Juan C; Nielsen, Jeppe L; Le, Vang Q; Kozlowski, Jessica A; Stein, Lisa Y; Lim, Chee Kent; Pommerening-Röser, Andreas; Martens-Habbena, Willm; Stahl, David A; Klotz, Martin G

    2015-01-01

    A Gram-negative, spiral-shaped, chemolithotrophic, ammonia-oxidizing bacterium, designated APG3(T), was isolated into pure culture from sandy lake sediment collected from Green Lake, Seattle, WA, USA. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain APG3(T) belongs to cluster 0 of the genus Nitrosospira, which is presently not represented by described species, with Nitrosospira multiformis (cluster 3) as the closest species with a validly published name (identity of 98.6 % to the type strain). Strain APG3(T) grew at 4 °C but could not grow at 35 °C, indicating that this bacterium is psychrotolerant. Remarkably, the strain was able to grow over a wide range of pH (pH 5-9), which was greater than the pH range of any studied ammonia-oxidizing bacteria in pure culture. The DNA G+C content of the APG3(T) genome is 53.5 %, which is similar to that of Nitrosospira multiformis ATCC 25196(T) (53.9 %) but higher than that of Nitrosomonas europaea ATCC 19718 (50.7 %) and Nitrosomonas eutropha C71 (48.5 %). The average nucleotide identity (ANI) calculated for the genomes of strain APG3(T) and Nitrosospira multiformis ATCC 25196(T) was 75.45 %, significantly lower than the value of 95 % ANI that corresponds to the 70 % species-level cut-off based on DNA-DNA hybridization. Overall polyphasic taxonomy study indicated that strain APG3(T) represents a novel species in the genus Nitrosospira, for which the name Nitrosospira lacus sp. nov. is proposed (type strain APG3(T) = NCIMB 14869(T) = LMG 27536(T) = ATCC BAA-2542(T)).

  2. Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants.

    PubMed

    Schmidt, Ingo; van Spanning, Rob J M; Jetten, Mike S M

    2004-12-01

    The phenotypes of three different Nitrosomonas europaea strains--wild-type, nitrite reductase (NirK)-deficient and nitric oxide reductase (NorB)-deficient strains--were characterized in chemostat cell cultures, and the effect of nitric oxide (NO) on metabolic activities was evaluated. All strains revealed similar aerobic ammonia oxidation activities, but the growth rates and yields of the knock-out mutants were significantly reduced. Dinitrogen (N2) was the main gaseous product of the wild-type, produced via its denitrification activity. The mutants were unable to reduce nitrite to N2, but excreted more hydroxylamine leading to the formation of almost equal amounts of NO, nitrous oxide (N2O) and N2 by chemical auto-oxidation and chemodenitrification of hydroxylamine. Under anoxic conditions Nsm. europaea wild-type gains energy for growth via nitrogen dioxide (NO2)-dependent ammonia oxidation or hydrogen-dependent denitrification using nitrite as electron acceptor. The mutant strains were restricted to NO and/or N2O as electron acceptor and consequently their growth rates and yields were much lower compared with the wild-type. When cells were transferred from anoxic (denitrification) to oxic conditions, the wild-type strain endogenously produced NO and recovered ammonia oxidation within 8 h. In contrast, the mutant strains remained inactive. For recovery of ammonia oxidation activity the NO concentration had to be adjusted to about 10 p.p.m. in the aeration gas.

  3. A rapid and simple respirometric biosensor with immobilized cells of Nitrosomonas europaea for detecting inhibitors of ammonia oxidation.

    PubMed

    Cui, Rong; Chung, Wook-Jin; Jahng, Deokjin

    2005-03-15

    As obligate chemolithotrophs, ammonia-oxidizing bacteria (AOB) grow very slowly and are known to be extremely sensitive to a wide variety of inhibitors. Since it is generally accepted that inhibition of ammonia oxidation by AOB results in a total failure of nitrogen removal, it is necessary to develop a method to detect inhibitors of ammonia oxidation in wastewater. Since ammonia oxidation accompanies oxygen consumption, ammonia oxidation can be easily evaluated by measuring oxygen consumption rate using a dissolved oxygen (DO) probe. In this study, a rapid and simple respirometric biosensor using the pure culture of Nitrosomonas europaea was developed. N. europaea was cultivated in a continuous fermentor operating at the dilution rate of 0.008 h(-1) to obtain physiologically constant cells and was immobilized onto the dialysis membrane through filtration. DO, determined by the biosensor, started to increase 30 s later after ammonia oxidation inhibitor was fed, and a new steady-state DO was obtained in 10-30 min. For this DO profile, steady-state kinetics was applied to evaluate ammonia oxidation efficiency. The concentration of a toxic compound causing 50% decrease of oxygen-consumption activity (EC50) was determined for different chemicals. The EC50 values obtained with the biosensor (0.018 mg l(-1) for allylthiourea, 0.027 mg l(-1) for thioacetamide, 1.10 mg l(-1) for phenol and 0.0 1mg l(-1) for thiourea) indicated that the developed biosensor was highly sensitive to a variety of the inhibitors. It was also shown that the biosensor is applicable for on-line real time monitoring.

  4. Complete Genome Sequence of Nitrosospira multiformis, an Ammonia-Oxidizing Bacterium from the Soil Environment▿ †

    PubMed Central

    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.

    2008-01-01

    The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196T) 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

  5. Effects of Soil on Ammonia, Ethylene, Chloroethane, and 1,1,1-Trichloroethane Oxidation by Nitrosomonas europaea†

    PubMed Central

    Hommes, Norman G.; Russell, Sterling A.; Bottomley, Peter J.; Arp, Daniel J.

    1998-01-01

    Ammonia monooxygenase (AMO) from Nitrosomonas europaea catalyzes the oxidation of ammonia to hydroxylamine and has been shown to oxidize a variety of halogenated and nonhalogenated hydrocarbons. As part of a program focused upon extending these observations to natural systems, a study was conducted to examine the influence of soil upon the cooxidative abilities of N. europaea. Small quantities of Willamette silt loam (organic carbon content, 1.8%; cation-exchange capacity, 15 cmol/kg of soil) were suspended with N. europaea cells in a soil-slurry-type reaction mixture. The oxidations of ammonia and three different hydrocarbons (ethylene, chloroethane, and 1,1,1-trichloroethane) were compared to results for controls in which no soil was added. The soil significantly inhibited nitrite production from 10 mM ammonium by N. europaea. Inhibition resulted from a combination of ammonium adsorption onto soil colloids and the exchangeable acidity of the soil lowering the pH of the reaction mixture. These phenomena resulted in a substantial drop in the concentration of NH4+ in solution (10 to 4.5 mM) and, depending upon the pH, in a reduction in the amount of available NH3 to concentrations (8 to 80 μM) similar to the Ks value of AMO for NH3 (∼29 μM). At a fixed initial pH (7.8), the presence of soil also modified the rates of oxidation of ethylene and chloroethane and changed the concentrations at which their maximal rates of oxidation occurred. The modifying effects of soil on nitrite production and on the cooxidation of ethylene and chloroethane could be circumvented by raising the ammonium concentration in the reaction mixture from 10 to 50 mM. Soil had virtually no effect on the oxidation of 1,1,1-trichloroethane. PMID:16349541

  6. Testing Silver Nanoparticle Toxicity Using the Ammonia Oxidizing Bacteria Nitrosomonas Europaea and a High-throughput Assay

    NASA Astrophysics Data System (ADS)

    Semprini, L.; Bartow, S.; Radniecki, T.

    2012-04-01

    Understanding the toxicity of nanoparticles on ecologically significant wastewater microbiota, specifically ammonia oxidizing bacteria (AOB), is critical due to the exponential increase in commercialization of nanoparticles as well as the sensitivity of AOB to inhibitors. A high-throughput activity assay was developed to rapidly screen for nanoparticle toxicity on AOB, using a multi-well plate method and AOB Nitrosomonas Europaea. This method demonstrated good agreement with previously established batch bottle assays utilizing both silver ions (Ag+) and nanoparticles (Ag-NPs) as nitrification inhibitors. The method was used to study the inhibition of Ag+ and Ag-NPs (20 nm) on the nitrification by N. Europaea cells grown in fill-and-draw reactors compared exponentially grown batch cells. Results indicate longer hydraulic residence times increased some protection against inhibition as measured by the production of nitrite over a three hour assay. The cells were more sensitive to Ag+ than Ag-NP, which is consistent with our past observations. Studies are currently being conducted to determine the effects that the presence of humic acid and cations on the inhibition and toxicity. Our initial results show that the presence of Mg++ provides protect from Ag-NP inhibition, which partly results from the aggregation of the Ag-NP and a decrease in the rate of oxidation of the Ag-NP to Ag+. The presence of humic acid also provides for some protection from Ag-NP inhibition.

  7. Physiologic and proteomic evidence for a role of nitric oxide in biofilm formation by Nitrosomonas europaea and other ammonia oxidizers.

    PubMed

    Schmidt, Ingo; Steenbakkers, Peter J M; op den Camp, Huub J M; Schmidt, Katrin; Jetten, Mike S M

    2004-05-01

    NO, a free radical gas, is the signal for Nitrosomonas europaea cells to switch between different growth modes. At an NO concentration of more than 30 ppm, biofilm formation by N. europaea was induced. NO concentrations below 5 ppm led to a reversal of the biofilm formation, and the numbers of motile and planktonic (motile-planktonic) cells increased. In a proteomics approach, the proteins expressed by N. europaea were identified. Comparison studies of the protein patterns of motile-planktonic and attached (biofilm) cells revealed several clear differences. Eleven proteins were found to be up or down regulated. Concentrations of other compounds such as ammonium, nitrite, and oxygen as well as different temperatures and pH values had no significant effect on the growth mode of and the proteins expressed by N. europaea.

  8. Physiologic and Proteomic Evidence for a Role of Nitric Oxide in Biofilm Formation by Nitrosomonas europaea and Other Ammonia Oxidizers

    PubMed Central

    Schmidt, Ingo; Steenbakkers, Peter J. M.; op den Camp, Huub J. M.; Schmidt, Katrin; Jetten, Mike S. M.

    2004-01-01

    NO, a free radical gas, is the signal for Nitrosomonas europaea cells to switch between different growth modes. At an NO concentration of more than 30 ppm, biofilm formation by N. europaea was induced. NO concentrations below 5 ppm led to a reversal of the biofilm formation, and the numbers of motile and planktonic (motile-planktonic) cells increased. In a proteomics approach, the proteins expressed by N. europaea were identified. Comparison studies of the protein patterns of motile-planktonic and attached (biofilm) cells revealed several clear differences. Eleven proteins were found to be up or down regulated. Concentrations of other compounds such as ammonium, nitrite, and oxygen as well as different temperatures and pH values had no significant effect on the growth mode of and the proteins expressed by N. europaea. PMID:15090520

  9. Physiological state, growth mode, and oxidative stress play a role in Cd(II)-mediated inhibition of Nitrosomonas europaea 19718.

    PubMed

    Chandran, Kartik; Love, Nancy G

    2008-04-01

    The goal of this study was to determine the impact of physiological growth states (batch exponential and batch stationary growth) and growth modes (substrate-limited chemostat, substrate-sufficient exponential batch, and substrate-depleted stationary batch growth) on several measures of growth and responses to Cd(II)-mediated inhibition of Nitrosomonas europaea strain 19718. The specific oxygen uptake rate (sOUR) was the most sensitive indicator of inhibition among the different responses analyzed, including total cell abundance, membrane integrity, intracellular 16S rRNA/DNA ratio, and amoA expression. This observation remained true irrespective of the physiological state, the growth mode, or the mode of Cd(II) exposure. Based on the sOUR, a strong time-dependent exacerbation of inhibition (in terms of an inhibition coefficient [K(i)]) in exponential batch cultures was observed. Long-term inhibition levels (based on K(i) estimates) in metabolically active chemostat and exponential batch cultures were also especially severe and comparable. In contrast, the inhibition level in stationary-phase cultures was 10-fold lower and invariable with exposure time. Different strategies for surviving substrate limitation (a 10-fold increase in amoA expression) and starvation (the retention of 16S rRNA levels) in N. europaea cultures were observed. amoA expression was most negatively impacted by Cd(II) exposure in the chemostat cultures, was less impacted in exponential batch cultures, and was least impacted in stationary batch cultures. Although the amoA response was consistent with that of the sOUR, the amoA response was not as strong. The intracellular 16S rRNA/DNA ratio, as determined by fluorescence in situ hybridization, also did not uniformly correlate with the sOUR under conditions of inhibition or no inhibition. Finally, Cd(II)-mediated inhibition of N. europaea was attributed partially to oxidative stress.

  10. Membrane tetraheme cytochrome c(m552) of the ammonia-oxidizing nitrosomonas europaea: a ubiquinone reductase.

    PubMed

    Kim, Hyung J; Zatsman, Anna; Upadhyay, Anup K; Whittaker, Mark; Bergmann, David; Hendrich, Michael P; Hooper, Alan B

    2008-06-24

    Cytochrome c(m552) (cyt c(m552)) from the ammonia-oxidizing Nitrosomonas europaea is encoded by the cycB gene, which is preceded in a gene cluster by three genes encoding proteins involved in the oxidation of hydroxylamine: hao, hydroxylamine oxidoreductase; orf2, a putative membrane protein; cycA, cyt c(554). By amino acid sequence alignment of the core tetraheme domain, cyt c(m552) belongs to the NapC/TorC family of tetra- or pentaheme cytochrome c species involved in electron transport from membrane quinols to a variety of periplasmic electron shuttles leading to terminal reductases. However, cyt c(m552) is thought to reduce quinone with electrons originating from HAO. In this work, the tetrahemic 27 kDa cyt c(m552) from N. europaea was purified after extraction from membranes using Triton X-100 with subsequent exchange into n-dodecyl beta-d-maltoside. The cytochrome had a propensity to form strong SDS-resistant dimers likely mediated by a conserved GXXXG motif present in the putative transmembrane segment. Optical spectra of the ferric protein contained a broad ligand-metal charge transfer band at approximately 625 nm indicative of a high-spin heme. Mossbauer spectroscopy of the reduced (57)Fe-enriched protein revealed the presence of high-spin and low-spin hemes in a 1:3 ratio. Multimode EPR spectroscopy of the native state showed signals from an electronically interacting high-spin/low-spin pair of hemes. Upon partial reduction, a typical high-spin heme EPR signal was observed. No EPR signals were observed from the other two low-spin hemes, indicating an electronic interaction between these hemes as well. UV-vis absorption data indicate that CO (ferrous enzyme) or CN(-) (ferric or ferrous enzyme) bound to more than one and possibly all hemes. Other anionic ligands did not bind. The four ferrous hemes of the cytochrome were rapidly oxidized in the presence of oxygen. Comparative modeling, based on the crystal structure and conserved residues of the homologous

  11. 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...

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

    SciTech Connect

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

    2008-01-01

    The complete genome of the ammonia-oxidizing bacterium, Nitrosospira multiformis (ATCC 25196T), consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2827 putative proteins. Of these, 2026 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 N. eutropha were the best match for 42% of the predicted genes in N. multiformis. The genome contains three nearly identical copies of amo and hao gene clusters as large repeats. Distinguishing features compared to N. europaea include: the presence of gene clusters encoding urease and hydrogenase, a RuBisCO-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 AOB genomes. 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 towards 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.

  13. Chemoorganoheterotrophic growth of Nitrosomonas europaea and Nitrosomonas eutropha.

    PubMed

    Schmidt, Ingo

    2009-08-01

    The ammonia oxidizers Nitrosomonas europaea and Nitrosomonas eutropha are able to grow chemoorganotrophically under anoxic conditions with pyruvate, lactate, acetate, serine, succinate, alpha-ketoglutarate, or fructose as substrate and nitrite as terminal electron acceptor. The growth yield of both bacteria is about 3.5 mg protein (mmol pyruvate)(-1) and the maximum growth rates of N. europaea and N. eutropha are 0.094 d(-1) and 0.175 d(-1), respectively. In the presence of pyruvate and CO2 about 80% of the incorporated carbon derives from pyruvate and about 20% from CO2. Pyruvate is used as energy and only carbon source in the absence of CO2 (chemoorganoheterotrophic growth). CO2 stimulates the chemoorganotrophic growth of both ammonia oxidizers and the expression of ribulose bisphosphate carboxylase/oxygenase is down-regulated at increasing CO2 concentration. Ammonium, although required as nitrogen source, is inhibitory for the chemoorganotrophic metabolism of N. europaea and N. eutropha. In the presence of ammonium pyruvate consumption and the expression of the genes aceE, ppc, gltA, odhA, and ppsA (energy conservation) as well as nirK, norB, and nsc (denitrification) are reduced.

  14. The transcription of the cbb operon in Nitrosomonas europaea.

    PubMed

    Wei, Xueming; Sayavedra-Soto, Luis A; Arp, Daniel J

    2004-06-01

    Nitrosomonas europaea is an aerobic ammonia-oxidizing bacterium that participates in the C and N cycles. N. europaea utilizes CO(2) as its predominant carbon source, and is an obligate chemolithotroph, deriving all the reductant required for energy and biosynthesis from the oxidation of ammonia (NH(3)) to nitrite (). This bacterium fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). The RubisCO operon is composed of five genes, cbbLSQON. This gene organization is similar to that of the operon for 'green-like' type I RubisCOs in other organisms. The cbbR gene encoding the putative regulatory protein for RubisCO transcription was identified upstream of cbbL. This study showed that transcription of cbb genes was upregulated when the carbon source was limited, while amo, hao and other energy-harvesting-related genes were downregulated. N. europaea responds to carbon limitation by prioritizing resources towards key components for carbon assimilation. Unlike the situation for amo genes, NH(3) was not required for the transcription of the cbb genes. All five cbb genes were only transcribed when an external energy source was provided. In actively growing cells, mRNAs from the five genes in the RubisCO operon were present at different levels, probably due to premature termination of transcription, rapid mRNA processing and mRNA degradation.

  15. 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.

  16. Quantification of Nitrosomonas oligotropha-Like Ammonia-Oxidizing Bacteria and Nitrospira spp. from Full-Scale Wastewater Treatment Plants by Competitive PCR

    PubMed Central

    Dionisi, Hebe M.; Layton, Alice C.; Harms, Gerda; Gregory, Igrid R.; Robinson, Kevin G.; Sayler, Gary S.

    2002-01-01

    Utilizing the principle of competitive PCR, we developed two assays to enumerate Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and nitrite-oxidizing bacteria belonging to the genus Nitrospira. The specificities of two primer sets, which were designed for two target regions, the amoA gene and Nitrospira 16S ribosomal DNA (rDNA), were verified by DNA sequencing. Both assays were optimized and applied to full-scale, activated sludge wastewater treatment plant (WWTP) samples. If it was assumed that there was an average of 3.6 copies of 16S rDNA per cell in the total population and two copies of the amoA gene per ammonia-oxidizing bacterial cell, the ammonia oxidizers examined represented 0.0033% ± 0.0022% of the total bacterial population in a municipal WWTP. N. oligotropha-like ammonia-oxidizing bacteria were not detected in an industrial WWTP. If it was assumed that there was one copy of the 16S rDNA gene per nitrite-oxidizing bacterial cell, Nitrospira spp. represented 0.39% ± 0.28% of the biosludge population in the municipal WWTP and 0.37% ± 0.23% of the population in the industrial WWTP. The number of Nitrospira sp. cells in the municipal WWTP was more than 62 times greater than the number of N. oligotropha-like cells, based on a competitive PCR analysis. The results of this study extended our knowledge of the comparative compositions of nitrifying bacterial populations in wastewater treatment systems. Importantly, they also demonstrated that we were able to quantify these populations, which ultimately will be required for accurate prediction of process performance and stability for cost-effective design and operation of WWTPs. PMID:11772633

  17. 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.

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

    PubMed

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

    2006-11-01

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

  19. Global analysis of the Nitrosomonas europaea iron starvation stimulon.

    PubMed

    Vajrala, Neeraja; Sayavedra-Soto, Luis A; Bottomley, Peter J; Arp, Daniel J

    2012-04-01

    The importance of iron to the metabolism of the ammonia-oxidizing bacterium Nitrosomonas europaea is well known. However, the mechanisms by which N. europaea acquires iron under iron limitation are less well known. To obtain insight into these mechanisms, transcriptional profiling of N. europaea was performed during growth under different iron availabilities. Of 2,355 N. europaea genes on DNA microarrays, transcripts for 247 genes were identified as differentially expressed when cells were grown under iron limitation compared to cells grown under iron-replete conditions. Genes with higher transcript levels in response to iron limitation included those with confirmed or assigned roles in iron acquisition. Genes with lower transcript levels included those encoding iron-containing proteins. Our analysis identified several potentially novel iron acquisition systems in N. europaea and provided support for the primary involvement of a TonB-dependent heme receptor gene in N. europaea iron homeostasis. We demonstrated that hemoglobin can act as an iron source under iron-depleted conditions for N. europaea. In addition, we identified a hypothetical protein carrying a lipocalin-like domain that may have the ability to chelate iron for growth in iron-limited media.

  20. Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea.

    PubMed

    Gvakharia, Barbara O; Tjaden, Brian; Vajrala, Neeraja; Sayavedra-Soto, Luis A; Arp, Daniel J

    2010-11-01

    Bacterial small noncoding RNAs (sRNAs) have been discovered in many genetically well-studied microorganisms and have been shown to regulate critical cellular processes at the post-transcriptional level. In this study, we used comparative genomics and microarray data to analyze the genome of the ammonia-oxidizing bacterium Nitrosomonas europaea for the presence and expression of sRNAs. Fifteen genes encoding putative sRNAs (psRNAs) were identified. Most of these genes showed altered expression in a variety of experimental conditions. The transcripts of two psRNAs were further characterized by mapping their 5'- and 3'-ends and by real-time PCR. The results of these analyses suggested that one of them, psRNA11, is involved in iron homeostasis in N. europaea.

  1. Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea.

    PubMed

    Wei, Xueming; Vajrala, Neeraja; Hauser, Loren; Sayavedra-Soto, Luis A; Arp, Daniel J

    2006-08-01

    Nitrosomonas europaea, as an ammonia-oxidizing bacterium, has a high Fe requirement and has 90 genes dedicated to Fe acquisition. Under Fe-limiting conditions (0.2 microM Fe), N. europaea was able to assimilate up to 70% of the available Fe in the medium even though it is unable to produce siderophores. Addition of exogenous siderophores to Fe-limited medium increased growth (final cell mass). Fe-limited cells had lower heme and cellular Fe contents, reduced membrane layers, and lower NH3- and NH2OH-dependent O2 consumption activities than Fe-replete cells. Fe acquisition-related proteins, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin and diffusion protein OmpC, were expressed to higher levels under Fe limitation, providing biochemical evidence for adaptation of N. europaea to Fe-limited conditions.

  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.

  3. 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

  4. 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.

  5. Detection and characterization of a multicopper oxidase from Nitrosomonas europaea.

    PubMed

    Lawton, Thomas J; Rosenzweig, Amy C

    2011-01-01

    Blue copper oxidase (BCO) is a multicopper oxidase (MCO) found in Nitrosomonas europaea as well as in other ammonia-oxidizing organisms. In this chapter, we detail methods used to detect, isolate, and characterize BCO from N. europaea. A method for identifying and classifying MCOs commonly found in nitrifiers based on primary sequence is also described.

  6. 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

  7. Superoxide production by a manganese-oxidizing bacterium facilitates iodide oxidation.

    PubMed

    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; Yeager, Chris M

    2014-05-01

    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 Mn(2+), 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.

  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. Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.

    PubMed

    Yong, Delicia; Ee, Robson; Lim, Yan-Lue; Yu, Choo-Yee; Ang, Geik-Yong; How, Kah-Yan; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

    2016-01-10

    Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.

  10. Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase.

    PubMed

    Kostera, Joshua; Youngblut, Matthew D; Slosarczyk, Jeffrey M; Pacheco, A Andrew

    2008-09-01

    Hydroxylamine oxidoreductase (HAO) from the ammonia-oxidizing bacterium Nitrosomonas europaea normally catalyzes the four-electron oxidation of hydroxylamine to nitrite, which is the second step in ammonia-dependent respiration. Here we show that, in the presence of methyl viologen monocation radical (MV(red)), HAO can catalyze the reduction of nitric oxide to ammonia. The process is analogous to that catalyzed by cytochrome c nitrite reductase, an enzyme found in some bacteria that use nitrite as a terminal electron acceptor during anaerobic respiration. The availability of a reduction pathway to ammonia is an important factor to consider when designing in vitro studies of HAO, and may also have some physiological relevance. The reduction of nitric oxide to ammonia proceeds in two kinetically distinct steps: nitric oxide is first reduced to hydroxylamine, and then hydroxylamine is reduced to ammonia at a tenfold slower rate. The second step was investigated independently in solutions initially containing hydroxylamine, MV(red), and HAO. Both steps show first-order dependence on nitric oxide and HAO concentrations, and zero-order dependence on MV(red) concentration. The rate constants governing each reduction step were found to have values of (4.7 +/- 0.3) x 10(5) and (2.06 +/- 0.04) x 10(4) M(-1) s(-1), respectively. A second reduction pathway, with second-order dependence on nitric oxide, may become available as the concentration of nitric oxide is increased. Such a pathway might lead to production of nitrous oxide. We estimate a maximum value of (1.5 +/- 0.05) x 10(10) M(-2) s(-1) for the rate constant of the alternative pathway, which is small and suggests that the pathway is not physiologically important.

  11. Physiological characterization of an anaerobic ammonium-oxidizing bacterium belonging to the "Candidatus scalindua" group.

    PubMed

    Awata, Takanori; Oshiki, Mamoru; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi; Okabe, Satoshi

    2013-07-01

    The phylogenetic affiliation and physiological characteristics (e.g., Ks and maximum specific growth rate [μmax]) of an anaerobic ammonium oxidation (anammox) bacterium, "Candidatus Scalindua sp.," enriched from the marine sediment of Hiroshima Bay, Japan, were investigated. "Candidatus Scalindua sp." exhibits higher affinity for nitrite and a lower growth rate and yield than the known anammox species.

  12. Influence of ammonia on silver nanoparticle dissolution and toxicity to Nitrosomonas europaea.

    PubMed

    Kostigen Mumper, Cameron; Ostermeyer, Ann-Kathrin; Semprini, Lewis; Radniecki, Tyler S

    2013-11-01

    Nitrosomonas europaea, a model ammonia oxidizing bacterium, was sensitive to both ionic silver (Ag(+)) and 20 nm citrate capped silver nanoparticles (AgNPs). AgNP toxicity has been previously shown to be primarily due to the dissolution of Ag(+). The rate of AgNP dissolution dramatically increased in test medium containing ammonium sulfate ((NH4)2SO4) and HEPES buffer compared to test medium containing either deionized water or HEPES buffer alone. The AgNP dissolution rates accelerated with increases in ammonia (NH3) concentrations either through increases in pH or through higher (NH4)2SO4 concentrations. Ammonia likely participated in the oxidation of the AgNP to form [Formula: see text] in solution leading to the observed increase in AgNP dissolution rates. AgNP toxicity was enhanced as NH3 concentrations increased. However, Ag(+) toxicity was constant at all NH3 concentrations tested. Therefore, it can be concluded that the increased AgNP toxicity was due to increased Ag(+) release and not due to a synergistic effect between NH3 and Ag(+). The results of this study may provide insights in the fate and toxicity of AgNPs in high NH3 environments including wastewater treatment plants, eutrophic waterways and alkaline environments.

  13. 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.

  14. Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium “Candidatus Brocadia sp. 40”

    PubMed Central

    Ali, Muhammad; Haroon, Mohamed Fauzi; Narita, Yuko; Zhang, Lei; Rangel Shaw, Dario; Okabe, Satoshi

    2016-01-01

    The anaerobic ammonium-oxidizing (anammox) bacterium “Candidatus Brocadia sp. 40” demonstrated the fastest growth rate compared to others in this taxon. Here, we report the 2.93-Mb draft genome sequence of this bacterium, which has 2,565 gene-coding regions, 41 tRNAs, and a single rrn operon. PMID:27932661

  15. Rapid and sensitive Nitrosomonas europaea biosensor assay for quantification of bioavailable ammonium sensu strictu in soil.

    PubMed

    Nguyen, Minh Dong; Risgaard-Petersen, Nils; Sørensen, Jan; Brandt, Kristian K

    2011-02-01

    Knowledge on bioavailable ammonium sensu strictu (i.e., immediately available for cellular uptake) in soil is required to understand nutrient uptake processes in microorganisms and thus of vital importance for plant production. We here present a novel ammonium biosensor approach based on the lithoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea transformed with a luxAB sensor plasmid. Bioluminescence-based ammonium detection was achieved within 10 min with a quantification limit in liquid samples of ∼20 μM and a linear response range up to 400 μM. Biosensor and conventional chemical quantification of ammonium in soil solutions agreed well across a range of sample and assay conditions. The biosensor was subsequently applied for a solid phase-contact assay allowing for direct interaction of biosensor cells with soil particle-associated (i.e., exchangeable plus fixed) ammonium. The assay successfully quantified bioavailable ammonium even in unfertilized soil and demonstrated markedly higher ratios of bioavailable ammonium to water- or 2 M KCl-exchangeable ammonium in anoxic soil than in corresponding oxic soil. Particle-associated ammonium contributed by at least 74% and 93% of the total bioavailable pool in oxic and anoxic soil, respectively. The N. europaea biosensor should have broad relevance for environmental monitoring of bioavailable ammonium and processes depending on ammonium bioavailability.

  16. Impacts of silver nanoparticle coating on the nitrification potential of Nitrosomonas europaea.

    PubMed

    Arnaout, Christina L; Gunsch, Claudia K

    2012-05-15

    Silver nanoparticles (AgNPs) are increasingly used as bacteriostatic agents to prevent microbial growth. AgNPs are manufactured with a variety of coatings, and their potential impacts on wastewater treatment in general are poorly understood. In the present study, Nitrosomonas europaea, a model ammonia oxidizing bacterium, was exposed to AgNPs with citrate, gum arabic (GA), and polyvinylpyrrolidone (PVP). GA and citrate AgNPs inhibited nitrification most strongly (67.9 ± 3.6% and 91.4 ± 0.2%, respectively at 2 ppm). Our data indicate that Ag(+) dissolution and colloid stability of AgNPs were the main factors in AgNP toxicity. In general, low amounts of dissolved Ag initially caused a post-transcriptional interruption of membrane-bound nitrifying enzyme function, reducing nitrification by 10% or more. A further increase in dissolved Ag resulted in heavy metal stress response (e.g., merA up-regulation) and ultimately led to membrane disruption. The highest effect on membrane disruption was observed for citrate AgNPs (64 ± 11% membranes compromised at 2 ppm), which had high colloidal stability. This study demonstrates that coating plays a very important role in determining Ag dissolution and ultimately toxicity to nitrifiers. More research is needed to characterize these parameters in complex growth media such as wastewater.

  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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Linking NE1545 gene expression with cell volume changes in Nitrosomonas europaea cells exposed to aromatic hydrocarbons.

    PubMed

    Radniecki, Tyler S; Gilroy, Caslin A; Semprini, Lewis

    2011-01-01

    Nitrosomonas europaea, a model ammonia oxidizing bacterium, was exposed to a wide variety of aromatic hydrocarbons in 3 h batch assays. The expression of NE1545, a phenol sentinel gene involved in fatty acid metabolism, was monitored via quantitative real-time polymerase chain reaction (qRT-PCR) and a Coulter Counter technique was used to monitor changes in cell volume. Decreases in cell volume and NE1545 gene expression correlated strongly with exposure to aromatic hydrocarbons that possessed a single polar group substitution (e.g. phenol and aniline). Aromatic hydrocarbons that contain no polar group substitutions (e.g. toluene) or multiple polar group substitutions (e.g. p-hydroquinone) caused negligible changes in NE1545 expression and cell volume. The oxidation of aromatic hydrocarbons by N. europaea from configurations without a single polar group to one with two polar groups (e.g. p-cresol oxidized to 4-hydroxybenzyl alcohol) and from configurations with no polar groups to one with a single polar group (e.g. ethylbenzene oxidized to 4-ethylphenol) greatly influenced NE1545 gene expression and observed changes in cell volume. Nitrification inhibition in N. europaea by the aromatic hydrocarbons was found to be completely reversible; however, the decreases in cell volume were not reversible suggesting a physical change in cell membrane composition. Ammonia monooxygenase blocking studies showed that the chemical exposure that was responsible for the cell volume decrease and up-regulation in gene expression and not the observed inhibition. N. europaea is the first bacterium shown to experience significant changes in cell volume when exposed to μM concentrations of aromatic hydrocarbons, three orders of magnitude lower than previous studies with other bacteria.

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

    PubMed

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

    2008-04-01

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

  7. Regulation of dissimilatory sulfur oxidation in the purple sulfur bacterium allochromatium vinosum.

    PubMed

    Grimm, Frauke; Franz, Bettina; Dahl, Christiane

    2011-01-01

    In the purple sulfur bacterium Allochromatium vinosum, thiosulfate oxidation is strictly dependent on the presence of three periplasmic Sox proteins encoded by the soxBXAK and soxYZ genes. It is also well documented that proteins encoded in the dissimilatory sulfite reductase (dsr) operon, dsrABEFHCMKLJOPNRS, are essential for the oxidation of sulfur that is stored intracellularly as an obligatory intermediate during the oxidation of thiosulfate and sulfide. Until recently, detailed knowledge about the regulation of the sox genes was not available. We started to fill this gap and show that these genes are expressed on a low constitutive level in A. vinosum in the absence of reduced sulfur compounds. Thiosulfate and possibly sulfide lead to an induction of sox gene transcription. Additional translational regulation was not apparent. Regulation of soxXAK is probably performed by a two-component system consisting of a multi-sensor histidine kinase and a regulator with proposed di-guanylate cyclase activity. Previous work already provided some information about regulation of the dsr genes encoding the second important sulfur-oxidizing enzyme system in the purple sulfur bacterium. The expression of most dsr genes was found to be at a low basal level in the absence of reduced sulfur compounds and enhanced in the presence of sulfide. In the present work, we focused on the role of DsrS, a protein encoded by the last gene of the dsr locus in A. vinosum. Transcriptional and translational gene fusion experiments suggest a participation of DsrS in the post-transcriptional control of the dsr operon. Characterization of an A. vinosum ΔdsrS mutant showed that the monomeric cytoplasmic 41.1-kDa protein DsrS is important though not essential for the oxidation of sulfur stored in the intracellular sulfur globules.

  8. Physiological characterization of anaerobic ammonium oxidizing bacterium 'Candidatus Jettenia caeni'.

    PubMed

    Ali, Muhammad; Oshiki, Mamoru; Awata, Takanori; Isobe, Kazuo; Kimura, Zenichiro; Yoshikawa, Hiroaki; Hira, Daisuke; Kindaichi, Tomonori; Satoh, Hisashi; Fujii, Takao; Okabe, Satoshi

    2015-06-01

    To date, six candidate genera of anaerobic ammonium-oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus 'Candidatus Jettenia'. Planctomycete KSU-1 was found to be a mesophilic (20-42.5°C) and neutrophilic (pH 6.5-8.5) bacterium with a maximum growth rate of 0.0020 h(-1) . Planctomycete KSU-1 cells showed typical physiological and structural features of anammox bacteria; i.e. (29) N2 gas production by coupling of (15) NH4 (+) and (14) NO2 (-) , accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone-7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl-CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU-1 cells. On the basis of these experimental results, we proposed the name 'Ca. Jettenia caeni' sp. nov. for the bacterial clade of the planctomycete KSU-1.

  9. 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.

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

    PubMed Central

    Bennett, Kristen; Sadler, Natalie C.; Wright, Aaron T.; Yeager, Chris

    2016-01-01

    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, and de novo protein 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

  11. A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus 'Methylomirabilis oxyfera'.

    PubMed

    Wu, Ming L; Ettwig, Katharina F; Jetten, Mike S M; Strous, Marc; Keltjens, Jan T; van Niftrik, Laura

    2011-01-01

    Biological methane oxidation proceeds either through aerobic or anaerobic pathways. The newly discovered bacterium Candidatus 'Methylomirabilis oxyfera' challenges this dichotomy. This bacterium performs anaerobic methane oxidation coupled to denitrification, but does so in a peculiar way. Instead of scavenging oxygen from the environment, like the aerobic methanotrophs, or driving methane oxidation by reverse methanogenesis, like the methanogenic archaea in sulfate-reducing systems, it produces its own supply of oxygen by metabolizing nitrite via nitric oxide into oxygen and dinitrogen gas. The intracellularly produced oxygen is then used for the oxidation of methane by the classical aerobic methane oxidation pathway involving methane mono-oxygenase. The present mini-review summarizes the current knowledge about this process and the micro-organism responsible for it.

  12. Dissecting iron uptake and homeostasis in Nitrosomonas europaea.

    PubMed

    Sayavedra-Soto, Luis A; Vajrala, Neeraja; Arp, Daniel J

    2011-01-01

    The chemolithoautotroph Nitrosomonas europaea oxidizes about 25 mol of NH(3) for each mole of CO(2) that is converted to biomass using an array of heme and nonheme Fe-containing proteins. Hence mechanisms of efficient iron (Fe) uptake and homeostasis are particularly important for this Betaproteobacterium. Among nitrifiers, N.europaea has been the most studied to date. Characteristics that make N.europaea a suitable model to study Fe uptake and homeostasis are as follows: (a) its sequenced genome, (b) its capability to grow relatively well in 0.2 μM Fe in the absence of heterologous siderophores, and (c) its amenability to mutagenesis. In this chapter, we describe the methodology we use in our laboratory to dissect Fe uptake and homeostasis in the ammonia oxidizer N. europaea.

  13. 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.

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

    PubMed

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

    2014-07-01

    This study investigated the influence of water hardness (Mg(2+) and Ca(2+)) 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 Mg(2+) to 2% and 33%, respectively, in the presence of 730 μM Mg(2+). Introduction of Mg(2+) resulted in the rapid aggregation of the AgNP suspensions and reduced the 3 h Ag(+) dissolution rates from 30%, in the absence of Mg(2+), to 9%, in the presence of 730 μM Mg(2+). 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 Mg(2+) increased the observed inhibition of nitrification, but was always less than what was observed in the absence of Mg(2+). The presence of Mg(2+) 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 Mg(2+) and Ag(+) for membrane binding sites and transport into the cells. Ca(2+) 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.

  15. Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns.

    PubMed

    Lu, Huijie; Ulanov, Alexander V; Nobu, Masaru; Liu, Wen-Tso

    2016-02-01

    The model ammonia-oxidizing bacterium Nitrosomonas europaea represents one of the environmentally and biotechnologically significant microorganisms. Genome-based studies over the last decade have led to many intriguing discoveries about its cellular biochemistry and physiology. However, knowledge regarding the regulation of overall metabolic routes in response to various environmental stresses is limited due to a lack of comprehensive, time-resolved metabolomic analyses. In this study, gas chromatography-mass spectrometry (GC-MS)-based metabolic profiling was performed to characterize the temporal variations of N. europaea 19718 intercellular metabolites in response to varied temperature (23 and 10 °C) and ammonia feeding patterns (shock loading and continuous feeding of 20 mg N/L). Approximately 87 metabolites were successfully identified and mapped to the existing pathways of N. europaea 19718, allowing interpretation of the influence of temperature and feeding pattern on metabolite levels. In general, varied temperature had a more profound influence on the overall metabolism than varied feeding patterns. Total extracellular metabolite concentrations (relative to internal standards and normalized to biomass weight) were lower under cold stress and shock loading conditions compared with the control (continuous feeding at 23 °C). Cold stress caused the widespread downregulation of metabolites involved in central carbon metabolism, amino acid, and lipid synthesis (e.g., malonic acid, succinic acid, putrescine, and phosphonolpyruvate). Metabolites that showed differences under varied feeding patterns were mainly involved in nucleotide acid, amino acid, and lipid metabolism (e.g., adenine, uracil, and spermidine). This study highlighted the roles of central carbon and nitrogen metabolism in countering cold stress and altered ammonia availability. In addition, transcriptomic, proteomic, and metabolomic data from three studies on N. europaea were compared to achieve a

  16. Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1

    PubMed Central

    Huang, Yinyan; Li, Hang; Rensing, Christopher; Zhao, Kai; Johnstone, Laurel

    2012-01-01

    Acidovorax sp. strain NO1, isolated from gold mine soil, was shown to be a facultative anaerobic arsenite-oxidizing and nitrate-reducing bacterium. The reported draft genome predicts the presence of genes involved in arsenic metabolism, nitrate reduction, phosphate transport, and multiple metal resistances and indicates putative horizontal gene transfer events. PMID:22374962

  17. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge.

    PubMed

    Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Bajic, Vladimir; Qian, Pei-Yuan

    2014-11-01

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body.

  18. Flavobacterium arsenitoxidans sp. nov., an arsenite-oxidizing bacterium from Thai soil.

    PubMed

    Khianngam, Saowapar; Akaracharanya, Ancharida; Lee, Jung-Sook; Lee, Keun Chul; Kim, Kyoung-Woong; Tanasupawat, Somboon

    2014-12-01

    An arsenite-oxidizing bacterium, strain S2-3H(T), was isolated from arsenic-contaminated soil sample collected from Dantchaeng district, Suphanburi province, Thailand and was characterized based on polyphasic taxonomic study. The strain was observed to be a Gram-stain negative, aerobic, yellow pigmented, non-spore forming and rod-shaped bacterium. Major menaquinone was MK-6. Iso-C15:0, iso-C15:0 3OH, C16:1 ω7c/C16:1 ω6c, C16:0, iso-C17:0 3OH, and C16:0 3OH were the predominant cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, unidentified phospholipids and unidentified aminophospholipids. The DNA G+C content was 37.0 mol%. Phylogenetic analysis using 16S rRNA sequence showed that strain S2-3H(T) is affiliated to the genus Flavobacterium, and is closely related to F. defluvii KCTC 12612(T) (97.0 %) and F. johnsoniae NBRC 14942(T) (97.0 %). The strain S2-3H(T) could be clearly distinguished from the related Flavobacterium species by its physiological and biochemical characteristics as well as its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Flavobacterium, for which the name Flavobacterium arsenitoxidans sp. nov. (type strain S2-3H(T) = KCTC 22507(T) = NBRC 109607(T) = PCU 331(T) = TISTR 2238(T)) is proposed.

  19. Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium

    PubMed Central

    Singh, Rahul; Grigg, Jason C.; Qin, Wei; Kadla, John F.; Murphy, Michael E.P.; Eltis, Lindsay D.

    2013-01-01

    DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn2+), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine, increased the enzyme’s apparent kcat and kcat/Km values for Mn2+ by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn2+ to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different to that of another bacterial Mn2+-oxidizing peroxidase. The first coordination sphere was entirely comprised of solvent, consistent with the variant’s high Km for Mn2+ (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin. PMID:23305326

  20. A new function of graphene oxide emerges: inactivating phytopathogenic bacterium Xanthomonas oryzae pv. Oryzae

    NASA Astrophysics Data System (ADS)

    Chen, Juanni; Wang, Xiuping; Han, Heyou

    2013-05-01

    Xanthomonas oryzae pv. oryzae ( Xoo) is one representative phytopathogenic bacterium causing bacteria infections in rice. The antibacterial activity of graphene suspended in different dispersants against Xoo was first investigated. Bacteriological test data, fluorescence microscope and transmission electron microscopy images are provided, which yield insight into the antibacterial action of the nanoscale materials. Surprisingly, the results showed graphene oxide (GO) exhibits superior bactericidal effect even at extremely low dose in water (250 μg/mL), almost killing 94.48 % cells, in comparison to common bactericide bismerthiazol with only 13.3 % mortality. The high efficiency in inactivating the bacteria on account of considerable changes in the cell membranes caused by the extremely sharp edges of graphene oxide and generation of reactive oxygen species, which may be the fatal factor for bacterial inactivation. Given the superior antibacterial effect of GO and the fact that GO can be mass-produced with low cost, we expect a new application could be developed as bactericide for controlling plant disease, which may be a matter of great importance for agricultural development.

  1. Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium.

    PubMed

    Singh, Rahul; Grigg, Jason C; Qin, Wei; Kadla, John F; Murphy, Michael E P; Eltis, Lindsay D

    2013-04-19

    DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn(2+)), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine increased the enzyme's apparent k(cat) and k(cat)/K(m) values for Mn(2+) by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn(2+) to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different from that of another bacterial Mn(2+)-oxidizing peroxidase. The first coordination sphere was entirely composed of solvent, consistent with the variant's high K(m) for Mn(2+) (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin.

  2. 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.

  3. Draft genome sequence of the sulfur-oxidizing bacterium "Candidatus Sulfurovum sediminum" AR, which belongs to the Epsilonproteobacteria.

    PubMed

    Park, Soo-Je; Ghai, Rohit; Martín-Cuadrado, Ana-Belén; Rodríguez-Valera, Francisco; Jung, Man-Young; Kim, Jong-Geol; Rhee, Sung-Keun

    2012-08-01

    Sulfur-oxidizing bacteria are common microorganisms in a variety of sulfide-rich environments. They play important roles in the global sulfur cycle on earth. Here, we present a high-quality draft genome sequence of a sulfur-oxidizing bacterium, "Candidatus Sulfurovum sediminum" strain AR, which belongs to the class Epsilonproteobacteria and dominated an enrichment culture from a marine sediment collected off Svalbard, within the Arctic Circle. Its genome contains genes for sulfur oxidation and carbon fixation. The size of the draft genome is 2.12 Mb, and the G+C content is 39.4%.

  4. L-Malate dehydrogenase activity in the reductive arm of the incomplete citric acid cycle of Nitrosomonas europaea.

    PubMed

    Deutch, Charles E

    2013-11-01

    The autotrophic nitrifying bacterium Nitrosomonas europaea does not synthesize 2-oxoglutarate (α-ketoglutarate) dehydrogenase under aerobic conditions and so has an incomplete citric acid cycle. L-malate (S-malate) dehydrogenase (MDH) from N. europaea was predicted to show similarity to the NADP(+)-dependent enzymes from chloroplasts and was separated from the NAD(+)-dependent proteins from most other bacteria or mitochondria. MDH activity in a soluble fraction from N. europaea ATCC 19718 was measured spectrophotometrically and exhibited simple Michaelis-Menten kinetics. In the reductive direction, activity with NADH increased from pH 6.0 to 8.5 but activity with NADPH was consistently lower and decreased with pH. At pH 7.0, the K m for oxaloacetate was 20 μM; the K m for NADH was 22 μM but that for NADPH was at least 10 times higher. In the oxidative direction, activity with NAD(+) increased with pH but there was very little activity with NADP(+). At pH 7.0, the K m for L-malate was 5 mM and the K m for NAD(+) was 24 μM. The reductive activity was quite insensitive to inhibition by L-malate but the oxidative activity was very sensitive to oxaloacetate. MDH activity was not strongly activated or inhibited by glycolytic or citric acid cycle metabolites, adenine nucleotides, NaCl concentrations, or most metal ions, but increased with temperature up to about 55 °C. The reductive activity was consistently 10-20 times higher than the oxidative activity. These results indicate that the L-malate dehydrogenase in N. europaea is similar to other NAD(+)-dependent MDHs (EC 1.1.1.37) but physiologically adapted for its role in a reductive biosynthetic sequence.

  5. Interaction of the mechanism-based inactivator acetylene with ammonia monooxygenase of Nitrosomonas europaea.

    PubMed

    Gilch, Stefan; Vogel, Manja; Lorenz, Matthias W; Meyer, Ortwin; Schmidt, Ingo

    2009-01-01

    The ammonia monooxygenase (AMO) of Nitrosomonas europaea is a metalloenzyme that catalyses the oxidation of ammonia to hydroxylamine. We have identified histidine 191 of AmoA as the binding site for the oxidized mechanism-based inactivator acetylene. Binding of acetylene changed the molecular mass of His-191 from 155.15 to 197.2 Da (+42.05), providing evidence that acetylene was oxidized to ketene (CH2CO; 42.04 Da) which binds specifically to His-191. It must be assumed that His-191 is part of the acetylene-activating site in AMO or at least directly neighbours this site.

  6. A soluble form of ammonia monooxygenase in Nitrosomonas europaea.

    PubMed

    Gilch, Stefan; Meyer, Ortwin; Schmidt, Ingo

    2009-09-01

    Ammonia monooxygenase (AMO) of Nitrosomonas europaea is a metalloenzyme that catalyzes the oxidation of ammonia to hydroxylamine. This study shows that AMO resides in the cytoplasm of the bacteria in addition to its location in the membrane and is distributed approximately equally in both subcellular fractions. AMO in both fractions catalyzes the oxidation of ammonia and binds [(14)C]acetylene, a mechanism-based inhibitor which specifically interacts with catalytically active AMO. Soluble AMO was purified 12-fold to electrophoretic homogeneity with a yield of 8%. AMO has a molecular mass of approximately 283 kDa with subunits of ca. 27 kDa (alpha-subunit, AmoA), ca. 42 kDa (beta-subunit, AmoB), and ca. 24 kDa (gamma-subunit, cytochrome c(1)) in an alpha(3)beta(3)gamma(3) sub-unit structure. Different from the beta-subunit of membrane-bound AMO, AmoB of soluble AMO possesses an N-terminal signal sequence. AMO contains Cu (9.4+/-0.6 mol per mol AMO), Fe (3.9+/-0.3 mol per mol AMO), and Zn (0.5 to 2.6 mol per mol AMO). Upon reduction the visible absorption spectrum of AMO reveals absorption bands characteristic of cytochrome c. Electron para-magnetic resonance spectroscopy of air-oxidized AMO at 50 K shows a paramagnetic signal originating from Cu(2+) and at 10 K a paramagnetic signal characteristic of heme-Fe.

  7. 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.

  8. Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation.

    PubMed

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

    2007-06-01

    The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (amoCAB operons) and CO(2) fixation (cbbLS), a third, lone copy of amoC (amoC(3)), and two representative housekeeping genes (glyA and rpsJ). Primer extension analysis of RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two amoCAB operons. The distal sigma(70) type amoCAB promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of amoC (amoC(3)) was expressed only during recovery. Both the proximal amoC(1,2) promoter and the amoC(3) promoter are similar to gram-negative sigma(E) promoters, thus implicating sigma(E) in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC(3) may modify the activity of the holoenzyme, characterization of a DeltaamoC(3) strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO(2) fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by sigma(E) and the coordinated regulation of catabolic and anabolic genes.

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

    PubMed Central

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

    2007-01-01

    The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for 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 regulated promoters upstream of the two amoCAB operons. The distal σ70 type amoCAB promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of amoC (amoC3) was expressed only during recovery. Both the proximal amoC1,2 promoter and the amoC3 promoter are similar to gram-negative σE promoters, thus implicating σE in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC3 may modify the activity of the holoenzyme, characterization of a ΔamoC3 strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO2 fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by σE and the coordinated regulation of catabolic and anabolic genes. PMID:17384196

  10. New Insights into Methyl Bromide Cooxidation by Nitrosomonas europaea Obtained by Experimenting with Moderately Low Density Cell Suspensions†

    PubMed Central

    Duddleston, Khrystyne N.; Bottomley, Peter J.; Porter, Angela J.; Arp, Daniel J.

    2000-01-01

    We examined the rates and sustainability of methyl bromide (MeBr) oxidation in moderately low density cell suspensions (∼6 × 107 cells ml−1) of the NH3-oxidizing bacterium Nitrosomonas europaea. In the presence of 10 mM NH4+ and 0.44, 0.22, and 0.11 mM MeBr, the initial rates of MeBr oxidation were sustained for 12, 12, and 24 h, respectively, despite the fact that only 10% of the NH4+, 18% of the NH4+, and 35% of the NH4+, respectively, were consumed. Although the duration of active MeBr oxidation generally decreased as the MeBr concentration increased, similar amounts of MeBr were oxidized with a large number of the NH4+-MeBr combinations examined (10 to 20 μmol mg [dry weight] of cells−1). Approximately 90% of the NH3-dependent O2 uptake activity and the NO2−-producing activity were lost after N. europaea was exposed to 0.44 mM MeBr for 24 h. After MeBr was removed and the cells were resuspended in fresh growth medium, NO2− production increased exponentially, and 48 to 60 h was required to reach the level of activity observed initially in control cells that were not exposed to MeBr. It is not clear what percentage of the cells were capable of cell division after MeBr oxidation because NO2− accumulated more slowly in the exposed cells than in the unexposed cells despite the fact that the latter were diluted 10-fold to create inocula which exhibited equal initial activities. The decreases in NO2−-producing and MeBr-oxidizing activities could not be attributed directly to NH4+ or NH3 limitation, to a decrease in the pH, to the composition of the incubation medium, or to toxic effects caused by accumulation of the end products of oxidation (NO2− and formaldehyde) in the medium. Additional cooxidation-related studies of N. europaea are needed to identify the mechanism(s) responsible for the MeBr-induced loss of cell activity and/or viability, to determine what percentages of cells damaged by cooxidative activities are culturable, and to determine if

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

    SciTech Connect

    Bennett, Kristen; Sadler, Natalie C.; Wright, Aaron T.; Yeager, Chris; Hyman, Michael R.; Löffler, F. E.

    2016-01-29

    Nitrosomonas europaeais 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 O2uptake byN. europaeaby 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

  12. 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).

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

    PubMed Central

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

    2006-01-01

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

  14. 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).

  15. Simple, rapid and effective preservation and reactivation of anaerobic ammonium oxidizing bacterium "Candidatus Brocadia sinica".

    PubMed

    Ali, Muhammad; Oshiki, Mamoru; Okabe, Satoshi

    2014-06-15

    It is still the biggest challenge to secure enough seeding biomass for rapid start-up of full-scale (anaerobic ammonium oxidation) anammox processes due to slow growth. Preservation of active anammox biomass could be one of the solutions. In this study, biomass of anammox bacterium, "Candidatus Brocadia sinica", immersed in various nutrient media were preserved at -80 °C, 4 °C and room temperature. After 45, 90 and 150 days of preservation, specific anammox activity (SAA) of the preserved anammox biomass was determined by measuring (29)N2 production rate and transcription levels of hzsA gene encoding hydrazine synthase alpha subunit. Storage in nutrient medium containing 3 mM of molybdate at room temperature with periodical (every 45 days) supply of NH4(+) and NO2(-) was proved to be the most effective storage technique for "Ca. Brocadia sinica" biomass. Using this preservation condition, 96, 92 and 65% of the initial SAA was sustained after 45, 90 and 150 days of storage, respectively. Transcription levels of hzsA gene in biomass correlated with the SAA (R(2) = 0.83), indicating it can be used as a genetic marker to evaluate the anammox activity of preserved biomass. Furthermore, the 90-day-stored biomass was successfully reactivated by immobilizing in polyvinyl alcohol (6%, w/v) and sodium alginate (2%, w/v) gel and then inoculated to up-flow column reactors. Total nitrogen removal rates rapidly increased to 7 kg-N m(-3) d(-1) within 35 days of operation. Based on these results, the room temperature preservation with molybdate addition is simple, cost-effective and feasible at a practical scale, which will accelerate the practical use of anammox process for wastewater treatment.

  16. Kinetic Studies of Ammonia Monooxygenase Inhibition in Nitrosomonas europaea by Hydrocarbons and Halogenated Hydrocarbons in an Optimized Whole-Cell Assay

    PubMed Central

    Keener, William K.; Arp, Daniel J.

    1993-01-01

    The inhibitory effects of 15 hydrocarbons and halogenated hydrocarbons on NH3 oxidation by ammonia monooxygenase (AMO) in intact cells of the nitrifying bacterium Nitrosomonas europaea were determined. Determination of AMO activity, measured as NO2- production, required coupling of hydroxylamine oxidoreductase (HAO) activity with NH3-dependent NH2OH production by AMO. Hydrazine, an alternate substrate for HAO, was added to the reaction mixtures as a source of reductant for AMO. Most inhibitors exhibited competitive or noncompetitive inhibition patterns. The competitive character generally decreased (KiE/KiES increased) as the molecular size of the inhibitors increased. For example, CH4 and C2H4 were competitive inhibitors of NH3 oxidation, whereas the remaining alkanes (up to C4) and monohalogenated (Cl, Br, I) alkanes were noncompetitive. Oxidation of C2H5Br (noncompetitive) increased as the NH4+ concentration increased up to 40 mM, whereas oxidations of inhibitors with competitive character (KiE ≪ KiES) were diminished at 40 mM NH4+. Multichlorinated compounds produced nonlinear Lineweaver-Burk plots. Iodinated alkanes (CH3I, C2H5I) and C2Cl4 were potent inhibitors of NH3 oxidation. Maximum rates of NH3, C2H4, and C2H6 oxidations were approximately equivalent, suggesting a common rate-determining step. These data support an active-site model for AMO consisting of an NH3-binding site and a second site that binds noncompetitive inhibitors, with oxidation occurring at either site. PMID:16349014

  17. Effect of free ammonia and free nitrous acid concentration on the anabolic and catabolic processes of an enriched Nitrosomonas culture.

    PubMed

    Vadivelu, Vel M; Keller, Jurg; Yuan, Zhiguo

    2006-12-05

    The effects of free ammonia (FA; NH(3)) and free nitrous acid (FNA; HNO(2)) concentrations on the metabolisms of an enriched ammonia oxidizing bacteria (AOB) culture were investigated using a method allowing the decoupling of growth and energy generation processes. A lab-scale sequencing batch reactor (SBR) was operated for the enrichment of an AOB culture. Fluorescent in-situ hybridization (FISH) analysis showed that 82% of the bacterial population in the SBR bound to the NEU probe specifically designed for Nitrosomonas europaea. Batch tests were carried out to measure the oxygen and ammonium consumption rates by the culture at various FA and FNA levels, in the presence or absence of inorganic carbon (CO(2), HCO(3) (-), and CO(3) (2-)). It was revealed that FA of up to 16.0 mgNH(3)-N . L(-1), which was the highest concentration used in this study, did not have any inhibitory effect on either the catabolic or anabolic processes of the Nitrosomonas culture. In contrast, FNA inhibited both the growth and energy production capabilities of the Nitrosomonas culture. The inhibition on growth initiated at approximately 0.10 mgHNO(2)-N . L(-1), and the data suggested that the biosynthesis was completely stopped at an FNA concentration of 0.40 mgHNO(2)-N . L(-1). The inhibition on energy generation initiated at a slightly lower level but the Nitrosomonas culture was still oxidizing ammonia at half of the maximum rate at an FNA concentration of 0.50-0.63 mgHNO(2)-N . L(-1). The affinity constant of the Nitrosomonas culture with respect to ammonia was determined to be 0.36 mgNH(3)-N . L(-1), independent of the presence or absence of inorganic carbon.

  18. 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.

  19. Genome-wide transcriptional responses of Nitrosomonas europaea to zinc.

    PubMed

    Park, Sunhwa; Ely, Roger L

    2008-06-01

    Nitrosomonas europaea, a Gram-negative obligate chemolithoautotroph, participates in global nitrogen cycling by carrying out nitrification and derives energy for growth through oxidation of ammonia. In this work, the physiological, proteomic, and transcriptional responses of N. europaea to zinc stress were studied. The nitrite production rate and ammonia-dependent oxygen uptake rate of the cells exposed to 3.4 microM ZnCl2 decreased about 61 and 69% within 30 min, respectively. Two proteins were notably up regulated in zinc treatment and the mRNA levels of their encoding genes started to increase by 1 h after the addition of zinc. A total of 27 genes were up regulated and 30 genes were down regulated. Up-regulated genes included mercury resistance genes (merTPCAD), inorganic ion transport genes, oxidative stress genes, toxin-antitoxin genes, and two-component signal transduction systems genes. merTPCAD was the highest up-regulated operon (46-fold). Down-regulated genes included the RubisCO operon (cbbO), biosynthesis (mrsA), and amino acid transporter.

  20. 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.

  1. Chlorobium ferrooxidans sp. nov., a phototrophic green sulfur bacterium that oxidizes ferrous iron in coculture with a "Geospirillum" sp. strain.

    PubMed

    Heising, S; Richter, L; Ludwig, W; Schink, B

    1999-08-01

    A green phototrophic bacterium was enriched with ferrous iron as sole electron donor and was isolated in defined coculture with a spirilloid chemoheterotrophic bacterium. The coculture oxidized ferrous iron to ferric iron with stoichiometric formation of cell mass from carbon dioxide. Sulfide, thiosulfate, or elemental sulfur was not used as electron donor in the light. Hydrogen or acetate in the presence of ferrous iron increased the cell yield of the phototrophic partner, and hydrogen could also be used as sole electron source. Complexed ferric iron was slowly reduced to ferrous iron in the dark, with hydrogen as electron source. Similar to Chlorobium limicola, the phototrophic bacterium contained bacteriochlorophyll c and chlorobactene as photosynthetic pigments, and also resembled representatives of this species morphologically. On the basis of 16S rRNA sequence comparisons, this organism clusters with Chlorobium, Prosthecochloris, and Pelodictyon species within the green sulfur bacteria phylum. Since the phototrophic partner in the coculture KoFox is only moderately related to the other members of the cluster, it is proposed as a new species, Chlorobium ferrooxidans. The chemoheterotrophic partner bacterium, strain KoFum, was isolated in pure culture with fumarate as sole substrate. The strain was identified as a member of the epsilon-subclass of the Proteobacteria closely related to "Geospirillum arsenophilum" on the basis of physiological properties and 16S rRNA sequence comparison. The "Geospirillum" strain was present in the coculture only in low numbers. It fermented fumarate, aspartate, malate, or pyruvate to acetate, succinate, and carbon dioxide, and could reduce nitrate to dinitrogen gas. It was not involved in ferrous iron oxidation but possibly provided a thus far unidentified growth factor to the phototrophic partner.

  2. Responses of the terrestrial ammonia-oxidizing archaeon Ca. Nitrososphaera viennensis and the ammonia-oxidizing bacterium Nitrosospira multiformis to nitrification inhibitors.

    PubMed

    Shen, Tianlin; Stieglmeier, Michaela; Dai, Jiulan; Urich, Tim; Schleper, Christa

    2013-07-01

    Nitrification inhibitors have been used for decades to improve nitrogen fertilizer utilization in farmland. However, their effect on ammonia-oxidizing Archaea (AOA) in soil is little explored. Here, we compared the impact of diverse inhibitors on nitrification activity of the soil archaeon Ca. Nitrososphaera viennensis EN76 and compared it to that of the ammonia-oxidizing bacterium (AOB) Nitrosospira multiformis. Allylthiourea, amidinothiourea, and dicyandiamide (DCD) inhibited ammonia oxidation in cultures of both N. multiformis and N. viennensis, but the effect on N. viennensis was markedly lower. In particular, the effective concentration 50 (EC50) of allylthiourea was 1000 times higher for the AOA culture. Among the tested nitrification inhibitors, DCD was the least potent against N. viennensis. Nitrapyrin had at the maximal soluble concentration only a very weak inhibitory effect on the AOB N. multiformis, but showed a moderate effect on the AOA. The antibiotic sulfathiazole inhibited the bacterium, but barely affected the archaeon. Only the NO-scavenger carboxy-PTIO had a strong inhibitory effect on the archaeon, but had little effect on the bacterium in the concentrations tested. Our results reflect the fundamental metabolic and cellular differences of AOA and AOB and will be useful for future applications of inhibitors aimed at distinguishing activities of AOA and AOB in soil environments.

  3. Monochloramine disinfection kinetics of Nitrosomonas europaea by propidium monoazide quantitative PCR and Live/dead BacLight methods.

    PubMed

    Wahman, David G; Wulfeck-Kleier, Karen A; Pressman, Jonathan G

    2009-09-01

    Monochloramine disinfection kinetics were determined for the pure-culture ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) by two culture-independent methods, namely, Live/Dead BacLight (LD) and propidium monoazide quantitative PCR (PMA-qPCR). Both methods were first verified with mixtures of heat-killed (nonviable) and non-heat-killed (viable) cells before a series of batch disinfection experiments with stationary-phase cultures (batch grown for 7 days) at pH 8.0, 25 degrees C, and 5, 10, and 20 mg Cl(2)/liter monochloramine. Two data sets were generated based on the viability method used, either (i) LD or (ii) PMA-qPCR. These two data sets were used to estimate kinetic parameters for the delayed Chick-Watson disinfection model through a Bayesian analysis implemented in WinBUGS. This analysis provided parameter estimates of 490 mg Cl(2)-min/liter for the lag coefficient (b) and 1.6 x 10(-3) to 4.0 x 10(-3) liter/mg Cl(2)-min for the Chick-Watson disinfection rate constant (k). While estimates of b were similar for both data sets, the LD data set resulted in a greater k estimate than that obtained with the PMA-qPCR data set, implying that the PMA-qPCR viability measure was more conservative than LD. For N. europaea, the lag phase was not previously reported for culture-independent methods and may have implications for nitrification in drinking water distribution systems. This is the first published application of a PMA-qPCR method for disinfection kinetic model parameter estimation as well as its application to N. europaea or monochloramine. Ultimately, this PMA-qPCR method will allow evaluation of monochloramine disinfection kinetics for mixed-culture bacteria in drinking water distribution systems.

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

    PubMed

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

    2016-09-01

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

  5. 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

  6. Monochloramine cometabolism by Nitrosomonas europaea under drinking water conditions.

    PubMed

    Maestre, Juan P; Wahman, David G; Speitel, Gerald E

    2013-09-01

    Chloramine is widely used in United States drinking water systems as a secondary disinfectant, which may promote the growth of nitrifying bacteria because ammonia is present. At the onset of nitrification, both nitrifying bacteria and their products exert a monochloramine demand, decreasing the residual disinfectant concentration in water distribution systems. This work investigated another potentially significant mechanism for residual disinfectant loss: monochloramine cometabolism by ammonia-oxidizing bacteria (AOB). Monochloramine cometabolism was studied with the pure culture AOB Nitrosomonas europaea (ATCC 19718) in batch kinetic experiments under drinking water conditions. Three batch reactors were used in each experiment: a positive control to estimate the ammonia kinetic parameters, a negative control to account for abiotic reactions, and a cometabolism reactor to estimate the cometabolism kinetic constants. Kinetic parameters were estimated in AQUASIM with a simultaneous fit to all experimental data. The cometabolism reactors showed a more rapid monochloramine decay than in the negative controls, demonstrating that cometabolism occurs. Cometabolism kinetics were best described by a pseudo first order model with a reductant term to account for ammonia availability. Monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (30-60% of the observed monochloramine decay). These results suggest that monochloramine cometabolism should occur in practice and may be a significant contribution to monochloramine decay during nitrification episodes in drinking water distribution systems.

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

    PubMed

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

    2016-03-03

    We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to form indigo by utilizing indole as the sole carbon source. The Alcaligenes species is increasingly reported for biodegradation of diverse toxicants and thus complete sequencing may provide insight into biodegradation capabilities and other phenotypes.

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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?.

  15. 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

  16. Metagenomic and biochemical characterizations of sulfur oxidation metabolism in uncultured large sausage-shaped bacterium in hot spring microbial mats.

    PubMed

    Tamazawa, Satoshi; Takasaki, Kazuto; Tamaki, Hideyuki; Kamagata, Yoichi; Hanada, Satoshi

    2012-01-01

    So-called "sulfur-turf" microbial mats in sulfide containing hot springs (55-70°C, pH 7.3-8.3) in Japan were dominated by a large sausage-shaped bacterium (LSSB) that is closely related to the genus Sulfurihydrogenibium. Several previous reports proposed that the LSSB would be involved in sulfide oxidation in hot spring. However, the LSSB has not been isolated yet, thus there has been no clear evidence showing whether it possesses any genes and enzymes responsible for sulfide oxidation. To verify this, we investigated sulfide oxidation potential in the LSSB using a metagenomic approach and subsequent biochemical analysis. Genome fragments of the LSSB (a total of 3.7 Mb sequence including overlapping fragments) were obtained from the metagenomic fosmid library constructed from genomic DNA of the sulfur-turf mats. The sequence annotation clearly revealed that the LSSB possesses sulfur oxidation-related genes coding sulfide dehydrogenase (SD), sulfide-quinone reductase and sulfite dehydrogenase. The gene encoding SD, the key enzyme for sulfide oxidation, was successfully cloned and heterologously expressed in Escherichia coli. The purified recombinant enzyme clearly showed SD activity with optimum temperature and pH of 60°C and 8.0, respectively, which were consistent with the environmental conditions in the hot spring where the sulfur-turf thrives. Furthermore, the affinity of SD to sulfide was relatively high, which also reflected the environment where the sulfide could be continuously supplied. This is the first report showing that the LSSB harbors sulfide oxidizing metabolism adapted to the hot spring environment and can be involved in sulfide oxidation in the sulfur-turf microbial mats.

  17. Metagenomic and Biochemical Characterizations of Sulfur Oxidation Metabolism in Uncultured Large Sausage-Shaped Bacterium in Hot Spring Microbial Mats

    PubMed Central

    Tamaki, Hideyuki; Kamagata, Yoichi; Hanada, Satoshi

    2012-01-01

    So-called “sulfur-turf” microbial mats in sulfide containing hot springs (55–70°C, pH 7.3–8.3) in Japan were dominated by a large sausage-shaped bacterium (LSSB) that is closely related to the genus Sulfurihydrogenibium. Several previous reports proposed that the LSSB would be involved in sulfide oxidation in hot spring. However, the LSSB has not been isolated yet, thus there has been no clear evidence showing whether it possesses any genes and enzymes responsible for sulfide oxidation. To verify this, we investigated sulfide oxidation potential in the LSSB using a metagenomic approach and subsequent biochemical analysis. Genome fragments of the LSSB (a total of 3.7 Mb sequence including overlapping fragments) were obtained from the metagenomic fosmid library constructed from genomic DNA of the sulfur-turf mats. The sequence annotation clearly revealed that the LSSB possesses sulfur oxidation-related genes coding sulfide dehydrogenase (SD), sulfide-quinone reductase and sulfite dehydrogenase. The gene encoding SD, the key enzyme for sulfide oxidation, was successfully cloned and heterologously expressed in Escherichia coli. The purified recombinant enzyme clearly showed SD activity with optimum temperature and pH of 60°C and 8.0, respectively, which were consistent with the environmental conditions in the hot spring where the sulfur-turf thrives. Furthermore, the affinity of SD to sulfide was relatively high, which also reflected the environment where the sulfide could be continuously supplied. This is the first report showing that the LSSB harbors sulfide oxidizing metabolism adapted to the hot spring environment and can be involved in sulfide oxidation in the sulfur-turf microbial mats. PMID:23185438

  18. A Bioluminescence Assay Using Nitrosomonas europaea for Rapid and Sensitive Detection of Nitrification Inhibitors

    PubMed Central

    Iizumi, Taro; Mizumoto, Masahiro; Nakamura, Kanji

    1998-01-01

    An expression vector for the luxAB genes, derived from Vibrio harveyi, was introduced into Nitrosomonas europaea. Although the recombinant strain produced bioluminescence due to the expression of the luxAB genes under normal growing conditions, the intensity of the light emission decreased immediately, in a time-and dose-dependent manner, with the addition of ammonia monooxygenase inhibitors, such as allylthiourea, phenol, and nitrapyrin. When whole cells were challenged with several nitrification inhibitors and toxic compounds, a close relationship was found between the change in the intensity of the light emission and the level of ammonia-oxidizing activity. The response of bioluminescence to the addition of allylthiourea was considerably faster than the change in the ammonia-oxidizing rate, measured as both the O2 uptake and NO2− production rates. The bioluminescence of cells inactivated by ammonia monooxygenase inhibitor was recovered rapidly by the addition of certain substrates for hydroxylamine oxidoreductase. These results suggested that the inhibition of bioluminescence was caused by the immediate decrease of reducing power in the cell due to the inactivation of ammonia monooxygenase, as well as by the destruction of other cellular metabolic pathways. We conclude that the assay system using luminous Nitrosomonas can be applied as a rapid and sensitive detection test for nitrification inhibitors, and it will be used to monitor the nitrification process in wastewater treatment plants. PMID:9758781

  19. A Specific Inorganic Triphosphatase from Nitrosomonas europaea

    PubMed Central

    Delvaux, David; Murty, Mamidanna R. V. S.; Gabelica, Valérie; Lakaye, Bernard; Lunin, Vladimir V.; Skarina, Tatiana; Onopriyenko, Olena; Kohn, Gregory; Wins, Pierre; De Pauw, Edwin; Bettendorff, Lucien

    2011-01-01

    The CYTH superfamily of proteins is named after its two founding members, the CyaB adenylyl cyclase from Aeromonas hydrophila and the human 25-kDa thiamine triphosphatase. Because these proteins often form a closed β-barrel, they are also referred to as triphosphate tunnel metalloenzymes (TTM). Functionally, they are characterized by their ability to bind triphosphorylated substrates and divalent metal ions. These proteins exist in most organisms and catalyze different reactions depending on their origin. Here we investigate structural and catalytic properties of the recombinant TTM protein from Nitrosomonas europaea (NeuTTM), a 19-kDa protein. Crystallographic data show that it crystallizes as a dimer and that, in contrast to other TTM proteins, it has an open β-barrel structure. We demonstrate that NeuTTM is a highly specific inorganic triphosphatase, hydrolyzing tripolyphosphate (PPPi) with high catalytic efficiency in the presence of Mg2+. These data are supported by native mass spectrometry analysis showing that the enzyme binds PPPi (and Mg-PPPi) with high affinity (Kd < 1.5 μm), whereas it has a low affinity for ATP or thiamine triphosphate. In contrast to Aeromonas and Yersinia CyaB proteins, NeuTTM has no adenylyl cyclase activity, but it shares several properties with other enzymes of the CYTH superfamily, e.g. heat stability, alkaline pH optimum, and inhibition by Ca2+ and Zn2+ ions. We suggest a catalytic mechanism involving a catalytic dyad formed by Lys-52 and Tyr-28. The present data provide the first characterization of a new type of phosphohydrolase (unrelated to pyrophosphatases or exopolyphosphatases), able to hydrolyze inorganic triphosphate with high specificity. PMID:21840996

  20. 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

  1. Biotreatment of ammonia in air by an immobilized Nitrosomonas europaea biofilter

    SciTech Connect

    Chung, Y.C.; Huang, C.

    1998-09-01

    The chemoautotrophic microorganism Nitrosomonas europaea has been utilized to remove gaseous ammonia in a continuous reactor. Extensive tests including removal characteristics, metabolic products, and removal efficiencies of ammonia by N. europaea were conducted. The operational principles governing the biofilter and the question of the heterotroph contamination were also studied. The optimum pH value and operating temperature required to effectively remove ammonia were found to be pH 7.5 and 30 C, respectively. When the diluted inlet ammonia concentration was 10 or 20 ppm, the biofilter achieved a 99% removal efficiency after 4 days of operation. However, higher ammonia inlet concentrations and heterotroph contamination resulted in a lower removal efficiency. The results showed that the maximum removal rate and apparent saturation constant were 1.11 g-N/day/kg-bead and 63.67 ppm, respectively. The mainly metabolic product of ammonia oxidation was determined to be nitrite, but the conversion ratio was dependent on whether the contaminations by heterotrophic bacteria were present. From an operating perspective, if the ammonia emission limit (i.e., 1 ppm) was to be achieved, the maximum inlet concentration could not exceed 75 ppm. These results suggest that the immobilized Nitrosomonas europaea biofilter provides a significant potential for treating ammonia in the gaseous phase.

  2. 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

  3. 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.

  4. Modeling the low pH limit of Nitrosomonas eutropha in high-strength nitrogen wastewaters.

    PubMed

    Fumasoli, Alexandra; Morgenroth, Eberhard; Udert, Kai M

    2015-10-15

    In wastewater treatment, the rate of ammonia oxidation decreases with pH and stops very often slightly below a pH of 6. Free ammonia (NH3) limitation, inhibition by nitrous acid (HNO2), limitation by inorganic carbon or direct effect of high proton concentrations have been proposed to cause the rate decrease with pH as well as the cessation of ammonia oxidation. In this study, we compare an exponential pH term common for food microbiology with conventionally applied rate laws based on Monod-type kinetics for NH3 limitation and non-competitive HNO2 inhibition as well as sigmoidal pH functions to model the low pH limit of ammonia oxidizing bacteria (AOB). For this purpose we conducted well controlled batch experiments which were then simulated with a computer model. The results showed that kinetics based on NH3 limitation and HNO2 inhibition can explain the rate decrease of ammonia oxidation between pH 7 and 6, but fail in predicting the pH limit of Nitrosomonas eutropha at pH 5.4 and rates close to that limit. This is where the exponential pH term becomes important: this term decreases the rate of ammonia oxidation to zero, as the pH limit approaches. Previously proposed sigmoidal pH functions that affect large pH regions, however, led to an overestimation of the pH effect and could therefore not be applied successfully. We show that the proposed exponential pH term can be explained quantitatively with thermodynamic principles: at low pH values, the energy available from the proton motive force is too small for the NADH production in Nitrosomonas eutropha and related AOB causing an energy limited state of the bacterial cell. Hence, energy limitation and not inhibition or limitation of enzymes is responsible for the cessation of the AOB activity at low pH values.

  5. Cultivation of an obligate Fe(II)-oxidizing lithoautotrophic bacterium using electrodes.

    PubMed

    Summers, Zarath M; Gralnick, Jeffrey A; Bond, Daniel R

    2013-01-29

    Fe(II)-oxidizing aerobic bacteria are poorly understood, due in part to the difficulties involved in laboratory cultivation. Specific challenges include (i) providing a steady supply of electrons as Fe(II) while (ii) managing rapid formation of insoluble Fe(III) oxide precipitates and (iii) maintaining oxygen concentrations in the micromolar range to minimize abiotic Fe(II) oxidation. Electrochemical approaches offer an opportunity to study bacteria that require problematic electron donors or acceptors in their respiration. In the case of Fe(II)-oxidizing bacteria, if the electron transport machinery is able to oxidize metals at the outer cell surface, electrodes poised at potentials near those of natural substrates could serve as electron donors, eliminating concentration issues, side reactions, and mineral end products associated with metal oxidation. To test this hypothesis, the marine isolate Mariprofundus ferrooxydans PV-1, a neutrophilic obligate Fe(II)-oxidizing autotroph, was cultured using a poised electrode as the sole energy source. When cells grown in Fe(II)-containing medium were transferred into a three-electrode electrochemical cell, a cathodic (negative) current representing electron uptake by bacteria was detected, and it increased over a period of weeks. Cultures scraped from a portion of the electrode and transferred into sterile reactors consumed electrons at a similar rate. After three transfers in the absence of Fe(II), electrode-grown biofilms were studied to determine the relationship between donor redox potential and respiration rate. Electron microscopy revealed that under these conditions, M. ferrooxydans PV-1 attaches to electrodes and does not produce characteristic iron oxide stalks but still appears to exhibit bifurcate cell division. IMPORTANCE Electrochemical cultivation, supporting growth of bacteria with a constant supply of electron donors or acceptors, is a promising tool for studying lithotrophic species in the laboratory

  6. Cultivation of an Obligate Fe(II)-Oxidizing Lithoautotrophic Bacterium Using Electrodes

    PubMed Central

    Summers, Zarath M.; Gralnick, Jeffrey A.; Bond, Daniel R.

    2013-01-01

    ABSTRACT Fe(II)-oxidizing aerobic bacteria are poorly understood, due in part to the difficulties involved in laboratory cultivation. Specific challenges include (i) providing a steady supply of electrons as Fe(II) while (ii) managing rapid formation of insoluble Fe(III) oxide precipitates and (iii) maintaining oxygen concentrations in the micromolar range to minimize abiotic Fe(II) oxidation. Electrochemical approaches offer an opportunity to study bacteria that require problematic electron donors or acceptors in their respiration. In the case of Fe(II)-oxidizing bacteria, if the electron transport machinery is able to oxidize metals at the outer cell surface, electrodes poised at potentials near those of natural substrates could serve as electron donors, eliminating concentration issues, side reactions, and mineral end products associated with metal oxidation. To test this hypothesis, the marine isolate Mariprofundus ferrooxydans PV-1, a neutrophilic obligate Fe(II)-oxidizing autotroph, was cultured using a poised electrode as the sole energy source. When cells grown in Fe(II)-containing medium were transferred into a three-electrode electrochemical cell, a cathodic (negative) current representing electron uptake by bacteria was detected, and it increased over a period of weeks. Cultures scraped from a portion of the electrode and transferred into sterile reactors consumed electrons at a similar rate. After three transfers in the absence of Fe(II), electrode-grown biofilms were studied to determine the relationship between donor redox potential and respiration rate. Electron microscopy revealed that under these conditions, M. ferrooxydans PV-1 attaches to electrodes and does not produce characteristic iron oxide stalks but still appears to exhibit bifurcate cell division. PMID:23362318

  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).

  8. Redox state dependence of axial ligand dynamics in Nitrosomonas europaea cytochrome c552.

    PubMed

    Kaur, Ravinder; Bren, Kara L

    2013-12-12

    Analysis of NMR spectra reveals that the heme axial Met ligand orientation and dynamics in Nitrosomonas europaea cytochrome c552 (Ne cyt c) are dependent on the heme redox state. In the oxidized state, the heme axial Met is fluxional, interconverting between two conformers related to each other by inversion through the Met δS atom. In the reduced state, there is no evidence of fluxionality, with the Met occupying one conformation similar to that seen in the homologous Pseudomonas aeruginosa cytochrome c551. Comparison of the observed and calculated pseudocontact shifts for oxidized Ne cyt c using the reduced protein structure as a reference structure reveals a redox-dependent change in the structure of the loop bearing the axial Met (loop 3). Analysis of nuclear Overhauser effects (NOEs) and existing structural data provides further support for the redox state dependence of the loop 3 structure. Implications for electron transfer function are discussed.

  9. Selenate-dependent anaerobic arsenite oxidation by a bacterium from Mono Lake, California.

    PubMed

    Fisher, Jenny C; Hollibaugh, James T

    2008-05-01

    Arsenate was produced when anoxic Mono Lake water samples were amended with arsenite and either selenate or nitrate. Arsenite oxidation did not occur in killed control samples or live samples with no added terminal electron acceptor. Potential rates of anaerobic arsenite oxidation with selenate were comparable to those with nitrate ( approximately 12 to 15 mumol.liter(-1) h(-1)). A pure culture capable of selenate-dependent anaerobic arsenite oxidation (strain ML-SRAO) was isolated from Mono Lake water into a defined salts medium with selenate, arsenite, and yeast extract. This strain does not grow chemoautotrophically, but it catalyzes the oxidation of arsenite during growth on an organic carbon source with selenate. No arsenate was produced in pure cultures amended with arsenite and nitrate or oxygen, indicating that the process is selenate dependent. Experiments with washed cells in mineral medium demonstrated that the oxidation of arsenite is tightly coupled to the reduction of selenate. Strain ML-SRAO grows optimally on lactate with selenate or arsenate as the electron acceptor. The amino acid sequences deduced from the respiratory arsenate reductase gene (arrA) from strain ML-SRAO are highly similar (89 to 94%) to those from two previously isolated Mono Lake arsenate reducers. The 16S rRNA gene sequence of strain ML-SRAO places it within the Bacillus RNA group 6 of gram-positive bacteria having low G+C content.

  10. 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

    2013-03-28

    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.

  11. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

    PubMed Central

    Sorokin, Dimitry Y; Lücker, Sebastian; Vejmelkova, Dana; Kostrikina, Nadezhda A; Kleerebezem, Robbert; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Le Paslier, Denis; Muyzer, Gerard; Wagner, Michael; van Loosdrecht, Mark C M; Daims, Holger

    2012-01-01

    Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25–63 °C) and low affinity for nitrite (Ks=1 mℳ), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO2, and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO2 fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems. PMID:22763649

  12. 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

  13. 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

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

    PubMed

    Wahman, David G; Speitel, Gerald E

    2015-01-01

    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 biological hydroxylamine oxidation to nitrite. In addition, monochloramine and hydroxylamine abiotically react, providing AOB a potential benefit by removing the disinfectant (monochloramine) and releasing growth substrate (ammonia). Alternatively and because biological hydroxylamine oxidation supplies the electrons (reductant) required for biological ammonia oxidation, the monochloramine/hydroxylamine abiotic reaction represents a possible inactivation mechanism by consuming hydroxylamine and inhibiting reductant generation. To investigate the abiotic monochloramine and hydroxylamine reaction's impact on AOB activity, the current study used batch experiments with Nitrosomonas europaea (AOB pure culture), ammonia, monochloramine, and hydroxylamine addition. To decipher whether hydroxylamine addition benefitted N. europaea activity by (i) removing monochloramine and releasing free ammonia or (ii) providing an additional effect (possibly the aforementioned reductant source), a previously developed cometabolism model was coupled with an abiotic monochloramine and hydroxylamine model for data interpretation. N. europaea maintained ammonia oxidizing activity when hydroxylamine was added before complete ammonia oxidation cessation. The impact could not be accounted for by monochloramine removal and free ammonia release alone and was concentration dependent for both monochloramine and hydroxylamine. In addition, a preferential negative impact occurred for ammonia versus hydroxylamine oxidation. These results suggest an additional benefit of exogenous hydroxylamine addition beyond monochloramine removal and free ammonia release, possibly providing reductant generation.

  16. A comparison of NO and N2O production by the autotrophic nitrifier Nitrosomonas europaea and the heterotrophic nitrifier Alcaligenes faecalis.

    PubMed Central

    Anderson, I C; Poth, M; Homstead, J; Burdige, D

    1993-01-01

    Soil microorganisms are important sources of the nitrogen trace gases NO and N2O for the atmosphere. Present evidence suggests that autotrophic nitrifiers such as Nitrosomonas europaea are the primary producers of NO and N2O in aerobic soils, whereas denitrifiers such as Pseudomonas spp. or Alcaligenes spp. are responsible for most of the NO and N2O emissions from anaerobic soils. It has been shown that Alcaligenes faecalis, a bacterium common in both soil and water, is capable of concomitant heterotrophic nitrification and denitrification. This study was undertaken to determine whether heterotrophic nitrification might be as important a source of NO and N2O as autotrophic nitrification. We compared the responses of N. europaea and A. faecalis to changes in partial O2 pressure (pO2) and to the presence of typical nitrification inhibitors. Maximal production of NO and N2O occurred at low pO2 values in cultures of both N. europaea (pO2, 0.3 kPa) and A. faecalis (pO2, 2 to 4 kPa). With N. europaea most of the NH4+ oxidized was converted to NO2-, with NO and N2O accounting for 2.6 and 1% of the end product, respectively. With A. faecalis maximal production of NO occurred at a pO2 of 2 kPa, and maximal production of N2O occurred at a pO2 of 4 kPa. At these low pO2 values there was net nitrite consumption. Aerobically, A. faecalis produced approximately the same amount of NO but 10-fold more N2O per cell than N. europaea did. Typical nitrification inhibitors were far less effective for reducing emissions of NO and N2O by A. faecalis than for reducing emissions of NO and N2O by N. europaea.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8285659

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

    PubMed Central

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

    2006-01-01

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

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

    PubMed

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

    2011-02-01

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

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

    PubMed

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

    2009-05-01

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

  1. 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

  2. Engineering of Nitrosomonas europaea to express Vitreoscilla hemoglobin enhances oxygen uptake and conversion of ammonia to nitrite.

    PubMed

    Kunkel, Stephanie A; Pagilla, Krishna R; Stark, Benjamin C

    2015-12-01

    Nitrosomonas europaea was transformed with a recombinant plasmid bearing the gene (vgb) encoding the hemoglobin (VHb) from the bacterium Vitreoscilla under control of the N. europaea amoC P1 promoter. Vgb was maintained stably and appeared to be expressed in the transformants at VHb levels of about 0.75 nmol/g wet weight. Expression of VHb in the N. europaea transformants was correlated with an approximately 2 fold increase in oxygen uptake rate by whole cells at oxygen concentrations in the range of 75-100% saturation, but no change in oxygen uptake rate at oxygen concentrations below 25% saturation. VHb expression was also correlated with an increase of as much as about 30% in conversion of ammonia to nitrite by growing cells. The results suggest that engineering of key aerobic wastewater bacteria to express bacterial hemoglobins may be a useful strategy to produce species with enhanced respiratory abilities.

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

    SciTech Connect

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

    1983-04-01

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

  4. DNA microarray mediated transcriptional profiling of Nitrosomonas europaea in response to linear alkylbenzene sulfonates.

    PubMed

    Urakawa, Hidetoshi; Matsumoto, Junpei; Inaba, Kazuho; Tsuneda, Satoshi

    2008-05-01

    Linear alkylbenzene sulfonates (LAS) constitute, quantitatively, the most important group of synthetic surfactants used today. We studied the gene expression of Nitrosomonas europaea in response to LAS using a DNA microarray because ammonia-oxidizers are thought to be more sensitive to LAS than other microorganisms. Our objective was to elucidate which genes are expressed for N. europaea in response to LAS exposure. Microarray analysis and real-time PCR assay revealed that c. 30 genes were significantly expressed after LAS exposure, in particular genes associated with energy production and conversion. Our findings demonstrate that physical disruption of membrane structures, which contain enzymes associated with energy production and conversion, might be an important explanation for the high sensitivity of N. europaea to LAS exposure.

  5. Role of Hydrophobicity in Adhesion of the Dissimilatory Fe(III)-Reducing Bacterium Shewanella alga to Amorphous Fe(III) Oxide

    PubMed Central

    Caccavo, F.; Schamberger, P. C.; Keiding, K.; Nielsen, P. H.

    1997-01-01

    The mechanisms by which the dissimilatory Fe(III)-reducing bacterium Shewanella alga adheres to amorphous Fe(III) oxide were examined through comparative analysis of S. alga BrY and an adhesion-deficient strain of this species, S. alga RAD20. Approximately 100% of S. alga BrY cells typically adhered to amorphous Fe(III) oxide, while less than 50% of S. alga RAD20 cells adhered. Bulk chemical analysis, isoelectric point analysis, and cell surface analysis by time-of-flight secondary-ion mass spectrometry and electron spectroscopy for chemical analysis demonstrated that the surfaces of S. alga BrY cells were predominantly protein but that the surfaces of S. alga RAD20 cells were predominantly exopolysaccharide. Physicochemical analyses and hydrophobic interaction assays demonstrated that S. alga BrY cells were more hydrophobic than S. alga RAD20 cells. This study represents the first quantitative analysis of the adhesion of a dissimilatory Fe(III)-reducing bacterium to amorphous Fe(III) oxide, and the results collectively suggest that hydrophobic interactions are a factor in controlling the adhesion of this bacterium to amorphous Fe(III) oxide. Despite having a reduced ability to adhere, S. alga RAD20 reduced Fe(III) oxide at a rate identical to that of S. alga BrY. This result contrasts with results of previous studies by demonstrating that irreversible cell adhesion is not requisite for microbial reduction of amorphous Fe(III) oxide. These results suggest that the interaction between dissimilatory Fe(III)-reducing bacteria and amorphous Fe(III) oxide is more complex than previously believed. PMID:16535706

  6. Changes in ammonia oxidiser population during transition to low pH in a biofilm reactor starting with Nitrosomonas europaea.

    PubMed

    Tarre, S; Shlafman, E; Beliavski, M; Green, M

    2007-01-01

    Recent experiments in our laboratory using both biofilm and suspended biomass reactors have demonstrated high rate nitrification at low pH with known autotrophic nitrifying bacteria originating from wastewater treatment plants refuting previous assumptions that nitrification is significantly inhibited at low pH. Since much of the earlier microbiological work regarding ammonia oxidising bacteria (AOB) physiology was carried out using Nitrosomonas europaea, this model bacterium's capability for high rate nitrification at low pH in a continuous biofilm reactor was tested. A biofilm reactor filled with sintered glass particles was inoculated with a pure culture of N. europaea. The reactor was first operated to high nitrification rates under conditions favourable to N. europaea (pH > 7; high ammonium concentrations). To eliminate inhibitory concentrations of nitrite at low pH, an enriched culture of Nitrospira (a nitrite oxidising bacterium) was then added. The transition from neutral to acidic conditions was attempted by sharply lowering the nitrification rate and by using a feeding solution containing insufficient buffer for complete nitrification. As opposed to other successful transitions, the pH in the N. europaea/Nitrospira reactor initially dropped only slightly and maintained pH > 6 for over two weeks. The reactor reached pH 4.5 only after four weeks. FISH results showed that while the percent of AOB and Nitrospira to eubacteria remained relatively constant at 51.1 +/- 8.2% and 40.8 +/- 6.4%, respectively, the AOB community changed completely in 60 days from 100% N. europaea to 100% Nitrosomonas oligotropha. Even though N. oligotropha was not intentionally introduced into the reactor, it is apparently much better adapted to conditions of low pH.

  7. Physiological characteristics of the anaerobic ammonium-oxidizing bacterium 'Candidatus Brocadia sinica'.

    PubMed

    Oshiki, Mamoru; Shimokawa, Masaki; Fujii, Naoki; Satoh, Hisashi; Okabe, Satoshi

    2011-06-01

    The present study investigated the phylogenetic affiliation and physiological characteristics of bacteria responsible for anaerobic ammonium oxidization (anammox); these bacteria were enriched in an anammox reactor with a nitrogen removal rate of 26.0 kg N m(-3) day(-1). The anammox bacteria were identified as representing 'Candidatus Brocadia sinica' on the basis of phylogenetic analysis of rRNA operon sequences. Physiological characteristics examined were growth rate, kinetics of ammonium oxidation and nitrite reduction, temperature, pH and inhibition of anammox. The maximum specific growth rate (μ(max)) was 0.0041 h(-1), corresponding to a doubling time of 7 days. The half-saturation constants (K(s)) for ammonium and nitrite of 'Ca. B. sinica' were 28±4 and 86±4 µM, respectively, higher than those of 'Candidatus Brocadia anammoxidans' and 'Candidatus Kuenenia stuttgartiensis'. The temperature and pH ranges of anammox activity were 25-45 °C and pH 6.5-8.8, respectively. Anammox activity was inhibited in the presence of nitrite (50 % inhibition at 16 mM), ethanol (91 % at 1 mM) and methanol (86 % at 1 mM). Anammox activities were 80 and 70 % of baseline in the presence of 20 mM phosphorus and 3 % salinity, respectively. The yield of biomass and dissolved organic carbon production in the culture supernatant were 0.062 and 0.005 mol C (mol NH (+)(-4))(-1), respectively. This study compared physiological differences between three anammox bacterial enrichment cultures to provide a better understanding of anammox niche specificity in natural and man-made ecosystems.

  8. Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor.

    PubMed

    Thandar, Soe Myat; Ushiki, Norisuke; Fujitani, Hirotsugu; Sekiguchi, Yuji; Tsuneda, Satoshi

    2016-01-01

    Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor. The pure culture of N. mobilis Ms1 was cultivated in liquid mineral medium with 30 mg-N L(-1) (2.14 mM) of ammonium at room temperature under dark conditions. The optimum growth of N. mobilis Ms1 occurred at 27°C and pH 8, with a maximum growth rate of 0.05-0.07 h(-1), which corresponded to a generation time of 10-14 h. The half saturation constant for ammonium uptake rate and the maximum ammonium uptake rate of N. mobilis Ms1 were 30.70 ± 0.51 μM NH4(+) and 0.01 ± 0.002 pmol NH4(+) cells(-1) h(-1), respectively. N. mobilis Ms1 had higher ammonia oxidation activity than N. europaea in this study. The oxygen uptake activity kinetics of N. mobilis Ms1 were Km(O2) = 21.74 ± 4.01 μM O2 and V max(O2) = 0.06 ± 0.02 pmol O2 cells(-1) h(-1). Ms1 grew well at ammonium and NaCl concentrations of up to 100 and 500 mM, respectively. The nitrite tolerance of N. mobilis Ms1 was extremely high (up to 300 mM) compared to AOB previously isolated from activated sludge and wastewater treatment plants. The average nucleotide identity between the genomes of N. mobilis Ms1 and other Nitrosomonas species indicated that N. mobilis Ms1 was distantly related to other Nitrosomonas species. The organization of the genes encoding protein inventory involved in ammonia oxidation and nitrifier denitrification processes were different from other Nitrosomonas species. The current

  9. Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor

    PubMed Central

    Thandar, Soe Myat; Ushiki, Norisuke; Fujitani, Hirotsugu; Sekiguchi, Yuji; Tsuneda, Satoshi

    2016-01-01

    Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor. The pure culture of N. mobilis Ms1 was cultivated in liquid mineral medium with 30 mg-N L-1 (2.14 mM) of ammonium at room temperature under dark conditions. The optimum growth of N. mobilis Ms1 occurred at 27°C and pH 8, with a maximum growth rate of 0.05–0.07 h-1, which corresponded to a generation time of 10–14 h. The half saturation constant for ammonium uptake rate and the maximum ammonium uptake rate of N. mobilis Ms1 were 30.70 ± 0.51 μM NH4+ and 0.01 ± 0.002 pmol NH4+ cells-1 h-1, respectively. N. mobilis Ms1 had higher ammonia oxidation activity than N. europaea in this study. The oxygen uptake activity kinetics of N. mobilis Ms1 were Km(O2) = 21.74 ± 4.01 μM O2 and V max(O2) = 0.06 ± 0.02 pmol O2 cells-1 h-1. Ms1 grew well at ammonium and NaCl concentrations of up to 100 and 500 mM, respectively. The nitrite tolerance of N. mobilis Ms1 was extremely high (up to 300 mM) compared to AOB previously isolated from activated sludge and wastewater treatment plants. The average nucleotide identity between the genomes of N. mobilis Ms1 and other Nitrosomonas species indicated that N. mobilis Ms1 was distantly related to other Nitrosomonas species. The organization of the genes encoding protein inventory involved in ammonia oxidation and nitrifier denitrification processes were different from other Nitrosomonas species. The current study

  10. Removal of multi-heavy metals using biogenic manganese oxides generated by a deep-sea sedimentary bacterium - Brachybacterium sp. strain Mn32.

    PubMed

    Wang, Wenming; Shao, Zongze; Liu, Yanjun; Wang, Gejiao

    2009-06-01

    A deep-sea manganese-oxidizing bacterium, Brachybacterium sp. strain Mn32, showed high Mn(II) resistance (MIC 55 mM) and Mn(II)-oxidizing/removing abilities. Strain Mn32 removed Mn(II) by two pathways: (1) oxidizing soluble Mn(II) to insoluble biogenic Mn oxides - birnessite (delta-MnO(2) group) and manganite (gamma-MnOOH); (2) the biogenic Mn oxides further adsorb more Mn(II) from the culture. The generated biogenic Mn oxides surround the cell surfaces of strain Mn32 and provide a high capacity to adsorb Zn(II) and Ni(II). Mn(II) oxidation by strain Mn32 was inhibited by both sodium azide and o-phenanthroline, suggesting the involvement of a metalloenzyme which was induced by Mn(II). X-ray diffraction analysis showed that the crystal structures of the biogenic Mn oxides were different from those of commercial pyrolusite (beta-MnO(2) group) and fresh chemically synthesized vernadite (delta-MnO(2) group). The biogenic Mn oxides generated by strain Mn32 showed two to three times higher Zn(II) and Ni(II) adsorption abilities than commercial and fresh synthetic MnO(2). The crystal structure and the biogenic MnO(2) types may be important factors for the high heavy metal adsorption ability of strain Mn32. This study provides potential applications of a new marine Mn(II)-oxidizing bacterium in heavy metal bioremediation and increases our basic knowledge of microbial manganese oxidation mechanisms.

  11. Phylogeny and functional expression of ribulose 1,5-bisphosphate carboxylase/oxygenase from the autotrophic ammonia-oxidizing bacterium Nitrosospira sp. isolate 40KI.

    PubMed

    Utåker, Janne B; Andersen, Kjell; Aakra, Agot; Moen, Birgitte; Nes, Ingolf F

    2002-01-01

    The autotrophic ammonia-oxidizing bacteria (AOB), which play an important role in the global nitrogen cycle, assimilate CO(2) by using ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we describe the first detailed study of RubisCO (cbb) genes and proteins from the AOB. The cbbLS genes from Nitrosospira sp. isolate 40KI were cloned and sequenced. Partial sequences of the RubisCO large subunit (CbbL) from 13 other AOB belonging to the beta and gamma subgroups of the class Proteobacteria are also presented. All except one of the beta-subgroup AOB possessed a red-like type I RubisCO with high sequence similarity to the Ralstonia eutropha enzyme. All of these new red-like RubisCOs had a unique six-amino-acid insert in CbbL. Two of the AOB, Nitrosococcus halophilus Nc4 and Nitrosomonas europaea Nm50, had a green-like RubisCO. With one exception, the phylogeny of the AOB CbbL was very similar to that of the 16S rRNA gene. The presence of a green-like RubisCO in N. europaea was surprising, as all of the other beta-subgroup AOB had red-like RubisCOs. The green-like enzyme of N. europaea Nm50 was probably acquired by horizontal gene transfer. Functional expression of Nitrosospira sp. isolate 40KI RubisCO in the chemoautotrophic host R. eutropha was demonstrated. Use of an expression vector harboring the R. eutropha cbb control region allowed regulated expression of Nitrosospira sp. isolate 40KI RubisCO in an R. eutropha cbb deletion strain. The Nitrosospira RubisCO supported autotrophic growth of R. eutropha with a doubling time of 4.6 h. This expression system may allow further functional analysis of AOB cbb genes.

  12. Phylogeny and Functional Expression of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from the Autotrophic Ammonia-Oxidizing Bacterium Nitrosospira sp.Isolate 40KI

    PubMed Central

    Utåker, Janne B.; Andersen, Kjell; Aakra, Ågot; Moen, Birgitte; Nes, Ingolf F.

    2002-01-01

    The autotrophic ammonia-oxidizing bacteria (AOB), which play an important role in the global nitrogen cycle, assimilate CO2 by using ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we describe the first detailed study of RubisCO (cbb) genes and proteins from the AOB. The cbbLS genes from Nitrosospira sp. isolate 40KI were cloned and sequenced. Partial sequences of the RubisCO large subunit (CbbL) from 13 other AOB belonging to the β and γ subgroups of the class Proteobacteria are also presented. All except one of the β-subgroup AOB possessed a red-like type I RubisCO with high sequence similarity to the Ralstonia eutropha enzyme. All of these new red-like RubisCOs had a unique six-amino-acid insert in CbbL. Two of the AOB, Nitrosococcus halophilus Nc4 and Nitrosomonas europaea Nm50, had a green-like RubisCO. With one exception, the phylogeny of the AOB CbbL was very similar to that of the 16S rRNA gene. The presence of a green-like RubisCO in N. europaea was surprising, as all of the other β-subgroup AOB had red-like RubisCOs. The green-like enzyme of N. europaea Nm50 was probably acquired by horizontal gene transfer. Functional expression of Nitrosospira sp. isolate 40KI RubisCO in the chemoautotrophic host R. eutropha was demonstrated. Use of an expression vector harboring the R. eutropha cbb control region allowed regulated expression of Nitrosospira sp. isolate 40KI RubisCO in an R. eutropha cbb deletion strain. The Nitrosospira RubisCO supported autotrophic growth of R. eutropha with a doubling time of 4.6 h. This expression system may allow further functional analysis of AOB cbb genes. PMID:11751824

  13. 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).

  14. Emergence of Competitive Dominant Ammonia-Oxidizing Bacterial Populations in a Full-Scale Industrial Wastewater Treatment Plant

    PubMed Central

    Layton, Alice C.; Dionisi, Hebe; Kuo, H.-W.; Robinson, Kevin G.; Garrett, Victoria M.; Meyers, Arthur; Sayler, Gary S.

    2005-01-01

    Ammonia-oxidizing bacterial populations in an industrial wastewater treatment plant were investigated with amoA and 16S rRNA gene real-time PCR assays. Nitrosomonas nitrosa initially dominated, but over time RI-27-type ammonia oxidizers, also within the Nitrosomonas communis lineage, increased from below detection to codominance. This shift occurred even though nitrification remained constant. PMID:15691975

  15. 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

  16. Biochemical studies of a soxF-encoded monomeric flavoprotein purified from the green sulfur bacterium Chlorobaculum tepidum that stimulates in vitro thiosulfate oxidation.

    PubMed

    Ogawa, Takuro; Furusawa, Toshinari; Shiga, Michiko; Seo, Daisuke; Sakurai, Hidehiro; Inoue, Kazuhito

    2010-01-01

    In the green sulfur bacterium Chlorobaculum tepidum, three sulfur oxidizing enzyme system (Sox) proteins, SoxAXK, SoxYZ, and SoxB (the core TOMES, thiosulfate oxidizing multi-enzyme system) are essential to in vitro thiosulfate oxidation. We purified monomeric flavoprotein SoxF from this bacterium, which had sulfide dehydrogenase activity. SoxF enhanced the thiosulfate oxidation activity of the purified core TOMES with various cytochromes as electron acceptors to different degrees without any change in the affinity for thiosulfate. The apparent reaction rates with 50 microM- C. tepidum cytochrome c-554 were slightly higher than with horse-heart cytochrome c, and the addition of 0.5 microM- SoxF increased the rate by 92%. The rates with 50 microM- horse-heart cytochrome c and 50 muM- horse-heart cytochrome c plus 0.5 muM- cytochrome c-554 were increased by SoxF by 31% and 120% respectively. We conclude that SoxF mediates electron transfer between the components of core TOMES and externally added cytochromes.

  17. 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

  18. Immobilization of iron- and manganese-oxidizing bacteria with a biofilm-forming bacterium for the effective removal of iron and manganese from groundwater.

    PubMed

    Li, Chunyan; Wang, Shuting; Du, Xiaopeng; Cheng, Xiaosong; Fu, Meng; Hou, Ning; Li, Dapeng

    2016-11-01

    In this study, three bacteria with high Fe- and Mn-oxidizing capabilities were isolated from groundwater well sludge and identified as Acinetobacter sp., Bacillus megaterium and Sphingobacterium sp. The maximum removal ratios of Fe and Mn (99.75% and 96.69%) were obtained by an optimal combination of the bacteria at a temperature of 20.15°C, pH 7.09 and an inoculum size of 2.08%. Four lab-scale biofilters were tested in parallel for the removal of iron and manganese ions from groundwater. The results indicated that the Fe/Mn removal ratios of biofilter R4, which was inoculated with iron- and manganese-oxidizing bacteria and a biofilm-forming bacterium, were approximately 95% for each metal during continuous operation and were better than the other biofilters. This study demonstrated that the biofilm-forming bacterium could promote the immobilization of the iron- and manganese-oxidizing bacteria on the biofilters and enhance the removal efficiency of iron and manganese ions from groundwater.

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

    DOE PAGES

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

    2015-11-19

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

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

    DOE PAGES

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

    2015-10-26

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

  1. A potentiometric flow biosensor based on ammonia-oxidizing bacteria for the detection of toxicity in water.

    PubMed

    Zhang, Qianyu; Ding, Jiawang; Kou, Lijuan; Qin, Wei

    2013-05-24

    A flow biosensor for the detection of toxicity in water using the ammonia-oxidizing bacterium (AOB) Nitrosomonas europaea as a bioreceptor and a polymeric membrane ammonium-selective electrode as a transducer is described. The system is based on the inhibition effects of toxicants on the activity of AOB, which can be evaluated by measuring the ammonium consumption rates with the ammonium-selective membrane electrode. The AOB cells are immobilized on polyethersulfone membranes packed in a holder, while the membrane electrode is placed downstream in the flow cell. Two specific inhibitors of the ammonia oxidation-allylthiourea and thioacetamide-have been tested. The IC50 values defined as the concentration of an inhibitor causing a 50% reduction in the ammonia oxidation activity have been measured as 0.17 μM and 0.46 μM for allylthiourea and thioacetamide, respectively. The proposed sensor offers advantages of simplicity, speed and high sensitivity for measuring toxicity in water.

  2. Physiological and transcriptional responses of Nitrosomonas europaea to toluene and benzene inhibition.

    PubMed

    Radniecki, Tyler S; Dolan, Mark E; Semprini, Lewis

    2008-06-01

    Ammonia oxidizing bacteria (AOB) are inhibited by many compounds found in wastewater treatment plant (WWTP) influent, including aromatic hydrocarbons. The detection of "sentinel genes" to identify the presence of aromatic hydrocarbons could be useful to WWTP operators. In this study, the transcriptomic responses of Nitrosomonas europaea during the cometabolism of benzene to phenol and toluene to benzyl alcohol and benzaldehyde were evaluated using whole genome Affymetrix microarrays and qRT-PCR. Benzyl alcohol and benzaldehyde were found not to inhibit N. europaea. However, phenol concentrations as low as 5 microM directly inhibited ammonia oxidation. Surprisingly, there were no significant up- or down-regulation of genes in N. europaea cells exposed to 20 microM toluene, which caused 50% inhibition of ammonia oxidation. Exposing N. europaea to 40 microM benzene, which caused a similar degree of inhibition, resulted in the up-regulation of seven adjacent genes, including NE 1545 (a putative pirin protein) and NE 1546 (a putative membrane protein), that appear to be involved with fatty-acid metabolism, lipid biosynthesis, and membrane protein synthesis. qRT-PCR analysis revealed that NE 1545 and NE 1546 were significantly up-regulated upon exposure to benzene and phenol, but not upon exposure to toluene. Transmission electron microscope images revealed a shift in outer cell structure in response to benzene exposure.

  3. X- and Q-band EPR Studies of the Tetraheme Cytochrome c554 from Nitrosomonas europaea

    NASA Astrophysics Data System (ADS)

    Petasis, Doros; Culver, Caleb; Hendrich, Michael

    2001-04-01

    Cytochrome c554 (cyt c554) is a tetraheme cytochrome from the bacteria Nitrosomonas europaea that participate in the assimilation of nitrogen into plants from industrially fixed Nsub2 by oxidizing ammonia to nitrite. These autotrophic bacteria metabolize ammonia as the sole source of energy through a two-step process. In the first step, the membrane-bound enzyme ammonia monooxygenase (AMO) catalyzes the oxidation of ammonia to hydroxylamine (NH3+O2+2e-+2H+ä_NH2OH+H2O). In the second step, hydroxylamine oxidoreductase (HAO) oxidizes hydroxylamine to nitrite (NH2OH+H2Oä_NO2-+4e-+5H+). Cyt c554 accepts electrons from HAO and transports them to either AMO or the ubiquinone pool. HAO is one of the most complicated heme systems known, consisting of 24 hemes in a circular arrangement. A large region of HAO matches the tertiary structure of cyt c554, so determining the electronic structure of the simpler protein cyt c554 will help in understanding the electronic structure of the active site of the more complex HAO enzyme. We have collected perpendicular and parallel mode EPR data at X- and Q-band frequencies (9 and 34 GHz respectively) of the native cyt c554 protein and a series of reduced samples in an effort to understand the role of each heme in electron transport. The novel features of these spectra were simulated using techniques developed at CMU and will be discussed.

  4. The partial characterization of purified nitrite reductase and hydroxylamine oxidase from Nitrosomonas europaea

    PubMed Central

    Ritchie, G. A. F.; Nicholas, D. J. D.

    1974-01-01

    Nitrite reductase has been separated from cell-free extracts of Nitrosomonas and partially purified from hydroxylamine oxidase by polyacrylamide-gel electrophoresis. In its oxidized state the enzyme, which did not contain haem, had an extinction maximum at 590nm, which was abolished on reduction. Sodium diethyldithiocarbamate was a potent inhibitor of nitrite reductase. Enzyme activity was stimulated 2.5-fold when remixed with hydroxylamine oxidase, but was unaffected by mammalian cytochrome c. The enzyme also exhibited a low hydroxylamine-dependent nitrite reductase activity. The results suggest that this enzyme is similar to the copper-containing `denitrifying enzyme' of Pseudomonas denitrificans. A dithionite-reduced, 465nm-absorbing haemoprotein was associated with homogeneous preparations of hydroxylamine oxidase. The band at 465nm maximum was not reduced during the oxidation of hydroxylamine although the extinction was abolished on addition of hydroxylamine, NO2− or CO. These last-named compounds when added to the oxidized enzyme precluded the appearance of the 465nm-absorption band on addition of dithionite. Several properties of 465nm-absorbing haemoprotein are described. PMID:4154745

  5. [A novel bacterium carrying out anaerobic ammonium oxidation in a reactor for biological treatment of the filtrate of wastewater fermented residue].

    PubMed

    Khramenkov, S V; Kozlov, M N; Krevbona, M V; Drofeev, A G; Kazakova, E A; Grachev, V A; Kuznetsov, B B; Poliakov, D Iu; Nikolaev, Iu A

    2013-01-01

    A new genus and species of bacteria capable of ammonium oxidation under anaerobic conditions in the presence of nitrite is described. The enrichment culture was obtained from the Moscow River silt by sequential cultivation in reactors with selective conditions for anaerobic ammonium oxidation. Bacterial cells were coccoid, -0.4 x 0.7 mm, with the intracellular membrane structures typical of bacteria capable of anaerobic ammonium oxidation (anammoxosome and paryphoplasm). The cells formed aggregates 5-25 μm in diameter (10 μm on average). They were readily adhered to solid surfaces. The cells were morphologically labile, they easily lost their content and changed their morphology during fixation for electron microscopy. The organism was capable of ammonium oxidation with nitrite. The semisaturation constants Ks for nitrite and ammonium were 0.38 mg N-NO2/L and 0.41 mg N-NH4/L, respectively. The maximal nitrite concentrations for growth were 90 and 75 mg N-NO2/L for single and continuous application, respectively. The doubling time was 32 days, μ(max) = 0.022 day(-1), the optimal temperature and pH were 20 degrees C and 7.8-8.3, respectively. According to the 16S rRNA gene sequencing, the bacterium was assigned to a new genus and species within the phylum Planctomycetes. The proposed name for the new bacterium is Candidatus Anammoximicrobium moscowii gen. nov., sp. nov. (a microorganisms carrying out anaerobia ammonium oxidation, isolated in the Moscow region).

  6. 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.

  7. Transcription of genes coding for metabolic key functions in Nitrosomonas europaea during aerobic and anaerobic growth.

    PubMed

    Beyer, Sonja; Gilch, Stefan; Meyer, Ortwin; Schmidt, Ingo

    2009-01-01

    Nitrosomonas europaea can grow under conditions of chemolithoautotrophic aerobic (oxygen as oxidant) as well as anaerobic [nitrogen dioxide (NO(2)) as oxidant] nitrification or chemoorganotrophic anaerobic pyruvate-dependent denitrification. In this study, the adaptation of the transcription (mRNA synthesis/concentration) of N. europaea to aerobic and anaerobic growth conditions was evaluated and the transcription of genes coding for metabolic key functions was analyzed: nitrogen and energy metabolism (amoA, hao, rh1, nirK, norB, nsc, aceE, ldhA, ppc, gltA, odhA, coxA), carbon dioxide fixation (cbbL), gluconeogenesis (ppsA), cell growth (ftsZ), and oxidative stress (sodB). During aerobic ammonia oxidation the specific activities of ammonia oxidation, nitrite reduction, and the growth rates correlated with the transcription level of the corresponding genes amoA/hao, nirK/norB/nsc, and cbbL/ftsZ. In anaerobically ammonia-oxidizing cells of N. europaea, the cellular mRNA concentrations of amoA, hao, rh1,coxA, cbbL, ftsZ, and sodB were reduced compared with aerobically nitrifying cells, but the mRNA levels of nirK, norB, and nsc were significantly increased. During anaerobic pyruvate-dependent denitrification, the mRNA abundance of nirK, norB, nsc, aceE, gltA, and odhA was increased, while the concentrations of amoA,hao, rh1, coxAcbbL, ftsZ, and sodB were significantly reduced. Temperature, pH value, and NH(4)(+), O(2), NO, and NO(2) concentrations had comparatively small effects on the transcription of the studied genes.

  8. /sup 15/N kinetic analysis of N/sub 2/O production by Nitrosomonas europaea: an examination of nitrifier denitrification

    SciTech Connect

    Poth, M.; Focht, D.D.

    1985-05-01

    A series of /sup 15/N isotope tracer experiments showed that Nitrosomonas europaea produces nitrous oxide only under oxygen-limiting conditions and that the labeled N from nitrite, but not nitrate, is incorporated into nitrous oxide, indicating the presence of the denitrifying enzyme nitrite reductase. A kinetic analysis of the m/z 44, 45, and 46 nitrous oxide produced by washed cell suspensions of N. europaea when incubated with 4 mM ammonium (99% /sup 14/N) and 0.4 mM nitrite (99% /sup 15/N) was performed. No labeled nitirte was reduced to ammonium. All labeled material added was accounted for as either nitrite or nitrous oxide. The hypothesis that nitrous oxide is produced directly from nitrification was rejected since (i) it does not allow for the large amounts of double-labeled (m/z 46) nitrous oxide observed; (ii) the observed patterns of m/z 44, 45, 46 nitrous oxide were completely consistent with a kinetic analysis based on denitrification as the sole mechanism of nitrous oxide production but not with a kinetic analysis based on both mechanisms; (iii) the asymptotic ratio of m/z 45 to m/z 46 nitrous oxide was consistent with denitrification kinetics but inconsistent with nitrification kinetics, which predicted no limit to m/z 45 production. It is concluded that N. europaea is a denitrifier which, under conditions of oxygen stress, uses nitrite as a terminal electron acceptor and produces nitrous oxide.

  9. Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane.

    PubMed

    Gvakharia, Barbara O; Permina, Elizabeth A; Gelfand, Mikhail S; Bottomley, Peter J; Sayavedra-Soto, Luis A; Arp, Daniel J

    2007-05-01

    Upon exposure of Nitrosomonas europaea to chloroform (7 microM, 1 h), transcripts for 175 of 2,460 genes were found at higher levels in treated cells than in untreated cells and transcripts for 501 genes were found at lower levels. With chloromethane (3.2 mM, 1 h), transcripts for 67 genes were at higher levels and transcripts for 148 genes were at lower levels. Transcripts for 37 genes were at higher levels following both treatments and included genes for heat shock proteins, sigma-factors of the extracytoplasmic function subfamily, and toxin-antitoxin loci. N. europaea has higher levels of transcripts for a variety of defense genes when exposed to chloroform or chloromethane.

  10. Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

    PubMed Central

    Tian, Ren-Mao; Zhang, Weipeng; Cai, Lin; Wong, Yue-Him; Ding, Wei

    2017-01-01

    ABSTRACT As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a new deep-sea SOB group. Microscopic observations suggest that Gsub is probably an extracellular symbiont. Gsub has complete sulfide oxidation and carbon fixation pathways, suggesting a chemoautotrophic lifestyle. Comparative genomics with other sponge-associated SOB and free-living SOB revealed significant genome reduction in Gsub, characterized by the loss of genes for carbohydrate metabolism, motility, DNA repair, and osmotic stress response. Intriguingly, this scenario of genome reduction is highly similar to those of the endosymbionts in deep-sea clams. However, Gsub has retained genes for phage defense and protein secretion, with the latter potentially playing a role in interactions with the sponge host. In addition, we recovered the genome of an ammonia-oxidizing archaeon (AOA), which may carry out ammonia oxidation and carbon fixation within the sponge body. IMPORTANCE Sponges and their symbionts are important players in the biogeochemical cycles of marine environments. As a unique habitat within marine ecosystems, cold seeps have received considerable interest in recent years. This study explores the lifestyle of a new symbiotic SOB in a cold seep sponge. The results demonstrate that both this sponge symbiont and endosymbionts in deep-sea clams employ similar strategies of genome reduction. However, this bacterium has retained unique functions for immunity and defense

  11. 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.

  12. NO Reductase Activity of the Tetraheme Cytochrome c554 of Nitrosomonas europaea

    PubMed Central

    Upadhyay, Anup K.; Hooper, Alan B.; Hendrich, Michael P.

    2009-01-01

    The tetraheme cytochrome c554 (cyt c554) from Nitrosomonas europaea is believed to function as an electron-transfer protein from hydroxylamine oxidoreductase (HAO). We show here that cyt c554 also has significant NO reductase activity. The protein contains one high-spin and three low-spin c-type hemes. HAO catalyzed reduction of the cyt c554, ligand binding, intermolecular electron transfer, and kinetics of NO reduction by cyt c554 have been investigated. We detect the formation of a NO-bound ferrous heme species in cyt c554 by EPR and Mössbauer spectroscopies during the HAO catalyzed oxidation of hydroxylamine, indicating that N-oxide intermediates produced from HAO readily bind to cyt c554. In the half-reduced state of cyt c554, we detect a spin interaction between the [FeNO]7 state of heme 2 and the low-spin ferric state of heme 4. We find that ferrous cyt c554 will reduce NO at a rate greater than 16 s−1, which is comparable to rates of other known NO reductases. Carbon monoxide or nitrite are shown not to bind to the reduced protein, and previous results indicate the reactions with O2 are slow and that a variety of ligands will not bind in the oxidized state. Thus, the enzymatic site is highly selective for NO. The NO reductase activity of cyt c554 may be important during ammonia oxidation in N. europaea at low oxygen concentrations to detoxify NO produced by reduction of nitrite or incomplete oxidation of hydroxylamine. PMID:16569009

  13. Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling.

    PubMed

    Lidbury, Ian D E A; Murrell, J Colin; Chen, Yin

    2015-03-01

    Bacteria of the marine Roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are methylated amines (MA) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after N2 gas, in the oceans. We investigated if the marine heterotrophic bacterium, Ruegeria pomeroyi DSS-3, could utilise TMA and TMAO as a supplementary energy source and whether this trait had any beneficial effect on growth. In R. pomeroyi, catabolism of TMA and TMAO resulted in the production of intracellular ATP which in turn helped to enhance growth rate and growth yield as well as enhancing cell survival during prolonged energy starvation. Furthermore, the simultaneous use of two different exogenous energy sources led to a greater enhancement of chemoorganoheterotrophic growth. The use of TMA and TMAO primarily as an energy source resulted in the remineralisation of nitrogen in the form of ammonium, which could cross feed into another bacterium. This study provides greater insight into the microbial metabolism of MAs in the marine environment and how it may affect both nutrient flow within marine surface waters and the flux of these climatically important compounds into the atmosphere.

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

    PubMed Central

    Parro, Víctor; Moreno-Paz, Mercedes

    2003-01-01

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

  15. Functional and physiological evidence for a rhesus-type ammonia transporter in Nitrosomonas europaea.

    PubMed

    Weidinger, Kerstin; Neuhäuser, Benjamin; Gilch, Stefan; Ludewig, Uwe; Meyer, Ortwin; Schmidt, Ingo

    2007-08-01

    Ammonium transporters form a conserved family of transport proteins and are widely distributed among all domains of life. The genome of Nitrosomonas europaea codes for a single gene (rh1) that belongs to the family of the AMT/Rh ammonium transporters. For the first time, this study provides functional and physiological evidence for a rhesus-type ammonia transporter in bacteria (N. europaea). The methylammonium (MA) transport activity of N. europaea correlated with the Rh1 expression. The K(m) value for the MA uptake of N. europaea was 1.8+/-0.2 mM (pH 7.25), and the uptake was competitively inhibited by ammonium [K(i)(NH(4) (+)) 0.3+/-0.1 mM at pH 7.25]. The MA uptake rate was pH dependent, indicating that the uncharged form of MA is transported by Rh1. An effect of the glutamine synthetase on the MA uptake was not observed. When expressed in Saccharomyces cerevisiae, the function of Rh1 from N. europaea as an ammonia/MA transporter was confirmed. The results suggest that Rh1 equilibrates the uncharged substrate species. A low pH value in the periplasmic space during ammonia oxidation seems to be responsible for the ammonium accumulation functioning as an acid NH(4) (+) trap.

  16. Influence of bovine serum albumin and alginate on silver nanoparticle dissolution and toxicity to Nitrosomonas europaea.

    PubMed

    Ostermeyer, Ann-Kathrin; Kostigen Mumuper, Cameron; Semprini, Lewis; Radniecki, Tyler

    2013-12-17

    Bovine serum albumin (BSA), a model protein, reduced the toxicity of 20 nm citrate silver nanoparticles (AgNP) toward Nitrosomonas europaea, a model ammonia oxidizing bacteria, through a dual-mode protection mechanism. BSA reduced AgNP toxicity by chelating the silver ions (Ag(+)) released from the AgNPs. BSA further reduced AgNP toxicity by binding to the AgNP surface thus preventing NH3-dependent dissolution from occurring. Due to BSA's affinity toward Ag(+) chemisorbed on the AgNP surface, increased concentrations of BSA lead to increased AgNP dissolution rates. This, however, did not increase AgNP toxicity as the dissolved Ag(+) were adsorbed onto the BSA molecules. Alginate, a model extracellular polysaccharide (EPS), lacks strong Ag(+) ligands and was unable to protect N. europaea from Ag(+) toxicity. However, at high concentrations, alginate reduced AgNP toxicity by binding to the AgNP surface and reducing AgNP dissolution rates. Unlike BSA, alginate only weakly interacted with the AgNP surface and was unable to completely prevent NH3-dependent AgNP dissolution from occurring. Based on these results, AgNP toxicity in high protein environments (e.g., wastewater) is expected to be muted while the EPS layers of wastewater biofilms may provide additional protection from AgNPs, but not from Ag(+) that have already been released.

  17. Crystallization and preliminary X-ray crystallographic analysis of a new crystal form of hydroxylamine oxidoreductase from Nitrosomonas europaea.

    PubMed

    Cedervall, Peder E; Hooper, Alan B; Wilmot, Carrie M

    2009-12-01

    Hydroxylamine oxidoreductase (HAO) from Nitrosomonas europaea is a homotrimeric protein that catalyzes the oxidation of hydroxylamine to nitrite. Each monomer, with a molecular weight of 67.1 kDa, contains seven c-type hemes and one heme P460, the porphyrin ring of which is covalently linked to a tyrosine residue from an adjacent subunit. HAO was first crystallized and structurally characterized at a resolution of 2.8 A in 1997. The structure was solved in space group P6(3) and suffered from merohedral twinning. Here, a crystallization procedure is presented that yielded untwinned crystals belonging to space group P2(1)2(1)2, which diffracted to 2.25 A resolution and contained one trimer in the asymmetric unit. The unit-cell parameters were a = 140.7, b = 142.6, c = 107.4 A.

  18. Electron paramagnetic studies of the copper and iron containing soluble ammonia monooxygenase from Nitrosomonas europaea.

    PubMed

    Gilch, Stefan; Meyer, Ortwin; Schmidt, Ingo

    2010-08-01

    Soluble ammonia monooxygenase (AMO) from Nitrosomonas europaea was purified to homogeneity and metals in the active sites of the enzyme (Cu, Fe) were analyzed by electron paramagnetic resonance (EPR) spectroscopy. EPR spectra were obtained for a type 2 Cu(II) site with g(parallel) = 2.24, A(parallel) = 18.4 mT and g(perpendicular) = 2.057 as well as for heme and non heme iron present in purified soluble AMO from N. europaea. A second type 2 Cu(II) EPR signal with g(parallel) = 2.29, A(parallel) = 16.1 mT and g(perpendicular) = 2.03 appeared in the spectrum of the ferricyanide oxidized enzyme and was attributed to oxidation of cuprous sites. Comparison of EPR-detectable Cu(2+) with total copper determined by inductively coupled plasma-mass spectrometry (ICP-MS) suggests that there are six paramagnetic Cu(2+) and three diamagnetic Cu(1+) per heterotrimeric soluble AMO (two paramagnetic and one diamagnetic Cu per alphabetagamma-protomer). A trigonal EPR signal at g = 6.01, caused by a high-spin iron, indicative for cytochrome bound iron, and a rhombic signal at g = 4.31, characteristic of specifically bound Fe(3+) was detectable. The binding of nitric oxide in the presence of reductant resulted in a ferrous S = 3/2 signal, characteristic of a ferrous nitrosyl complex. Inactivation of soluble AMO with acetylene did neither diminish the ferrous signal nor the intensity of the Cu(2+)-EPR signal.

  19. Fe(II)EDTA-NO reduction coupled with Fe(II)EDTA oxidation by a nitrate- and Fe(III)-reducing bacterium.

    PubMed

    Dong, Xiyang; Zhang, Yu; Zhou, Jiti; Chen, Mingxiang; Wang, Xiaojun; Shi, Zhuang

    2013-06-01

    The nitrate- and Fe(III)-reducing bacterium Paracoccus versutus LYM was characterized in terms of its ability to perform Fe(II)EDTA-NO reduction coupled with Fe(II)EDTA oxidation (NO-dependent Fe(II)EDTA oxidation, NDFO). It experienced a single anaerobic FeEDTA redox cycling through NDFO and dissimilatory Fe(III)EDTA reduction in FeEDTA culture. The increase in the Fe(II)EDTA concentration contributed to the ascending Fe(II)EDTA-NO reduction rate. The amount of glucose controlled the rate and extent of Fe(II) oxidation during NDFO. Without glucose addition, Fe(II)EDTA-NO reduction rate was at a rather slow rate even in presence of relatively sufficient Fe(II)EDTA. Unlike aqueous Fe(2+) and solid-phase Fe(II), Fe(II)EDTA could prevent cells from encrustations. These findings suggested the occurrence of NDFO preferred being beneficial via a mixotrophic physiology in the presence of an organic cosubstrate to being out of consideration for metabolic strategy.

  20. A soxA Gene, Encoding a Diheme Cytochrome c, and a sox Locus, Essential for Sulfur Oxidation in a New Sulfur Lithotrophic Bacterium

    PubMed Central

    Mukhopadhyaya, Pratap N.; Deb, Chirajyoti; Lahiri, Chandrajit; Roy, Pradosh

    2000-01-01

    A mobilizable suicide vector, pSUP5011, was used to introduce Tn5-mob in a new facultative sulfur lithotrophic bacterium, KCT001, to generate mutants defective in sulfur oxidation (Sox−). The Sox− mutants were unable to oxidize thiosulfate while grown mixotrophically in the presence of thiosulfate and succinate. The mutants were also impaired in oxidizing other reduced sulfur compounds and elemental sulfur as evident from the study of substrate oxidation by the whole cells. Sulfite oxidase activity was significantly diminished in the cell extracts of all the mutants. A soxA gene was identified from the transposon-adjacent genomic DNA of a Sox− mutant strain. The sequence analysis revealed that the soxA open reading frame (ORF) is preceded by a potential ribosome binding site and promoter region with −10- and −35-like sequences. The deduced nucleotide sequence of the soxA gene was predicted to code for a protein of 286 amino acids. It had a signal peptide of 26 N-terminal amino acids. The amino acid sequence showed similarity with a putative gene product of Aquifex aeolicus, soluble cytochrome c551 of Chlorobium limicola, and the available partial SoxA sequence of Paracoccus denitrificans. The soxA-encoded product seems to be a diheme cytochrome c for KCT001 and A. aeolicus, but the amino acid sequence of C. limicola cytochrome c551 revealed a single heme-binding region. Another transposon insertion mutation was mapped within the soxA ORF. Four other independent transposon insertion mutations were mapped in the 4.4-kb soxA contiguous genomic DNA region. The results thus suggest that a sox locus of KCT001, essential for sulfur oxidation, was affected by all these six independent insertion mutations. PMID:10894738

  1. Copper toxicity to bioluminescent Nitrosomonas europaea in soil is explained by the free metal ion activity in pore water.

    PubMed

    Ore, S; Mertens, J; Brandt, K K; Smolders, E

    2010-12-01

    The terrestrial biotic ligand model (BLM) for metal toxicity in soil postulates that metal toxicity depends on the free metal ion activity in solution and on ions competing for metal sorption to the biotic ligand. Unequivocal evidence for the BLM assumptions is most difficult to obtain for native soil microorganisms because the abiotic and biotic compartments cannot be experimentally separated. Here, we report copper (Cu) toxicity to a bioluminescent Nitrosomonas europaea reporter strain that was used in a solid phase-contact assay and in corresponding soil extracts and artificial soil solutions. The Cu(2+) ion activities that halve bioluminescence (EC50) in artificial solutions ranged 10(-5) to 10(-7) M and increased with increasing activities of H(+), Ca(2+) and Mg(2+) according to the BLM concept. The solution based Cu(2+) EC50 values of N. europaea in six contaminated soils ranged 2 × 10(-6) to 2 × 10(-9) M and these thresholds for both solid phase or soil extract based assays were well predicted by the ion competition model fitted to artificial solution data. In addition, solution based Cu(2+) EC50 of the solid phase-contact assay were never smaller than corresponding values in soil extracts suggesting no additional solid phase toxic route. By restricting the analysis to the same added species, we show that the Cu(2+) in solution represents the toxic species to this bacterium.

  2. Characterization of the ferrioxamine uptake system of Nitrosomonas europaea.

    PubMed

    Wei, Xueming; Sayavedra-Soto, Luis A; Arp, Daniel J

    2007-12-01

    The chemolithoautotroph Nitrosomonas europaea has two genes predicted to encode outer-membrane (OM) ferrioxamine transporters. Expression of the ferrioxamine uptake system required induction, as shown by the shorter lag phase in ferrioxamine-containing cultures when ferrioxamine-exposed cells were used as an inoculum. The two OM ferrioxamine siderophore transporters encoded by foxA(1) (NE1097) and foxA(2) (NE1088) were produced only in cells grown in Fe-limited ferrioxamine-containing medium. The inactivation of foxA(1), singly or in combination with foxA(2), prevented growth in Fe-limited medium containing excess desferrioxamine (DFX). The foxA(2)-disrupted single mutant grew poorly in the regular Fe-limited (0.2 microM) medium with 10 microM DFX, but grew well when the Fe level was raised to 1.0 microM with 10 microM DFX. For efficient acquisition of Fe-loaded ferrioxamine, N. europaea needs both ferrioxamine transporters FoxA(1) and FoxA(2). FoxA(1) probably regulates its own production, and it controls the production of FoxA(2) as well.

  3. 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

  4. 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

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

    PubMed

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

    2009-10-01

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

  6. 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

  7. Characterization of the norCBQD genes, encoding nitric oxide reductase, in the nitrogen fixing bacterium Bradyrhizobium japonicum.

    PubMed

    Mesa, Socorro; Velasco, Leonardo; Manzanera, Maximino E; Delgado, María J; Bedmar, Eulogio J

    2002-11-01

    The genes norCBQD that encode the bc-type nitric oxide reductase from Bradyrhizobium japonicum USDA110 have been isolated and characterized. norC and norB encode the cytochrome c-containing subunit II and cytochrome b-containing subunit I of nitric oxide reductase, respectively. norQ encodes a protein with an ATP/GTP-binding motif, and the predicted norD gene product shows similarity with NorD from other denitrifiers. Mutational analysis indicates that the two structural norC and norB genes are required for microaerobic growth under nitrate-respiring conditions. A mutant strain lacking a functional norC gene also lacked the 16 kDa c-type cytochrome that is normally detectable by haem-staining of proteins from membranes of microaerobically grown wild-type cells. Expression of a transcriptional fusion of the nor promoter region to the reporter gene lacZ (P(norC)-lacZ) was not detected in aerobically grown cells of USDA110, but the fusion was induced threefold when the cells were cultured under microaerobic conditions (1% O(2)) with either nitrite or nitric oxide, and about 18-fold when nitrate was the N oxide present in the medium. The P(norC)-lacZ fusion was not expressed in the B. japonicum fixK(2) mutant strain 9043, but complementation of the mutant with the fixK(2) gene restored beta-galactosidase activity to levels similar to those found in the parental strain. The promoter region of the norCBQD genes has been characterized by primer extension. A major transcript initiates 45.5 bp downstream of the centre of a putative binding site for the transcription factor FixK(2).

  8. A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum.

    PubMed

    Weissgerber, Thomas; Sylvester, Marc; Kröninger, Lena; Dahl, Christiane

    2014-04-01

    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).

  9. Endogenous nitric oxide regulates the recovery of the radiation-resistant bacterium Deinococcus radiodurans from exposure to UV light

    PubMed Central

    Patel, Bhumit A.; Moreau, Magali; Widom, Joanne; Chen, Huan; Yin, Longfei; Hua, Yuejin; Crane, Brian R.

    2009-01-01

    Deinococcus radiodurans (Dr) withstands desiccation, reactive oxygen species, and doses of radiation that would be lethal to most organisms. Deletion of a gene encoding a homolog of mammalian nitric oxide synthase (NOS) severely compromises the recovery of Dr from ultraviolet (UV) radiation damage. The Δnos defect can be complemented with recombinant NOS, rescued by exogenous nitric oxide (NO) and mimicked in the wild-type strain with an NO scavenging compound. UV radiation induces both upregulation of the nos gene and cellular NO production on similar time scales. Growth recovery does not depend on NO being present during UV irradiation, but rather can be manifested by NO addition hours after exposure. Surprisingly, nos deletion does not increase sensitivity to oxidative damage, and hydrogen peroxide does not induce nos expression. However, NOS-derived NO upregulates transcription of obgE, a gene involved in bacterial growth proliferation and stress response. Overexpression of the ObgE GTPase in the Δnos background substantially alleviates the growth defect after radiation damage. Thus, NO acts as a signal for the transcriptional regulation of growth in D. radiodurans. PMID:19841256

  10. Influence of liberated silver from silver nanoparticles on nitrification inhibition of Nitrosomonas europaea.

    PubMed

    Radniecki, Tyler S; Stankus, Dylan P; Neigh, Arianne; Nason, Jeffrey A; Semprini, Lewis

    2011-09-01

    The ecotoxicity of silver nanoparticles (Ag-NPs) to wastewater biota, including ammonia oxidizing bacteria (AOB), is gaining increasing interest as the number of products containing Ag-NPs continues to rise exponentially and they are expected to accumulate in wastewater treatment plants. This research demonstrated that the addition order of Ag-NP and the media constituents had a profound influence on the stability of the Ag-NP suspension and the corresponding repeatability of results and sensitivity of Nitrosomonas europaea. N. europaea, a model AOB, was found to be extremely sensitive to ionic silver (Ag(+)) and two sizes of Ag-NPs (20 and 80 nm). Ag(+) exposures resulted in the highest level of toxicity with smaller Ag-NPs (20 nm) being more toxic than larger Ag-NPs (80 nm). The increased sensitivity of N. europaea to smaller Ag-NPs was caused by their higher rates of dissolved silver (dAg) release, via dissolution, due to a greater surface area to volume ratio. dAg was shown to be responsible for the vast majority of the observed Ag-NP toxicity, as determined by abiotic Ag-NP dissolution tests. For the sizes of Ag-NP studied (20 and 80 nm), there appears to be a negligible nanoparticle-specific toxicity. This was further supported by similarities in inhibition mechanisms between Ag(+) and Ag-NP, with both causing decreases in AMO activity and destabilization of the outer-membrane of N. europaea. Finally, equal concentrations of total silver were found to be tightly associated to both Ag(+) and Ag-NP-exposed cells despite Ag-NP concentrations being five times greater, by mass, than Ag(+) concentrations.

  11. Candidate stress genes of Nitrosomonas europaea for monitoring inhibition of nitrification by heavy metals.

    PubMed

    Park, Sunhwa; Ely, Roger L

    2008-09-01

    Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury on Nitrosomonas europaea were studied in quasi-steady-state batch reactors. When cells were exposed to 1 microM CdCl2, 6 microM HgCl2, or 8 microM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses of N. europaea to cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 microM CdCl2 for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 microM CdCl2, with merA (mercuric reductase) showing 297-fold upregulation. In N. europaea cells exposed to 6 microM HgCl2 or to 8 microM CuCl2, merA showed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes and amoA, but no such recovery was evident in Cd2+-exposed cells even though merTPCADE were highly upregulated. We suggest that the upregulation of merA in response to CdCl2 and HgCl2 exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals.

  12. Candidate Stress Genes of Nitrosomonas europaea for Monitoring Inhibition of Nitrification by Heavy Metals ▿

    PubMed Central

    Park, Sunhwa; Ely, Roger L.

    2008-01-01

    Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury on Nitrosomonas europaea were studied in quasi-steady-state batch reactors. When cells were exposed to 1 μM CdCl2, 6 μM HgCl2, or 8 μM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses of N. europaea to cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 μM CdCl2 for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 μM CdCl2, with merA (mercuric reductase) showing 297-fold upregulation. In N. europaea cells exposed to 6 μM HgCl2 or to 8 μM CuCl2, merA showed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes and amoA, but no such recovery was evident in Cd2+-exposed cells even though merTPCADE were highly upregulated. We suggest that the upregulation of merA in response to CdCl2 and HgCl2 exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals. PMID:18606795

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

    PubMed

    Kodama, Yumiko; Watanabe, Kazuya

    2004-11-01

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

  14. Zinc Oxide Nanorods-Decorated Graphene Nanoplatelets: A Promising Antimicrobial Agent against the Cariogenic Bacterium Streptococcus mutans

    PubMed Central

    Zanni, Elena; Chandraiahgari, Chandrakanth Reddy; De Bellis, Giovanni; Montereali, Maria Rita; Armiento, Giovanna; Ballirano, Paolo; Polimeni, Antonella; Sarto, Maria Sabrina; Uccelletti, Daniela

    2016-01-01

    Nanomaterials are revolutionizing the field of medicine to improve the quality of life due to the myriad of applications stemming from their unique properties, including the antimicrobial activity against pathogens. In this study, the antimicrobial and antibiofilm properties of a novel nanomaterial composed by zinc oxide nanorods-decorated graphene nanoplatelets (ZNGs) are investigated. ZNGs were produced by hydrothermal method and characterized through field-emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDX) and X-ray diffraction (XRD) techniques. The antimicrobial activity of ZNGs was evaluated against Streptococcus mutans, the main bacteriological agent in the etiology of dental caries. Cell viability assay demonstrated that ZNGs exerted a strikingly high killing effect on S. mutans cells in a dose-dependent manner. Moreover, FE-SEM analysis revealed relevant mechanical damages exerted by ZNGs at the cell surface of this dental pathogen rather than reactive oxygen species (ROS) generation. In addition, inductively coupled plasma mass spectrometry (ICP-MS) measurements showed negligible zinc dissolution, demonstrating that zinc ion release in the suspension is not associated with the high cell mortality rate. Finally, our data indicated that also S. mutans biofilm formation was affected by the presence of graphene-zinc oxide (ZnO) based material, as witnessed by the safranin staining and growth curve analysis. Therefore, ZNGs can be a remarkable nanobactericide against one of the main dental pathogens. The potential applications in dental care and therapy are very promising. PMID:28335307

  15. 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

  16. 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

  17. 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

  18. Solubilization of Fe(III) oxide-bound trace metals by a dissimilatory Fe(III) reducing bacterium

    NASA Astrophysics Data System (ADS)

    Zachara, John M.; Fredrickson, Jim K.; Smith, Steven C.; Gassman, Paul L.

    2001-01-01

    Trace metals associate with Fe(III) oxides as adsorbed or coprecipitated species, and consequently, the biogeochemical cycles of iron and the trace metals are closely linked. This communication investigated the solubilization of coprecipitated Co(III) and Ni(II) from goethite (α-FeOOH) during dissimilatory bacterial iron reduction to provide insights on biogeochemical factors controlling trace-element fluxes in anoxic environments. Suspensions of homogeneously substituted Co-FeOOH (50 mmol/L as Co 0.01Fe 0.99OOH; 57Co-labeled) in eight different buffer/media solutions were inoculated with a facultative, metal-reducing bacteria isolated from groundwater ( Shewanella putrefacians CN32), and incubated under strictly anaerobic conditions for periods up to 32 days. Lactate (30 mmol/L) was provided as an electron donor. Growth and non-growth promoting conditions were established by adding or withholding PO 4 and/or trace metals ( 60Co-labeled) from the incubation media. Anthraquinone disulfonate (AQDS; 100 μmol/L) was added to most suspensions as an electron shuttle to enhance bacterial reduction. Solutions were buffered at circumneutral pH with either PIPES or bicarbonate buffers. Solid and liquid samples were analyzed at intermediate and final time points for aqueous and sorbed/precipitated (by HCl extraction) Fe(II) and Co(II). The bioreduced solids were analyzed by X-ray diffraction and field-emission electron microscopy at experiment termination. Ni-FeOOH (Ni 0.01Fe 0.99OOH) was used for comparison in select experiments. Up to 45% of the metal containing FeOOH was bioreduced; growth-supporting conditions did not enhance reduction. The biogenic Fe(II) strongly associated with the residual Fe(III) oxide as an undefined sorbed phase at low fractional reduction in PIPES buffer, and as siderite (FeCO 3) in bicarbonate buffer or as vivianite [Fe 3(PO 4) 2 · 8H 2O] when P was present. Cobalt(III) was reduced to Co(II) in proportion to its mole ratio in the solid. The

  19. Energy-mediated vs. ammonium-regulated gene expression in the obligate ammonia-oxidizing bacterium, Nitrosococcus oceani

    PubMed Central

    Stein, Lisa Y.; Campbell, Mark A.; Klotz, Martin G.

    2013-01-01

    Ammonia serves as the source of energy and reductant and as a signaling molecule that regulates gene expression in obligate ammonia-oxidizing chemolithotrophic microorganisms. The gammaproteobacterium, Nitrosococcus oceani, was the first obligate ammonia-oxidizer isolated from seawater and is one of the model systems for ammonia chemolithotrophy. We compared global transcriptional responses to ammonium and the catabolic intermediate, hydroxylamine, in ammonium-starved and non-starved cultures of N. oceani to discriminate transcriptional effects of ammonium from a change in overall energy and redox status upon catabolite availability. The most highly expressed genes from ammonium- or hydroxylamine-treated relative to starved cells are implicated in catabolic electron flow, carbon fixation, nitrogen assimilation, ribosome structure and stress tolerance. Catabolic inventory-encoding genes, including electron flow-terminating Complexes IV, FoF1 ATPase, transporters, and transcriptional regulators were among the most highly expressed genes in cells exposed only to ammonium relative to starved cells, although the differences compared to steady-state transcript levels were less pronounced. Reduction in steady-state mRNA levels from hydroxylamine-treated relative to starved-cells were less than five-fold. In contrast, several transcripts from ammonium-treated relative to starved cells were significantly less abundant including those for forward Complex I and a gene cluster of cytochrome c encoding proteins. Identified uneven steady-state transcript levels of co-expressed clustered genes support previously reported differential regulation at the levels of transcription and transcript stability. Our results differentiated between rapid regulation of core genes upon a change in cellular redox status vs. those responsive to ammonium as a signaling molecule in N. oceani, both confirming and extending our knowledge of metabolic modules involved in ammonia chemolithotrophy. PMID

  20. 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.

  1. Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.).

    PubMed

    Anandham, Rangasamy; Indiragandhi, Pandiyan; Kwon, Soon Wo; Sa, Tong Min; Jeon, Che Ok; Kim, Yong Ki; Jee, Hyeong Jin

    2010-01-01

    A facultatively chemolithoautotrophic, thiosulfate-oxidizing, Gram-negative, aerobic, motile, rod-shaped bacterial strain, designated ATSB16(T), was isolated from rhizosphere soils of sesame (Sesamum indicum L.). 16S rRNA gene sequence analysis demonstrated that this strain was closely related to Pandoraea pnomenusa LMG 18087(T) (96.7 % similarity), P. pulmonicola LMG 18016(T) (96.5 %), P. apista LMG 16407(T) (96.2 %), P. norimbergensis LMG 18379(T) (96.1 %) and P. sputorum LMG 18819(T) (96.0 %). Strain ATSB16(T) shared 96.0-96.4 % sequence similarity with four unnamed genomospecies of Pandoraea. The major cellular fatty acids of the strain ATSB16(T) were C(17 : 0) cyclo (33.0 %) and C(16 : 0) (30.6 %). Q-8 was the predominant respiratory quinone. The major polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified aminophospholipids. Hydroxyputrescine and putrescine were the predominant polyamines. The genomic DNA G+C content of the strain was 64.0 mol%. On the basis of the results obtained from this study, strain ATSB16(T) represents a novel species of the genus Pandoraea, for which the name Pandoraea thiooxydans sp. nov. is proposed. The type strain is ATSB16(T) (=KACC 12757(T) =LMG 24779(T)).

  2. An antioxidant exopolysaccharide devoid of pro-oxidant activity produced by the soil bacterium Bordetella sp. B4.

    PubMed

    Lin, Yanliang; Liu, Jinglei; Hu, Yibo; Song, Xin; Zhao, Yueran

    2012-11-01

    An exopolysaccharide (EPS) with a molecular weight of 230 kDa, was isolated from Bordetella sp. B4. The EPS was identified as linear alpha-1,6-(6-methyl)-glucan with N-acetyl-D-glucosamine branches at alpha-1, 4-linkages by IR and NMR spectroscopy. The free radical scavenging capacities of EPS on 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(+)), H(2)O(2), -OH and lipid peroxidation were 2-, 86-, 134- and 18-fold higher than that of ascorbic acid, respectively. Compared with ascorbic acid, the EPS was more effective in preventing DNA and protein from free radical damage induced by 2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH). More significantly, the EPS did not degrade DNA and protein by the pro-oxidant effect in the presence of copper ions and H(2)O(2). Furthermore, EPS could protect human umbilical vein endothelium cells (HUVECs) from high glucose-mediated damage. The production of EPS reached 10.2 g/L in the fermentation medium containing 3.0 g/L cholesterol, suggesting that Bordetella sp. B4 was a potential producer of antioxidant EPS.

  3. Final Intrinsic Remediation Engineering Evaluation/Cost Analysis for the FT-002 Site, Plattsburg Air Force Base, New York

    DTIC Science & Technology

    1995-04-01

    of trichloroethylene by the ammonia-oxidizing bacterium Nitrosomonas europaea : Biochem. Biophys. Res. Commun., vol. 159, p. 640-643. I Atlas, R.M...aliphatic compounds by the ammonia-oxidizing bacterium Nitrosomonas europaea : Appl. Environ. Microbiol., vol. 56, no. 4, p. 1169-1171. * Verschueren, K

  4. 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.

  5. Modulation of the ligand-field anisotropy in a series of ferric low-spin cytochrome c mutants derived from Pseudomonas aeruginosa cytochrome c-551 and Nitrosomonas europaea cytochrome c-552: a nuclear magnetic resonance and electron paramagnetic resonance study.

    PubMed

    Zoppellaro, Giorgio; Harbitz, Espen; Kaur, Ravinder; Ensign, Amy A; Bren, Kara L; Andersson, K Kristoffer

    2008-11-19

    Cytochromes of the c type with histidine-methionine (His-Met) heme axial ligation play important roles in electron-transfer reactions and in enzymes. In this work, two series of cytochrome c mutants derived from Pseudomonas aeruginosa (Pa c-551) and from the ammonia-oxidizing bacterium Nitrosomonas europaea (Ne c-552) were engineered and overexpressed. In these proteins, point mutations were induced in a key residue (Asn64) near the Met axial ligand; these mutations have a considerable impact both on heme ligand-field strength and on the Met orientation and dynamics (fluxionality), as judged by low-temperature electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectra. Ne c-552 has a ferric low-spin (S = 1/2) EPR signal characterized by large g anisotropy with g(max) resonance at 3.34; a similar large g(max) value EPR signal is found in the mitochondrial complex III cytochrome c1. In Ne c-552, deletion of Asn64 (NeN64Delta) changes the heme ligand field from more axial to rhombic (small g anisotropy and g(max) at 3.13) and furthermore hinders the Met fluxionality present in the wild-type protein. In Pa c-551 (g(max) at 3.20), replacement of Asn64 with valine (PaN64V) induces a decrease in the axial strain (g(max) at 3.05) and changes the Met configuration. Another set of mutants prepared by insertion (ins) and/or deletion (Delta) of a valine residue adjacent to Asn64, resulting in modifications in the length of the axial Met-donating loop (NeV65Delta, NeG50N/V65Delta, PaN50G/V65ins), did not result in appreciable alterations of the originally weak (Ne c-552) or very weak (Pa c-551) axial field but had an impact on Met orientation, fluxionality, and relaxation dynamics. Comparison of the electronic fingerprints in the overexpressed proteins and their mutants reveals a linear relationship between axial strain and average paramagnetic heme methyl shifts, irrespective of Met orientation or dynamics. Thus, for these His-Met axially coordinated Fe

  6. Whole-genome transcriptional and physiological responses of Nitrosomonas europaea to cyanide: identification of cyanide stress response genes.

    PubMed

    Park, Sunhwa; Ely, Roger L

    2009-04-15

    Nitrosomonas europaea (ATCC 19718) is one of several nitrifying species that participate in the biological removal of nitrogen from wastewater by oxidizing ammonia to nitrite, the first step in nitrification. Because nitrification is quite sensitive to cyanide, a compound often encountered in wastewater treatment plants, we characterized the physiological and transcriptional responses of N. europaea cells to cyanide. The cells were extremely sensitive to low concentrations of cyanide, with NO-(2)production and ammonia-dependent oxygen uptake rates decreasing by 50% within 30 min of exposure to 1 microM NaCN. Whole-genome transcriptional responses of cells exposed to 1 microM NaCN were examined using Affymetrix microarrays to identify stress-induced genes. The transcript levels of 35 genes increased more than 2-fold while transcript levels of 29 genes decreased more than 20-fold. A gene cluster that included moeZ (NE2353), encoding a rhodanese homologue and thought to be involved in detoxification of cyanide, showed the highest up-regulation (7-fold). The down-regulated genes included genes encoding proteins involved in the sulfate reduction pathway, signal transduction mechanisms, carbohydrate transport, energy production, coenzyme metabolism, and amino acid transport.

  7. Application of an integrated statistical design for optimization of culture condition for ammonium removal by Nitrosomonas europaea.

    PubMed

    Bao, Yingling; Zhengfang, Ye

    2013-01-01

    Statistical methodology was applied to the optimization of the ammonium oxidation by Nitrosomonas europaea for biomass concentration (C(B)), nitrite yield (Y(N)) and ammonium removal (R(A)). Initial screening by Plackett-Burman design was performed to select major variables out of nineteen factors, among which NH4Cl concentration (C(N)), trace element solution (TES), agitation speed (AS), and fermentation time (T) were found to have significant effects. Path of steepest ascent and response surface methodology was applied to optimize the levels of the selected factors. Finally, multi-objective optimization was used to obtain optimal condition by compromise of the three desirable objectives through a combination of weighted coefficient method coupled with entropy measurement methodology. These models enabled us to identify the optimum operation conditions (C(N)= 84.1 mM; TES = 0.74 ml; AS= 100 rpm and T = 78 h), under which C(B)= 3.386×10(8) cells/ml; Y(N)= 1.98 mg/mg and R(A) = 97.76% were simultaneously obtained. The optimized conditions were shown to be feasible through verification tests.

  8. Application of an Integrated Statistical Design for Optimization of Culture Condition for Ammonium Removal by Nitrosomonas europaea

    PubMed Central

    yingling, Bao; zhengfang, Ye

    2013-01-01

    Statistical methodology was applied to the optimization of the ammonium oxidation by Nitrosomonas europaea for biomass concentration (CB), nitrite yield (YN) and ammonium removal (RA). Initial screening by Plackett-Burman design was performed to select major variables out of nineteen factors, among which NH4Cl concentration (CN), trace element solution (TES), agitation speed (AS), and fermentation time (T) were found to have significant effects. Path of steepest ascent and response surface methodology was applied to optimize the levels of the selected factors. Finally, multi-objective optimization was used to obtain optimal condition by compromise of the three desirable objectives through a combination of weighted coefficient method coupled with entropy measurement methodology. These models enabled us to identify the optimum operation conditions (CN = 84.1 mM; TES = 0.74 ml; AS = 100 rpm and T = 78 h), under which CB = 3.386×108 cells/ml; YN = 1.98 mg/mg and RA = 97.76% were simultaneously obtained. The optimized conditions were shown to be feasible through verification tests. PMID:23565225

  9. 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.

  10. 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

  11. Metabolism of Nitrogen Oxides in Ammonia-Oxidizing Bacteria

    NASA Astrophysics Data System (ADS)

    Kozlowski, J.; Stein, L. Y.

    2014-12-01

    Ammonia-oxidizing bacteria (AOB) are key microorganisms in the transformation of nitrogen intermediates in most all environments. Until recently there was very little work done to elucidate the physiology of ammonia-oxidizing bacteria cultivated from variable trophic state environments. With a greater variety of ammonia-oxidizers now in pure culture the importance of comparative physiological and genomic analysis is crucial. Nearly all known physiology of ammonia-oxidizing bacteria lies within the Nitrosomonas genus with Nitrosomonas europaea strain ATCC 19718 as the model. To more broadly characterize and understand the nature of obligate ammonia chemolithotrophy and the contribution of AOB to production of nitrogen oxides, Nitrosomonas spp. and Nitrosospira spp. isolated from variable trophic states and with sequenced genomes, were utilized. Instantaneous ammonia- and hydroxylamine-oxidation kinetics as a function of oxygen and substrate concentration were measured using an oxygen micro-sensor. The pathway intermediates nitric oxide and nitrous oxide were measured in real time using substrate-specific micro-sensors to elucidate whether production of these molecules is stoichiometric with rates of substrate oxidation. Genomic inventory was compared among the strains to identify specific pathways and modules to explain physiological differences in kinetic rates and production of N-oxide intermediates as a condition of their adaptation to different ammonium concentrations. This work provides knowledge of how nitrogen metabolism is differentially controlled in AOB that are adapted to different concentrations of ammonium. Overall, this work will provide further insight into the control of ammonia oxidizing chemolithotrophy across representatives of the Nitrosomonas and Nitrosospira genus, which can then be applied to examine additional genome-sequenced AOB isolates.

  12. Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park.

    PubMed

    Sokolova, Tatyana G; González, Juan M; Kostrikina, Nadezhda A; Chernyh, Nikolai A; Slepova, Tatiana V; Bonch-Osmolovskaya, Elizaveta A; Robb, Frank T

    2004-11-01

    A new anaerobic, thermophilic, facultatively carboxydotrophic bacterium, strain Nor1(T), was isolated from a hot spring at Norris Basin, Yellowstone National Park. Cells of strain Nor1(T) were curved motile rods with a length of 2.6-3 microm, a width of about 0.5 microm and lateral flagellation. The cell wall structure was of the Gram-negative type. Strain Nor1(T) was thermophilic (temperature range for growth was 40-68 degrees C, with an optimum at 60 degrees C) and neutrophilic (pH range for growth was 6.5-7.6, with an optimum at 6.8-7.0). It grew chemolithotrophically on CO (generation time, 1.15 h), producing equimolar quantities of H(2) and CO(2) according to the equation CO+H(2)O-->CO(2)+H(2). During growth on CO in the presence of ferric citrate or amorphous ferric iron oxide, strain Nor1(T) reduced ferric iron but produced H(2) and CO(2) at a ratio close to 1 : 1, and growth stimulation was slight. Growth on CO in the presence of sodium selenite was accompanied by precipitation of elemental selenium. Elemental sulfur, thiosulfate, sulfate and nitrate did not stimulate growth of strain Nor1(T) on CO and none of these chemicals was reduced. Strain Nor1(T) was able to grow on glucose, sucrose, lactose, arabinose, maltose, fructose, xylose and pyruvate, but not on cellobiose, galactose, peptone, yeast extract, lactate, acetate, formate, ethanol, methanol or sodium citrate. During glucose fermentation, acetate, H(2) and CO(2) were produced. Thiosulfate was found to enhance the growth rate and cell yield of strain Nor1(T) when it was grown on glucose, sucrose or lactose; in this case, acetate, H(2)S and CO(2) were produced. In the presence of thiosulfate or ferric iron, strain Nor1(T) was also able to grow on yeast extract. Lactate, acetate, formate and H(2) were not utilized either in the absence or in the presence of ferric iron, thiosulfate, sulfate, sulfite, elemental sulfur or nitrate. Growth was completely inhibited by penicillin, ampicillin, streptomycin

  13. 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.

  14. Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations.

    PubMed

    Oishi, Ryu; Tada, Chika; Asano, Ryoki; Yamamoto, Nozomi; Suyama, Yoshihisa; Nakai, Yutaka

    2012-05-01

    A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.

  15. 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.

  16. An electrophoretic study of the thermal- and reductant-dependent aggregation of the 27 kDa component of ammonia monooxygenase from Nitrosomonas europaea.

    PubMed

    Hyman, M R; Arp, D J

    1993-07-01

    Standard protocols for sample preparation for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) typically involve the combined use of heat and a reductant to fully disrupt protein-protein interactions and allow for constant ratios of SDS-binding to individual polypeptides. However, 14C-labeled forms of the membrane-bound, active-site-containing 27 kDa polypeptide of ammonia monooxygenase from Nitrosomonas europaea undergo an aggregation reaction when cells or membranes are heated in the presence of SDS-PAGE sample buffer. The aggregate produced after heating at 100 degrees C is a soluble complex which fails to enter the stacking gel in discontinuous SDS-PAGE gels. The extent of the aggregation reaction is dependent on the temperature of sample preparation, and the reaction exhibits first-order kinetics at 65 degrees C and 100 degrees C (rates constants = 0.07 and 0.35 min-1, respectively). The rate of the aggregation reaction is further dependent on the concentration of reductant used in the sample buffer. However, the concentration of SDS does not significantly affect the rate of aggregation. The aggregated form of the 27 kDA polypeptide can be isolated by gel-permeation chromatography in the presence of SDS. The aggregated protein can also be returned to the monomeric state by incubation at high pH in the presence of SDS. The aggregation reaction also occurs with 14C2H2-labeled polypeptides in other species of autotrophic nitrifiers and a methanotrophic bacterium which expresses the particulate form of methane monooxygenase. We conclude that strongly hydrophobic amino acid sequences present in ammonia monooxygenase are responsible for the aggregation phenomenon.

  17. Regulation of membrane fixation and energy production/conversion for adaptation and recovery of ZnO nanoparticle impacted Nitrosomonas europaea.

    PubMed

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

    2017-04-01

    The ZnO nanoparticle (NP) effects on typical ammonia-oxidizing bacteria, Nitrosomonas europaea in a chemostat bioreactor, and the cells' toxicity adaptation and recovery potentials were explored. Hardly any inhibition was observed when the NP concentration was high up to 10 mg/L. The cells exposed to 50 mg/L ZnO NPs displayed time-dependent impairment and recovery potentials in terms of cell density, membrane integrity, nitrite production rate, and ammonia monooxygenase activity. The 6-h NP stress impaired cells were nearly completely restored during a 12-h recovery incubation, while the longer exposure time would cause irretrievable cell damage. Microarray analysis further indicated the transcriptional adaptation of N. europaea to NP stress. The regulations of genes encoding for membrane permeability or osmoprotectant, membrane integrity preservation, and inorganic ion transport during NP exposure and cell recovery revealed the importance of membrane fixation and the associated metabolisms for cells' self-protection and the following recovery from NP stress. The oxidative phosphorylation, carbon assimilation, and tricarboxylic acid (TCA) cycling pathways involved in the cells' antitoxicity activities and would promote the energy production/conversion efficiency for cell recovery. The heavy metal resistance, histidine metabolism, toxin-antitoxin defense, glycolysis, and sulfate reduction pathways were also suggested to participate in the cell detoxication and recovery processes. All these findings provided valuable insights into the mechanisms of cell-mediated ZnO NP cytotoxicity and their potential impacts on wastewater nitrogen removal system.

  18. 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.

  19. 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

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

    PubMed

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

    2016-06-04

    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.

  1. Removal of ammonia by immobilized Nitrosomonas europaea in a biotrickling filter packed with polyurethane foam.

    PubMed

    Ramírez, Martín; Gómez, José Manuel; Aroca, Germán; Cantero, Domingo

    2009-03-01

    A biotrickling filter with Nitrosomonas europaea immobilized on polyurethane foam is proposed for treating ammonia contaminated air. The effect of the surface velocity of the recirculation medium, nitrite concentration, pH, empty bed residence time (EBRT) and ammonia inlet load on the NH(3) removal process was investigated. The total amount of biomass immobilized on the carrier was 3.29+/-0.52 x 10(10) cells g(-1) dry carrier. The maximum elimination capacity of the biotrickling filter was 270 g Nm(-3)h(-1) at pH 7.5, an EBRT of 11s, and nitrite concentrations below 100mM. These results show that system studied can be considered as a viable alternative for the treatment of gaseous emissions containing high concentrations of ammonia.

  2. Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process.

    PubMed

    Dahl, Christiane; Franz, Bettina; Hensen, Daniela; Kesselheim, Anne; Zigann, Renate

    2013-12-01

    In phototrophic sulfur bacteria, sulfite is a well-established intermediate during reduced sulfur compound oxidation. Sulfite is generated in the cytoplasm by the reverse-acting dissimilatory sulfite reductase DsrAB. Many purple sulfur bacteria can even use externally available sulfite as a photosynthetic electron donor. Nevertheless, the exact mode of sulfite oxidation in these organisms is a long-standing enigma. Indirect oxidation in the cytoplasm via adenosine-5'-phosphosulfate (APS) catalysed by APS reductase and ATP sulfurylase is neither generally present nor essential. The inhibition of sulfite oxidation by tungstate in the model organism Allochromatium vinosum indicated the involvement of a molybdoenzyme, but homologues of the periplasmic molybdopterin-containing SorAB or SorT sulfite dehydrogenases are not encoded in genome-sequenced purple or green sulfur bacteria. However, genes for a membrane-bound polysulfide reductase-like iron-sulfur molybdoprotein (SoeABC) are universally present. The catalytic subunit of the protein is predicted to be oriented towards the cytoplasm. We compared the sulfide- and sulfite-oxidizing capabilities of A. vinosum WT with single mutants deficient in SoeABC or APS reductase and the respective double mutant, and were thus able to prove that SoeABC is the major sulfite-oxidizing enzyme in A. vinosum and probably also in other phototrophic sulfur bacteria. The genes also occur in a large number of chemotrophs, indicating a general importance of SoeABC for sulfite oxidation in the cytoplasm. Furthermore, we showed that the periplasmic sulfur substrate-binding protein SoxYZ is needed in parallel to the cytoplasmic enzymes for effective sulfite oxidation in A. vinosum and provided a model for the interplay between these systems despite their localization in different cellular compartments.

  3. Methylobacter tundripaludum sp. nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78 degrees N).

    PubMed

    Wartiainen, Ingvild; Hestnes, Anne Grethe; McDonald, Ian R; Svenning, Mette M

    2006-01-01

    A Gram-negative, rod-shaped, non-motile, non-spore forming bacterium (SV96T) was isolated from wetland soil near Ny-Alesund, Svalbard. On the basis of 16S rRNA gene sequence similarity, strain SV96T was shown to belong to the Gammaproteobacteria, related to Methylobacter psychrophilus Z-0021T (99.1 %), Methylobacter luteus ATCC 49878T (97.3 %), Methylobacter marinus A45T (97.0 %) and Methylobacter whittenburyi ATCC 51738T (95.8 %); the closest related species within the genus Methylomicrobium with a validly published name was Methylomicrobium album ATCC 33003T (95.0 %). Chemotaxonomic data (including the major fatty acids: 16 : 1omega8, 16 : 1omega7 and 16 : 1omega5t) supported the affiliation of strain SV96T to the genus Methylobacter. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV96T from the four Methylobacter species mentioned above. Strain SV96T therefore represents a novel species, for which the name Methylobacter tundripaludum sp. nov. is proposed (type strain SV96T = DSM 17260T = ATCC BAA-1195T).

  4. Isolation and characterization of a thermophilic bacterium which oxidizes acetate in syntrophic association with a methanogen and which grows acetogenically on H/sub 2/-CO/sub 2/

    SciTech Connect

    Lee, M.J.; Zinder, S.H.

    1988-01-01

    The authors previously described a thermophilic (60/sup 0/C), syntrophic, two-membered culture which converted acetate to methane via a two-step mechanism in which acetate was oxidized to H/sub 2/ and CO/sub 2/. While the hydrogenotrophic methanogen Methanobacterium sp. strain THF in the biculture was readily isolated, we were unable to find a substrate that was suitable for isolation of the acetate-oxidizing member of the biculture. In this study, we found that the biculture grew on ethylene glycol, and an acetate-oxidizing, rod-shape bacterium (AOR) was isolated from the biculture by dilution into medium containing ethylene glycol as the growth substrate. When the axenic culture of the AOR was recombined with a pure culture of Methanobacterium sp. strain THF, the reconstituted biculture grew on acetate and converted it to CH/sub 4/. The AOR used ethylene glycol, 1,2-propanediol, formate, pyruvate, glycine-betaine, and H/sub 2/-CO/sub 2/ as growth substrates. Acetate was the major fermentation product detected from these substrates, except for 1,2-propanediol, which was converted to 1-propanol and propionate. N,N-Dimethylglycine was also formed from glycine-betaine. Acetate was formed in stoichiometric amounts during growth on H/sub 2/-CO/sub 2/, demonstrating that the AOR is an acetogen. This reaction, which was carried out by the pure culture of the AOR in the presence of high partial pressures of H/sub 2/, was the reverse of the acetate oxidation reaction carried out by the AOR when hydrogen partial pressures were kept low by coculturing it with Methanobacterium sp. strain THF. The DNA base composition of the AOR was 47 mol% guanine plus cytosine, and no cytochromes were detected.

  5. Effects of Nitrogen Dioxide and Anoxia on Global Gene and Protein Expression in Long-Term Continuous Cultures of Nitrosomonas eutropha C91

    PubMed Central

    Kartal, Boran; Wessels, Hans J. C. T.; van der Biezen, Erwin; Francoijs, Kees-Jan; Jetten, Mike S. M.; Klotz, Martin G.

    2012-01-01

    Nitrosomonas eutropha is an ammonia-oxidizing betaproteobacterium found in environments with high ammonium levels, such as wastewater treatment plants. The effects of NO2 on gene and protein expression under oxic and anoxic conditions were determined by maintaining N. eutropha strain C91 in a chemostat fed with ammonium under oxic, oxic-plus-NO2, and anoxic-plus-NO2 culture conditions. Cells remained viable but ceased growing under anoxia; hence, the chemostat was switched from continuous to batch cultivation to retain biomass. After several weeks under each condition, biomass was harvested for total mRNA and protein isolation. Exposure of N. eutropha C91 to NO2 under either oxic or anoxic conditions led to a decrease in proteins involved in N and C assimilation and storage and an increase in proteins involved in energy conservation, including ammonia monooxygenase (AmoCAB). Exposure to anoxia plus NO2 resulted in increased representation of proteins and transcripts reflective of an energy-deprived state. Several proteins implicated in N-oxide metabolism were expressed and remained unchanged throughout the experiment, except for NorCB nitric oxide reductase, which was not detected in the proteome. Rather, NorY nitric oxide reductase was expressed under oxic-plus-NO2 and anoxic-plus-NO2 conditions. The results indicate that exposure to NO2 results in an energy-deprived state of N. eutropha C91 and that anaerobic growth could not be supported with NO2 as an oxidant. PMID:22562996

  6. Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area.

    PubMed

    Sorokin, Dimitry Yu; Tourova, Tatjana P; Spiridonova, Elizaveta M; Rainey, Fred A; Muyzer, Gerard

    2005-05-01

    Strain TL 2(T) was isolated on mineral medium with thiosulfate from a near-shore sulfidic hydrothermal area in Matupi Harbour on the island of New Britain, Papua New Guinea. The cells varied from long filaments with swollen ends, often aggregated, to short rods, depending on the growth conditions. The bacterium was obligately aerobic and grew autotrophically with thiosulfate as energy source or heterotrophically with organic acids and sugars. In thiosulfate-limited continuous culture, mu(max) and Y(max) for autotrophic growth were 0.1 h(-1) and 3 g protein mol(-1), respectively. From the various reduced sulfur compounds tested, only thiosulfate and sulfide supported active respiration. Inorganic carbon was assimilated via the Calvin cycle. Presence of the 'green'-type of form I RubisCO gene was detected. Growth was possible from 15 to 47 degrees C with an optimum at 35 degrees C, pH 6.5-8.5 with an optimum at pH 8.0, and between 10 and 90 g NaCl l(-1) with an optimum at 35 g l(-1). Phylogenetic analysis based on 16S rRNA and cbbL gene sequences demonstrated that strain TL 2(T) forms a separate lineage within the alpha-3 subdivision of the Proteobacteria, distantly related to the genera Rhodovulum and Rhodobacter. On the basis of these results, a novel genus and species, Thioclava pacifica gen. nov., sp. nov., is proposed to accommodate strain TL 2(T) (= DSM 10166(T) = UNIQEM 229(T)).

  7. Selective Inhibition of Ammonium Oxidation and Nitrification-Linked N2O Formation by Methyl Fluoride and Dimethyl Ether

    PubMed Central

    Miller, Laurence G.; Coutlakis, M. Denise; Oremland, Ronald S.; Ward, Bess 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. PMID:16349011

  8. 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.

  9. A Potentiometric Flow Biosensor Based on Ammonia-Oxidizing Bacteria for the Detection of Toxicity in Water

    PubMed Central

    Zhang, Qianyu; Ding, Jiawang; Kou, Lijuan; Qin, Wei

    2013-01-01

    A flow biosensor for the detection of toxicity in water using the ammonia-oxidizing bacterium (AOB) Nitrosomonas europaea as a bioreceptor and a polymeric membrane ammonium-selective electrode as a transducer is described. The system is based on the inhibition effects of toxicants on the activity of AOB, which can be evaluated by measuring the ammonium consumption rates with the ammonium-selective membrane electrode. The AOB cells are immobilized on polyethersulfone membranes packed in a holder, while the membrane electrode is placed downstream in the flow cell. Two specific inhibitors of the ammonia oxidation—allylthiourea and thioacetamide—have been tested. The IC50 values defined as the concentration of an inhibitor causing a 50% reduction in the ammonia oxidation activity have been measured as 0.17 μM and 0.46 μM for allylthiourea and thioacetamide, respectively. The proposed sensor offers advantages of simplicity, speed and high sensitivity for measuring toxicity in water. PMID:23708274

  10. Characterization of metabolites formed during the biotransformation of 17alpha-ethinylestradiol by Nitrosomonas europaea in batch and continuous flow bioreactors.

    PubMed

    Skotnicka-Pitak, J; Khunjar, W O; Love, N G; Aga, D S

    2009-05-15

    The biotransformation of 17alpha-ethinylestradiol (EE2) by an ammonia oxidizing bacteria, Nitrosomonas europaea, grown in batch (ammonia-rich) and continuous flow (chemostat, ammonia-limited) reactors was investigated. Both C-14 labeled EE2 (10 gammag/L) and unlabeled EE2 (1 mg/L) were used to facilitate metabolite identification under environmentally relevant physiological conditions. Whole cell ammonia monooxygenase (AMO) activity was not inhibited at the EE2 concentrations used in this study. Characterization of the primary metabolite formed during batch cultivation by liquid chromatography/ion-trap mass spectrometry (LC-ITMS) and nuclear magnetic resonance (NMR) spectroscopy showed modification at the ethinyl group and addition of a carboxyl group. This metabolite (M386) (revealed by m/z 385 in negative mode electrospray LC/ MS) was not formed in the abiotic control. In contrast, biotransformation of EE2 under continuous flow conditions showed formation of a monohydroxylated EE2 (revealed by m/z 311), but not M386. Furthermore, nitrated EE2 derivatives were formed in both batch and continuous flow cultures, as a result of abiotic transformation of EE2 in the presence of high concentrations of nitrite in the bioreactors. Results from this study underscore the importance of physiological state and growth conditions as critical variables that can dictate the metabolic pathway for EE2 biodegradation and the nature of byproducts formed.

  11. 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.

  12. 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.

  13. Identification of a Novel Arsenite Oxidase Gene, arxA, in the Haloalkaliphilic, Arsenite-Oxidizing Bacterium Alkalilimnicola ehrlichii Strain MLHE-1 ▿

    PubMed Central

    Zargar, Kamrun; Hoeft, Shelley; Oremland, Ronald; Saltikov, Chad W.

    2010-01-01

    Although arsenic is highly toxic to most organisms, certain prokaryotes are known to grow on and respire toxic metalloids of arsenic (i.e., arsenate and arsenite). Two enzymes are known to be required for this arsenic-based metabolism: (i) the arsenate respiratory reductase (ArrA) and (ii) arsenite oxidase (AoxB). Both catalytic enzymes contain molybdopterin cofactors and form distinct phylogenetic clades (ArrA and AoxB) within the dimethyl sulfoxide (DMSO) reductase family of enzymes. Here we report on the genetic identification of a “new” type of arsenite oxidase that fills a phylogenetic gap between the ArrA and AoxB clades of arsenic metabolic enzymes. This “new” arsenite oxidase is referred to as ArxA and was identified in the genome sequence of the Mono Lake isolate Alkalilimnicola ehrlichii MLHE-1, a chemolithoautotroph that can couple arsenite oxidation to nitrate reduction. A genetic system was developed for MLHE-1 and used to show that arxA (gene locus ID mlg_0216) was required for chemoautotrophic arsenite oxidation. Transcription analysis also showed that mlg_0216 was only expressed under anaerobic conditions in the presence of arsenite. The mlg_0216 gene is referred to as arxA because of its greater homology to arrA relative to aoxB and previous reports that implicated Mlg_0216 (ArxA) of MLHE-1 in reversible arsenite oxidation and arsenate reduction in vitro. Our results and past observations support the position that ArxA is a distinct clade within the DMSO reductase family of proteins. These results raise further questions about the evolutionary relationships between arsenite oxidases (AoxB) and arsenate respiratory reductases (ArrA). PMID:20453090

  14. Submarine Basaltic Glass Colonization by the Heterotrophic Fe(II)-Oxidizing and Siderophore-Producing Deep-Sea Bacterium Pseudomonas stutzeri VS-10: The Potential Role of Basalt in Enhancing Growth.

    PubMed

    Sudek, Lisa A; Wanger, Greg; Templeton, Alexis S; Staudigel, Hubert; Tebo, Bradley M

    2017-01-01

    Phylogenetically and metabolically diverse bacterial communities have been found in association with submarine basaltic glass surfaces. The driving forces behind basalt colonization are for the most part unknown. It remains ambiguous if basalt provides ecological advantages beyond representing a substrate for surface colonization, such as supplying nutrients and/or energy. Pseudomonas stutzeri VS-10, a metabolically versatile bacterium isolated from Vailulu'u Seamount, was used as a model organism to investigate the physiological responses observed when biofilms are established on basaltic glasses. In Fe-limited heterotrophic media, P. stutzeri VS-10 exhibited elevated growth in the presence of basaltic glass. Diffusion chamber experiments demonstrated that physical attachment or contact of soluble metabolites such as siderophores with the basaltic glass plays a pivotal role in this process. Electrochemical data indicated that P. stutzeri VS-10 is able to use solid substrates (electrodes) as terminal electron donors and acceptors. Siderophore production and heterotrophic Fe(II) oxidation are discussed as potential mechanisms enhancing growth of P. stutzeri VS-10 on glass surfaces. In correlation with that we discuss the possibility that metabolic versatility could represent a common and beneficial physiological trait in marine microbial communities being subject to oligotrophic and rapidly changing deep-sea conditions.

  15. Submarine Basaltic Glass Colonization by the Heterotrophic Fe(II)-Oxidizing and Siderophore-Producing Deep-Sea Bacterium Pseudomonas stutzeri VS-10: The Potential Role of Basalt in Enhancing Growth

    PubMed Central

    Sudek, Lisa A.; Wanger, Greg; Templeton, Alexis S.; Staudigel, Hubert; Tebo, Bradley M.

    2017-01-01

    Phylogenetically and metabolically diverse bacterial communities have been found in association with submarine basaltic glass surfaces. The driving forces behind basalt colonization are for the most part unknown. It remains ambiguous if basalt provides ecological advantages beyond representing a substrate for surface colonization, such as supplying nutrients and/or energy. Pseudomonas stutzeri VS-10, a metabolically versatile bacterium isolated from Vailulu’u Seamount, was used as a model organism to investigate the physiological responses observed when biofilms are established on basaltic glasses. In Fe-limited heterotrophic media, P. stutzeri VS-10 exhibited elevated growth in the presence of basaltic glass. Diffusion chamber experiments demonstrated that physical attachment or contact of soluble metabolites such as siderophores with the basaltic glass plays a pivotal role in this process. Electrochemical data indicated that P. stutzeri VS-10 is able to use solid substrates (electrodes) as terminal electron donors and acceptors. Siderophore production and heterotrophic Fe(II) oxidation are discussed as potential mechanisms enhancing growth of P. stutzeri VS-10 on glass surfaces. In correlation with that we discuss the possibility that metabolic versatility could represent a common and beneficial physiological trait in marine microbial communities being subject to oligotrophic and rapidly changing deep-sea conditions. PMID:28344573

  16. The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea.

    PubMed

    Berube, Paul M; Stahl, David A

    2012-07-01

    The ammonia monooxygenase of chemolithotrophic ammonia-oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB(1,2)). Several AOB, including N. europaea, also possess a divergent monocistronic copy of amoC (amoC(3)) of unknown function. Previous work suggested a possible functional role for amoC(3) as part of the σ(E) stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC(3) is part of a general poststarvation cellular response system in N. europaea. We also found that amoC(3) is required for an efficient response to some stress conditions, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ(32) global stress response regulator demonstrated that the heat shock regulon plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC(3) subunit which appears to function as a stress-responsive subunit capable of maintaining ammonia oxidation activity under stress conditions. While this study was limited to starvation and heat shock, it is possible that the AmoC(3) subunit may be responsive to other membrane stressors (e.g., solvent or osmotic shocks) that are prevalent in the environments of AOB.

  17. The Divergent AmoC3 Subunit of Ammonia Monooxygenase Functions as Part of a Stress Response System in Nitrosomonas europaea

    PubMed Central

    Berube, Paul M.

    2012-01-01

    The ammonia monooxygenase of chemolithotrophic ammonia-oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB1,2). Several AOB, including N. europaea, also possess a divergent monocistronic copy of amoC (amoC3) of unknown function. Previous work suggested a possible functional role for amoC3 as part of the σE stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC3 is part of a general poststarvation cellular response system in N. europaea. We also found that amoC3 is required for an efficient response to some stress conditions, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ32 global stress response regulator demonstrated that the heat shock regulon plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC3 subunit which appears to function as a stress-responsive subunit capable of maintaining ammonia oxidation activity under stress conditions. While this study was limited to starvation and heat shock, it is possible that the AmoC3 subunit may be responsive to other membrane stressors (e.g., solvent or osmotic shocks) that are prevalent in the environments of AOB. PMID:22544266

  18. Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture.

    PubMed

    Pérez, José; Buchanan, Alex; Mellbye, Brett; Ferrell, Rebecca; Chang, Jeffrey H; Chaplen, Frank; Bottomley, Peter J; Arp, Daniel J; Sayavedra-Soto, Luis A

    2015-01-01

    Nitrosomonas europaea and Nitrobacter winogradskyi were grown singly and in co-culture in chemostats to probe for physiological differences between the two growth conditions. Co-culture growth medium containing 60 mM NH4 (+) resulted in a cell density (0.20-0.29 OD600) greater than the sum of the densities in single chemostat cultures, i.e., 0.09-0.14 OD600 for N. europaea with 60 mM NH4 (+)and 0.04-0.06 OD600 for N. winogradskyi with 60 mM NO2 (-). The NO2 (-)- and NH4 (+)-dependent O2 uptake rates, qRT-PCR, and microscopic observations indicated that in co-culture, N. europaea contributed ~0.20 OD600 (~80 %) and N. winogradskyi ~0.05 OD600 (~20 %). In co-culture, the transcriptomes showed that the mRNA levels of 773 genes in N. europaea (30.2 % of the genes) and of 372 genes in N. winogradskyi (11.8 % of the genes) changed significantly. Total cell growth and the analysis of the transcriptome revealed that in co-culture, N. europaea benefits more than N. winogradskyi.

  19. Inactivation of Nitrosomonas europaea and pathogenic Escherichia coli by chlorine and monochloramine.

    PubMed

    Chauret, Christian; Smith, Curtis; Baribeau, Hélène

    2008-09-01

    The purpose of this study was to measure the chlorine and monochloramine inactivation kinetics of Nitrosomonas europaea at 21 degrees C in the presence and absence of particles. The inactivation kinetics rates were compared with those obtained with Escherichia coli O157:H7. The results show that, in pure water, the use of free chlorine produced 4 log10 of N. europaea inactivation at a CT value of 0.8 mg.min l(-1), whereas monochloramine yielded 4 log10 of inactivation at CT values of approximately 9.9-16.4mg.min l(-1). With E. coli, chlorine produced approximately 4 1og10 of inactivation at a CT of 0.13 mg.min l(-1), whereas monochloramine resulted in 4 logo10 of inactivation at a CT of approximately 9.2 mg.min l(-1). These results suggest that N. europaea is more resistant to monochloramine and chlorine than E. coli. Corrosion debris, soil material and wastewater had no statistically significant (p < 0.05) impact on the inactivation of N. europaea by either chlorine or monochloramine. It seems likely that the CT values present in distribution systems would be sufficient to control suspended cells of these two organisms, especially under conditions of breakpoint chlorination, which could be used to control nitrification. Adequate disinfection should prevent the growth of these organisms in a distribution system.

  20. Crystallization and preliminary X-ray crystallographic analysis of MxaJ, a component of the methanol-oxidizing system operon from the marine bacterium Methylophaga aminisulfidivorans MPT

    PubMed Central

    Choi, Jin Myung; Kang, Jung Hun; Lee, Dong-Woo; Kim, Si Wouk; Lee, Sung Haeng

    2013-01-01

    The methanol-oxidizing system (mox) is essential for methylotrophic bacteria to extract energy during the oxidoreduction reaction and consists of a series of electron-transfer proteins encoded by the mox operon. One of the key enzymes is the α2β2 methanol dehydrogenase complex (type I MDH), which converts methanol to formaldehyde during the 2e− transfer through the prosthetic group pyrroloquinoline quinone. MxaJ, a product of mxaJ of the mox operon, is a component of the MDH complex and enhances the methanol-converting activity of the MDH complex. However, the exact functional mechanism of MxaJ in the complex is not clearly known. To investigate the functional role of MxaJ in MDH activity, an attempt was made to determine its crystal structure. Diffraction data were collected from a selenomethionine-substituted crystal to 1.92 Å resolution at the peak wavelength. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 37.127, b = 63.761, c = 99.246 Å. The asymmetric unit contained one MxaJ molecule with a calculated Matthews coefficient of 2.11 Å3 Da−1 and a solvent content of 41.7%. Three-dimensional structure determination of the MxaJ protein is currently in progress by the single-wavelength anomalous dispersion technique and model building. PMID:23908039

  1. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

    PubMed

    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.

  2. Genome of ‘Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut

    PubMed Central

    Kuwahara, Hirokazu; Yuki, Masahiro; Izawa, Kazuki; Ohkuma, Moriya; Hongoh, Yuichi

    2017-01-01

    The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, ‘Candidatus Endomicrobium trichonymphae' and ‘Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of ‘Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of ‘Ca. Desulfovibrio trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of ‘Ca. Endomicrobium trichonymphae'. An amino acid permease gene has apparently been transferred between the ancestors of these two symbionts; a lateral gene transfer has affected their metabolic capacity. Notably, ‘Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates common in desulfovibrios are pseudogenized or missing. Thus, ‘Ca. Desulfovibrio trichonymphae' is specialized to consume hydrogen that may otherwise inhibit fermentation processes in both T. agilis and ‘Ca. Endomicrobium trichonymphae'. The small pore may be necessary to take up sulfate. This study depicts a genome-based model of a multipartite symbiotic system within a cellulolytic protist cell in the termite gut. PMID:27801909

  3. 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

  4. 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.

  5. Binding and Direct Electrochemistry of OmcA, an Outer-Membrane Cytochrome from an Iron Reducing Bacterium, with Oxide Electrodes: A Candidate Biofuel Cell System

    SciTech Connect

    Eggleston, Carrick M.; Voros, Janos; Shi, Liang; Lower, Brian H.; Droubay, Timothy C.; Colberg, Patricia J.

    2008-02-15

    Dissimilatory iron-reducing bacteria transfer electrons to solid ferric respiratory electron acceptors. Outer-membrane cytochromes expressed by these organisms are of interest in both microbial fuel cells and biofuel cells. We use optical waveguide lightmode spectroscopy (OWLS) to show that OmcA, an 85 kDa decaheme outer-membrane c-type cytochrome from Shewanella oneidensis MR-1, adsorbs to isostructural Al2O3 and Fe2O3 in similar amounts. Adsorption is ionic-strength and pH dependent (peak adsorption at pH 6.5–7.0). The thickness of the OmcA layer on Al2O3 at pH 7.0 [5.8 ± 1.1 (2r) nm] from OWLS is similar, within error, to that observed using atomic force microscopy (4.8 ± 2 nm). The highest adsorption density observed was 334 ng cm 2 (2.4 · 1012 molecules cm 2), corresponding to a monolayer or 9.9 nm diameter spheres or submonolayer coverage by smaller molecules. Direct electrochemistry of OmcA on Fe2O3 electrodes was observed using cyclic voltammetry, with cathodic peak potentials of 380 to 320 mV versus Ag/AgCl. Variations in the cathodic peak positions are speculatively attributed to redox-linked conformation change or changes in molecular orientation. OmcA can exchange electrons with ITO electrodes at higher current densities than with Fe2O3. Overall, OmcA can bind to and exchange electrons with several oxides, and thus its utility in fuel cells is not restricted to Fe2O3.

  6. Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure.

    PubMed

    Can, Mehmet; Krucinska, Jolanta; Zoppellaro, Giorgio; Andersen, Niels H; Wedekind, Joseph E; Hersleth, Hans-Petter; Andersson, K Kristoffer; Bren, Kara L

    2013-09-23

    Nitrosomonas europaea cytochrome c-552 (Ne c-552) variants with the same His/Met axial ligand set but with different EPR spectra have been characterized structurally, to aid understanding of how molecular structure determines heme electronic structure. Visible light absorption, Raman, and resonance Raman spectroscopy of the protein crystals was performed along with structure determination. The structures solved are those of Ne c-552, which displays a "HALS" (or highly anisotropic low-spin) EPR spectrum, and of the deletion mutant Ne N64Δ, which has a rhombic EPR spectrum. Two X-ray crystal structures of wild-type Ne c-552 are reported; one is of the protein isolated from N. europaea cells (Ne c-552n, 2.35 Å resolution), and the other is of recombinant protein expressed in Escherichia coli (Ne c-552r, 1.63 Å resolution). Ne N64Δ crystallized in two different space groups, and two structures are reported [monoclinic (2.1 Å resolution) and hexagonal (2.3 Å resolution)]. Comparison of the structures of the wild-type and mutant proteins reveals that heme ruffling is increased in the mutant; increased ruffling is predicted to yield a more rhombic EPR spectrum. The 2.35 Å Ne c-552n structure shows 18 molecules in the asymmetric unit; analysis of the structure is consistent with population of more than one axial Met configuration, as seen previously by NMR. Finally, the mutation was shown to yield a more hydrophobic heme pocket and to expel water molecules from near the axial Met. These structures reveal that heme pocket residue 64 plays multiple roles in regulating the axial ligand orientation and the interaction of water with the heme. These results support the hypothesis that more ruffled hemes lead to more rhombic EPR signals in cytochromes c with His/Met axial ligation.

  7. A specific inorganic triphosphatase from Nitrosomonas europaea: structure and catalytic mechanism.

    PubMed

    Delvaux, David; Murty, Mamidanna R V S; Gabelica, Valérie; Lakaye, Bernard; Lunin, Vladimir V; Skarina, Tatiana; Onopriyenko, Olena; Kohn, Gregory; Wins, Pierre; De Pauw, Edwin; Bettendorff, Lucien

    2011-09-30

    The CYTH superfamily of proteins is named after its two founding members, the CyaB adenylyl cyclase from Aeromonas hydrophila and the human 25-kDa thiamine triphosphatase. Because these proteins often form a closed β-barrel, they are also referred to as triphosphate tunnel metalloenzymes (TTM). Functionally, they are characterized by their ability to bind triphosphorylated substrates and divalent metal ions. These proteins exist in most organisms and catalyze different reactions depending on their origin. Here we investigate structural and catalytic properties of the recombinant TTM protein from Nitrosomonas europaea (NeuTTM), a 19-kDa protein. Crystallographic data show that it crystallizes as a dimer and that, in contrast to other TTM proteins, it has an open β-barrel structure. We demonstrate that NeuTTM is a highly specific inorganic triphosphatase, hydrolyzing tripolyphosphate (PPP(i)) with high catalytic efficiency in the presence of Mg(2+). These data are supported by native mass spectrometry analysis showing that the enzyme binds PPP(i) (and Mg-PPP(i)) with high affinity (K(d) < 1.5 μm), whereas it has a low affinity for ATP or thiamine triphosphate. In contrast to Aeromonas and Yersinia CyaB proteins, NeuTTM has no adenylyl cyclase activity, but it shares several properties with other enzymes of the CYTH superfamily, e.g. heat stability, alkaline pH optimum, and inhibition by Ca(2+) and Zn(2+) ions. We suggest a catalytic mechanism involving a catalytic dyad formed by Lys-52 and Tyr-28. The present data provide the first characterization of a new type of phosphohydrolase (unrelated to pyrophosphatases or exopolyphosphatases), able to hydrolyze inorganic triphosphate with high specificity.

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

    PubMed

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

    2012-11-01

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

  9. Expression of merA, amoA and hao in continuously cultured Nitrosomonas europaea cells exposed to zinc chloride additions.

    PubMed

    Radniecki, Tyler S; Semprini, Lewis; Dolan, Mark E

    2009-02-01

    The effects of ZnCl2 additions on a mercuric reductase, merA, ammonia monooxygenase, amoA, and hydroxylamine (NH2OH) oxidoreductase, hao, gene expression were examined in continuously cultured Nitrosomonas europaea cells. The reactor was operated for 85 days with a 6.9 d hydraulic retention time and with four successive additions of ZnCl2 achieving maximum concentrations from 3 to 90 microM Zn2+. Continuously cultured N. europaea cells were more resistant to Zn2+ inhibition than previously examined batch cultured cells due to the presence of Mg2+ in the growth media, suggesting that Zn2+ enters the cell through Mg2+ import channels. The maximum merA up-regulation was 45-fold and expression increased with increases in Zn2+ concentration and decreased as Zn2+ concentrations decreased. Although Zn2+ irreversibly inactivated ammonia oxidation in N. europaea, the addition of either 600 microM CuSO4 or 2250 microM MgSO4 protected N. europaea from ZnCl2 inhibition, indicating a competition between Zn2+ and Cu2+/Mg2+ for uptake and/or AMO active sites. Since ZnCl2 inhibition is irreversible and amoA was up-regulated at 30 and 90 microM additions, it is hypothesized that de novo synthesis of the AMO enzyme is needed to overcome inhibition. The up-regulation of merA during exposure to non-inhibitory Zn2+ levels indicates that merA is an excellent early warning signal for Zn2+ inhibition.

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

    PubMed Central

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

    2012-01-01

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

  11. Growth modelling of Nitrosomonas europaea ATCC® 19718 and Nitrobacter winogradskyi ATCC® 25391: A new online indicator of the partial nitrification.

    PubMed

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

    2016-11-01

    The aim of the present work was to study the growth of two nitrifying bacteria. For modelling the nitrifying subsystem of the MELiSSA loop, Nitrosomonas europaea ATCC® 19718 and Nitrobacter winogradskyi ATCC® 25931 were grown separately and in cocultures. The kinetic parameters of a stoichiometric mass balanced Pirt model were identified: μmax=0.054h(-1), decay rate b=0.003h(-1) and maintenance rate m=0.135gN-NH4(+)·gX(-1)·h(-1) for Nitrosomonas europaea; μmax=0.024h(-1), b=0.001h(-1) and m=0.467gN-NO2(-)·gX(-1)·h(-1) for Nitrobacter winogradskyi. A predictive structured model of nitrification in co-culture was developed. The online evolution of the addition of KOH is correlated to the nitritation; the dissolved oxygen concentration is correlated to both nitritation and nitratation. The model suitably represents these two variables so that transient partial nitrification is assessed. This is a clue for avoiding partial nitrification by predictive functional control.

  12. 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 ...

  13. 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.

  14. Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history.

    PubMed

    Bergmann, David J; Hooper, Alan B; Klotz, Martin G

    2005-09-01

    Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c(554); and cycB, cytochrome c(m)(552). The deduced protein sequences of HAO, c(554), and c(m)(552) were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c(m)(552), NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c(554) gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c(554) gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.

  15. Structure and Sequence Conservation of hao Cluster Genes of Autotrophic Ammonia-Oxidizing Bacteria: Evidence for Their Evolutionary History

    PubMed Central

    Bergmann, David J.; Hooper, Alan B.; Klotz, Martin G.

    2005-01-01

    Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c554; and cycB, cytochrome cm552. The deduced protein sequences of HAO, c554, and cm552 were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes cm552, NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c554 gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c554 gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB. PMID:16151127

  16. Transcript Analysis of Multiple Copies of amo (Encoding Ammonia Monooxygenase) and hao (Encoding Hydroxylamine Oxidoreductase) in Nitrosomonas europaea

    PubMed Central

    Hommes, Norman G.; Sayavedra-Soto, Luis A.; Arp, Daniel J.

    2001-01-01

    The genes encoding ammonia monooxygenase (amoCAB), hydroxylamine oxidoreductase (hao), and the c-type cytochrome c-554 (hcy) are present in multiple copies in the genome of Nitrosomonas europaea. The upstream regions of the two copies of amoC, the three copies of hao, and one copy of hcy were cloned and sequenced. Primer extension reactions were done to identify transcription start sites for these genes, as well as for amoA. Putative ς70 promoter sequences were found associated with all but one of the mapped transcription start sites. Primer extensions were done with amoC primers using RNA harvested from cells incubated with and without ammonium. The experiments suggested that N. europaea cells may be able to use different promoters in the presence and absence of ammonium. PMID:11208810

  17. Role of nitrogen oxides in the metabolism of ammonia-oxidizing bacteria.

    PubMed

    Kampschreur, M J; Tan, N C G; Picioreanu, C; Jetten, M S M; Schmidt, I; van Loosdrecht, M C M

    2006-02-01

    Ammonia-oxidizing bacteria (AOB) can use oxygen and nitrite as electron acceptors. Nitrite reduction by Nitrosomonas is observed under three conditions: (i) hydrogen-dependent denitrification, (ii) anoxic ammonia oxidation with nitrogen dioxide (NO(2)) and (iii) NO(x)-induced aerobic ammonia oxidation. NO(x) molecules play an important role in the conversion of ammonia and nitrite by AOB. Absence of nitric oxide (NO), which is generally detectable during ammonia oxidation, severely impairs ammonia oxidation by AOB. The lag phase of recovery of aerobic ammonia oxidation was significantly reduced by NO(2) addition. Acetylene inhibition tests showed that NO(2)-dependent and oxygen-dependent ammonia oxidation can be distinguished. Addition of NO(x) increased specific activity of ammonia oxidation, growth rate and denitrification capacity. Together, these findings resulted in a hypothetical model on the role of NO(x) in ammonia oxidation: the NO(x) cycle.

  18. 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.

  19. Diversity in the Ammonia-Oxidizing Nitrifier Population of a Soil †

    PubMed Central

    Belser, L. W.; Schmidt, E. L.

    1978-01-01

    Multiple genera of ammonia-oxidizing chemoautotrophic nitrifiers in a soil were detected, isolated, and studied by means of modified most-probable-number (MPN) techniques. The soil examined was a Waukegon silt loam treated with ammonium nitrate or sewage effluent. The genera Nitrosomonas and Nitrosospira were found to occur more commonly than the genus Nitrosolobus. Three different MPN media gave approximately the same overall ammonia oxidizer counts within statistical error after prolonged incubation but differed markedly in ratios of Nitrosomonas to Nitrosospira. Selectivity and counting efficiency of MPN media were studied by observing the growth response of representative pure cultures isolated from the soil. Selectivity was evident in each medium with respect to all strains tested, and the media differed greatly in incubation times required to obtain maximum counts. PMID:16345319

  20. Expression, purification, crystallization and preliminary X-ray diffraction of a novel Nitrosomonas europaea cytochrome, cytochrome P460

    SciTech Connect

    Elmore, Bradley O.; Pearson, Arwen R.; Wilmot, Carrie M.; Hooper, Alan B.

    2006-04-01

    Cytochrome P460 from N. europaea, a novel mono-heme protein containing an unusual lysine cross-link to the porphyrin ring, has been recombinantly expressed and purified from E. coli and crystallized. The crystals belong to the trigonal space group P3{sub 1/2}21, with unit-cell parameters a = b = 53.3, c = 127.1 Å, one monomer in the asymmetric unit and diffract to 1.7 Å on a Cu Kα rotating-anode X-ray source. Cytochrome P460 from Nitrosomonas europaea, a novel mono-heme protein containing an unusual cross-link between a conserved lysine and the porphyrin ring, has been recombinantly expressed and purified from Escherichia coli. The protein crystallizes readily and diffraction to 1.7 Å has been obtained in-house. The crystals belong to the trigonal space group P3{sub 1/2}21, with unit-cell parameters a = b = 53.3, c = 127.1 Å, and contain one monomer in the asymmetric unit.

  1. Role of Nitrosomonas europaea NitABC iron transporter in the uptake of Fe3+-siderophore complexes.

    PubMed

    Vajrala, Neeraja; Sayavedra-Soto, Luis A; Bottomley, Peter J; Arp, Daniel J

    2010-11-01

    Nitrosomonas europaea has a single three-gene operon (nitABC) encoding an iron ABC transporter system (NitABC). Phylogenetic analysis clustered the subunit NitB with Fe(3+)-ABC transporter permease components from other organisms. The N. europaea strain deficient in nitB (nitB::kan) grew well in either Fe-replete or Fe-limited media and in Fe-limited medium containing the catecholate-type siderophore, enterobactin or the citrate-based dihydroxamate-type siderophore, aerobactin. However, the nitB::kan mutant strain was unable to grow in Fe-limited media containing either the hydroxamate-type siderophores, ferrioxamine and ferrichrome or the mixed-chelating type siderophore, pyoverdine. Exposure of N. europaea cells to a ferrichrome analog coupled to the fluorescent moiety naphthalic diimide (Fhu-NI) led to increase in fluorescence in the wild type but not in nitB::kan mutant cells. Spheroplasts prepared from N. europaea wild type exposed to Fhu-NI analog retained the fluorescence, while spheroplasts of the nitB::kan mutant were not fluorescent. NitABC transports intact Fe(3+)-ferrichrome complex into the cytoplasm and is an atypical ABC type iron transporter for Fe(3+) bound to ferrioxamine, ferrichrome or pyoverdine siderophores into the cytoplasm. The mechanisms to transport iron in either the Fe(3+) or Fe(2+) forms or Fe(3+) associated with enterobactin or aerobactin siderophores into the cell across the cytoplasmic membrane are as yet undetermined.

  2. Expression and purification of recombinant proteins in Escherichia coli tagged with a small metal-binding protein from Nitrosomonas europaea.

    PubMed

    Vargas-Cortez, Teresa; Morones-Ramirez, Jose Ruben; Balderas-Renteria, Isaias; Zarate, Xristo

    2016-02-01

    Escherichia coli is still the preferred organism for large-scale production of recombinant proteins. The use of fusion proteins has helped considerably in enhancing the solubility of heterologous proteins and their purification with affinity chromatography. Here, the use of a small metal-binding protein (SmbP) from Nitrosomonas europaea is described as a new fusion protein for protein expression and purification in E. coli. Fluorescent proteins tagged at the N-terminal with SmbP showed high levels of solubility, compared with those of maltose-binding protein and glutathione S-transferase, and low formation of inclusion bodies. Using commercially available IMAC resins charged with Ni(II), highly pure recombinant proteins were obtained after just one chromatography step. Proteins may be purified from the periplasm of E. coli if SmbP contains the signal sequence at the N-terminal. After removal of the SmbP tag from the protein of interest, high-yields are obtained since SmbP is a protein of just 9.9 kDa. The results here obtained suggest that SmbP is a good alternative as a fusion protein/affinity tag for the production of soluble recombinant proteins in E. coli.

  3. 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...

  4. 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 representative Nitrosomonas 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.

  5. 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...

  6. 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...

  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. Community shift of ammonia-oxidizing bacteria along an anthropogenic pollution gradient from the Pearl River Delta to the South China Sea.

    PubMed

    Cao, Huiluo; Hong, Yiguo; Li, Meng; Gu, Ji-Dong

    2012-04-01

    The phylogenetic diversity and abundance of ammonia-oxidizing beta-proteobacteria (beta-AOB) was analyzed along an anthropogenic pollution gradient from the coastal Pearl River Delta to the South China Sea using the ammonia monooxygenase subunit A (amoA) gene. Along the gradient from coastal to the open ocean, the phylogenetic diversity of the dominant genus changed from Nitrosomonas to Nitrosospira, indicating the niche specificity by these two genera as both salinity and anthropogenic influence were major factors involved. The diversity of bacterial amoA gene was also variable along the gradient, with the highest in the deep-sea sediments, followed by the marshes sediments and the lowest in the coastal areas. Within the Nitrosomonas-related clade, four distinct lineages were identified including a putative new one (A5-16) from the different sites over the large geographical area. In the Nitrosospira-related clade, the habitat-specific lineages to the deep-sea and coastal sediments were identified. This study also provides strong support that Nitrosomonas genus, especially Nitrosomonas oligotropha lineage (6a) could be a potential bio-indicator species for pollution or freshwater/wastewater input into coastal environments. A suite of statistical analyses used showed that water depth and temperature were major factors shaping the community structure of beta-AOB in this study area.

  9. A "MICROTUBULE" IN A BACTERIUM

    PubMed Central

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

    1967-01-01

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

  10. Disruption of sucA, which encodes the E1 subunit of alpha-ketoglutarate dehydrogenase, affects the survival of Nitrosomonas europaea in stationary phase.

    PubMed

    Hommes, Norman G; Kurth, Elizabeth G; Sayavedra-Soto, Luis A; Arp, Daniel J

    2006-01-01

    Although Nitrosomonas europaea lacks measurable alpha-ketoglutarate dehydrogenase activity, the recent completion of the genome sequence revealed the presence of the genes encoding the enzyme. A knockout mutation was created in the sucA gene encoding the E1 subunit. Compared to wild-type cells, the mutant strain showed an accelerated loss of ammonia monooxygenase and hydroxylamine oxidoreductase activities upon entering stationary phase. In addition, unlike wild-type cells, the mutant strain showed a marked lag in the ability to resume growth in response to pH adjustments in late stationary phase.

  11. Ammonia- and Nitrite-Oxidizing Bacterial Communities in a Pilot-Scale Chloraminated Drinking Water Distribution System

    PubMed Central

    Regan, John M.; Harrington, Gregory W.; Noguera, Daniel R.

    2002-01-01

    Nitrification in drinking water distribution systems is a common operational problem for many utilities that use chloramines for secondary disinfection. The diversity of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the distribution systems of a pilot-scale chloraminated drinking water treatment system was characterized using terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene (ribosomal DNA [rDNA]) cloning and sequencing. For ammonia oxidizers, 16S rDNA-targeted T-RFLP indicated the presence of Nitrosomonas in each of the distribution systems, with a considerably smaller peak attributable to Nitrosospira-like AOB. Sequences of AOB amplification products aligned within the Nitrosomonas oligotropha cluster and were closely related to N. oligotropha and Nitrosomonas ureae. The nitrite-oxidizing communities were comprised primarily of Nitrospira, although Nitrobacter was detected in some samples. These results suggest a possible selection of AOB related to N. oligotropha and N. ureae in chloraminated systems and demonstrate the presence of NOB, indicating a biological mechanism for nitrite loss that contributes to a reduction in nitrite-associated chloramine decay. PMID:11772611

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

    SciTech Connect

    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; 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, Loanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy; Hazen, Terry C.; Fields, Matthew W.

    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.

  13. 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...

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

    PubMed

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

    2015-01-01

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

  15. 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.

  16. Peeking under the Iron Curtain: Development of a Microcosm for Imaging the Colonization of Steel Surfaces by Mariprofundus sp. Strain DIS-1, an Oxygen-Tolerant Fe-Oxidizing Bacterium.

    PubMed

    Mumford, Adam C; Adaktylou, Irini J; Emerson, David

    2016-11-15

    Microbially influenced corrosion (MIC) is a major cause of damage to steel infrastructure in the marine environment. Despite their ability to grow directly on Fe(II) released from steel, comparatively little is known about the role played by neutrophilic iron-oxidizing bacteria (FeOB). Recent work has shown that FeOB grow readily on mild steel (1018 MS) incubated in situ or as a substrate for pure cultures in vitro; however, details of how they colonize steel surfaces are unknown yet are important for understanding their effects. In this study, we combine a novel continuously upwelling microcosm with confocal laser scanning microscopy (CLSM) to determine the degree of colonization of 1018 MS by the marine FeOB strain DIS-1. 1018 MS coupons were incubated with sterile seawater (pH 8) inoculated with strain DIS-1. Incubations were performed both under oxic conditions and in an anoxic-to-oxic gradient. Following incubations of 1 to 10 days, the slides were removed from the microcosms and stained to visualize both cells and stalk structures. Stained coupons were visualized by CLSM after being mounted in a custom frame to preserve the three-dimensional structure of the biofilm. The incubation of 1018 MS coupons with strain DIS-1 under oxic conditions resulted in initial attachment of cells within 2 days and nearly total coverage of the coupon with an ochre film within 5 days. CLSM imaging revealed a nonadherent biofilm composed primarily of the Fe-oxide stalks characteristic of strain DIS-1. When incubated with elevated concentrations of Fe(II), DIS-1 colonization of 1018 MS was inhibited.

  17. Analysis of ammonia-oxidizing bacteria dominating in lab-scale bioreactors with high ammonium bicarbonate loading.

    PubMed

    Vejmelkova, Dana; Sorokin, Dimitry Y; Abbas, Ben; Kovaleva, Olga L; Kleerebezem, Robbert; Kampschreur, Marlies J; Muyzer, Gerard; van Loosdrecht, Mark C M

    2012-01-01

    The ammonia-oxidizing bacterial community (AOB) was investigated in two types of laboratory-scale bioreactors performing partial oxidation of ammonia to nitrite or nitrate at high (80 mM) to extremely high (428 mM) concentrations of ammonium bicarbonate. At all conditions, the dominant AOB was affiliated to the Nitrosomonas europaea lineage as was determined by fluorescence in situ hybridization and polymerase chain reaction in combination with denaturing gradient gel electrophoresis. Molecular analysis of the mixed populations, based on the 16S rRNA and cbbL genes, demonstrated the presence of two different phylotypes of Nitrosomonas, while microbiological analysis produced a single phylotype, represented by three different morphotypes. One of the most striking features of the AOB populations encountered in the bioreactors was the domination of highly aggregated obligate microaerophilic Nitrosomonas, with unusual cellular and colony morphology, commonly observed in nitrifying bioreactors but rarely investigated by cultural methods. The latter is probably not an adaptation to stressful conditions created by high ammonia or nitrite concentrations, but oxygen seems to be a stressful factor in these bioreactors.

  18. Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary*

    PubMed Central

    Li, Xiao-ran; Xiao, Yi-ping; Ren, Wen-wei; Liu, Zeng-fu; Shi, Jin-huan; Quan, Zhe-xue

    2012-01-01

    Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages. PMID:23024044

  19. Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi in an autotrophic nitrifying biofilm reactor as depicted by molecular analyses and mathematical modelling.

    PubMed

    Montràs, Anna; Pycke, Benny; Boon, Nico; Gòdia, Francesc; Mergeay, Max; Hendrickx, Larissa; Pérez, Julio

    2008-03-01

    The autotrophic two-species biofilm from the packed bed reactor of a life-support system, containing Nitrosomonas europaea ATCC 19718 and Nitrobacter winogradskyi ATCC 25391, was analysed after 4.8 years of continuous operation performing complete nitrification. Real-time quantitative polymerase chain reaction (Q-PCR) was used to quantify N. europaea and N. winogradskyi along the vertical axis of the reactor, revealing a spatial segregation of N. europaea and N. winogradskyi. The main parameters influencing the spatial segregation of both nitrifiers along the bed were assessed through a multi-species one-dimensional biofilm model generated with AQUASIM software. The factor that contributed the most to this distribution profile was a small deviation from the flow pattern of a perfectly mixed tank towards plug-flow. The results indicate that the model can estimate the impact of specific biofilm parameters and predict the nitrification efficiency and population dynamics of a multispecies biofilm.

  20. 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.

  1. 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.

  2. Dissimilatory Nitrite Reductase Genes from Autotrophic Ammonia-Oxidizing Bacteria

    PubMed Central

    Casciotti, Karen L.; Ward, Bess B.

    2001-01-01

    The presence of a copper-containing dissimilatory nitrite reductase gene (nirK) was discovered in several isolates of β-subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were designed based on published nirK sequences from denitrifying bacteria and used to amplify a 540-bp fragment of the nirK gene from Nitrosomonas marina and five additional isolates of ammonia-oxidizing bacteria. Amplification products of the expected size were cloned and sequenced. Alignment of the nucleic acid and deduced amino acid (AA) sequences shows significant similarity (62 to 75% DNA, 58 to 76% AA) between nitrite reductases present in these nitrifiers and the copper-containing nitrite reductase found in classic heterotrophic denitrifiers. While the presence of a nitrite reductase in Nitrosomonas europaea is known from early biochemical work, preliminary sequence data from its genome indicate a rather low similarity to the denitrifier nirKs. Phylogenetic analysis of the partial nitrifier nirK sequences indicates that the topology of the nirK tree corresponds to the 16S rRNA and amoA trees. While the role of nitrite reduction in the metabolism of nitrifying bacteria is still uncertain, these data show that the nirK gene is present in closely related nitrifying isolates from many oceanographic regions and suggest that nirK sequences retrieved from the environment may include sequences from ammonia-oxidizing bacteria. PMID:11319103

  3. Population diversity of ammonium oxidizers investigated by specific PCR amplification

    USGS Publications Warehouse

    Ward, B.B.; Voytek, M.A.; Witzel, K.-P.

    1997-01-01

    The species composition of ammonia-oxidizing bacteria in aquatic environments was investigated using PCR primers for 16S rRNA genes to amplify specific subsets of the total ammonia-oxidizer population. The specificity of the amplification reactions was determined using total genomic DNA from known nitrifying strains and non-nitrifying strains identified as having similar rDNA sequences. Specificity of amplification was determined both for direct amplification, using the nitrifier specific primers, and with nested amplification, in which the nitrifier primers were used to reamplify a fragment obtained from direct amplification with Eubacterial universal primers. The present level of specificity allows the distinction between Nitrosomonas europaea, Nitrosomonas sp. (marine) and the other known ammonia-oxidizers in the beta subclass of the Proteobacteria. Using total DNA extracted from natural samples, we used direct amplification to determine presence/absence of different species groups. Species composition was found to differ among depths in vertical profiles of lake samples and among samples and enrichments from various other aquatic environments. Nested PCR yielded several more positive reactions, which implies that nitrifier DNA was present in most samples, but often at very low levels.

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

    PubMed

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

    1999-11-19

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

  5. Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria

    SciTech Connect

    Jiang, Q.Q.; Bakken, L.R.

    1999-06-01

    Ammonia-oxidizing bacteria (AOB) are thought to contribute significantly to N{sub 2}O production and methane oxidation in soils. Most knowledge derives from experiments with Nitrosomonas europaea, which appears to be of minor importance in most soils compared to Nitrosospira spp. The authors have conducted a comparative study of levels of aerobic N{sub 2}O production in six phylogenetically different Nitrosospira strains newly isolated from soils and in two N. europaea and Nitrosospira multiformis type strains. The fraction of oxidized ammonium released as N{sub 2}O during aerobic growth was remarkably constant for all the Nitrosospira strains, irrespective of the substrate supply (urea versus ammonium), the pH, or substrate limitation. N. europaea and Nitrosospira multiformis released similar fractions of N{sub 2}O when they were supplied with ample amounts of substrates, but the fractions rose sharply when they were restricted by a low pH or substrate limitation. Phosphate buffer doubled the N{sub 2}O release for all types of AOB. No detectable oxidation of atmospheric methane was detected. Calculations based on detection limits as well as data in the literature on CH{sub 4} oxidation by AOB bacteria prove that none of the tested strains contribute significantly to the oxidation of atmospheric CH{sub 4} in soils.

  6. 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

  7. Population dynamics of ammonia-oxidizing bacteria in an aerated submerged biofilm reactor for micropolluted raw water pretreatment.

    PubMed

    Qin, Ying-Ying; Zhang, Xiao-Wen; Ren, Hong-Qiang; Li, Dao-Tang; Yang, Hong

    2008-05-01

    Population dynamics of ammonia-oxidizing bacteria (AOB) in a full-scale aerated submerged biofilm reactor for micropolluted raw water pretreatment was investigated using molecular techniques for a period of 1 year. The ammonia monooxygenase (amoA) gene fragments were amplified from DNA and RNA extracts of biofilm samples. Denaturing gradient gel electrophoresis (DGGE) profile based on the amoA messenger RNA approach exhibited a more variable pattern of temporal dynamics of AOB communities than the DNA-derived approach during the study. Phylogenetic analysis of excised DGGE bands revealed three AOB groups affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage, and an unknown Nitrosomonas group. The population size of betaproteobacterial AOB, quantified with 16S ribosomal RNA gene real-time polymerase chain reaction assay, ranged from 6.63 x 10(5) to 2.67 x 10(9) cells per gram of dry biofilm and corresponded to 0.23-1.8% of the total bacterial fraction. Quantitative results of amoA gene of the three specific AOB groups revealed changes in competitive dominance between AOB of the N. oligotropha lineage and N. communis lineage. Water temperature is shown to have major influence on AOB population size in the reactor by the statistic analysis, and a positive correlation between AOB cell numbers and ammonia removal efficiency is suggested (r = 0.628, P < 0.05).

  8. Paradigms: examples from the bacterium Xylella fastidiosa.

    PubMed

    Purcell, Alexander

    2013-01-01

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

  9. Pneumonia caused by a previously undescribed bacterium.

    PubMed Central

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

    1982-01-01

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

  10. Characterization of a novel extremely alkalophilic bacterium

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

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

  11. 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.

  12. Stresses exerted by ZnO, CeO2 and anatase TiO2 nanoparticles on the Nitrosomonas europaea.

    PubMed

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

    2010-08-15

    Recent studies have shown that nano-bio interfaces are the most complex and the least understood. Notably, nanotoxicity of these nanoparticles is not even well recognized. In this work, we examined the toxic effects of different nanoparticles on bacteria cells (Nitrosomonas europaea). The four nanoparticles involved are: 25 nm anatase TiO(2), 200 nm anatase TiO(2), ZnO and CeO(2) particles. These particles will have different electrical charges in the cell cultivating media. It has been observed that even with only 4 h of dosing, all of the particles caused apparent morphological damage to the cells. Experimental results suggest that ZnO particles exert the stress on cells by its dissolution and releasing of Zn(2+) ions. The TEM and AUC (analytical ultracentrifuge) result suggest that cells become heavier in presence of CeO(2) and TiO(2) particles. No visible clear intrusions of bulk nanoparticles were observed. However, both the analytical ultracentrifuge and TEM results show that cells are heavier when being damaged.

  13. 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.

  14. 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.

  15. The Distribution of Ammonia-Oxidizing Betaproteobacteria in Stands of Black Mangroves (Avicennia germinans).

    PubMed

    Laanbroek, Hendrikus J; Keijzer, Rosalinde M; Verhoeven, Jos T A; Whigham, Dennis F

    2012-01-01

    The distribution of species of aerobic chemolitho-autotrophic microorganisms such as ammonia-oxidizing bacteria are governed by pH, salinity, and temperature as well as the availability of oxygen, ammonium, carbon dioxide, and other inorganic elements required for growth. Impounded mangrove forests in the Indian River Lagoon, a coastal estuary on the east coast of Florida, are dominated by mangroves, especially stands of Black mangrove (Avicennia germinans) that differ in the size and density of individual plants. In March 2009, the management of one impoundment was changed to a regime of pumping estuarine water into the impoundment at critical times of the year to eliminate breeding sites for noxious insects. We collected soil samples in three different Black mangrove habitats before and after the change in management to determine the impacts of the altered hydrologic regimes on the distribution of 16s rRNA genes belonging to ammonia-oxidizing betaproteobacteria (β-AOB). We also sampled soils in an adjacent impoundment in which there had not been any hydrologic alteration. At the level of 97% mutual similarity in the 16s rRNA gene, 13 different operational taxonomic units were identified; the majority related to the lineages of Nitrosomonas marina (45% of the total clones), Nitrosomonas sp. Nm143 (23%), and Nitrosospira cluster 1 (19%). Long-term summer flooding of the impoundment in 2009, after initiation of the pumping regime, reduced the percentage of N. marina by half between 2008 and 2010 in favor of the two other major lineages and the potential ammonia-oxidizing activity decreased by an average of 73%. Higher interstitial salinities, probably due to a prolonged winter drought, had a significant effect on the composition of the β-AOB in March 2009 compared to March 2008: Nitrosomonas sp. Nm143 was replaced by Nitrosospira cluster 1 as the second most important lineage. There were small, but significant differences in the bacterial communities between the

  16. Draft Genome Sequence of the Suttonella ornithocola Bacterium

    PubMed Central

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

    2017-01-01

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

  17. Identification of function and mechanistic insights of guanine deaminase from Nitrosomonas europaea: role of the C-terminal loop in catalysis.

    PubMed

    Bitra, Aruna; Hussain, Bhukya; Tanwar, Ajay Singh; Anand, Ruchi

    2013-05-21

    NE0047 from Nitrosomonas europaea has been annotated as a zinc-dependent deaminase; however, the substrate specificity is unknown because of the low level of structural similarity and sequence identity compared to other family members. In this study, the function of NE0047 was established as a guanine deaminase (catalytic efficiency of 1.2 × 10(5) M(-1) s(-1)), exhibiting secondary activity towards ammeline. The structure of NE0047 in the presence of the substrate analogue 8-azaguanine was also determined to a resolution of 1.9 Å. NE0047 crystallized as a homodimer in an asymmetric unit. It was found that the extreme nine-amino acid C-terminal loop forms an active site flap; in one monomer, the flap is in the closed conformation and in the other in the open conformation with this loop region exposed to the solvent. Calorimetric data obtained using the full-length version of the enzyme fit to a sequential binding model, thus supporting a cooperative mode of ligand occupancy. In contrast, the mutant form of the enzyme (ΔC) with the deletion of the extreme nine amino acids follows an independent model of ligand occupancy. In addition, the ΔC mutant also does not exhibit any enzyme activity. Therefore, we propose that the progress of the reaction is communicated via changes in the conformation of the C-terminal flap and the closed form of the enzyme is the catalytically active form, while the open form allows for product release. The catalytic mechanism of deamination was also investigated, and we found that the mutagenesis of the highly conserved active site residues Glu79 and Glu143 resulted in a complete loss of activity and concluded that they facilitate the reaction by serving as proton shuttles.

  18. Solid-Phase Contact Assay That Uses a lux-Marked Nitrosomonas europaea Reporter Strain To Estimate Toxicity of Bioavailable Linear Alkylbenzene Sulfonate in Soil

    PubMed Central

    Brandt, Kristian K.; Pedersen, Anders; Sørensen, Jan

    2002-01-01

    Information about in situ toxicity of the bioavailable pools of adsorptive soil pollutants is a prerequisite for proper ecological risk assessment in contaminated soils. Such toxicity data may be obtained by assays allowing for direct exposure of introduced test microorganisms to the toxicants, as they appear in solid solution equilibria in the natural soil. We describe a novel sensitive solid-phase contact assay for in situ toxicity testing of soil pollutants based on a recombinant bioluminescent reporter strain of Nitrosomonas europaea. A slurry of the reporter strain and soil sample was shaken for 1 h, after which bioluminescence was measured either directly (soil slurry protocol) or in the supernatant obtained after centrifugation (soil extract protocol). The assay was validated for both protocols by using linear alkylbenzene sulfonate (LAS) as a toxic and adsorptive model compound in the soil samples. Interestingly, LAS showed the same toxicity to the reporter strain with either soil incubation (both protocols) or pure culture, suggesting that adsorbed LAS pools contributed to the observed toxicity. The solid-phase contact assay that used the reporter strain of lux-marked N. europaea was slightly more sensitive for the detection of LAS toxicity in soil than activity-based assays targeting indigenous nitrifiers and much more sensitive than assays targeting indigenous heterotrophic microbes. We conclude that the new solid-phase contact assay, which is based on direct interaction of the test microorganisms with bioavailable pools of the toxicants in soil, provides a most sensitive and relevant method for evaluating the in situ toxicity and assessing the risks of soil contaminants. PMID:12089034

  19. 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

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

    PubMed

    Petroff, Alexander; Libchaber, Albert

    2014-02-04

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

  1. Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans

    PubMed Central

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

    2009-01-01

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

  2. 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.

  3. The complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium Bradyrhizobium japonicum.

    PubMed

    Bedmar, E J; Robles, E F; Delgado, M J

    2005-02-01

    Denitrification is an alternative form of respiration in which bacteria sequentially reduce nitrate or nitrite to nitrogen gas by the intermediates nitric oxide and nitrous oxide when oxygen concentrations are limiting. In Bradyrhizobium japonicum, the N(2)-fixing microsymbiont of soya beans, denitrification depends on the napEDABC, nirK, norCBQD, and nosRZDFYLX gene clusters encoding nitrate-, nitrite-, nitric oxide- and nitrous oxide-reductase respectively. Mutational analysis of the B. japonicum nap genes has demonstrated that the periplasmic nitrate reductase is the only enzyme responsible for nitrate respiration in this bacterium. Regulatory studies using transcriptional lacZ fusions to the nirK, norCBQD and nosRZDFYLX promoter region indicated that microaerobic induction of these promoters is dependent on the fixLJ and fixK(2) genes whose products form the FixLJ-FixK(2) regulatory cascade. Besides FixK(2), another protein, nitrite and nitric oxide respiratory regulator, has been shown to be required for N-oxide regulation of the B. japonicum nirK and norCBQD genes. Thus nitrite and nitric oxide respiratory regulator adds to the FixLJ-FixK(2) cascade an additional control level which integrates the N-oxide signal that is critical for maximal induction of the B. japonicum denitrification genes. However, the identity of the signalling molecule and the sensing mechanism remains unknown.

  4. An oleaginous bacterium that intrinsically accumulates long-chain free Fatty acids in its cytoplasm.

    PubMed

    Katayama, Taiki; Kanno, Manabu; Morita, Naoki; Hori, Tomoyuki; Narihiro, Takashi; Mitani, Yasuo; Kamagata, Yoichi

    2014-02-01

    Medium- and long-chain fatty acids are present in organisms in esterified forms that serve as cell membrane constituents and storage compounds. A large number of organisms are known to accumulate lipophilic materials as a source of energy and carbon. We found a bacterium, designated GK12, that intrinsically accumulates free fatty acids (FFAs) as intracellular droplets without exhibiting cytotoxicity. GK12 is an obligatory anaerobic, mesophilic lactic acid bacterium that was isolated from a methanogenic reactor. Phylogenetic analysis based on 16S rRNA gene sequences showed that GK12 is affiliated with the family Erysipelotrichaceae in the phylum Firmicutes but is distantly related to type species in this family (less than 92% similarity in 16S rRNA gene sequence). Saturated fatty acids with carbon chain lengths of 14, 16, 18, and 20 were produced from glucose under stress conditions, including higher-than-optimum temperatures and the presence of organic solvents that affect cell membrane integrity. FFAs were produced at levels corresponding to up to 25% (wt/wt) of the dry cell mass. Our data suggest that FFA accumulation is a result of an imbalance between excess membrane fatty acid biosynthesis due to homeoviscous adaptation and limited β-oxidation activity due to anaerobic growth involving lactic acid fermentation. FFA droplets were not further utilized as an energy and carbon source, even under conditions of starvation. A naturally occurring bacterium that accumulates significant amounts of long-chain FFAs with noncytotoxicity would provide useful strategies for microbial biodiesel production.

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

    DOE PAGES

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

    2015-10-26

    Thioalkalivibrio thiocyanoxidans strain ARh 2T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na+. This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. In conclusion, this organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

  6. 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.

  7. Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu).

    PubMed

    Hou, Jie; Song, Chunlei; Cao, Xiuyun; Zhou, Yiyong

    2013-05-01

    Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic ecosystems. Recent findings have expanded the known ammonia-oxidizing prokaryotes from Bacteria to Archaea. However, the relative importance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in nitrification is still debated. Here we showed that, in two large eutrophic lakes in China (Lake Taihu and Lake Chaohu), the abundance of AOA and AOB varied in opposite patterns according to the trophic state, although both AOA and AOB were abundant. In detail, from mesotrophic to eutrophic sites, the AOA abundance decreased, while the AOB increased in abundance and outnumbered the AOA at hypertrophic sites. In parallel, the nitrification rate increased along these trophic gradients and was significantly correlated with both the AOB abundance and the numerical ratio of AOB to AOA. Phylogenetic analysis of bacterial amoA sequences showed that Nitrosomonas oligotropha- and Nitrosospira-affiliated AOB dominated in both lakes, while Nitrosomonas communis-related AOB were only detected at the eutrophic sites. The diversity of AOB increased from mesotrophic to eutrophic sites and was positively correlated with the nitrification rate. Overall, this study enhances our understanding of the ecology of ammonia-oxidizing prokaryotes by elucidating conditions that AOB may numerically predominated over AOA, and indicated that AOA may play a less important role than AOB in the nitrification process of eutrophic lakes.

  8. 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)

  9. 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.

  10. Relationship between ion requirements for respiration and membrane transport in a marine bacterium.

    PubMed

    Khanna, G; DeVoe, L; Brown, L; Niven, D F; MacLeod, R A

    1984-01-01

    Intact cells of the marine bacterium Alteromonas haloplanktis 214 oxidized NADH, added to the suspending medium, by a process which was stimulated by Na+ or Li+ but not K+. Toluene-treated cells oxidized NADH at three times the rate of untreated cells by a mechanism activated by Na+ but not by Li+ or K+. In the latter reaction, K+ spared the requirement for Na+. Intact cells of A. haloplanktis oxidized ethanol by a mechanism stimulated by either Na+ or Li+. The uptake of alpha-aminoisobutyric acid by intact cells of A. haloplanktis in the presence of either NADH or ethanol as an oxidizable substrate required Na+, and neither Li+ nor K+ could replace it. The results indicate that exogenous and endogenous NADH and ethanol are oxidized by A. haloplanktis by processes distinguishable from one another by their requirements for alkali metal ions and from the ion requirements for membrane transport. Intact cells of Vibrio natriegens and Photobacterium phosphoreum oxidized NADH, added externally, by an Na+-activated process, and intact cells of Vibrio fischeri oxidized NADH, added externally, by a K+-activated process. Toluene treatment caused the cells of all three organisms to oxidize NADH at much faster rates than untreated cells by mechanisms which were activated by Na+ and spared by K+.

  11. Abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a chinese shallow eutrophic urban lake

    PubMed Central

    Qiu, Shanlian; Chen, Guoyuan; Zhou, Yiyong

    2010-01-01

    The measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a Chinese shallow eutrophic urban lake (Lake Yuehu). Among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 105 cells g-1 dry weight) in sediment significantly. Furthermore, the diversity of ammonia-oxidizing bacteria were determined by means of PCR primers targeting the amoA gene with five gene libraries created and restriction pattern analysis. The 13 restriction patterns were recorded with 4 ones being common among all sampling sites. The 8 restriction patterns including 4 unique ones were found at the site with the highest NH4+ concentrations in interstitial water, while, there were only common patterns without unique ones at the site with the lowest NH4+ concentrations in interstitial water. Phylogenetic analysis showed that the amoA fragments retrieved belong to Nitrosomonas oligotropha & ureae lineage, N. europaea lineage, N. communis lineage and Nitrosospira lineage, most of which were affiliated with the genus Nitrosomonas. The N. oligotropha & ureae-like bacteria were the dominant species. Thus, the abundance and diversity of sediment AOB is closely linked to ammonium status in eutrophic lakes. PMID:24031484

  12. Quantitative analysis of ammonia-oxidizing bacteria in a combined system of MBR and worm reactors treating synthetic wastewater.

    PubMed

    Liu, Jia; Tian, Yu; Wang, Dezhen; Lu, Yaobin; Zhang, Jun; Zuo, Wei

    2014-12-01

    The Static Sequencing Batch Worm Reactor (SSBWR) followed by the MBR (S-MBR) is one of the advanced excess sludge treatments. In this paper, the control MBR (C-MBR) and the SSBWR-MBR were operated in parallel to study the changes of NH3-N removal and ammonia oxidizing bacteria (AOB). The results showed that the capacity of NH3-N removal of the S-MBR was improved by the worm reactors along with the operation. The S-MBR was favorable because it selected for the higher activity of the ammonia oxidization and better cells appearance of the sludge. The five species (Nitrosomonas, Betaproteobacteria, Clostridium, Dechloromonas and Bacteria) were found to be significantly correlate with the ammonia oxidization functions and performance of NH3-N removal in the C-MBR and S-MBR. The Nitrosomonas, Betaproteobacteria and Dechloromonas remained and eventually enriched in the S-MBR played a primary role in the NH3-N removal of the S-MBR.

  13. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

    NASA Astrophysics Data System (ADS)

    Gao, Jing-Feng; Fan, Xiao-Yan; Pan, Kai-Ling; Li, Hong-Yu; Sun, Li-Xin

    2016-12-01

    Increasing ammonia emissions could exacerbate air pollution caused by fine particulate matter (PM2.5). Therefore, it is of great importance to investigate ammonia oxidation in PM2.5. This study investigated the diversity, abundance and activity of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and complete ammonia oxidizers (Comammox) in PM2.5 collected in Beijing-Tianjin-Hebei megalopolis, China. Nitrosopumilus subcluster 5.2 was the most dominant AOA. Nitrosospira multiformis and Nitrosomonas aestuarii were the most dominant AOB. Comammox were present in the atmosphere, as revealed by the occurrence of Candidatus Nitrospira inopinata in PM2.5. The average cell numbers of AOA, AOB and Ca. N. inopinata were 2.82 × 104, 4.65 × 103 and 1.15 × 103 cell m‑3 air, respectively. The average maximum nitrification rate of PM2.5 was 0.14 μg (NH4+-N) [m3 air·h]‑1. AOA might account for most of the ammonia oxidation, followed by Comammox, while AOB were responsible for a small part of ammonia oxidation. Statistical analyses showed that Nitrososphaera subcluster 4.1 was positively correlated with organic carbon concentration, and Nitrosomonas eutropha showed positive correlation with ammonia concentration. Overall, this study expanded our knowledge concerning AOA, AOB and Comammox in PM2.5 and pointed towards an important role of AOA and Comammox in ammonia oxidation in PM2.5.

  14. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

    PubMed Central

    Gao, Jing-Feng; Fan, Xiao-Yan; Pan, Kai-Ling; Li, Hong-Yu; Sun, Li-Xin

    2016-01-01

    Increasing ammonia emissions could exacerbate air pollution caused by fine particulate matter (PM2.5). Therefore, it is of great importance to investigate ammonia oxidation in PM2.5. This study investigated the diversity, abundance and activity of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and complete ammonia oxidizers (Comammox) in PM2.5 collected in Beijing-Tianjin-Hebei megalopolis, China. Nitrosopumilus subcluster 5.2 was the most dominant AOA. Nitrosospira multiformis and Nitrosomonas aestuarii were the most dominant AOB. Comammox were present in the atmosphere, as revealed by the occurrence of Candidatus Nitrospira inopinata in PM2.5. The average cell numbers of AOA, AOB and Ca. N. inopinata were 2.82 × 104, 4.65 × 103 and 1.15 × 103 cell m−3 air, respectively. The average maximum nitrification rate of PM2.5 was 0.14 μg (NH4+-N) [m3 air·h]−1. AOA might account for most of the ammonia oxidation, followed by Comammox, while AOB were responsible for a small part of ammonia oxidation. Statistical analyses showed that Nitrososphaera subcluster 4.1 was positively correlated with organic carbon concentration, and Nitrosomonas eutropha showed positive correlation with ammonia concentration. Overall, this study expanded our knowledge concerning AOA, AOB and Comammox in PM2.5 and pointed towards an important role of AOA and Comammox in ammonia oxidation in PM2.5. PMID:27941955

  15. 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.

  16. 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.

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

    PubMed

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

    2014-11-01

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

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

    USGS Publications Warehouse

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

    1996-01-01

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

  19. 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.

  20. Epiphyton as a niche for ammonia-oxidizing bacteria: detailed comparison with benthic and pelagic compartments in shallow freshwater lakes.

    PubMed

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

    2008-04-01

    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.

  1. 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

  2. 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.

  3. 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.

  4. Quantitative proteomics of Chlorobaculum tepidum: insights into the sulfur metabolism of a phototrophic green sulfur bacterium.

    PubMed

    Falkenby, Lasse G; Szymanska, Monika; Holkenbrink, Carina; Habicht, Kirsten S; Andersen, Jens S; Miller, Mette; Frigaard, Niels-Ulrik

    2011-10-01

    Chlorobaculum (Cba.) tepidum is a green sulfur bacterium that oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. To gain insight into the sulfur metabolism, the proteome of Cba. tepidum cells sampled under different growth conditions has been quantified using a rapid gel-free, filter-aided sample preparation (FASP) protocol with an in-solution isotopic labeling strategy. Among the 2245 proteins predicted from the Cba. tepidum genome, approximately 970 proteins were detected in unlabeled samples, whereas approximately 630-640 proteins were detected in labeled samples comparing two different growth conditions. Wild-type cells growing on thiosulfate had an increased abundance of periplasmic cytochrome c-555 and proteins of the periplasmic thiosulfate-oxidizing SOX enzyme system when compared with cells growing on sulfide. A dsrM mutant of Cba. tepidum, which lacks the dissimilatory sulfite reductase DsrM protein and therefore is unable to oxidize sulfur globules to sulfite, was also investigated. When compared with wild type, the dsrM cells exhibited an increased abundance of DSR enzymes involved in the initial steps of sulfur globule oxidation (DsrABCL) and a decreased abundance of enzymes putatively involved in sulfite oxidation (Sat-AprAB-QmoABC). The results show that Cba. tepidum regulates the cellular levels of enzymes involved in sulfur metabolism and other electron-transferring processes in response to the availability of reduced sulfur compounds.

  5. Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.

    PubMed

    Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Wen, Donghui

    2015-05-01

    Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.

  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. 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

  8. 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

  9. 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.

  10. 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

  11. Stimulatory Effect of Xenobiotics on Oxidative Electron Transport of Chemolithotrophic Nitrifying Bacteria Used as Biosensing Element

    PubMed Central

    Woznica, Andrzej; Nowak, Agnieszka; Ziemski, Przemyslaw; Kwasniewski, Mirosław; Bernas, Tytus

    2013-01-01

    Electron transport chain (ETCh) of ammonium (AOB) and nitrite oxidizing bacteria (NOB) participates in oxidation of ammonium to nitrate (nitrification). Operation of ETCh may be perturbed by a range of water-soluble xenobiotics. Therefore, consortia of nitrifying bacteria may be used as a biosensor to detect water contamination. A surprising feature of this system is an increase of oxygen consumption, detected in the presence of certain inhibitors of ETCh. Thus, to shed light on the mechanism of this effect (and other differences between inhibitors) we monitored separately respiration of the bacteria of the first (AOB - Nitrosomonas) and second (NOB -Nitrobacter) stages of nitrification. Furthermore, we measured plasma membrane potential and the level of reduction of NAD(P)H. We propose a novel model of ETCh in NOB to explain the role of reverse electron transport in the stimulation of oxygen consumption (previously attributed to hormesis). PMID:23326438

  12. 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.

  13. Microbial community structure and occurrence of diverse autotrophic ammonium oxidizing microorganisms in the anammox process.

    PubMed

    Bae, H; Chung, Y-C; Jung, J-Y

    2010-01-01

    The enrichment of anaerobic ammonium oxidizing (anammox) bacteria using an upflow anaerobic sludge bioreactor was successfully conducted for 400 days of continuous operation. The bacterial community structure of anammox bioreactor included Proteobacteria (42%), Chloroflexi (22%), Planctomycetes (20%), Chlorobi (7%), Bacteroidetes (5%), Acidobacteria (2%), and Actinobacteria (2%). All clones of Planctomycetes were affiliated with the anammox bacteria, Planctomycete KSU-1 (AB057453). The presence and diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) were identified by terminal restriction fragment length polymorphism (T-RFLP) based on the amoA gene sequences. The AOB in anammox bioreactor were affiliated with the Nitrosomonas europaea cluster. The T-RFLP result of AOA showed the diverse microbial community structure of AOA with three terminal restriction fragments (T-RFs).

  14. 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.

  15. 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.

  16. 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

  17. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana.

    PubMed

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

    2015-06-04

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

  18. The Symbiotic Bacterium Fuels the Energy Metabolism of the Host Trypanosomatid Strigomonas culicis.

    PubMed

    Loyola-Machado, Ana Carolina; Azevedo-Martins, Allan Cézar; Catta-Preta, Carolina Moura Costa; de Souza, Wanderley; Galina, Antonio; Motta, Maria Cristina M

    2017-02-28

    The mutualistic relationship between trypanosomatids and their respective endosymbiotic bacteria represents an excellent model for studying metabolic co-evolution since the symbiont completes essential biosynthetic routes of the host cell. In this work, we investigated the influence of the endosymbiont on the energy metabolism of Strigomonas culicis by comparing the wild strain with aposymbiotic protists. The bacterium maintains a frequent and close association with glycosomes, which are distributed around the prokaryote. Furthermore, 3D reconstructions revealed that the shape and distribution of glycosomes are different in symbiont-bearing protists compared to symbiont-free cells. Results of bioenergetic assays showed that the presence of the symbiont enhances the O2 consumption of the host cell. When the quantity of intracellular or released glycerol was evaluated, the aposymbiotic strain presented higher values when compared to symbiont-containing cells. Furthermore, inhibition of oxidative phosphorylation by potassium cyanide increased the rate of glycerol release and slightly diminished the ATP content in cells without the symbiont, indicating that the host trypanosomatid enhances its fermentative activity when the bacterium is lost.

  19. Thiorhodococcus mannitoliphagus sp. nov., a purple sulfur bacterium from the White Sea.

    PubMed

    Rabold, Sandra; Gorlenko, Vladimir M; Imhoff, Johannes F

    2006-08-01

    A novel purple sulfur bacterium, strain WS(T), was isolated from a microbial mat from an estuary of the White Sea. Individual cells are coccoid shaped, motile by flagella and do not contain gas vesicles. The mean cell diameter is 1.85 mum (range 1.5-2.0 mum). Cell suspensions exhibit a purple-violet colour. They contain bacteriochlorophyll a and carotenoids of the rhodopinal series as photosynthetic pigments. The novel bacterium is an anoxygenic photoautotroph, using sulfide, thiosulfate, sulfite and elemental sulfur as electron donors for photosynthesis and is capable of photoassimilating several organic carbon sources in the presence of carbonate and a reduced sulfur source (sulfide and/or thiosulfate). Sulfur globules, formed during oxidation of sulfide, are stored transiently inside the cells. Optimal salinity and pH for growth are at 0.5-2.0 % NaCl and pH 7.0-7.5. The DNA base composition of strain WS(T) is 61.8 mol% G+C. 16S rRNA gene sequence analysis showed that the new isolate belongs to the genus Thiorhodococcus, with Thiorhodococcus minor CE2203(T) as the nearest relative (sequence similarity of 97.3 %). Several distinct differences from described species necessitate the description of a novel species. Thiorhodococcus mannitoliphagus sp. nov. is the proposed name, with strain WS(T) (=ATCC BAA-1228(T)=VKM B-2393(T)) as the type strain.

  20. 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

  1. 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

  2. Treatability Study in Support of the Intrinsic Remediation Option at the Current Fire Training Area, Westover Air Reserves Base, Chicopee, Massachusetts

    DTIC Science & Technology

    1997-02-01

    physical and chemical conditions of the groundwater and phreat’. soil at the site are not likely to 0 inhibit microorganism growth . Fuel-hydrocarbon...Arciero, D., Vannelli, T., Logan, M., and Hooper, A.B., 1989, Degradation of trichloroethylene by the ammonia-oxidizing bacterium Nitrosomonas europaea ...5-3 5.3.1 Grid Design and Boundary Conditions ..................................... 5-3 5.3.2 Groundwater Elevation and

  3. 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.

  4. 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...

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

    PubMed

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

    2010-09-01

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

  6. Distribution and abundance of archaeal and bacterial ammonia oxidizers in the sediments of the Dongjiang River, a drinking water supply for Hong Kong.

    PubMed

    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.

  7. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions.

    PubMed

    Laanbroek, Hendrikus J; Keijzer, Rosalinde M; Verhoeven, Jos T A; Whigham, Dennis F

    2013-01-01

    In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.

  8. 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

  9. Biosynthesis of the respiratory toxin bongkrekic acid in the pathogenic bacterium Burkholderia gladioli.

    PubMed

    Moebius, Nadine; Ross, Claudia; Scherlach, Kirstin; Rohm, Barbara; Roth, Martin; Hertweck, Christian

    2012-09-21

    Bongkrekic acid (BA), an infamous respiratory toxin of the pathogenic bacterium Burkholderia gladioli, causes lethal intoxications when tempe bongkrek is produced with contaminated Rhizopus oligosporus cultures. Genome sequencing of B. gladioli pathovar cocovenenans unveiled the genetic basis for BA biosynthesis, and pointed to a homologous bon gene cluster in a B. gladioli strain from an infected rice plant. For functional genetics in B. gladioli λ Red recombination was established. Dissection of the modular type I polyketide synthase (a trans-AT PKS) provided insights into complex polyketide assembly. Isoprenoid-like β-branching events and a six-electron oxidation of a methyl group to a carboxylic acid give rise to the unique branched tricarboxylic fatty acid. The role of the cytochrome P450 monooxygenase, BonL, was proven by structural elucidation of deoxybongkrekic acid from a mutant.

  10. Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16.

    PubMed

    Pohlmann, Anne; Fricke, Wolfgang Florian; Reinecke, Frank; Kusian, Bernhard; Liesegang, Heiko; Cramm, Rainer; Eitinger, Thomas; Ewering, Christian; Pötter, Markus; Schwartz, Edward; Strittmatter, Axel; Voss, Ingo; Gottschalk, Gerhard; Steinbüchel, Alexander; Friedrich, Bärbel; Bowien, Botho

    2006-10-01

    The H(2)-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically versatile organism capable of subsisting, in the absence of organic growth substrates, on H(2) and CO(2) as its sole sources of energy and carbon. R. eutropha H16 first attracted biotechnological interest nearly 50 years ago with the realization that the organism's ability to produce and store large amounts of poly[R-(-)-3-hydroxybutyrate] and other polyesters could be harnessed to make biodegradable plastics. Here we report the complete genome sequence of the two chromosomes of R. eutropha H16. Together, chromosome 1 (4,052,032 base pairs (bp)) and chromosome 2 (2,912,490 bp) encode 6,116 putative genes. Analysis of the genome sequence offers the genetic basis for exploiting the biotechnological potential of this organism and provides insights into its remarkable metabolic versatility.

  11. 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.

  12. Ultrastructure of the denitrifying methanotroph "Candidatus Methylomirabilis oxyfera," a novel polygon-shaped bacterium.

    PubMed

    Wu, Ming L; van Teeseling, Muriel C F; Willems, Marieke J R; van Donselaar, Elly G; Klingl, Andreas; Rachel, Reinhard; Geerts, Willie J C; Jetten, Mike S M; Strous, Marc; van Niftrik, Laura

    2012-01-01

    "Candidatus Methylomirabilis oxyfera" is a newly discovered denitrifying methanotroph that is unrelated to previously known methanotrophs. This bacterium is a member of the NC10 phylum and couples methane oxidation to denitrification through a newly discovered intra-aerobic pathway. In the present study, we report the first ultrastructural study of "Ca. Methylomirabilis oxyfera" using scanning electron microscopy, transmission electron microscopy, and electron tomography in combination with different sample preparation methods. We observed that "Ca. Methylomirabilis oxyfera" cells possess an atypical polygonal shape that is distinct from other bacterial shapes described so far. Also, an additional layer was observed as the outermost sheath, which might represent a (glyco)protein surface layer. Further, intracytoplasmic membranes, which are a common feature among proteobacterial methanotrophs, were never observed under the current growth conditions. Our results indicate that "Ca. Methylomirabilis oxyfera" is ultrastructurally distinct from other bacteria by its atypical cell shape and from the classical proteobacterial methanotrophs by its apparent lack of intracytoplasmic membranes.

  13. Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium Pseudoalteromonas haloplanktis TAC125 ▿ †

    PubMed Central

    Wilmes, Boris; Kock, Holger; Glagla, Susanne; Albrecht, Dirk; Voigt, Birgit; Markert, Stephanie; Gardebrecht, Antje; Bode, Rüdiger; Danchin, Antoine; Feller, Georges; Hecker, Michael; Schweder, Thomas

    2011-01-01

    The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments. PMID:21183643

  14. Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group.

    PubMed

    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-2(T). A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.

  15. Thiorhodospira sibirica gen. nov., sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake.

    PubMed

    Bryantseva, I; Gorlenko, V M; Kompantseva, E I; Imhoff, J F; Süling, J; Mityushina, L

    1999-04-01

    A new purple sulfur bacterium was isolated from microbial films on decaying plant mass in the near-shore area of the soda lake Malyi Kasytui (pH 9.5, 0.2% salinity) located in the steppe of the Chita region of south-east Siberia. Single cells were vibrioid- or spiral-shaped (3-4 microns wide and 7-20 microns long) and motile by means of a polar tuft of flagella. Internal photosynthetic membranes were of the lamellar type. Lamellae almost filled the whole cell, forming strands and coils. Photosynthetic pigments were bacteriochlorophyll a and carotenoids of the spirilloxanthin group. The new bacterium was strictly anaerobic. Under anoxic conditions, hydrogen sulfide and elemental sulfur were used as photosynthetic electron donors. During growth on sulfide, sulfur globules were formed as intermediate oxidation products. They were deposited outside the cytoplasm of the cells, in the peripheral periplasmic space and extracellularly. Thiosulfate was not used. Carbon dioxide, acetate, pyruvate, propionate, succinate, fumarate and malate were utilized as carbon sources. Optimum growth rates were obtained at pH 9.0 and optimum temperature was 30 degrees C. Good growth was observed in a mineral salts medium containing 5 g sodium bicarbonate l-1 without sodium chloride. The new bacterium tolerated up to 60 g sodium chloride l-1 and up to 80 g sodium carbonates l-1. Growth factors were not required. The DNA G + C composition was 56.0-57.4 mol%. Based on physiological, biochemical and genetic characteristics, the newly isolated bacterium is recognized as a new species of a new genus with the proposed name Thiorhodospira sibirica.

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

    USGS Publications Warehouse

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

    2016-01-01

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

  17. Expression, and Molecular and Enzymatic Characterization of Cu-Containing Nitrite Reductase from a Marine Ammonia-Oxidizing Gammaproteobacterium, Nitrosococcus oceani

    PubMed Central

    Kondo, Keitaro; Yoshimatsu, Katsuhiko; Fujiwara, Taketomo

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) remove intracellular nitrite to prevent its toxicity by a nitrifier denitrification pathway involving two denitrifying enzymes, nitrite reductase and nitric oxide reductase. Here, a Cu-containing nitrite reductase from Nitrosococcus oceani strain NS58, a gammaproteobacterial marine AOB, was expressed in Escherichia coli and purified to homogeneity. Sequence homology analysis indicated that the nitrite reductase from N. oceani was phylogenetically closer to its counterparts from denitrifying bacteria than that of the betaproteobacterium Nitrosomonas europaea. The recombinant enzyme was a homotrimer of a 32 kDa subunit molecule. The enzyme was green in the oxidized state with absorption peaks at 455 nm and 575 nm. EPR spectroscopy indicated the presence of type 2 Cu. Molecular activities and the affinity constant for the nitrite were determined to be 1.6×103 s−1 and 52 μM, respectively. PMID:22641151

  18. 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).

  19. 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.

  20. Nitrogen cycling and community structure of proteobacterial beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments.

    PubMed

    McCaig, A E; Phillips, C J; Stephen, J R; Kowalchuk, G A; Harvey, S M; Herbert, R A; Embley, T M; Prosser, J I

    1999-01-01

    A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantly disrupted directly beneath the fish cage, with inhibition of nitrification and denitrification. Although visual examination indicated some slight changes in sediment appearance at 20 m, all other measurements were similar to those obtained at 40 m, where the sediment was considered pristine. The community structures of proteobacterial beta-subgroup ammonia-oxidizing bacteria at the sampling sites were compared by PCR amplification of 16S ribosomal DNA (rDNA), using primers which target this group. PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE) and with oligonucleotide hybridization probes specific for different ammonia oxidizers. A DGGE doublet observed in PCR products from the highly polluted fish cage sediment sample was present at a lower intensity in the 20-m sample but was absent from the pristine 40-m sample station. Band migration, hybridization, and sequencing demonstrated that the doublet corresponded to a marine Nitrosomonas group which was originally observed in 16S rDNA clone libraries prepared from the same sediment samples but with different PCR primers. Our data suggest that this novel Nitrosomonas subgroup was selected for within polluted fish farm sediments and that the relative abundance of this group was influenced by the extent of pollution.

  1. Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

    PubMed Central

    Bartelme, Ryan P.; McLellan, Sandra L.; Newton, Ryan J.

    2017-01-01

    Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while

  2. 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.

  3. 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

  4. Initiation of Chromosomal Replication in Predatory Bacterium Bdellovibrio bacteriovorus

    PubMed Central

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

    2016-01-01

    Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase) and replicating cells (the intracellular-growth phase). The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although, we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC) is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box [5′-NN(A/T)TCCACA-3′]. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus). We compared the architecture of the DnaA–oriC complexes (orisomes) in homologous (oriC and DnaA from B. bacteriovorus) and heterologous (BdoriC and DnaA from prey, Escherichia coli or Pseudomonas aeruginosa) systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium. PMID:27965633

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

    PubMed

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

    1976-01-01

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

  6. Distribution of sediment ammonia-oxidizing microorganisms in plateau freshwater lakes.

    PubMed

    Liu, Yong; Zhang, Jingxu; Zhao, Lei; Li, Yuzhao; Dai, Yu; Xie, Shuguang

    2015-05-01

    Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can play important roles in ammonia biotransformation in ecosystems. However, the factors regulating the distribution of these microorganisms in lacustrine ecosystems remain essentially unclear. The present study investigated the effects of geographic location on the distribution of sediment AOA and AOB in 13 freshwater lakes on the Yunnan Plateau (China). The spatial dissimilarity in the abundance and structure of sediment AOA and AOB communities was observed in these plateau lakes. AOA abundance was usually less than AOB abundance, and the AOA/AOB ratio was positively correlated with water depth. Nitrososphaera-like AOA occurred in most of the studied lakes and were dominant in two lakes. Nitrosospira was the dominant AOB species in most of the lakes, while Nitrosomonas showed high abundance only in three lakes. In addition, geographic location was found to affect lake sediment AOB community structure.

  7. 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.

    PubMed

    Wahman, David G; Schrantz, Karen A; Pressman, Jonathan G

    2010-12-01

    Various medium compositions (phosphate, 1 to 50 mM; ionic strength, 2.8 to 150 meq/liter) significantly affected Nitrosomonas europaea monochloramine disinfection kinetics, as determined by the Live/Dead BacLight (LD) and propidium monoazide quantitative PCR (PMA-qPCR) methods (lag coefficient, 37 to 490 [LD] and 91 to 490 [PMA-qPCR] mg·min/liter; Chick-Watson rate constant, 4.0 × 10(-3) to 9.3 × 10(-3) [LD] and 1.6 × 10(-3) to 9.6 × 10(-3) [PMA-qPCR] liter/mg·min). Two competing effects may account for the variation in disinfection kinetic parameters: (i) increasing kinetics (disinfection rate constant [k] increased, lag coefficient [b] decreased) with increasing phosphate concentration and (ii) decreasing kinetics (k decreased, b increased) with increasing ionic strength. The results support development of a standard medium for evaluating disinfection kinetics in drinking water.

  8. Enrichment and Physiological Characterization of a Novel Nitrospira-Like Bacterium Obtained from a Marine Sponge ▿

    PubMed Central

    Off, Sandra; Alawi, Mashal; Spieck, Eva

    2010-01-01

    Members of the nitrite-oxidizing genus Nitrospira are most likely responsible for the second step of nitrification, the conversion of nitrite (NO2−) to nitrate (NO3−), 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°C and 30°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

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

    PubMed

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

    2017-02-01

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

  10. 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

  11. Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir.

    PubMed

    Feio, Maria J; Zinkevich, Vitaly; Beech, Iwona B; Llobet-Brossa, Enric; Eaton, Peter; Schmitt, Jürgen; Guezennec, Jean

    2004-09-01

    A novel sulphate-reducing bacterium (Al1T) was recovered from a soured oil well in Purdu Bay, Alaska. Light and atomic force microscopy observations revealed that cells were Gram-negative, vibrio-shaped and motile by means of a single polar flagellum. The carbon and energy sources used by the isolate and the salinity, temperature and pH ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. Analysis of the fatty acid profile revealed that C(18 : 0), isoC(15 : 0) and isoC(17 : 1)omega7c were the predominant species. Fatty acid profile and complete 16S rRNA gene sequencing demonstrated the similarity between strain Al1T and members of the genus Desulfovibrio. The position of strain Al1T within the phylogenetic tree indicated that it clustered closely with Desulfovibrio vietnamensis DSM 10520T (98.9 % sequence similarity), a strain recovered from a similar habitat. However, whole-cell protein profiles, Fourier-transform infrared studies and DNA-DNA hybridization demonstrated that, in spite of the high level of 16S rRNA gene sequence similarity, there is sufficient dissimilarity at the DNA sequence level between D. vietnamensis DSM 10520T and strain Al1T (10.2 % similarity) to propose that strain Al1T belongs to a separate species within the genus Desulfovibrio. Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (= NCIMB 13491T = DSM 16109T) as the type strain.

  12. 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

  13. Molecular Characterization and In Vitro Analyses of a Sporogenous Bacterium with Potential Probiotic Properties.

    PubMed

    Sen, Ramkrishna; Pal, Dibyarupa; Kodali, Vidya Prabhakar; Das, Subhasish; Ghosh, Sudip Kumar

    2010-10-01

    The Gram-positive thin rods of a Bacillus species were identified and designated as Bacillus coagulans RK - 02 through the standard microbiological and biochemical characterization procedures, followed by data analysis and comparison with the characteristics given in Bergey's manual of systematic bacteriology. The culture was further characterized and confirmed as Bacillus coagulans by 16S rDNA sequence analysis wherein about 755 nucleotides of 16S rDNA was amplified and cloned in pGEM-T vector and subsequently sequenced. Sequence was blasted against the nr database of NCBI. Multiple alignments were done with some selected and related sequences using Clustal W. Phylogenetic trees were drawn with the same software after the distances were determined by neighbor-joining algorithm. The in vitro studies on the probiotic properties demonstrated that our isolate could prove to be a potential probiotic with spore-forming and lactic acid-producing abilities coupled with acid and bile tolerance properties and antimicrobial action. In addition to these characteristics, the bacterium also produced enzymes such as amylase, cellulase, lipase, protease, lactase and catalase, which can help in improving digestion and overall health, alleviate lactose intolerance and remove oxidative stresses, required for the well-being of the consumers. In our previously reported studies, an exopolysaccharide (EPS), a probioactive molecule produced by the same bacterium, showed very significant antioxidant, antihyperglycemic and emulsification activities. Thus, Bacillus coagulans RK - 02 is a well-characterized promising probiotic for its potential commercial applications to pharmaceutical, nutraceutical and functional food formulations with care-free storage.

  14. Effect of ammonium nitrogen concentration on the ammonia-oxidizing bacteria community in a membrane bioreactor for the treatment of anaerobically digested swine wastewater.

    PubMed

    Sui, Qianwen; Liu, Chong; Dong, Hongmin; Zhu, Zhiping

    2014-09-01

    A membrane bioreactor (MBR) was developed for the treatment of anaerobically digested swine wastewater and to investigate the effect of ammonium nitrogen concentration on biological nitrogen removal and ammonia-oxidizing bacteria (AOB) community structures. The MBR achieved a high NH4(+)-N removal efficiency of 0.08 kgNMLSS(-1)d(-1) and removed 95% of the influent NH4(+)-N. The TN removal rate was highest of 82.62% at COD/TN and BOD5/TN ratios of 8.76 ± 0.30 and 3.02 ± 0.09, respectively. With the decrease in ammonium nitrogen concentrations, the diversity of the AOB community declined and showed a simple pattern of DGGE. However, the AOB population size remained high, with abundance of 10(7)-10(9) copies mL(-1). With the decrease of ammonium nitrogen concentrations, Nitrosomonas eutropha gradually disappeared, whereas Nitrosomonas sp. OZK11 showed constant adaptability to survive during each treatment stage. The selective effect of ammonium concentration on AOB species could be due to the affinity for NH4(+)-N. In this study, the changes of ammonium nitrogen concentrations in digested swine wastewater were found to have selective effects on the composition of AOB community, and biological nitrogen removal was improved by optimising the influencing parameters.

  15. Effect of pH and HNO2 concentration on the activity of ammonia-oxidizing bacteria in a partial nitritation reactor.

    PubMed

    Claros, J; Jiménez, E; Aguado, D; Ferrer, J; Seco, A; Serralta, J

    2013-01-01

    Ammonia-oxidizing bacteria (AOB) are very sensitive to environmental conditions and wastewater treatment plant operational parameters. One of the most important factors affecting their activity is pH. Its effect is associated with: NH3/NH4(+) and HNO2/NO2(-) chemical equilibriums and biological reaction rates. The aim of this study was to quantify and model the effect of pH and free nitrous acid (FNA) concentration on the activity of AOB present in a lab-scale partial nitritation reactor. For this purpose, two sets of batch experiments were carried out using biomass from this reactor. Fluorescent in situ hybridization analysis showed that Nitrosomona eutropha and Nitrosomona europaea species were dominant in the partial nitritation reactor (>94%). The experimental results showed that FNA inhibits the AOB activity. This inhibition was properly modelled by the non-competitive inhibition function and the half inhibition constant value was determined as 1.32 mg HNO2-N L(-1). The optimal pH for these AOB was found to be in the range 7.4-7.8. The pH inhibitory effect was stronger at high pH values than at low pH values. Therefore, an asymmetric inhibition function was proposed to represent the pH effect on these bacteria. A combination of two sigmoidal functions was able to reproduce the experimental results obtained.

  16. 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.

  17. Elongated magnetite nanoparticle formation from a solid ferrous precursor in a magnetotactic bacterium

    PubMed Central

    Menguy, Nicolas; Gonzalez, Teresa Perez; Morin, Guillaume; Widdrat, Marc; Faivre, Damien

    2016-01-01

    Magnetotactic bacteria are aquatic microorganisms that intracellularly mineralize ferrimagnetic nanoparticles enabling the cells to align with the geomagnetic field. The bacteria produce a magnetic mineral of species-specific phase (magnetite Fe(II)Fe(III)2O4 or greigite Fe(II)Fe(III)2S4), size, morphology and particle assembly. Several species produce crystals of unusual elongated particle shapes, which break the symmetry of the thermodynamically favoured isometric morphology. Such morphologies are thought to affect domain size and orientation of the internal magnetization. Therefore, they are interesting study objects to develop new synthetic strategies for the morphological control of nanoparticles. We investigate the formation of such irregularly shaped nanomagnets in the species Desulfovibrio magneticus RS-1. In contrast to previously described organisms, this bacterium accumulates iron predominantly as Fe(II) rather than Fe(III) consistent with an alternative oxidative biomineralization route. Further, using high-resolution electron microscopy, we observe an epitaxial relationship between precursor and the final mineral phase supporting the notion of a solid-state transformation pathway. The precursor is likely a green rust previously thought to convert to magnetite only by dissolution and re-precipitation. Our findings represent a novel observation in the interconversion of iron (oxyhydr)oxide materials and suggest that solid-state growth processes could be required to produce irregularly shaped, elongated magnetite nanocrystals. PMID:27881802

  18. Hydrogen peroxide-dependent uptake of iodine by marine Flavobacteriaceae bacterium strain C-21.

    PubMed

    Amachi, Seigo; Kimura, Koh; Muramatsu, Yasuyuki; Shinoyama, Hirofumi; Fujii, Takaaki

    2007-12-01

    The cells of the marine bacterium strain C-21, which is phylogenetically closely related to Arenibacter troitsensis, accumulate iodine in the presence of glucose and iodide (I-). In this study, the detailed mechanism of iodine uptake by C-21 was determined using a radioactive iodide tracer, 125I-. In addition to glucose, oxygen and calcium ions were also required for the uptake of iodine. The uptake was not inhibited or was only partially inhibited by various metabolic inhibitors, whereas reducing agents and catalase strongly inhibited the uptake. When exogenous glucose oxidase was added to the cell suspension, enhanced uptake of iodine was observed. The uptake occurred even in the absence of glucose and oxygen if hydrogen peroxide was added to the cell suspension. Significant activity of glucose oxidase was found in the crude extracts of C-21, and it was located mainly in the membrane fraction. These findings indicate that hydrogen peroxide produced by glucose oxidase plays a key role in the uptake of iodine. Furthermore, enzymatic oxidation of iodide strongly stimulated iodine uptake in the absence of glucose. Based on these results, the mechanism was considered to consist of oxidation of iodide to hypoiodous acid by hydrogen peroxide, followed by passive translocation of this uncharged iodine species across the cell membrane. Interestingly, such a mechanism of iodine uptake is similar to that observed in iodine-accumulating marine algae.

  19. 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.

  20. 1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum.

    SciTech Connect

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

    2011-03-04

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

  1. 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

  2. The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

    PubMed Central

    van de Vossenberg, Jack; Woebken, Dagmar; Maalcke, Wouter J; Wessels, Hans J C T; Dutilh, Bas E; Kartal, Boran; Janssen-Megens, Eva M; Roeselers, Guus; Yan, Jia; Speth, Daan; Gloerich, Jolein; Geerts, Wim; van der Biezen, Erwin; Pluk, Wendy; Francoijs, Kees-Jan; Russ, Lina; Lam, Phyllis; Malfatti, Stefanie A; Tringe, Susannah Green; Haaijer, Suzanne C M; Op den Camp, Huub J M; Stunnenberg, Henk G; Amann, Rudi; Kuypers, Marcel M M; Jetten, Mike S M

    2013-01-01

    Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm. PMID:22568606

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

    PubMed

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

    2015-03-01

    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.

  4. 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.

  5. 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

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

    PubMed

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

    2010-09-01

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

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

    PubMed

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

    2005-03-11

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

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

    PubMed Central

    Johansson, B C; Gest, H

    1976-01-01

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

  9. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    PubMed Central

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

    1984-01-01

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

  10. 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.

  11. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE PAGES

    Gardner, Jeffrey G.

    2016-06-04

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

  12. 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.

  13. 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

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

    PubMed

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

    2004-01-01

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

  15. 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

  16. 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.

  17. Effects of copper on the abundance and diversity of ammonia oxidizers during dairy cattle manure composting.

    PubMed

    Yin, Yanan; Song, Wen; Gu, Jie; Zhang, Kaiyu; Qian, Xun; Zhang, Xin; Zhang, Yajun; Li, Yang; Wang, Xiaojuan

    2016-12-01

    This study investigated the effects of adding Cu(II) at two exposure levels (50 and 500mgkg(-1), i.e., Cu50 and Cu500 treatments, respectively) on the activity of ammonia-oxidizing microorganisms during dairy cattle manure composting. The results showed that the pH, NH4(+)-N, NO3(-)-N, and potential ammonia oxidation values were inhibited significantly by the addition of Cu(II). Furthermore, the abundances of the ammonia-oxidizing archaea (AOA) amoA gene and ammonia-oxidizing bacteria (AOB) amoA gene were determined by quantitative PCR, and their compositions were evaluated by denaturing gradient gel electrophoresis (DGGE). AOA was the dominant ammonia oxidizing microorganism, of which the abundance was much higher than AOB during composting. Cu50 and Cu500 had significant inhibitory effects on the abundance of the amoA gene. The DGGE profile and statistical analysis showed that Cu(II) changed the AOA and AOB community structure and diversity, where Nitrosomonas and Crenarchaeota dominated throughout the composting process.

  18. [Diversity and community structure of soil ammonia-oxidizing bacteria in Hulunbeier Grassland, Inner Mongolia].

    PubMed

    Wendu, Ri-le; Li, Gang; Yang, Dian-lin; Zhang, Jing-ni; Yi, Jin

    2011-04-01

    By the methods of polymerase chain reaction-denaturing gradient gel electrophoresis and sequence analysis, a comparative study was conducted on the diversity and community structure of soil ammonia-oxidizing bacteria in the Filifolium sibiricum steppe, Stipa baicalensis steppe, Leymus chinensis steppe, Stipa grandis steppe, and Stipa kryrowi steppe in Hulunbeier Grassland, Inner Mongolia. A significant difference was observed in the community structure of soil ammonia-oxidizing bacteria among the five steppes, with the similarity lower than 50%. The diversity of soil ammonia-oxidizing bacteria was the highest in F. sibiricum steppe, followed by in S. baicalensis steppe, L. chinensis steppe, S. kryrowi steppe, and S. grandis steppe. In the five steppes, Nitrosospira cluster 3 was the dominant group, and the Nitrosospira cluster 1, 2, and 4 as well as Nitrosomonas were also found. The community structure of soil ammonia oxidizing bacteria in F. sibiricum steppe was most complex, while that in L. chinensis steppe and S. grandis steppe was relatively simple. Correlation analysis indicated that there existed significant positive correlations between the diversity of soil ammonia-oxidizing bacteria and the soil moisture, total nitrogen, total organic carbon, and C/N ratio (P<0.05).

  19. Short-term effect of ammonia concentration and salinity on activity of ammonia oxidizing bacteria.

    PubMed

    Claros, J; Jiménez, E; Borrás, L; Aguado, D; Seco, A; Ferrer, J; Serralta, J

    2010-01-01

    A continuously aerated SHARON (single reactor high activity ammonia removal over nitrite) system has been operated to achieve partial nitritation. Two sets of batch experiments were carried out to study the effect of ammonia concentration and salinity on the activity of ammonia-oxidizing bacteria (AOB). Activity of AOB raised as free ammonia concentration was increased reaching its maximum value at 4.5 mg NH3-N l(-1). The half saturation constant for free ammonia was determined (K(NH3)=0.32 mg NH3-N l(-1)). Activity decreased at TAN (total ammonium-nitrogen) concentration over 2,000 mg NH4-N l(-1). No free ammonia inhibition was detected. The effect of salinity was studied by adding different concentrations of different salts to the biomass. No significant differences were observed between the experiments carried out with a salt containing or not containing NH4. These results support that AOB are inhibited by salinity, not by free ammonia. A mathematical expression to represent this inhibition is proposed. To compare substrate affinity and salinity inhibitory effect on different AOB populations, similar experiments were carried out with biomass from a biological nutrient removal pilot plant. The AOB activity reached its maximum value at 0.008 mg NH3-N l(-1) and decreased at TAN concentration over 400 mg NH4-N l(-1). These differences can be explained by the different AOB predominating species: Nitrosomonas europaea and N. eutropha in the SHARON biomass and Nitrosomonas oligotropha in the pilot plant.

  20. 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.

  1. Gene sequencing and characterization of the light-harvesting complex 2 from thermophilic purple sulfur bacterium Thermochromatium tepidum.

    PubMed

    Sekine, Fumie; Horiguchi, Kentaro; Kashino, Yasuhiro; Shimizu, Yuuki; Yu, Long-Jiang; Kobayashi, Masayuki; Wang, Zheng-Yu

    2012-03-01

    In this study, gene sequences coding for the light-harvesting (LH) 2 polypeptides from a thermophilic purple sulfur bacterium Thermochromatium tepidum are reported and characterization of the LH2 complex is described. Three sets of pucBA genes have been identified, and the gene products have been analyzed by electrophoresis and reversed-phase chromatography. The result shows that all of the genes are expressed but the distribution of the expression is not uniform. The gene products undergo post-translational modification, where two of the β-polypeptides appear to be N-terminally methylated. Absorption spectrum of the purified LH2 complex exhibits Q (y) transitions at 800 and 854 nm in dodecyl β-maltopyranoside solution, and the circular dichroism spectrum shows a "molischianum"-like characteristic. No spectral change was observed for the LH2 when the bacterium was cultured under different conditions of light intensity. In lauryl dimethylamine N-oxide (LDAO) solution, significant changes in the absorption spectrum were observed. The B850 peak decreased and blue-shifted with increasing the LDAO concentration, whereas the B800 intensity increased without change in the peak position. The spectral changes can be partially or almost completely reversed by addition of metal ions, and the divalent cations seem to be more effective. The results indicate that ionic interactions may exist between LH2, detergent molecules and metal ions. Possible mechanisms involved in the detergent- and cation-induced spectral changes are discussed.

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

    PubMed

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

    2004-11-01

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

  3. Expression of merA, trxA, amoA, and hao in continuously cultured Nitrosomonas europaea cells exposed to cadmium sulfate additions.

    PubMed

    Radniecki, Tyler S; Semprini, Lewis; Dolan, Mark E

    2009-12-01

    The effects of CdSO(4) additions on the gene expressions of a mercury reductase, merA, an oxidative stress protein, trxA, the ammonia-monooxygenase enzyme (AMO), amoA, and the hydroxylamine oxidoreductase enzyme (HAO), hao, were examined in continuously cultured N. europaea cells. The reactor was fed 50 mM NH(4)+ and was operated for 78 days with a 6.9 days hydraulic retention time. Over this period, six successive batch additions of CdSO(4) were made with increasing maximum concentrations ranging from 1 to 60 microM Cd(2+). The expression of merA was highly correlated with the level of Cd(2+) within the reactor (Rs = 0.90) with significant up-regulation measured at non-inhibitory Cd(2+) concentrations. Cd(2+) appears to target AMO specifically at lower concentrations and caused oxidative stress at higher concentrations, as indicated by the SOURs (specific oxygen uptake rates) and the up-regulation of trxA. Since Cd(2+) inhibition is irreversible and amoA was up-regulated in response to Cd(2+) inhibition, it is hypothesized that de novo synthesis of the AMO enzyme occurred and was responsible for the observed recovery in activity. Continuously cultured N. europaea cells were more resistant to Cd(2+) inhibition than previously examined batch cultured cells due to the presence of Mg(2+) and Ca(2+) in the growth media, suggesting that Cd(2+) enters the cell through Mg(2+) and Ca(2+) import channels. The up-regulation of merA during exposure to non-inhibitory Cd(2+) levels indicates that merA is an excellent early warning signal for Cd(2+) inhibition.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-09-08

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

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

    DOE PAGES

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

    2015-09-24

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

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

    PubMed

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

    2014-05-15

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

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

    PubMed Central

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

    1997-01-01

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

  11. Flow cytometric evaluation of the intracellular bacterium, Wolbachia pipientis, in mosquito cells

    PubMed Central

    Fallon, Ann M

    2014-01-01

    Wolbachia is an obligate intracellular bacterium (Anaplasmataceae, Rickettisales) that occurs in arthropods and filarial worms, and spreads by vertical transmission in the oocyte cytoplasm. In insects, reproductive distortions associated with Wolbachia, such as cytoplasmic incompatibility in mosquitoes, have potential value for controlling pests, including species that transmit human, animal and plant diseases. Wolbachia strains that propagate as a persistent infection in insect cell lines provide an important resource for developing the genetic tools that will facilitate these applications. Here I describe conditions for flow cytometric evaluation of Wolbachia growth in persistently infected mosquito cells. Cytometry parameters were established using uninfected mosquito cells and Escherichia coli as a surrogate for Wolbachia, and quantitation was correlated with cell counts determined with a Coulter electronic cell counter and bacterial counts based on optical density. The protocol was validated by showing depletion of Wolbachia in medium containing tetracycline and rifampicin, and sensitivity of Wolbachia to treatment of host cells with paraquat, an oxidizing agent, and lumiflavin, an inhibitor of riboflavin uptake. The Wolbachia peak on the flow cytometry histogram was shown to contain Wolbachia by DNA analysis using the polymerase chain reaction, and by infection of naive recipient cells. This approach will streamline investigation of Wolbachia growth in insect cell lines and facilitate identification of culture conditions that select for Wolbachia-infected cells. PMID:25300665

  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. 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.

  14. Tolerance of the nanocellulose-producing bacterium Gluconacetobacter xylinus to lignocellulose-derived acids and aldehydes.

    PubMed

    Zhang, Shuo; Winestrand, Sandra; Chen, Lin; Li, Dengxin; Jönsson, Leif J; Hong, Feng

    2014-10-08

    Lignocellulosic biomass serves as a potential alternative feedstock for production of bacterial nanocellulose (BNC), a high-value-added product of bacteria such as Gluconacetobacter xylinus. The tolerance of G. xylinus to lignocellulose-derived inhibitors (formic acid, acetic acid, levulinic acid, furfural, and 5-hydroxymethylfurfural) was investigated. Whereas 100 mM formic acid completely suppressed the metabolism of G. xylinus, 250 mM of either acetic acid or levulinic acid still allowed glucose metabolism and BNC production to occur. Complete suppression of glucose utilization and BNC production was observed after inclusion of 20 and 30 mM furfural and 5-hydroxymethylfurfural, respectively. The bacterium oxidized furfural and 5-hydroxymethylfurfural to furoic acid and 5-hydroxymethyl-2-furoic acid, respectively. The highest yields observed were 88% for furoic acid/furfural and 76% for 5-hydroxymethyl-2-furoic acid/5-hydroxymethylfurfural. These results are the first demonstration of the capability of G. xylinus to tolerate lignocellulose-derived inhibitors and to convert furan aldehydes.

  15. Prosthecochloris indica sp. nov., a novel green sulfur bacterium from a marine aquaculture pond, Kakinada, India.

    PubMed

    Anil Kumar, Pinnaka; Naga Radha Srinivas, Tanuku; Sasikala, Chintalapati; Venkata Ramana, Chintalapati; Süling, Jorg; Imhoff, Johannes

    2009-04-01

    A green sulfur bacterium, strain JAGS6T was isolated from a marine aquaculture pond located near Kakinada on the east coast of India. Cells of strain JAGS6T were Gram-negative, non-motile, coccoid, 1-1.2 microm in diameter, with prosthecae. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JAGS6T clusters with members of the genus Prosthecochloris and the sequence similarity with the nearest relative, Prosthecochloris vibrioformis, is 96.7%. Cultures of strain JAGS6T are green in color and the cells contain bacteriochlorophyll c and most likely carotenoids of the chlorobactene series as photosynthetic pigments. Strain JAGS6T is mesophilic, halotolerant (up to 7% NaCl) and is obligately phototrophic, utilizing sulfide but not thiosulfate as a photosynthetic electron donor. Sulfur globules are deposited outside the cells during oxidation of sulfide. On the basis of 16S rRNA gene sequence analysis and its morphological and physiological characteristics, strain JAGS6T is distinct from described species of the genus Prosthecochloris and we propose to describe it as a new species, Prosthecochloris indica, sp. nov. The type strain is JAGS6T (=JCM 13299T=ATCC BAA1214T).

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

    SciTech Connect

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

    1997-06-06

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

  17. 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.

  18. 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.

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

    PubMed

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

    2015-07-08

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

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

    PubMed

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

    2005-06-28

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

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

    PubMed Central

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

    2010-01-01

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

  2. The domestication of the probiotic bacterium Lactobacillus acidophilus.

    PubMed

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

    2014-11-26

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

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

    PubMed

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

    2006-10-20

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

  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. 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

  6. Metabolism of 2-methylpropene (isobutylene) by the aerobic bacterium Mycobacterium sp. strain ELW1.

    PubMed

    Kottegoda, Samanthi; Waligora, Elizabeth; Hyman, Michael

    2015-03-01

    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.

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. True Chemotaxis in Oxygen Gradients of the Sulfur-Oxidizing Bacterium Thiovulum majus

    PubMed Central

    Thar, Roland; Fenchel, Tom

    2001-01-01

    Observations of free-swimming Thiovulum majus cells show that these bacteria exhibit a phobic response as well as true chemotaxis in oxygen gradients. Both phenomena of their chemotactic behavior are integrated into a single model of helical klinotaxis, which is demonstrated by computer simulations. PMID:11425757

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

  14. 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.

  15. Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii

    PubMed Central

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

    2016-01-01

    Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic

  16. 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

  17. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions

    PubMed Central

    Laanbroek, Hendrikus J.; Keijzer, Rosalinde M.; Verhoeven, Jos T. A.; Whigham, Dennis F.

    2013-01-01

    In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests. PMID:24312088

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

    PubMed

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

    1988-12-01

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

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

    SciTech Connect

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

    2016-02-23

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

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

    DOE PAGES

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

    2016-02-23

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

  1. 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.

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

    PubMed

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

    2013-07-01

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

  3. The lipopolysaccharide of a chloridazon-degrading bacterium.

    PubMed

    Weisshaar, R; Lingens, F

    1983-12-01

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

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

    PubMed

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

    2016-02-23

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

  5. 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

  6. 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

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

    PubMed

    Dudley, Margaret; Salamone, Anna; Nerenberg, Robert

    2008-05-01

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

  8. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7.

    PubMed

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

    2015-09-29

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

  9. 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

  10. The Mismetallation of Enzymes during Oxidative Stress*

    PubMed Central

    Imlay, James A.

    2014-01-01

    Mononuclear iron enzymes can tightly bind non-activating metals. How do cells avoid mismetallation? The model bacterium Escherichia coli may control its metal pools so that thermodynamics favor the correct metallation of each enzyme. This system is disrupted, however, by superoxide and hydrogen peroxide. These species oxidize ferrous iron and thereby displace it from many iron-dependent mononuclear enzymes. Ultimately, zinc binds in its place, confers little activity, and imposes metabolic bottlenecks. Data suggest that E. coli compensates by using thiols to extract the zinc and by importing manganese to replace the catalytic iron atom. Manganese resists oxidants and provides substantial activity. PMID:25160623

  11. [Ammonia-oxidizing bacteria community composition at the root zones of aquatic plants after ecological restoration].

    PubMed

    Xing, Peng; Kong, Fan-xiang; Chen, Kai-ning; Chen, Mei-jun; Wu, Xiao-dong

    2008-08-01

    To investigate the effects of aquatic plants on ammonia-oxidizing bacteria (AOB) at their root zones, four species of aquatic plants were selected, Phragmites communis, Typha angustifolia L., Potamogeton crispus L., and Limnanthemun nymphoides, which were widely used in ecological restorations. AOB in the samples were enumerated by most-probable-number (MPN) method. Nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) procedures were performed with ammonia oxidizer-selective primers. Main DGGE bands were excised from the gel and sequenced for phylogenetic affiliation. Results indicate that AOB densities are always higher at the root zones of emergent plants (Phragmites communis 2.8 x 10(5) cells/g and Typha angustifolia L.4.3 x 10(5) cells/g) than those of submerged and floating-leaved plant (Potamogeton crispus L. 9.3 x 10(4) cells/g and Limnanthemun nymphoides 7.7 x 10(4) cells/g). At the root zones, the oxidation-reduction potential is above zero and NH4+ concentration is lower than it in the bare surface sediment. Fourteen major bands were recovered from the DGGE gel, re-amplified and sequenced. Although the identified bands have their respective similar sequences in GenBank, most of them are related to Nitrosomonas-like. This type of bacteria would play an important role of nitrogen cycle in lake sediment after ecological restoration.

  12. 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.

  13. 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...

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

    PubMed

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

    2014-12-04

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

  15. 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...

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

    PubMed

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

    2013-08-22

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

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

    EPA Science Inventory

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

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

    PubMed

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

    2015-07-20

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

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

    PubMed

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

    1981-12-04

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

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

    PubMed

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

    2008-04-01

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

  1. Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

    PubMed

    Caffrey, Sean M; Park, Hyung-Soo; Voordouw, Johanna K; He, Zhili; Zhou, Jizhong; Voordouw, Gerrit

    2007-09-01

    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen>50% hydrogen>lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.

  2. 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

  3. Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough▿ †

    PubMed Central

    Caffrey, Sean M.; Park, Hyung-Soo; Voordouw, Johanna K.; He, Zhili; Zhou, Jizhong; Voordouw, Gerrit

    2007-01-01

    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase. PMID:17601789

  4. 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

  5. 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

  6. 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

  7. 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.

  8. The S-Layer Protein of the Anammox Bacterium Kuenenia stuttgartiensis Is Heavily O-Glycosylated

    PubMed Central

    van Teeseling, Muriel C. F.; Maresch, Daniel; Rath, Cornelia B.; Figl, Rudolf; Altmann, Friedrich; Jetten, Mike S. M.; Messner, Paul; Schäffer, Christina; van Niftrik, Laura

    2016-01-01

    Anaerobic ammonium oxidation (anammox) bacteria are a distinct group of Planctomycetes that are characterized by their unique ability to perform anammox with nitrite to dinitrogen gas in a specialized organelle. The cell of anammox bacteria comprises three membrane-bound compartments and is surrounded by a two-dimensional crystalline S-layer representing the direct interaction zone of anammox bacteria with the environment. Previous results from studies with the model anammox organism Kuenenia stuttgartiensis suggested that the protein monomers building the S-layer lattice are glycosylated. In the present study, we focussed on the characterization of the S-layer protein glycosylation in order to increase our knowledge on the cell surface characteristics of anammox bacteria. Mass spectrometry (MS) analysis showed an O-glycan attached to 13 sites distributed over the entire 1591-amino acid S-layer protein. This glycan is composed of six monosaccharide residues, of which five are N-acetylhexosamine (HexNAc) residues. Four of these HexNAc residues have been identified as GalNAc. The sixth monosaccharide in the glycan is a putative dimethylated deoxyhexose. Two of the HexNAc residues were also found to contain a methyl group, thereby leading to an extensive degree of methylation of the glycan. This study presents the first characterization of a glycoprotein in a planctomycete and shows that the S-layer protein Kustd1514 of K. stuttgartiensis is heavily glycosylated with an O-linked oligosaccharide which is additionally modified by methylation. S-layer glycosylation clearly contributes to the diversification of the K. stuttgartiensis cell surface and can be expected to influence the interaction of the bacterium with other cells or abiotic surfaces. PMID:27847504