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Sample records for acidophilic methanotroph isolate

  1. Detection, Isolation, and Characterization of Acidophilic Methanotrophs from Sphagnum Mosses

    OpenAIRE

    N. Kip; Ouyang, W.J.; van der Winden, J.; Raghoebarsing, A.; van Niftrik, L.; De Pol, A.; Pan, Y.; L. Bodrossy; van Donselaar, E. G.; G. J. Reichart; M. S. M. Jetten; J. S. Sinninghe Damsté; Op den Camp, H.J.M.

    2011-01-01

    Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphapr...

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

    OpenAIRE

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

    2011-01-01

    Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphapr...

  3. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

    Directory of Open Access Journals (Sweden)

    Stott Matthew B

    2008-07-01

    Full Text Available Abstract Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. Results We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely

  4. Acidophilic Methanotrophic Communities from Sphagnum Peat Bogs

    OpenAIRE

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

    1998-01-01

    Highly enriched methanotrophic communities (>25 serial transfers) were obtained from acidic ombrotrophic peat bogs from four boreal forest sites. The enrichment strategy involved using media conditions that were associated with the highest rates of methane uptake by the original peat samples, namely, the use of diluted mineral medium of low buffering capacity, moderate incubation temperature (20°C), and pH values of 3 to 6. Enriched communities contained a mixture of rod-shaped bacteria arran...

  5. Draft Genomes of Gammaproteobacterial Methanotrophs Isolated from Terrestrial Ecosystems

    OpenAIRE

    Hamilton, R.(University of Iowa, 52242, Iowa City, Iowa, USA); Kits, K.D.; Ramonovskaya, V.A.; Rozova, O.N.; Yurimoto, H; Iguchi, H.; Khmelenina, V.N.; Sakai, Y.; Dunfield, P.F.; Klotz, M G; Knief, C.; Camp, H.J.M. op den; M. S. M. Jetten; Bringel, F.; Vuilleumier, S.

    2015-01-01

    Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.

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

    Directory of Open Access Journals (Sweden)

    David Barrie Johnson

    2012-09-01

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

  7. Bacteriohopanepolyol signatures as markers for methanotrophic bacteria in peat moss

    OpenAIRE

    van Winden, J.F.; H. M. Talbot; N. Kip; G. J. Reichart; De Pol, A.; N. P. McNamara; M. S. M. Jetten; Op den Camp, H.J.M.; J. S. Sinninghe Damsté

    2012-01-01

    Bacteriohopanepolyols (BHPs) are bacterial biomarkers with a likely potential to identify present and past methanotrophic communities. To unravel the methanotrophic community in peat bogs, we report the BHP signatures of type I and type II methanotrophs isolated from Sphagnum mosses and of an extreme acidophilic verrucomicrobial methanotroph. A type I Methylovulum-like strain (M200) contains a remarkable combination of BHPs, including a complete suite of mono-unsaturated aminobacteriohopanepe...

  8. Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.

    Science.gov (United States)

    Hamilton, Richard; Kits, K Dimitri; Ramonovskaya, Victoria A; Rozova, Olga N; Yurimoto, Hiroya; Iguchi, Hiroyuki; Khmelenina, Valentina N; Sakai, Yasuyoshi; Dunfield, Peter F; Klotz, Martin G; Knief, Claudia; Op den Camp, Huub J M; Jetten, Mike S M; Bringel, Françoise; Vuilleumier, Stéphane; Svenning, Mette M; Shapiro, Nicole; Woyke, Tanja; Trotsenko, Yuri A; Stein, Lisa Y; Kalyuzhnaya, Marina G

    2015-01-01

    Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems. PMID:26044417

  9. ISOLATION AND CHARACTERIZATION OF METHANOTROPHIC BACTERIA FROM RICE FIELDS

    OpenAIRE

    IMAN RUSMANA; ALINA AKHDIYA

    2009-01-01

    Methane is a greenhouse gas capable of depleting the ozone layer. Rice fields are significant sources of atmospheric methane. The application of chemical fertilizer in rice fields increases the methane emission. Methanotrophic bacteria has a unique ability as it can utilize methane as a source of carbon and energy. This research was able to isolate and characterize successfully the methanotrophic bacteria from rice fields in Bogor and Sukabumi, in West Java, Indonesia. Methane oxidation was...

  10. ISOLATION AND CHARACTERIZATION OF METHANOTROPHIC BACTERIA FROM RICE FIELDS

    Directory of Open Access Journals (Sweden)

    IMAN RUSMANA

    2009-01-01

    Full Text Available Methane is a greenhouse gas capable of depleting the ozone layer. Rice fields are significant sources of atmospheric methane. The application of chemical fertilizer in rice fields increases the methane emission. Methanotrophic bacteria has a unique ability as it can utilize methane as a source of carbon and energy. This research was able to isolate and characterize successfully the methanotrophic bacteria from rice fields in Bogor and Sukabumi, in West Java, Indonesia. Methane oxidation was determined through Gas Chromatography and it shows that all isolates performed methane oxidation activity. The highest methane oxidation activity was performed by BGM 9 isolate. And the DNA amplification of BGM 9 genome was performed by a single band of mmoX in the size of 500 bp and three bands of pmoA in the size of 1000, 750 and 500 bp respectively

  11. Isolation of methanotrophic bacteria from termite gut.

    Science.gov (United States)

    Reuss, Julia; Rachel, Reinhard; Kämpfer, Peter; Rabenstein, Andreas; Küver, Jan; Dröge, Stefan; König, Helmut

    2015-10-01

    The guts of termites feature suitable conditions for methane oxidizing bacteria (MOB) with their permanent production of CH4 and constant supply of O2 via tracheae. In this study, we have isolated MOB from the gut contents of the termites Incisitermes marginipennis, Mastotermes darwiniensis, and Neotermes castaneus for the first time. The existence of MOB was indicated by detecting pmoA, the gene for the particulate methane monooxygenase, in the DNA of gut contents. Fluorescence in situ hybridization and quantitative real-time polymerase chain reaction supported those findings. The MOB cell titer was determined to be 10(2)-10(3) per gut. Analyses of the 16S rDNA from isolates indicated close similarity to the genus Methylocystis. After various physiological tests and fingerprinting methods, no exact match to a known species was obtained, indicating the isolation of new MOB species. However, MALDI-TOF MS analyses revealed a close relationship to Methylocystis bryophila and Methylocystis parvus. PMID:26411892

  12. Biological conversion of biogas to methanol using methanotrophs isolated from solid-state anaerobic digestate.

    Science.gov (United States)

    Sheets, Johnathon P; Ge, Xumeng; Li, Yueh-Fen; Yu, Zhongtang; Li, Yebo

    2016-02-01

    The aim of this work was to isolate methanotrophs (methane oxidizing bacteria) that can directly convert biogas produced at a commercial anaerobic digestion (AD) facility to methanol. A methanotrophic bacterium was isolated from solid-state anaerobic digestate. The isolate had characteristics comparable to obligate methanotrophs from the genus Methylocaldum. This newly isolated methanotroph grew on biogas or purified CH4 and successfully converted biogas from AD to methanol. Methanol production was achieved using several methanol dehydrogenase (MDH) inhibitors and formate as an electron donor. The isolate also produced methanol using phosphate with no electron donor or using formate with no MDH inhibitor. The maximum methanol concentration (0.43±0.00gL(-1)) and 48-h CH4 to methanol conversion (25.5±1.1%) were achieved using biogas as substrate and a growth medium containing 50mM phosphate and 80mM formate. PMID:26630583

  13. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems.

    Science.gov (United States)

    Flynn, James D; Hirayama, Hisako; Sakai, Yasuyoshi; Dunfield, Peter F; Klotz, Martin G; Knief, Claudia; Op den Camp, Huub J M; Jetten, Mike S M; Khmelenina, Valentina N; Trotsenko, Yuri A; Murrell, J Colin; Semrau, Jeremy D; Svenning, Mette M; Stein, Lisa Y; Kyrpides, Nikos; Shapiro, Nicole; Woyke, Tanja; Bringel, Françoise; Vuilleumier, Stéphane; DiSpirito, Alan A; Kalyuzhnaya, Marina G

    2016-01-01

    The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems. PMID:26798114

  14. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems

    OpenAIRE

    Flynn, James D.; Hirayama, Hisako; Sakai, Yasuyoshi; Dunfield, Peter F.; Klotz, Martin G.; Knief, Claudia; Op Den Camp, Huub J M; Jetten, Mike S. M.; Khmelenina, Valentina N; Trotsenko, Yuri A.; Murrell, J. Colin; Semrau, Jeremy D.; Svenning, Mette M.; Stein, Lisa Y.; Kyrpides, Nikos

    2016-01-01

    The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems.

  15. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems

    Science.gov (United States)

    Flynn, James D.; Hirayama, Hisako; Sakai, Yasuyoshi; Dunfield, Peter F.; Knief, Claudia; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Khmelenina, Valentina N.; Trotsenko, Yuri A.; Murrell, J. Colin; Semrau, Jeremy D.; Svenning, Mette M.; Stein, Lisa Y.; Kyrpides, Nikos; Shapiro, Nicole; Woyke, Tanja; Bringel, Françoise; Vuilleumier, Stéphane; DiSpirito, Alan A.

    2016-01-01

    The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems. PMID:26798114

  16. Isolate 761M: a new type I methanotroph that possesses a complete tricarboxylic acid cycle

    International Nuclear Information System (INIS)

    A methanotrophic bacterium, isolate 761M, grows slowly with methane as the sole carbon and energy source. Growth was stimulated by peptone, casein hydrolysate, glucose, and acetate plus malate. Sugars other than glucose did not stimulate growth. Growth yields, based on the amount of methane consumed, increased when other carbon sources were present, and less methane carbon was assimilated under these conditions. Methane was obligatorily required for growth of isolate 761M. This bacterium does not grow on rich media. Isolate 761M was found to possess hexulose phosphate synthase and intracytoplasmic membranes characteristic of other type I methanotrophs. Unlike other type I methanotrophs, this bacterium possessed alpha-ketoglutarate dehydrogenase and oxidized (2-14C)acetate to carbon dioxide. 32 references, 1 figure, 6 tables

  17. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Lake Washington Sediment

    OpenAIRE

    Kalyuzhnaya, Marina G.; Lamb, Andrew E.; McTaggart, Tami L.; Oshkin, Igor Y.; Shapiro, Nicole; Woyke, Tanja; Chistoserdova, Ludmila

    2015-01-01

    The genomes of Methylosarcina lacus LW14T (=ATCC BAA-1047T = JCM 13284T), Methylobacter sp. strain 21/22, Methylobacter sp. strain 31/32, Methylomonas sp. strain LW13, Methylomonas sp. strain MK1, and Methylomonas sp. strain 11b were sequenced and are reported here. All the strains are obligately methanotrophic bacteria isolated from the sediment of Lake Washington.

  18. Separation of Methanotrophic Bacteria by Using Percoll and Its Application to Isolation of Mixed and Pure Cultures

    OpenAIRE

    Putzer, K. P.; Buchholz, L. A.; Lidstrom, M E; Remsen, C. C.

    1991-01-01

    Type I and II methanotrophic bacteria can be cleanly separated by using Percoll buoyant density gradients. This simple and inexpensive method can be used to screen new isolates rapidly for preliminary classification. In addition, Percoll gradients can also be used to enhance standard enrichment techniques for methanotrophs from natural water samples.

  19. Isolate 761M: a New Type I Methanotroph That Possesses a Complete Tricarboxylic Acid Cycle

    OpenAIRE

    Zhao, Shu-Jie; Hanson, R S

    1984-01-01

    A methanotrophic bacterium, isolate 761M, grows slowly with methane as the sole carbon and energy source. Growth was stimulated by peptone, casein hydrolysate, glucose, and acetate plus malate. Sugars other than glucose did not stimulate growth. Growth yields, based on the amount of methane consumed, increased when other carbon sources were present, and less methane carbon was assimilated under these conditions. Methane was obligately required for growth of isolate 761M. This bacterium does n...

  20. Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field.

    Science.gov (United States)

    Rahalkar, Monali C; Pandit, Pranitha S; Dhakephalkar, Prashant K; Pore, Soham; Arora, Preeti; Kapse, Neelam

    2016-04-01

    Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph. PMID:26547566

  1. Draft genome sequences of gammaproteobacterial methanotrophs isolated from lake washington sediment.

    Science.gov (United States)

    Kalyuzhnaya, Marina G; Lamb, Andrew E; McTaggart, Tami L; Oshkin, Igor Y; Shapiro, Nicole; Woyke, Tanja; Chistoserdova, Ludmila

    2015-01-01

    The genomes of Methylosarcina lacus LW14(T) (=ATCC BAA-1047(T) = JCM 13284(T)), Methylobacter sp. strain 21/22, Methylobacter sp. strain 31/32, Methylomonas sp. strain LW13, Methylomonas sp. strain MK1, and Methylomonas sp. strain 11b were sequenced and are reported here. All the strains are obligately methanotrophic bacteria isolated from the sediment of Lake Washington. PMID:25767239

  2. Ardrea characterisation of acidophilic micro-organisms isolated from gold mines in Marmato, Colombia

    Directory of Open Access Journals (Sweden)

    Edna Judith Márquez F.

    2008-02-01

    Full Text Available Mineral bio-oxidation improves the extraction of valuable metals and also decreases the impact caused by mining waste; however, the interactions between the micro-organisms so involved are little known. Double-layer solid culture media techniques and amplified ribosomal DNA restriction enzyme analysis (Ardrea, using Eco72I, Eco24I, XcmI and BsaAI enzymes, were used for characterising four micro-organisms isolated from gold mines located in Marmato, Colombia. This work was aimed at better understanding of native acidophilic micro-organisms’ microbial interactions in mixed cultures. Iron and sulphur oxidising isolates revealed similar restriction patterns to those previously reported for Acidithiobacillus ferrooxidans; however, one of them exhibited different colony morphology compared to previously reported morphology. The iron non-oxidising isolate presented a restriction pattern agreeing with theoretical analysis of Acidithiobacillus thiooxidans database sequences. ARDREA proved to be a viable technique for differentiating between At. ferrooxidans and At. thiooxidans; in turn, it enabled checking isolates’ identity with their physiological traits and colony morphology.

  3. Isolation and identification of moderately thermophilic acidophilic iron-oxidizing bacterium and its bioleaching characterization

    Institute of Scientific and Technical Information of China (English)

    ZENG Wei-min; WU Chang-bin; ZHANG Ru-bing; HU Pei-lei; QIU Guan-zhou; GU Guo-hua; ZHOU Hong-bo

    2009-01-01

    A moderately thermophilic acidophilic iron-oxidizing bacterium ZW-1 was isolated from Dexing mine, Jiangxi Province, China. The morphological, biochemical and physiological characteristics, 16S rRNA sequence and bioleaching characterization of strain ZW-1 were studied. The optimum growth temperature is 48 ℃, and the optimum initial pH is 1.9. The strain can grow autotrophically by using ferrous iron or elemental sulfur as sole energy sources. The strain is also able to grow heterotrophically by using peptone and yeast extract powder, but not glucose. The cell density of strain ZW-1 can reach up to 1.02×108 /mL with addition of 0.4 g/L peptone. A phylogenetic tree was constructed by comparing with the published 16S rRNA sequences of the relative bacteria species. In the phylogenetic tree, strain ZW-1 is closely relative to Sulfobacilus acidophilus with more than 99% sequence similarity. The results of bioleaching experiments indicate that the strain could oxidize Fe2+ efficiently, and the maximum oxidizing rate is 0.295 g/(L·h). It could tolerate high concentration of Fe3+ and Cu2+ (35 g/L and 25 g/L, respectively). After 20 d, 44.6% of copper is extracted from chalcopyrite by using strain ZW-1 as inocula.

  4. Isolation of methanotrophic bacteria from a london landfill: a preliminary study using molecular and stable isotopic techniques.

    Science.gov (United States)

    Sriskantharajah, S.; Cutting, S.; Lowry, D.; Grassineau, N.; Nisbet, E.

    2003-04-01

    Methane emissions from landfills are an important source of European greenhouse emissions, and could be reduced by a biological management program that used methanotrophs in landfill cover soils. Topsoil samples taken from a London Landfill were incubated on Nitrate Mineral Salts medium in the presence of methane. The resulting colonies were probed for methanotrophic DNA using PCR amplification. DNA from methanotroph positive colonies was cloned and sequenced for identification. Isolates belonging to the genera Methylocaldum, Methylomonas and Methylosinus were detected. Phylogenetic analysis suggests the presence of possible new species. In addition dried samples of the isolates were analysed for their stable carbon isotope (δ 13C) composition. The results were δ 13C values of -27 per mil and -25 per mil for Methylomonas isolates, -35 per mil and -44 per mil for Methylosinus isolates, -58 per mil and -60 per mil for some of the Methylocaldum isolates and -35 per mil and -45 per mil for the others. This isotopic variation is reflected in a phylogenetic tree of the isolates. The differences shown in the δ 13C analysis could be due to differing biochemical properties, and if the technique is further developed, it may be used for rapid identification of bacteria useful in landfill management for reducing methane emissions. The results suggest that useful reductions in methane emissions could be achieved by a careful design of landfill cover to culture methanotrophs.

  5. Diversity and Ecophysiology of New Isolates of Extremely Acidophilic CS2-Converting Acidithiobacillus Strains

    Science.gov (United States)

    Smeulders, Marjan J.; Pol, Arjan; Zandvoort, Marcel H.; Jetten, Mike S. M.

    2013-01-01

    Biofiltration of industrial carbon disulfide (CS2)-contaminated waste air streams results in the acidification of biofilters and therefore reduced performance, high water use, and increased costs. To address these issues, we isolated 16 extremely acidophilic CS2-converting Acidithiobacillus thiooxidans strains that tolerated up to 6% (vol/vol) sulfuric acid. The ecophysiological properties of five selected strains (2Bp, Sts 4-3, S1p, G8, and BBW1) were compared. These five strains had pH optima between 1 (2Bp) and 2 (S1p). Their affinities for CS2 ranged between 80 (G8) and 130 (2Bp) μM. Strains S1p, G8, and BBW1 had more hydrophobic cell surfaces and produced less extracellular polymeric substance than did strains 2Bp and Sts 4-3. All five strains converted about 80% of the S added as CS2 to S0 when CS2 was supplied in excess. The rate of S0 consumption varied between 7 (Sts 4-3) and 63 (S1p) nmol O2 min−1 ml culture−1. Low S0 consumption rates correlated partly with low levels of cell attachment to externally produced S0 globules. During chemostat growth, the relative amount of CS2 hydrolase in the cell increased with decreasing growth rates. This resulted in more S0 accumulation during CS2 overloads at low growth rates. Intermittent interruptions of the CS2 supply affected all five strains. Strains S1p, G8, and BBW1 recovered from 24 h of starvation within 4 h, and strains 2Bp and Sts 4-3 recovered within 24 h after CS2 was resupplied. We recommend the use of mixtures of Acidithiobacillus strains in industrial biofilters. PMID:23995926

  6. Solid and liquid media for isolating and cultivating acidophilic and acid-tolerant sulfate-reducing bacteria.

    Science.gov (United States)

    Ňancucheo, Ivan; Rowe, Owen F; Hedrich, Sabrina; Johnson, D Barrie

    2016-05-01

    Growth media have been developed to facilitate the enrichment and isolation of acidophilic and acid-tolerant sulfate-reducing bacteria (aSRB) from environmental and industrial samples, and to allow their cultivation in vitro The main features of the 'standard' solid and liquid devised media are as follows: (i) use of glycerol rather than an aliphatic acid as electron donor; (ii) inclusion of stoichiometric concentrations of zinc ions to both buffer pH and to convert potentially harmful hydrogen sulphide produced by the aSRB to insoluble zinc sulphide; (iii) inclusion of Acidocella aromatica (an heterotrophic acidophile that does not metabolize glycerol or yeast extract) in the gel underlayer of double layered (overlay) solid media, to remove acetic acid produced by aSRB that incompletely oxidize glycerol and also aliphatic acids (mostly pyruvic) released by acid hydrolysis of the gelling agent used (agarose). Colonies of aSRB are readily distinguished from those of other anaerobes due to their deposition and accumulation of metal sulphide precipitates. Data presented illustrate the effectiveness of the overlay solid media described for isolating aSRB from acidic anaerobic sediments and low pH sulfidogenic bioreactors. PMID:27036143

  7. Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem.

    Science.gov (United States)

    Dedysh, Svetlana N; Didriksen, Alena; Danilova, Olga V; Belova, Svetlana E; Liebner, Susanne; Svenning, Mette M

    2015-10-01

    An aerobic methanotrophic bacterium was isolated from a collapsed palsa soil in northern Norway and designated strain NE2T. Cells of this strain were Gram-stain-negative, non-motile, non-pigmented, slightly curved thick rods that multiplied by normal cell division. The cells possessed a particulate methane monooxygenase enzyme (pMMO) and utilized methane and methanol. Strain NE2T grew in a wide pH range of 4.1–8.0 (optimum pH 5.2–6.5) at temperatures between 6 and 32 °C (optimum 18–25 °C), and was capable of atmospheric nitrogen fixation under reduced oxygen tension. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω7c, and the DNA G+C content was 61.7 mol%. The isolate belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the facultative methanotroph Methylocapsa aurea KYGT (98.3 % 16S rRNA gene sequence similarity and 84 % PmoA sequence identity). However, strain NE2T differed from Methylocapsa aurea KYGT by cell morphology, the absence of pigmentation, inability to grow on acetate, broader pH growth range, and higher tolerance to NaCl. Therefore, strain NE2T represents a novel species of the genus Methylocapsa, for which we propose the name Methylocapsa palsarum sp. nov. The type strain is NE2T ( = LMG 28715T = VKM B-2945T). PMID:26297585

  8. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps

    OpenAIRE

    Islam, Tajul; Torsvik, Vigdis; Larsen, Øivind; Bodrossy, Levente; Øvreås, Lise; Birkeland, Nils-Kåre

    2016-01-01

    Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and uti...

  9. Genome Sequence of the Acidophilic Ferrous Iron-Oxidizing Isolate Acidithrix ferrooxidans Strain Py-F3, the Proposed Type Strain of the Novel Actinobacterial Genus Acidithrix

    Science.gov (United States)

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

    2015-01-01

    Extremely acidophilic iron-oxidizing Gram-positive bacteria comprise species within the phyla Firmicutes and Actinobacteria. Here, we report the 4.02-Mb draft genome of Acidithrix ferrooxidans Py-F3, which was isolated from a stream draining an abandoned copper mine and proposed as the type species of a new genus of Actinobacteria. PMID:25931603

  10. Acid-tolerant moderately thermophilic methanotrophs of the class Gammaproteobacteria isolated from tropical topsoil with methane seeps

    Directory of Open Access Journals (Sweden)

    Tajul eIslam

    2016-06-01

    Full Text Available Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0 and at a temperature range of 30–60oC (optimal 51–55oC. 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity. The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems.

  11. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps

    Science.gov (United States)

    Islam, Tajul; Torsvik, Vigdis; Larsen, Øivind; Bodrossy, Levente; Øvreås, Lise; Birkeland, Nils-Kåre

    2016-01-01

    Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems. PMID:27379029

  12. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps.

    Science.gov (United States)

    Islam, Tajul; Torsvik, Vigdis; Larsen, Øivind; Bodrossy, Levente; Øvreås, Lise; Birkeland, Nils-Kåre

    2016-01-01

    Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2-7.5 (optimal 5.5-6.0) and at a temperature range of 30-60°C (optimal 51-55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1-94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems. PMID:27379029

  13. Alicyclobacillus sp. strain CC2, a thermo-acidophilic bacterium isolated from Deception Island (Antarctica) containing a thermostable superoxide dismutase enzyme

    Institute of Scientific and Technical Information of China (English)

    Daniela N. Correa-Llantén; Maximiliano J. Amenábar; Patricio A. Muñoz; María T. Monsalves; Miguel E. Castro; Jenny M.Blamey

    2014-01-01

    A gram-positive, rod-shaped, aerobic, thermo-acidophilic bacterium CC2 (optimal temperature 55℃and pH 4.0), belonging to the genus Alicyclobacillus was isolated from geothermal soil collected from“Cerro Caliente”, Deception Island, Antarctica. Owing to the harsh environmental conditions found in this territory, microorganisms are exposed to conditions that trigger the generation of reactive oxygen species (ROS). They must have an effective antioxidant defense system to deal with this oxidative stress. We focused on one of the most important enzymes: superoxide dismutase, which was partially purified and characterized. This study presents the ifrst report of a thermo-acidophilic bacterium isolated from Deception Island with a thermostable superoxide dismutase (SOD).

  14. Methanotrophs and Methanogens in Masonry

    OpenAIRE

    Kussmaul, Martin; Wilimzig, Markus; Bock, Eberhard

    1998-01-01

    Methanotrophs were present in 48 of 225 stone samples which were removed from 19 historical buildings in Germany and Italy. The average cell number of methanotrophs was 20 CFU per g of stone, and their activities ranged between 11 and 42 pmol of CH4 g of stone−1 day−1. Twelve strains of methane-oxidizing bacteria were isolated. They belonged to the type II methanotrophs of the genera Methylocystis, Methylosinus, and Methylobacterium. In masonry, growth substrates like methane or methanol are ...

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

    Science.gov (United States)

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

    2014-12-01

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

  16. Methanobactin: a copper binding compound having antibiotic and antioxidant activity isolated from methanotrophic bacteria

    Science.gov (United States)

    DiSpirito, Alan A.; Zahn, James A.; Graham, David W.; Kim, Hyung J.; Alterman, Michail; Larive, Cynthia

    2007-04-03

    A means and method for treating bacterial infection, providing antioxidant activity, and chelating copper using a copper binding compound produced by methanotrophic bacteria is described. The compound, known as methanobactin, is the first of a new class of antibiotics having gram-positive activity. Methanobactin has been sequenced, and its structural formula determined.

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

    Directory of Open Access Journals (Sweden)

    Jiannan Ding

    2011-06-01

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

  18. Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere.

    Science.gov (United States)

    Khalifa, Ashraf; Lee, Chol Gyu; Ogiso, Takuya; Ueno, Chihoko; Dianou, Dayéri; Demachi, Toyoko; Katayama, Arata; Asakawa, Susumu

    2015-10-01

    An aerobic, methane-oxidizing bacterium (strain RS11D-PrT) was isolated from rice rhizosphere. Cells of strain RS11D-PrT were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20–37 °C (optimum 31–33 °C), at pH 6.8–7.4 (range 5.5–9.0) and with 0–0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). pmoA and mmoX genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-PrT is related closely to the genera Methylococcus, Methylocaldum, Methyloparacoccus and Methylogaea in the family Methylococcaceae. The similarity was low (94.6 %) between strain RS11D-PrT and the most closely related type strain (Methyloparacoccus murrellii R-49797T). The DNA G+C content was 64.1 mol%. Results of phylogenetic analysis of the pmoA gene and chemotaxonomic data regarding the major cellular fatty acids (C16 : 1ω7c, C16 : 0 and C14 : 0) and the major respiratory quinone (MQ-8) also indicated the affiliation of strain RS11D-PrT to the Methylococcus–Methylocaldum–Methyloparacoccus–Methylogaea clade. On the basis of phenotypic, genotypic and phylogenetic characteristics, strain RS11D-PrT is considered to represent a novel genus and species within the family Methylococcaceae, for which the name Methylomagnum ishizawai gen. nov., sp. nov. is proposed. The type strain is RS11D-PrT ( = JCM 18894T = NBRC 109438T = DSM 29768T = KCTC 4681T). PMID:26297568

  19. Enumeration and Characterization of Acidophilic Microorganisms Isolated from a Pilot Plant Stirred-Tank Bioleaching Operation

    OpenAIRE

    Okibe, Naoko; Gericke, Mariekie; Hallberg, Kevin B.; Johnson, D. Barrie

    2003-01-01

    Microorganisms were enumerated and isolated on selective solid media from a pilot-scale stirred-tank bioleaching operation in which a polymetallic sulfide concentrate was subjected to biologically accelerated oxidation at 45°C. Four distinct prokaryotes were isolated: three bacteria (an Acidithiobacillus caldus-like organism, a thermophilic Leptospirillum sp., and a Sulfobacillus sp.) and one archaeon (a Ferroplasma-like isolate). The relative numbers of these prokaryotes changed in the three...

  20. Alicyclobacillus dauci sp. nov., a slightly thermophilic, acidophilic bacterium isolated from a spoiled mixed vegetable and fruit juice product.

    Science.gov (United States)

    Nakano, Chisa; Takahashi, Naoto; Tanaka, Naoto; Okada, Sanae

    2015-02-01

    A novel, moderately thermophilic, acidophilic, Gram-variable, rod-shaped, endospore-forming bacterium was isolated from a spoiled mixed vegetable and fruit juice product that had the off-flavour of guaiacol. The bacterium, strain 4F(T), grew aerobically at 20-50 °C (optimum 40 °C) and pH 3.0-6.0 (optimum pH 4.0) and produced acid from glycerol, d-galactose and d-glucose. It contained menaquinone-7 (MK-7) as the major isoprenoid quinone and the DNA G+C content was 49.6 mol%. The predominant cellular fatty acids of strain 4F(T) were ω-alicyclic (ω-cyclohexane fatty acids), which are characteristic of the genus Alicyclobacillus. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to the Alicyclobacillus cluster, and is related most closely to the type strains of Alicyclobacillus acidoterrestris (97.4 % similarity) and Alicyclobacillus fastidiosus (97.3 %). Strain 4F(T) produced guaiacol from vanillic acid. It can be distinguished from related species by its acid production type and guaiacol production. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness values, it can be concluded that the strain represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus dauci sp. nov. is proposed; the type strain is 4F(T) ( = DSM 28700(T) = NBRC 108949(T) = NRIC 0938(T)). PMID:25505343

  1. Methanotrophic bacteria.

    OpenAIRE

    Hanson, R S; Hanson, T. E.

    1996-01-01

    Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehy...

  2. A new iron-oxidizing/O2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans.

    Science.gov (United States)

    Castelle, Cindy; Guiral, Marianne; Malarte, Guillaume; Ledgham, Fouzia; Leroy, Gisèle; Brugna, Myriam; Giudici-Orticoni, Marie-Thérèse

    2008-09-19

    The iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans involves various metalloenzymes. Here we demonstrate that the oxygen reduction pathway from ferrous iron (named downhill pathway) is organized as a supercomplex constituted of proteins located in the outer and inner membranes as well as in the periplasm. For the first time, the outer membrane-bound cytochrome c Cyc2 was purified, and we showed that it is responsible for iron oxidation and determined that its redox potential is the highest measured to date for a cytochrome c. The organization of metalloproteins inside the supramolecular structure was specified by protein-protein interaction experiments. The isolated complex spanning the two membranes had iron oxidase as well as oxygen reductase activities, indicating functional electron transfer between the first iron electron acceptor, Cyc2, and the Cu(A) center of cytochrome c oxidase aa(3). This is the first characterization of a respirasome from an acidophilic bacterium. In Acidithiobacillus ferrooxidans,O(2) reduction from ferrous iron must be coupled to the energy-consuming reduction of NAD(+)(P) from ferrous iron (uphill pathway) required for CO(2) fixation and other anabolic processes. Besides the proteins involved in the O(2) reduction, there were additional proteins in the supercomplex, involved in uphill pathway (bc complex and cytochrome Cyc(42)), suggesting a possible physical link between these two pathways.

  3. Cultivation and detection of endophytic aerobic methanotrophs isolated from Sphagnum species as a perspective for environmental biotechnology

    OpenAIRE

    Stępniewska, Zofia; Kuźniar, Agnieszka

    2014-01-01

    Enriched cultures of microorganisms are an essential step in the production of inoculum of these organisms for biotechnology and bioengineering. The potential application of methanotrophic microorganisms for removal of methane produced from landfills and coal mines as well as biodegradation of toxic compounds has been widely studied. Therefore, searching for new sources of methanotrophs can contribute to increasing the possibilities of biotechnology and bioengineering. Enrichment cultures of ...

  4. Bacteriohopanepolyol signatures as markers for methanotrophic bacteria in peat moss

    NARCIS (Netherlands)

    Winden, J.F. van; Talbot, H.M.; Kip, N.; Reichart, G.-J.; Pol, A.; McNamara, N.P.; Jetten, M.S.M.; Camp, H.J.M. Op den; Sinninghe Damsté, J.S.

    2012-01-01

    Bacteriohopanepolyols (BHPs) are bacterial biomarkers with a likely potential to identify present and past methanotrophic communities. To unravel the methanotrophic community inpeat bogs, we report the BHP signatures of type I and type II methanotrophs isolated from Sphagnummosses and of an extreme

  5. Bacteriohopanepolyol signatures as markers for methanotrophic bacteria in peat moss

    NARCIS (Netherlands)

    van Winden, J.F.; Talbot, H.M.; Kip, N.; Reichart, G.J.; Pol, A.; McNamara, N.P.; Jetten, M.S.M.; Op den Camp, H.J.M.; Sinninghe Damsté, J.S.

    2012-01-01

    Bacteriohopanepolyols (BHPs) are bacterial biomarkers with a likely potential to identify present and past methanotrophic communities. To unravel the methanotrophic community in peat bogs, we report the BHP signatures of type I and type II methanotrophs isolated from Sphagnum mosses and of an extrem

  6. Expanding the verrucomicrobial methanotrophic world: description of three novel species of Methylacidimicrobium gen. nov.

    Science.gov (United States)

    van Teeseling, Muriel C F; Pol, Arjan; Harhangi, Harry R; van der Zwart, Sietse; Jetten, Mike S M; Op den Camp, Huub J M; van Niftrik, Laura

    2014-11-01

    Methanotrophic Verrucomicrobia have been found in geothermal environments characterized by high temperatures and low pH values. However, it has recently been hypothesized that methanotrophic Verrucomicrobia could be present under a broader range of environmental conditions. Here we describe the isolation and characterization of three new species of mesophilic acidophilic verrucomicrobial methanotrophs from a volcanic soil in Italy. The three new species showed 97% to 98% 16S rRNA gene identity to each other but were related only distantly (89% to 90% on the 16S rRNA level) to the thermophilic genus Methylacidiphilum. We propose the new genus Methylacidimicrobium, including the novel species Methylacidimicrobium fagopyrum, Methylacidimicrobium tartarophylax, and Methylacidimicrobium cyclopophantes. These mesophilic Methylacidimicrobium spp. were more acid tolerant than their thermophilic relatives; the most tolerant species, M. tartarophylax, still grew at pH 0.5. The variation in growth temperature optima (35 to 44°C) and maximum growth rates (µmax; 0.013 to 0.040 h(-1)) suggested that all species were adapted to a specific niche within the geothermal environment. All three species grew autotrophically using the Calvin cycle. The cells of all species contained glycogen particles and electron-dense particles in their cytoplasm as visualized by electron microscopy. In addition, the cells of one of the species (M. fagopyrum) contained intracytoplasmic membrane stacks. The discovery of these three new species and their growth characteristics expands the known diversity of verrucomicrobial methanotrophs and shows that they are present in many more ecosystems than previously assumed. PMID:25172849

  7. Thermoanaerobacterium aotearoense sp. nov., a slightly acidophilic, anaerobic thermophile isolated from various hot springs in New Zealand, and emendation of the genus Thermoanaerobacterium

    Energy Technology Data Exchange (ETDEWEB)

    Shu-Ying Liu; Wiegel, J. [Univ. of Georiga, Athens, GA (United States); Rainey, F.A. [Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig (Germany)] [and others

    1996-04-01

    Six moderately acidophilic, thermophilic bacterial strains with similar properties were isolated from geothermally heated water and sediment samples collected in New Zealand. These Gram stain-negative but Gram type-positive, rod-shaped bacteria formed oval terminal endospores. The cells were peritrichously flagellated and exhibited tumbling motility. At 60{degrees}C the pH range for growth was 3.8 to 6.8, and the optimum pH was 5.2 when the organisms were grown with xylose. At pH 5.2 the temperature range for growth was 35 to 66{degrees}C, and the optimum temperature was 60 to 63{degrees}C. The fermentation products from flucose or xylose were ethanol, acetate, lactate, CO{sub 2}, and H{sub 2}. The DNA G+C content was 34.5 to 35 mol%. On the basis of properties such as formation of elemental sulfur from thiosulfate, growth at acidic pH values at elevated temperatures, and the results of a 16S rRNA sequence comparison performed with previously validly published species belonging to the genus Thermoanaerobacterium, we propose that strain JW/SL-NZ613{sup T} (T = type strain) and five similar strains isolated from samples collected in New Zealand represent a new species, Thermoanaerobacterium aotearoense. Strain JW/SL-NZ613{sup T} (= DSM 10170) is the type strain of this species.

  8. Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine.

    Science.gov (United States)

    Mardanov, Andrey V; Panova, Inna A; Beletsky, Alexey V; Avakyan, Marat R; Kadnikov, Vitaly V; Antsiferov, Dmitry V; Banks, David; Frank, Yulia A; Pimenov, Nikolay V; Ravin, Nikolai V; Karnachuk, Olga V

    2016-08-01

    Microbial sulfate reduction in acid mine drainage is still considered to be confined to anoxic conditions, although several reports have shown that sulfate-reducing bacteria occur under microaerophilic or aerobic conditions. We have measured sulfate reduction rates of up to 60 nmol S cm(-3) day(-1) in oxidized layers of gold mine tailings in Kuzbass (SW Siberia). A novel, acidophilic, copper-tolerant Desulfosporosinus sp. I2 was isolated from the same sample and its genome was sequenced. The genomic analysis and physiological data indicate the involvement of transporters and additional mechanisms to tolerate metals, such as sequestration by polyphosphates. Desulfosporinus sp. I2 encodes systems for a metabolically versatile life style. The genome possessed a complete Embden-Meyerhof pathway for glycolysis and gluconeogenesis. Complete oxidation of organic substrates could be enabled by the complete TCA cycle. Genomic analysis found all major components of the electron transfer chain necessary for energy generation via oxidative phosphorylation. Autotrophic CO2 fixation could be performed through the Wood-Ljungdahl pathway. Multiple oxygen detoxification systems were identified in the genome. Taking into account the metabolic activity and genomic analysis, the traits of the novel isolate broaden our understanding of active sulfate reduction and associated metabolism beyond strictly anaerobic niches. PMID:27222219

  9. Molecular characterization of methanotrophic communities in forest soils that consume atmospheric methane.

    Science.gov (United States)

    Lau, Evan; Ahmad, Azeem; Steudler, Paul A; Cavanaugh, Colleen M

    2007-06-01

    Methanotroph abundance was analyzed in control and long-term nitrogen-amended pine and hardwood soils using rRNA-targeted quantitative hybridization. Family-specific 16S rRNA and pmoA/amoA genes were analyzed via PCR-directed assays to elucidate methanotrophic bacteria inhabiting soils undergoing atmospheric methane consumption. Quantitative hybridizations suggested methanotrophs related to the family Methylocystaceae were one order of magnitude more abundant than Methyloccocaceae and more sensitive to nitrogen-addition in pine soils. 16S rRNA gene phylotypes related to known Methylocystaceae and acidophilic methanotrophs and pmoA/amoA gene sequences, including three related to the upland soil cluster Alphaproteobacteria (USCalpha) group, were detected across different treatments and soil depths. Our results suggest that methanotrophic members of the Methylocystaceae and Beijerinckiaceae may be the candidates for soil atmospheric methane consumption. PMID:17391332

  10. Bacteria that degrade hazardous waste: The isolation of trichloroethylene-degrading methanotrophic bacteria and development of monoclonal antibodies specific to them

    International Nuclear Information System (INIS)

    Trichloroethylene (TCE), a suspected carcinogen, is one of the most frequently reported groundwater contaminants at hazardous waste sites in the US. An aerobic, methane-oxidizing bacterium was isolated that degrades TCE in pure culture at concentrations commonly observed in contaminated groundwater. Strain 46-1, a Type I methanotrophic bacterium, degraded TCE when growing on methane or methanol, producing CO2 and water-soluble products. Gas chromatography and 14C radiotracer techniques were used to determine the rate, methane dependence, and mechanism of TCE biodegradation. TCE biodegradation by strain 46-1 appears to be a co-metabolic process that occurs when the organism is actively metabolizing a suitable growth substrate such as methane or methanol. Five mouse monoclonal antibodies (MABS) that specifically bind strain 46-1 were prepared by conventional hybridoma technology. These MABS are apparently biochemically distinct and were used to develop enzyme-linked and fluorescent immunoassays to detect strain 46-1 cells in environmental samples. A fluorescent immunoassay utilizing four of these MABS easily distinguished laboratory-grown 46-1 cells from other methanotrophic and heterotrophic bacteria, but failed to detect 46-1 cells in groundwater samples and cultures

  11. Detection of Methanotrophs in Groundwater by PCR†

    OpenAIRE

    Cheng, Y S; Halsey, J. L.; Fode, K. A.; Remsen, C. C.; Collins, M. L. P.

    1999-01-01

    Methanotrophic bacteria have significant potential for bioremediation, which would require methods for monitoring the presence and activity of these organisms in environmental samples. In this study, PCR was used to detect methanotrophic bacteria. Primers were designed on the basis of a partial sequence of pmoA, which encodes one of the proteins of the particulate methane monooxygenase. Specific amplification of a portion of pmoA was obtained with template DNA isolated from lab strains of met...

  12. Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09

    Energy Technology Data Exchange (ETDEWEB)

    Boden, Rich [University of Warwick, UK; Cunliffe, Michael [University of Warwick, UK; Scanlan, Julie [University of Warwick, UK; Moussard, Helene [University of Warwick, UK; Kits, K. Dimitri [University of Alberta, Edmondton, Canada; Klotz, Martin G [University of Louisville, Louisville; Jetten, MSM [Radboud University Nijmegen, The Netherlands; Vuilleumier, Stephane [University of Strasbourg; Han, James [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Stein, Lisa Y. [University of Alberta, Edmondton, Canada; Murrell, Collin [University of Warwick, UK

    2011-01-01

    Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.

  13. Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02

    DEFF Research Database (Denmark)

    Servín-Garcidueñas, Luis E.; Garrett, Roger A.; Amils, Ricardo;

    2013-01-01

    Here, we report the draft genome sequence of Acidocella sp. strain MX-AZ02, an acidophilic and heterotrophic alphaproteobacterium isolated from a geothermal lake in western Mexico.......Here, we report the draft genome sequence of Acidocella sp. strain MX-AZ02, an acidophilic and heterotrophic alphaproteobacterium isolated from a geothermal lake in western Mexico....

  14. Isolation of a New Broad-Host-Range IncQ-Like Plasmid, pTC-F14, from the Acidophilic Bacterium Acidithiobacillus caldus and Analysis of the Plasmid Replicon

    OpenAIRE

    Gardner, Murray N.; Deane, Shelly M.; Rawlings, Douglas E

    2001-01-01

    A moderately thermophilic (45 to 50°C), highly acidophilic (pH 1.5 to 2.5), chemolithotrophic Acidithiobacillus caldus strain, f, was isolated from a biooxidation process used to treat nickel ore. Trans-alternating field electrophoresis analysis of total DNA from the A. caldus cells revealed two plasmids of approximately 14 and 45 kb. The 14-kb plasmid, designated pTC-F14, was cloned and shown by replacement of the cloning vector with a kanamycin resistance gene to be capable of autonomous re...

  15. Production of poly-β-hydroxybutyrate (PHB) by Methylobacterium organophilum isolated from a methanotrophic consortium in a two-phase partition bioreactor

    International Nuclear Information System (INIS)

    The biodegradation of methane, a greenhouse gas, and the accumulation of poly-β-hydroxybutyrate (PHB) were studied using a methanotrophic consortium and an isolated strain thereof. The specific rates for methane consumption were 100 and 17mgCH4gx-1 h-1 for the isolate and the consortium, respectively. Also the effect of including 10% (v v-1) of silicone oil in a two-phase partitioning bioreactor (TPPB) was assayed for the elimination of 1% methane in air stream. TPPB allowed a 33-45% increase of methane elimination under growing conditions. Nitrogen limitation was assayed in bioreactors to promote PHB production. Under this condition, the specific methane degradation rate remained unchanged for the consortium and decreased to 36mgCH4gx-1 h-1 for the isolated strain. The accumulated PHB in the reactor was 34% and 38% (w w-1) for the consortium and the isolate, respectively. The highest productivity was obtained in the TPPB and was 1.61mgPHBgx-1 h-1. The CZ-2 isolate was identified as Methylobacterium organophilum, this is the first study that reports this species as being able to grow on methane and accumulate up to 57% (w w-1) of PHB under nitrogen limitation in microcosm experiments.

  16. Production of poly-{beta}-hydroxybutyrate (PHB) by Methylobacterium organophilum isolated from a methanotrophic consortium in a two-phase partition bioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Zuniga, C., E-mail: cristal7n@gmail.com [Universidad Autonoma Metropolitana-Cuajimalpa, Departamento de Procesos y Tecnologia, Artificios 40, Col. Miguel Hidalgo, C.P. 01120, Mexico D.F. (Mexico); Morales, M., E-mail: mmorales@correo.cua.uam.mx [Universidad Autonoma Metropolitana-Cuajimalpa, Departamento de Procesos y Tecnologia, Artificios 40, Col. Miguel Hidalgo, C.P. 01120, Mexico D.F. (Mexico); Le Borgne, S., E-mail: sylvielb@correo.cua.uam.mx [Universidad Autonoma Metropolitana-Cuajimalpa, Departamento de Procesos y Tecnologia, Artificios 40, Col. Miguel Hidalgo, C.P. 01120, Mexico D.F. (Mexico); Revah, S., E-mail: srevah@correo.cua.uam.mx [Universidad Autonoma Metropolitana-Cuajimalpa, Departamento de Procesos y Tecnologia, Artificios 40, Col. Miguel Hidalgo, C.P. 01120, Mexico D.F. (Mexico)

    2011-06-15

    The biodegradation of methane, a greenhouse gas, and the accumulation of poly-{beta}-hydroxybutyrate (PHB) were studied using a methanotrophic consortium and an isolated strain thereof. The specific rates for methane consumption were 100 and 17mg{sub CH{sub 4}}g{sub x}{sup -1} h{sup -1} for the isolate and the consortium, respectively. Also the effect of including 10% (v v{sup -1}) of silicone oil in a two-phase partitioning bioreactor (TPPB) was assayed for the elimination of 1% methane in air stream. TPPB allowed a 33-45% increase of methane elimination under growing conditions. Nitrogen limitation was assayed in bioreactors to promote PHB production. Under this condition, the specific methane degradation rate remained unchanged for the consortium and decreased to 36mg{sub CH{sub 4}}g{sub x}{sup -1} h{sup -1} for the isolated strain. The accumulated PHB in the reactor was 34% and 38% (w w{sup -1}) for the consortium and the isolate, respectively. The highest productivity was obtained in the TPPB and was 1.61mg{sub PHB}g{sub x}{sup -1} h{sup -1}. The CZ-2 isolate was identified as Methylobacterium organophilum, this is the first study that reports this species as being able to grow on methane and accumulate up to 57% (w w{sup -1}) of PHB under nitrogen limitation in microcosm experiments.

  17. Draft genome sequence of extremely acidophilic bacterium Acidithiobacillus ferrooxidans DLC-5 isolated from acid mine drainage in Northeast China

    Directory of Open Access Journals (Sweden)

    Peng Chen

    2015-12-01

    Full Text Available Acidithiobacillus ferrooxidans type strain DLC-5, isolated from Wudalianchi in Heihe of Heilongjiang Province, China. Here, we present the draft genome of strain DLC-5 which contains 4,232,149 bp in 2745 contigs with 57.628% GC content and includes 32,719 protein-coding genes and 64 tRNA-encoding genes. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. JNNH00000000.1.

  18. Bacteriophages of methanotrophic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Tyutikow, F.M. (All-Union Research Inst. for Genetics and Selection of Industrial Microorganisms, Moscow, USSR); Bespalova, I.A.; Rebentish, B.A.; Aleksandrushkina, N.N.; Krivisky, A.S.

    1980-10-01

    Bacteriophages of methanotrophic bacteria have been found in 16 out of 88 studied samples (underground waters, pond water, soil, gas and oil installation waters, fermentor cultural fluids, bacterial paste, and rumen of cattle) taken in different geographic zones of the Soviet Union. Altogether, 23 phage strains were isolated. By fine structure, the phages were divided into two types (with very short or long noncontractile tails); by host range and serological properties, they fell into three types. All phages had guanine- and cytosine-rich double-stranded deoxyribonucleic acid consisting of common nitrogen bases. By all of the above-mentioned properties, all phages within each of the groups were completely identical to one another, but differed from phages of other groups.

  19. Genome Sequence of the Moderately Acidophilic Sulfate-Reducing Firmicute Desulfosporosinus acididurans (Strain M1T)

    Science.gov (United States)

    Petzsch, Patrick; Poehlein, Anja; Johnson, D. Barrie; Daniel, Rolf; Schlömann, Michael

    2015-01-01

    Microbial dissimilatory sulfate reduction is commonplace in many anaerobic environments, though few acidophilic bacteria are known to mediate this process. We report the 4.64-Mb draft genome of the type strain of the moderate acidophile Desulfosporosinus acididurans, which was isolated from acidic sediment in a river draining the Soufrière volcano, Montserrat. PMID:26251501

  20. [Decline of Activity and Shifts in the Methanotrophic Community Structure of an Ombrotrophic Peat Bog after Wildfire].

    Science.gov (United States)

    Danilova, O V; Belova, S E; Kulichevskaya, I S; Dedysh, S N

    2015-01-01

    This study examined potential disturbances of methanotrophic communities playing a key role in reducing methane emissions from the peat bog Tasin Borskoye, Vladimir oblast, Russia as a result of the 2007 wildfire. The potential activity of the methane-oxidizing filter in the burned peatland site and the abundance of indigenous methanotrophic bacteria were significantly reduced in comparison to the undisturbed site. Molecular analysis of methanotrophic community structure by means of PCR amplification and cloning of the pmoAgene encoding particulate methane monooxygenase revealed the replacement of typical peat-inhabiting, acidophilic type II methanotrophic bacteria with type I methanotrophs, which are less active in acidic environments. In summary, both the structure and the activity of the methane-oxidizing filter in burned peatland sites underwent significant changes, which were clearly pronounced even after 7 years of the natural ecosystem recovery. These results point to the long-term character of the disturbances caused by wildfire in peatlands. PMID:27169243

  1. Heat-tolerant methanotrophic bacteria from the hot water effluent of a natural gas field.

    OpenAIRE

    L. Bodrossy; Murrell, J.C.; Dalton, H; Kalman, M; Puskas, L. G.; Kovacs, K L

    1995-01-01

    Methanotrophic bacteria were isolated from a natural environment potentially favorable to heat-tolerant methanotrophs. An improved colony plate assay was developed and used to identify putative methanotrophic colonies with high confidence. Fourteen new isolates were purified and partially characterized. These new isolates exhibit a DNA sequence homology of up to 97% with the conserved regions in the mmoX and mmoC genes of the soluble methane monooxygenase (MMO)-coding gene cluster of Methyloc...

  2. The importance of methanotrophic activity in geothermal soils of Pantelleria island (Italy)

    Science.gov (United States)

    D'Alessandro, Walter; Gagliano, Antonina Lisa; Quatrini, Paola; Parello, Francesco

    2013-04-01

    were investigated by culturing and culture-independent techniques. The diversity of proteobacterial methanotrophs was investigated by creating a clone library of the amplified methane mono-oxygenase encoding gene, pmoA. Clone sequencing indicates the presence of Gammaproteobacteria in the soils of Favara Grande. Enrichment cultures, on a mineral medium in a CH4-enriched atmosphere, led to the isolation of different strains that were identified as Methylocistis spp., which belong to the Alphaproteobacteria. The presence of Verrucomicrobia was detected by amplification of pmoA gene using newly designed primers. Soils from Favara Grande show therefore the largest spectrum of methanotrophic microorganisms until now detected in a geothermal environment. While the presence of Verrucomicrobia in geothermal soils was predictable due to their thermophilic and acidophilic character, the presence of both Alpha and Gamma proteobacteria was unexpected. Their presence is limited to the shallowest part of the soil were temperatures are lower and is probably favored by a soil pH that is not too low (pH ~5) and their contribution to biological methane oxidation at Pantelleria is significant. Understanding the ecology of methanotrophy in geothermal sites will increase our knowledge of the role of soils in methane emissions in such environments.

  3. Detection and Enumeration of Methanotrophs in Acidic Sphagnum Peat by 16S rRNA Fluorescence In Situ Hybridization, Including the Use of Newly Developed Oligonucleotide Probes for Methylocella palustris

    OpenAIRE

    Dedysh, Svetlana N.; Derakshani, Manigee; Liesack, Werner

    2001-01-01

    Two 16S rRNA-targeted oligonucleotide probes, Mcell-1026 and Mcell-181, were developed for specific detection of the acidophilic methanotroph Methylocella palustris using fluorescence in situ hybridization (FISH). The fluorescence signal of probe Mcell-181 was enhanced by its combined application with the oligonucleotide helper probe H158. Mcell-1026 and Mcell-181, as well as 16S rRNA oligonucleotide probes with reported group specificity for either type I methanotrophs (probes M-84 and M-705...

  4. Aerobic and Anaerobic Starvation Metabolism in Methanotrophic Bacteria

    OpenAIRE

    Roslev, P.; King, G. M.

    1995-01-01

    The capacity for anaerobic metabolism of endogenous and selected exogenous substrates in carbon- and energy-starved methanotrophic bacteria was examined. The methanotrophic isolate strain WP 12 survived extended starvation under anoxic conditions while metabolizing 10-fold less endogenous substrate than did parallel cultures starved under oxic conditions. During aerobic starvation, the cell biomass decreased by 25% and protein and lipids were the preferred endogenous substrates. Aerobic prote...

  5. [Culturable psychrotolerant methanotrophic bacteria in landfill cover soil].

    Science.gov (United States)

    Kallistova, A Iu; Montonen, L; Jurgens, G; Munster, U; Kevbrina, M V; Nozhevnikova, A N

    2014-01-01

    Methanotrophs closely related to psychrotolerant members of the genera Methylobacter and Methylocella were identified in cultures enriched at 10@C from landfill cover soil samples collected in the period from April to November. Mesophilic methanotrophs of the genera Methylobacter and Methylosinus were found in cultures enriched at 20 degrees C from the same cover soil samples. A thermotolerant methanotroph related to Methylocaldum gracile was identified in the culture enriched at 40 degrees C from a sample collected in May (the temperature of the cover soil was 11.5-12.5 degrees C). In addition to methanotrophs, methylobacteria of the genera Methylotenera and Methylovorus and members of the genera Verrucomicrobium, Pseudomonas, Pseudoxanthomonas, Dokdonella, Candidatus Protochlamydia, and Thiorhodospira were also identified in the enrichment cultures. A methanotroph closely related to the psychrotolerant species Methylobacter tundripaludum (98% sequence identity of 16S r-RNA genes with the type strain SV96(T)) was isolated in pure culture. The introduction of a mixture of the methanotrophic enrichments, grown at 15 degrees C, into the landfill cover soil resulted in a decrease in methane emission from the landfill surface in autumn (October, November). The inoculum used was demonstrated to contain methanotrophs closely related to Methylobacter tundripaludum SV96.

  6. Genetic Tools for the Industrially Promising Methanotroph Methylomicrobium buryatense

    Energy Technology Data Exchange (ETDEWEB)

    Puri, AW; Owen, S; Chu, F; Chavkin, T; Beck, DAC; Kalyuzhnaya, MG; Lidstrom, ME

    2015-02-10

    Aerobic methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. In this work, we developed and validated genetic tools for Methylomicrobium buryatense, a haloalkaliphilic gammaproteobacterial (type I) methanotroph. M. buryatense was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other methanotrophic species. As a proof of concept, we used a sucrose counterselection system to eliminate glycogen production in M. buryatense by constructing unmarked deletions in two redundant glycogen synthase genes. We also selected for a more genetically tractable variant strain that can be conjugated with small incompatibility group P (IncP)-based broad-host-range vectors and determined that this capability is due to loss of the native plasmid. These tools make M. buryatense a promising model system for studying aerobic methanotroph physiology and enable metabolic engineering in this bacterium for industrial biocatalysis of methane.

  7. Methanotrophic activity and diversity of methanotrophs in volcanic geothermal soils at Pantelleria (Italy)

    Science.gov (United States)

    Gagliano, A. L.; D'Alessandro, W.; Tagliavia, M.; Parello, F.; Quatrini, P.

    2014-10-01

    Volcanic and geothermal systems emit endogenous gases by widespread degassing from soils, including CH4, a greenhouse gas twenty-five times as potent as CO2. Recently, it has been demonstrated that volcanic or geothermal soils are not only a source of methane, but are also sites of methanotrophic activity. Methanotrophs are able to consume 10-40 Tg of CH4 a-1 and to trap more than 50% of the methane degassing through the soils. We report on methane microbial oxidation in the geothermally most active site of Pantelleria (Italy), Favara Grande, whose total methane emission was previously estimated at about 2.5 Mg a-1 (t a-1). Laboratory incubation experiments with three top-soil samples from Favara Grande indicated methane consumption values of up to 59.2 nmol g-1 soil d.w. h-1. One of the three sites, FAV2, where the highest oxidation rate was detected, was further analysed on a vertical soil profile, the maximum methane consumption was measured in the top-soil layer, and values greater than 6.23 nmol g-1 h-1 were still detected up to a depth of 13 cm. The highest consumption rate was measured at 37 °C, but a still detectable consumption at 80 °C (> 1.25 nmol g-1 h-1) was recorded. The soil total DNA extracted from the three samples was probed by Polymerase Chain Reaction (PCR) using standard proteobacterial primers and newly designed verrucomicrobial primers, targeting the unique methane monooxygenase gene pmoA; the presence of methanotrophs was detected at sites FAV2 and FAV3, but not at FAV1, where harsher chemical-physical conditions and negligible methane oxidation were detected. The pmoA gene libraries from the most active site (FAV2) pointed to a high diversity of gammaproteobacterial methanotrophs, distantly related to Methylocaldum-Metylococcus genera, and the presence of the newly discovered acido-thermophilic Verrucomicrobia methanotrophs. Alphaproteobacteria of the genus Methylocystis were isolated from enrichment cultures under a methane

  8. Diversity and activity of methanotrophs in alkaline soil from a Chinese coal mine

    Energy Technology Data Exchange (ETDEWEB)

    Han, Bing; Chen, Yin; Abell, Guy; Jiang, Hao; Bodrossy, Levente; Zhao, Jiangang; Murrell, J. Colin; Xing, Xin-Hui [Tsinghua University, Beijing (China). Dept. of Chemical Engineering

    2009-11-15

    Culture-independent molecular biological techniques, including 16S rRNA gene and functional gene clone libraries and microarray analyses using pmoA (encoding a key subunit of particulate methane monooxygenase), were applied to investigate the methanotroph community structure in alkaline soil from a Chinese coal mine. This environment contained a high diversity of methanotrophs, including the type II methanotrophs Methylosinus/Methylocystis, type I methanotrophs related to Methylobacter/Methylosoma and Methylococcus, and a number of as yet uncultivated methanotrophs. In order to identify the metabolically active methane-oxidizing bacteria from this alkaline environment, DNA stable isotope probing (DNA-SIP) experiments using {sup 13}CH{sub 4} were carried out. This showed that both type I and type II methanotrophs were active, together with methanotrophs related to Methylocella, which had previously been found only in acidic environments. Methylotrophs, including Methylopila and Hyphomicrobium, were also detected in soil DNA and after DNA-SIP experiments. DNA sequence information on the most abundant, active methanotrophs in this alkaline soil will facilitate the design of oligonucleotide probes to monitor enrichment cultures when isolating key alkaliphilic methanotrophs from such environments.

  9. Members of the methanotrophic genus Methylomarinum inhabit inland mud pots.

    Science.gov (United States)

    Fradet, Danielle T; Tavormina, Patricia L; Orphan, Victoria J

    2016-01-01

    Proteobacteria capable of converting the greenhouse gas methane to biomass, energy, and carbon dioxide represent a small but important sink in global methane inventories. Currently, 23 genera of methane oxidizing (methanotrophic) proteobacteria have been described, although many are represented by only a single validly described species. Here we describe a new methanotrophic isolate that shares phenotypic characteristics and phylogenetic relatedness with the marine methanotroph Methylomarinum vadi. However, the new isolate derives from a terrestrial saline mud pot at the northern terminus of the Eastern Pacific Rise (EPR). This new cultivar expands our knowledge of the ecology of Methylomarinum, ultimately towards a fuller understanding of the role of this genus in global methane cycling. PMID:27478692

  10. Methane oxidation and molecular characterization of methanotrophs from a former mercury mine impoundment

    Science.gov (United States)

    Baesman, Shaun; Miller, Laurence G.; Wei, Jeremy H.; Cho, Yirang; Matys, Emily D.; Summons, Roger E.; Welander, Paula V.; Oremland, Ronald S.

    2015-01-01

    The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO2 with some CH4 present. The δ13CH4 value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively 12C-enriched CO2 suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.

  11. Methane Oxidation and Molecular Characterization of Methanotrophs from a Former Mercury Mine Impoundment

    Directory of Open Access Journals (Sweden)

    Shaun M. Baesman

    2015-06-01

    Full Text Available The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO2 with some CH4 present. The δ13CH4 value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively 12C-enriched CO2 suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5 medium via methane oxidation.

  12. The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments.

    Directory of Open Access Journals (Sweden)

    Evan Lau

    Full Text Available The mxaF gene, coding for the large (α subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mxaF and 16S rRNA gene phylogenies were constructed based on over 100 database sequences of known proteobacterial methanotrophs and other methylotrophs to assess their evolutionary histories. Topology tests revealed that mxaF and 16S rDNA genes of methanotrophs do not show congruent evolutionary histories, with incongruencies in methanotrophic taxa in the Methylococcaceae, Methylocystaceae, and Beijerinckiacea. However, known methanotrophs generally formed coherent clades based on mxaF gene sequences, allowing for phylogenetic discrimination of major taxa. This feature highlights the mxaF gene's usefulness as a biomarker in studying the molecular diversity of proteobacterial methanotrophs in nature. To verify this, PCR-directed assays targeting this gene were used to detect novel methanotrophs from diverse environments including soil, peatland, hydrothermal vent mussel tissues, and methanotroph isolates. The placement of the majority of environmental mxaF gene sequences in distinct methanotroph-specific clades (Methylocystaceae and Methylococcaceae detected in this study supports the use of mxaF as a biomarker for methanotrophic proteobacteria.

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

    Science.gov (United States)

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

    2015-01-01

    Extremely acidophilic iron-oxidizing bacteria have largely been characterized for the phyla Proteobacteria and Nitrospira. Here, we report the draft genome of an iron-oxidizing and -reducing heterotrophic mesophile of the Actinobacteria, Ferrimicrobium acidiphilum, which was isolated from an abandoned pyrite mine. The genome sequence comprises 3.08 Mb. PMID:25931604

  14. Genome Sequence of the Acidophilic Sulfate-Reducing Peptococcaceae Strain CEB3

    Science.gov (United States)

    Petzsch, Patrick; Poehlein, Anja; Johnson, D. Barrie; Daniel, Rolf; Schlömann, Michael

    2015-01-01

    We report the draft genome of the Peptococcaceae strain CEB3 that originated from an acidic (pH 2.5) stream draining an abandoned copper mine. Strain CEB3 is one of the very few reported acidophilic sulfate-reducing isolates. The 5.04-Mb draft genome harbors 5,069 predicted protein-encoding and 66 RNA genes. PMID:26251503

  15. Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia.

    OpenAIRE

    Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi

    2011-01-01

    Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest...

  16. Stimulation of Methanotrophic Growth in Cocultures by Cobalamin Excreted by Rhizobia▿†

    OpenAIRE

    Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi

    2011-01-01

    Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest...

  17. Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense.

    Science.gov (United States)

    Puri, Aaron W; Owen, Sarah; Chu, Frances; Chavkin, Ted; Beck, David A C; Kalyuzhnaya, Marina G; Lidstrom, Mary E

    2015-03-01

    Aerobic methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. In this work, we developed and validated genetic tools for Methylomicrobium buryatense, a haloalkaliphilic gammaproteobacterial (type I) methanotroph. M. buryatense was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other methanotrophic species. As a proof of concept, we used a sucrose counterselection system to eliminate glycogen production in M. buryatense by constructing unmarked deletions in two redundant glycogen synthase genes. We also selected for a more genetically tractable variant strain that can be conjugated with small incompatibility group P (IncP)-based broad-host-range vectors and determined that this capability is due to loss of the native plasmid. These tools make M. buryatense a promising model system for studying aerobic methanotroph physiology and enable metabolic engineering in this bacterium for industrial biocatalysis of methane. PMID:25548049

  18. Response and resilience of methanotrophs to disturbances

    OpenAIRE

    Ho, Adrian Kah Wye

    2011-01-01

    Methanotrophic bacteria are the only known biological sink for the greenhouse gas methane. Therefore, methanotrophs play a key function in carbon cycling, an important biogeochemical process that affects global climate change. Yet, little is known of their vulnerability and resilience to disturbances. Driven by the gap of knowledge, this PhD thesis is a seminal study focusing on the recovery of methanotrophs from disturbances with...

  19. Methylocella Species Are Facultatively Methanotrophic

    OpenAIRE

    Svetlana N. Dedysh; Knief, Claudia; Dunfield, Peter F.

    2005-01-01

    All aerobic methanotrophic bacteria described to date are unable to grow on substrates containing carbon-carbon bonds. Here we demonstrate that members of the recently discovered genus Methylocella are an exception to this. These bacteria are able to use as their sole energy source the one-carbon compounds methane and methanol, as well as the multicarbon compounds acetate, pyruvate, succinate, malate, and ethanol. To conclusively verify facultative growth, acetate and methane were used as mod...

  20. Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches.

    Science.gov (United States)

    Pandit, Pranitha S; Rahalkar, Monali C; Dhakephalkar, Prashant K; Ranade, Dilip R; Pore, Soham; Arora, Preeti; Kapse, Neelam

    2016-04-01

    Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India. PMID:26547567

  1. Bioleaching of metals from electronic scrap by moderately thermophilic acidophilic bacteria

    NARCIS (Netherlands)

    Ilyas, Sadia; Anwar, Munir A.; Niazi, Shahida B.; Ghauri, M. Afzal

    2007-01-01

    The present work was aimed at studying the bioleachability of metals from electronic scrap by the selected moderately thermophilic strains of acidophilic chemolithotrophic and acidophilic heterotrophic bacteria. These included Sulfobacillus thermosulfidooxidans and an unidentified acidophilic hetero

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

    Science.gov (United States)

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

    2011-01-01

    Coccomyxa acidophila is an extremophile eukaryotic microalga isolated from the Tinto River mining area in Huelva, Spain. Coccomyxa acidophila accumulates relevant amounts of β-carotene and lutein, well-known carotenoids with many biotechnological applications, especially in food and health-related industries. The acidic culture medium (pH cultivation from non-desired microorganism growth is one of the main advantages of acidophile microalgae production. Conversely, acidophile microalgae growth rates are usually very low compared to common microalgae growth rates. In this work, we show that mixotrophic cultivation on urea efficiently enhances growth and productivity of an acidophile microalga up to typical values for common microalgae, therefore approaching acidophile algal production towards suitable conditions for feasible outdoor production. Algal productivity and potential for carotenoid accumulation were analyzed as a function of the nitrogen source supplied. Several nitrogen conditions were assayed: nitrogen starvation, nitrate and/or nitrite, ammonia and urea. Among them, urea clearly led to the best cell growth (~4 × 10(8) cells/mL at the end of log phase). Ammonium led to the maximum chlorophyll and carotenoid content per volume unit (220 μg·mL(·1) and 35 μg·mL(·1), respectively). Interestingly, no significant differences in growth rates were found in cultures grown on urea as C and N source, with respect to those cultures grown on nitrate and CO(2) as nitrogen and carbon sources (control cultures). Lutein accumulated up to 3.55 mg·g(·1) in the mixotrophic cultures grown on urea. In addition, algal growth in a shaded culture revealed the first evidence for an active xanthophylls cycle operative in acidophile microalgae. PMID:21339944

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

    Directory of Open Access Journals (Sweden)

    Carlos Vilchez

    2010-12-01

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

  4. Revisiting Methanotrophic Communities in Sewage Treatment Plants

    OpenAIRE

    Ho, Adrian; Vlaeminck, Siegfried E.; Ettwig, Katharina F.; Schneider, Bellinda; Frenzel, Peter; Boon, Nico

    2013-01-01

    The methanotrophic potential in sewage treatment sludge was investigated. We detected a diverse aerobic methanotrophic community that potentially plays a significant role in mitigating methane emission in this environment. The results suggest that community structure was determined by conditions specific to the processes in a sewage treatment plant.

  5. Methanotrophic Bacteria and Facilitated Transport of Pollutants in Aquifer Material

    OpenAIRE

    Jenkins, Michael B.; Chen, Jyh-Herng; Kadner, Debra J.; Lion, Leonard W.

    1994-01-01

    In situ stimulation of methanotrophic bacteria has been considered as a methodology for aquifer remediation. Chlorinated aliphatic hydrocarbons such as trichloroethylene are fortuitously oxidized by the methane monooxygenase produced by methanotrophic bacteria. Experimental results are presented that indicate that both colloidal suspensions containing methanotrophic cells and the soluble extracellular polymers produced by methanotrophic cells have the potential to enhance the transport and re...

  6. Distribution and diversity of Verrucomicrobia methanotrophs in geothermal and acidic environments.

    Science.gov (United States)

    Sharp, Christine E; Smirnova, Angela V; Graham, Jaime M; Stott, Matthew B; Khadka, Roshan; Moore, Tim R; Grasby, Stephen E; Strack, Maria; Dunfield, Peter F

    2014-06-01

    Recently, methanotrophic members of the phylum Verrucomicrobia have been described, but little is known about their distribution in nature. We surveyed methanotrophic bacteria in geothermal springs and acidic wetlands via pyrosequencing of 16S rRNA gene amplicons. Putative methanotrophic Verrucomicrobia were found in samples covering a broad temperature range (22.5-81.6°C), but only in acidic conditions (pH 1.8-5.0) and only in geothermal environments, not in acidic bogs or fens. Phylogenetically, three 16S rRNA gene sequence clusters of putative methanotrophic Verrucomicrobia were observed. Those detected in high-temperature geothermal samples (44.1-81.6°C) grouped with known thermoacidiphilic 'Methylacidiphilum' isolates. A second group dominated in moderate-temperature geothermal samples (22.5-40.1°C) and a representative mesophilic methanotroph from this group was isolated (strain LP2A). Genome sequencing verified that strain LP2A possessed particulate methane monooxygenase, but its 16S rRNA gene sequence identity to 'Methylacidiphilum infernorum' strain V4 was only 90.6%. A third group clustered distantly with known methanotrophic Verrucomicrobia. Using pmoA-gene targeted quantitative polymerase chain reaction, two geothermal soil profiles showed a dominance of LP2A-like pmoA sequences in the cooler surface layers and 'Methylacidiphilum'-like pmoA sequences in deeper, hotter layers. Based on these results, there appears to be a thermophilic group and a mesophilic group of methanotrophic Verrucomicrobia. However, both were detected only in acidic geothermal environments.

  7. Novel Methanotrophs of the Family Methylococcaceae from Different Geographical Regions and Habitats

    Directory of Open Access Journals (Sweden)

    Tajul Islam

    2015-08-01

    Full Text Available Terrestrial methane seeps and rice paddy fields are important ecosystems in the methane cycle. Methanotrophic bacteria in these ecosystems play a key role in reducing methane emission into the atmosphere. Here, we describe three novel methanotrophs, designated BRS-K6, GFS-K6 and AK-K6, which were recovered from three different habitats in contrasting geographic regions and ecosystems: waterlogged rice-field soil and methane seep pond sediments from Bangladesh; and warm spring sediments from Armenia. All isolates had a temperature range for growth of 8–35 °C (optimal 25–28 °C and a pH range of 5.0–7.5 (optimal 6.4–7.0. 16S rRNA gene sequences showed that they were new gammaproteobacterial methanotrophs, which form a separate clade in the family Methylococcaceae. They fell into a cluster with thermotolerant and mesophilic growth tendency, comprising the genera Methylocaldum-Methylococcus-Methyloparacoccus-Methylogaea. So far, growth below 15 °C of methanotrophs from this cluster has not been reported. The strains possessed type I intracytoplasmic membranes. The genes pmoA, mxaF, cbbL, nifH were detected, but no mmoX gene was found. Each strain probably represents a novel species either belonging to the same novel genus or each may even represent separate genera. These isolates extend our knowledge of methanotrophic Gammaproteobacteria and their physiology and adaptation to different ecosystems.

  8. A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity.

    Science.gov (United States)

    Sherry, Angela; Osborne, Kate A; Sidgwick, Frances R; Gray, Neil D; Talbot, Helen M

    2016-02-01

    River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary. PMID:26617278

  9. Methanotrophic activity and bacterial diversity in volcanic-geothermal soils at Pantelleria island (Italy)

    Science.gov (United States)

    Gagliano, A. L.; D'Alessandro, W.; Tagliavia, M.; Parello, F.; Quatrini, P.

    2014-04-01

    Verrucomicrobia. Alphaproteobacteria of the genus Methylocystis were isolated from enrichment cultures, under a methane containing atmosphere at 37 °C. The isolates grow at pH 3.5-8 and temperatures of 18-45 °C, and show a methane oxidation rate of ~ 450 μmol mol-1 h-1. Soils from Favara Grande showed the largest diversity of methanotrophic bacteria until now detected in a geothermal soil. While methanotrophic Verrucomicrobia are reported to dominate highly acidic geothermal sites, our results suggest that slightly acidic soils, in high enthalpy geothermal systems, host a more diverse group of both culturable and uncultivated methanotrophs.

  10. Secretion of Flavins by Three Species of Methanotrophic Bacteria▿ †

    OpenAIRE

    Balasubramanian, Ramakrishnan; Levinson, Benjamin T; Rosenzweig, Amy C.

    2010-01-01

    We detected flavins in the growth medium of the methanotrophic bacterium Methylocystis species strain M. Flavin secretion correlates with growth stage and increases under iron starvation conditions. Two other methanotrophs, Methylosinus trichosporium OB3b and Methylococcus capsulatus (Bath), secrete flavins, suggesting that flavin secretion may be common to many methanotrophic bacteria.

  11. Genetics of particulate methane monooxygenase in methanotrophs

    Energy Technology Data Exchange (ETDEWEB)

    Peeples, T.L.; Lebron, J.; Costello, A.Y. [California Institute of Technology, Pasadena, CA (United States)

    1995-12-01

    The ability of methanotrophs to co-metabolize halocarbons such as trichloroethylene (TCE) by way of the enzyme methane monooxygenase (MMO) is of interest in the development of bioremediation technologies. The presence and the regulation of expression of soluble (sMMO) and membrane-bound (pMMO) forms is important in the design and optimization of such processing schemes. Because the pMMO is found in all methanotrophic species, this form is relevant to in situ remediation technologies. Recently, multiple copies of genes encoding for pMMO have been identified in several species of methanotrophs. Genes encoding the 45 and 27 kDa subunits of the PMMO have been cloned and sequenced. We will discuss the possible implications of multiple copies of pMMO genes in the regulation of pMMO expression. These data may give insights into how MMO activity in natural environments may be manipulated for increased TCE biodegradation.

  12. Particulate methane monooxygenase genes in methanotrophs.

    OpenAIRE

    Semrau, J. D.; Chistoserdov, A; Lebron, J.; Costello, A; Davagnino, J.; Kenna, E; Holmes, A. J.; Finch, R; Murrell, J.C.; Lidstrom, M E

    1995-01-01

    A 45-kDa membrane polypeptide that is associated with activity of the particulate methane monooxygenase (pMMO) has been purified from three methanotrophic bacteria, and the N-terminal amino acid sequence was found to be identical in 17 of 20 positions for all three polypeptides and identical in 14 of 20 positions for the N terminus of AmoB, the 43- kDa subunit of ammonia monooxygenase. DNA from a variety of methanotrophs was screened with two probes, an oligonucleotide designed from the N-ter...

  13. Biodegradation of trichloroethylene (TCE) by methanotrophic community.

    Science.gov (United States)

    Shukla, Awadhesh K; Vishwakarma, Pranjali; Upadhyay, S N; Tripathi, Anil K; Prasana, H C; Dubey, Suresh K

    2009-05-01

    Laboratory incubation experiments were carried out to assess the potential of methanotrophic culture for degrading TCE. Measurements of the growth rate and TCE degradation showed that the methanotrophs not only grew in presence of TCE but also degraded TCE. The rate of TCE degradation was found to be 0.19 ppm h(-1). The reverse transcriptase-PCR test was conducted to quantify expression of pmoA and mmoX genes. RT-PCR revealed expression of pmoA gene only. This observation provides evidence that the pmoA gene was functionally active for pMMO enzyme during the study. The diversity of the methanotrophs involved in TCE degradation was assessed by PCR amplification, cloning, restriction fragment length polymorphism and phylogenetic analysis of pmoA genes. Results suggested the occurrence of nine different phylotypes belonging to Type II methanotrophs in the enriched cultures. Out of the nine, five clustered with, genera Methylocystis and rest got clustered in to a separate group. PMID:19157866

  14. Identification of Methanotrophic Biomarker Lipids in the Symbiont-Containing Gills of Seep Mussels

    Science.gov (United States)

    Jahnke, L. L.; Zahiralis, K. D.; Klein, H. P.; Morrison, David (Technical Monitor)

    1994-01-01

    Mussels collected from hydrocarbon seeps in the Gulf of Mexico grow with methane as sole carbon and energy source due to a symbiotic association with methane-oxidizing bacteria. Transmission electron micrographs of mussel gills show cells with stacked intracytoplasmic membranes similar to type I methanotrophic bacteria. Methanotrophs are known to synthesize several types of cyclic triterpenes, hopanoids and methyl sterols, as well as unique monounsaturated fatty acid, double bond positional isomers that serve as biomarkers for this group. Lipid analysis of dissected mussels demonstrated the presence of these biomarkers predominantly in the gill tissue with much smaller amounts in mantle and remaining body tissues. Gill tissue contained 1150 micrograms/g dry wt. of hopanepolyol derivatives and diplopterol while the mantle tissue contained only 17 micrograms/g. The C16 monounsaturated fatty acids (16:1) characteristic of type I methanotrophic membranes dominated the gill tissue making up 53% of the total while only 5% 16:1 was present in the mantle tissue. The methyl sterol distribution was more dispersed. The predominant sterol in all tissues was cholesterol with lesser amounts of other desmethyl and 4-methyl sterols. The gill and mantle tissues contained 3461 micrograms (17% methyl) and 2750 micrograms (5% methyl) sterol per gm dry wt., respectively. Methyl sterol accounted for 44% of the sterol esters isolated from the gill, suggesting active demethylation of the methanotrophic sterols in this tissue. The use of lipid biomarkers could provide an effective means for identifying host-symbiont relationships.

  15. Flow cytometry based techniques to study testicular acidophilic granulocytes from the protandrous fish gilthead seabream (Sparus aurata L.

    Directory of Open Access Journals (Sweden)

    Chaves-Pozo Elena

    2004-01-01

    Full Text Available The gilthead seabream is a protandrous seasonal breeding teleost that is an excellent model for studying the testicular regression process which occurs in both seasonal testicular involution and sex reversion. Little is known about the cell types and the molecular mechanisms involved in such processes, mainly because of the lack of appropriate methods for testis dissociation, and testicular cell isolation, culture and functional characterization. We have previously reported that gilthead seabream acidophilic granulocytes infiltrate the testis at post-spawning stage, settle close to the spermatogonia and accumulate intracellular interleukin-1&bgr;. In this paper, we report several flow cytometry based assays which allow to establish the role played by gilthead seabream testicular acidophilic granulocytes and permits their quantification.

  16. High diversity of methanotrophic bacteria in geothermal soils affected by high methane fluxes

    Science.gov (United States)

    D'Alessandro, Walter; Gagliano, Antonina Lisa; Quatrini, Paola; Parello, Francesco

    2014-05-01

    Volcanic and geothermal systems emit endogenous gases by widespread degassing from soils, including CH4, a greenhouse gas 25 times as potent as CO2. Recently, it has been demonstrated that volcanic/geothermal soils act as source, but also as biological filter for methane release to the atmosphere. For long time, volcanic/geothermal soils has been considered inhospitable for methanotrophic microorganisms, but new extremophile methanotrophs belonging to Verrucomicrobia were identified in three different areas (Pozzuoli, Italy; Hell's Gate, New Zealand; Kamchatka, Russia), explaining anomalous behaviours in methane leakages of several geothermal/volcanic sites. Our aim was to increase the knowledge of the relationship between methane emissions from volcanic/geothermal areas and biological methane oxidation, by investigating a geothermal site of Pantelleria island (Italy). Pantelleria Island hosts a high enthalpy geothermal system characterized by high temperature, high CH4 and very low H2S fluxes. Such characteristics are reflected in potentially great supply of methane for methanotrophs and scarce presence of inhibitors of their activity (H2S and NH3) in the Pantelleria soils. Potential methanotrophic activity within these soils was already evidenced by the CH4/CO2 ratio of the flux measurements which was lower than that of the respective fumarolic manifestations indicating a loss of CH4 during the gas travel towards the earth's surface. In this study laboratory incubation experiments using soils sampled at Favara Grande, the main hydrothermal area of Pantelleria, showed very high methane consumption rates (up to 9500 ng CH4 h-1 g-1). Furthermore, microbiological and culture-independent molecular analyses allowed to detect the presence of methanotrophs affiliated to Gamma- and Alpha-Proteobacteria and to the newly discovered acidothermophilic methanotrophs Verrucomicrobia. Culturable methanotrophic Alpha-proteobacteria of the genus Methylocystis were isolated by

  17. Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile.

    Science.gov (United States)

    Messerli, Mark A; Amaral-Zettler, Linda A; Zettler, Erik; Jung, Sung-Kwon; Smith, Peter J S; Sogin, Mitchell L

    2005-07-01

    Organisms growing in acidic environments, pHpH. We begin to investigate this premise by determining the magnitude of the transmembrane electrochemical H+ gradient in an acidophilic Chlamydomonas sp. (ATCC PRA-125) isolated from the Rio Tinto, a heavy metal laden, acidic river (pH 1.7-2.5). This acidophile grows most rapidly at pH 2 but is capable of growth over a wide pH range (1.5-7.0), while Chlamydomonas reinhardtii is restricted to growth at pH>or=3 with optimal growth between pH 5.5 and 8.5. With the fluorescent H+ indicator, 2',7'-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein (BCECF), we show that the acidophilic Chlamydomonas maintains an average cytosolic pH of 6.6 in culture medium at both pH 2 and pH 7 while Chlamydomonas reinhardtii maintains an average cytosolic pH of 7.1 in pH 7 culture medium. The transmembrane electric potential difference of Chlamydomonas sp., measured using intracellular electrodes at both pH 2 and 7, is close to 0 mV, a rare value for plants, animals and protists. The 40,000-fold difference in [H+] could be the result of either active or passive mechanisms. Evidence for active maintenance was detected by monitoring the rate of ATP consumption. At the peak, cells consume about 7% more ATP per second in medium at pH 2 than at pH 7. This increased rate of consumption is sufficient to account for removal of H+ entering the cytosol across a membrane with relatively high permeability to H+ (7x10(-8) cm s-1). Our results indicate that the small increase in the rate of ATP consumption can account for maintenance of the transmembrane H+ gradient without the imposition of cell surface H+ barriers.

  18. Genomics and Metagenomics of Extreme Acidophiles in Biomining Environments

    Science.gov (United States)

    Holmes, D. S.

    2015-12-01

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

  19. Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242)

    Energy Technology Data Exchange (ETDEWEB)

    Stein, Lisa Y. [University of Alberta, Edmondton, Canada; Bringel, Francoise O. [University of Strasbourg; DiSpiritto, Alan A. [University of Iowa; Han, Sukkyun [University of Alberta, Edmondton, Canada; Jetten, MSM [Radboud University Nijmegen, The Netherlands; Kalyuzhnaya, Marina G. [University of Washington, Seattle; Kits, K. Dimitri [University of Alberta, Edmondton, Canada; Klotz, Martin G [University of Louisville, Louisville; Op den Camp, HJM [Radboud University Nijmegen, The Netherlands; Semrau, Jeremy D. [University of Michigan; Vuilleumier, Stephane [University of Strasbourg; Bruce, David [Los Alamos National Laboratory (LANL); Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Davenport, Karen W. [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Lajus, Aurelie [Genoscope/Centre National de la Recherche Scientifique-Unite Mixte de Recherche; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Medigue, Claudine [Genoscope/Centre National de la Recherche Scientifique-Unite Mixte de Recherche; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Methylocystis sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing Alphaproteobacterium isolated from an aquifer in southern California. Unlike most methanotrophs in the Methylocystaceae family, this strain has a single pmo operon encoding particulate methane monooxygenase and no evidence of the genes encoding soluble methane monooxygenase. This is the first reported genome sequence of a member of the Methylocystis species of the Methylocystaceae family in the order Rhizobiales.

  20. Termites Facilitate Methane Oxidation and Shape the Methanotrophic Community

    OpenAIRE

    Ho, Adrian; Erens, Hans; Mujinya, Basile Bazirake; Boeckx, Pascal; Baert, Geert; Schneider, Bellinda; Frenzel, Peter; Boon, Nico; Van Ranst, Eric

    2013-01-01

    Termite-derived methane contributes 3 to 4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (methanotrophs). However, a considerable fraction of the methane produced can be consumed by methanotrophs that inhabit the mound material, yet the methanotroph ecology in these environments is virtually unknown. The potential for methane oxidation was determined using slurry incubations under conditions with high (12%) and in situ (∼0.004%) metha...

  1. Modelling the growth of a methanotrophic biofilm

    DEFF Research Database (Denmark)

    Arcangeli, J.-P.; Arvin, E.

    1999-01-01

    This article discusses the growth of methanotrophic biofilms. Several independent biofilm growths scenarios involving different inocula were examined. Biofilm growth, substrate removal and product formation were monitored throughout the experiments. Based on the oxygen consumption it was concluded...... that heterotrophs and nitrifiers co-existed with methanotrophs in the biofilm. Heterotrophic biomass grew on soluble polymers formed by the hydrolysis of dead biomass entrapped in the biofilm. Nitrifier populations developed because of the presence of ammonia in the mineral medium. Based on these experimental...... was performed on this model. It indicated that the most influential parameters were those related to the biofilm (i.e. density; solid-volume fraction; thickness). This suggests that in order to improve the model, further research regarding the biofilm structure and composition is needed....

  2. Methanotrophic microbiomes as drivers for environmental biotechnology

    OpenAIRE

    van der Ha, David

    2013-01-01

    Since the industrial revolution, the average temperature on Earth has risen considerably, mainly due to the enormous emissions of greenhouse gases. This doctoral research focused on microbial mitigation strategies for methane (CH4), the second most important greenhouse gas after CO2. Therefore, methanotrophic microbiomes were used, the latter being entire microbial communities depending on CH4 for their activity. In a first phase, the effects of external growth parameters on the activity and ...

  3. Methanotrophic microbiomes from North Sea sediment

    OpenAIRE

    Vekeman, B.

    2016-01-01

    Methane is the most abundant organic greenhouse gas in our atmosphere, and has a strong infrared absorbance, being 25 to 30 times more effective than carbon dioxide on a 100 years scale. Methane therefore plays an important role in the climate warming regulation. Methanotrophs are microorganisms that can consume methane and utilize it as their sole source of carbon and energy. These organisms are the most important biological sink of methane. Their importance is especially demonstrated in mar...

  4. Methanotrophic activity and diversity of methanotrophs in volcanic-geothermal soils at Pantelleria island (Italy)

    OpenAIRE

    A. L. Gagliano; W. D'Alessandro; M. Tagliavia; Parello, F.; Quatrini, P.

    2014-01-01

    Volcanic and geothermal systems emit endogenous gases by widespread degassing from soils, including CH4, a greenhouse gas twenty-five times as potent as CO2. Recently, it has been demonstrated that volcanic or geothermal soils are not only a source of methane, but are also sites of methanotrophic activity. Methanotrophs are able to consume 10–40 Tg of CH4 a−1 and to trap more than 50% of the methane degassing through the soils. We report on methane microbial oxidation in the...

  5. PCR-mediated detection of acidophilic, bioleaching-associated bacteria.

    OpenAIRE

    De Wulf-Durand, P; Bryant, L J; Sly, L I

    1997-01-01

    The detection of acidophilic microorganisms from mining environments by culture methods is time consuming and unreliable. Several PCR approaches were developed to amplify small-subunit rRNA sequences from the DNA of six bacterial phylotypes associated with acidic mining environments, permitting the detection of the target DNA at concentrations as low as 10 fg.

  6. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria.

    Science.gov (United States)

    Wegener, Gunter; Krukenberg, Viola; Riedel, Dietmar; Tegetmeyer, Halina E; Boetius, Antje

    2015-10-22

    The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. In marine sediments, AOM is performed by dual-species consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) inhabiting the methane-sulfate transition zone. The biochemical pathways and biological adaptations enabling this globally relevant process are not fully understood. Here we study the syntrophic interaction in thermophilic AOM (TAOM) between ANME-1 archaea and their consortium partner SRB HotSeep-1 (ref. 6) at 60 °C to test the hypothesis of a direct interspecies exchange of electrons. The activity of TAOM consortia was compared to the first ANME-free culture of an AOM partner bacterium that grows using hydrogen as the sole electron donor. The thermophilic ANME-1 do not produce sufficient hydrogen to sustain the observed growth of the HotSeep-1 partner. Enhancing the growth of the HotSeep-1 partner by hydrogen addition represses methane oxidation and the metabolic activity of ANME-1. Further supporting the hypothesis of direct electron transfer between the partners, we observe that under TAOM conditions, both ANME and the HotSeep-1 bacteria overexpress genes for extracellular cytochrome production and form cell-to-cell connections that resemble the nanowire structures responsible for interspecies electron transfer between syntrophic consortia of Geobacter. HotSeep-1 highly expresses genes for pili production only during consortial growth using methane, and the nanowire-like structures are absent in HotSeep-1 cells isolated with hydrogen. These observations suggest that direct electron transfer is a principal mechanism in TAOM, which may also explain the enigmatic functioning and specificity of other methanotrophic ANME-SRB consortia. PMID:26490622

  7. Methanotrophic production of polyhydroxybutyrate-co-hydroxyvalerate with high hydroxyvalerate content.

    Science.gov (United States)

    Cal, Andrew J; Sikkema, W Dirk; Ponce, Maria I; Franqui-Villanueva, Diana; Riiff, Timothy J; Orts, William J; Pieja, Allison J; Lee, Charles C

    2016-06-01

    Type II methanotrophic bacteria are a promising production platform for PHA biopolymers. These bacteria are known to produce pure poly-3-hydroxybutyrate homopolymer (PHB). We isolated a strain, Methylocystis sp. WRRC1, that was capable of producing a wide range of polyhydroxybutyrate-co-hydroxyvalerate copolymers (PHB-co-HV) when co-fed methane and valerate or n-pentanol. The ratio of HB to HV monomer was directly related to the concentration of valeric acid in the PHA accumulation media. We observed increased incorporation of HV and total polymer under copper-free growth conditions. The PHB-co-HV copolymers produced had decreased melting temperatures and crystallinity compared with methanotroph-produced PHB. PMID:26920242

  8. Methanotrophic activity and bacterial diversity in volcanic-geothermal soils at Pantelleria island (Italy

    Directory of Open Access Journals (Sweden)

    A. L. Gagliano

    2014-04-01

    -thermophilic methanotrophs Verrucomicrobia. Alphaproteobacteria of the genus Methylocystis were isolated from enrichment cultures, under a methane containing atmosphere at 37 °C. The isolates grow at pH 3.5–8 and temperatures of 18–45 °C, and show a methane oxidation rate of ~ 450 μmol mol−1 h−1. Soils from Favara Grande showed the largest diversity of methanotrophic bacteria until now detected in a geothermal soil. While methanotrophic Verrucomicrobia are reported to dominate highly acidic geothermal sites, our results suggest that slightly acidic soils, in high enthalpy geothermal systems, host a more diverse group of both culturable and uncultivated methanotrophs.

  9. Oxidation of inorganic sulfur compounds in acidophilic prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Rohwerder, T.; Sand, W. [Universitaet Duisburg-Essen, Biofilm Centre, Aquatic Biotechnology, Duisburg (Germany)

    2007-07-15

    The oxidation of reduced inorganic sulfur compounds to sulfuric acid is of great importance for biohydrometallurgical technologies as well as the formation of acidic (below pH 3) and often heavy metal-contaminated environments. The use of elemental sulfur as an electron donor is the predominant energy-yielding process in acidic natural sulfur-rich biotopes but also at mining sites containing sulfidic ores. Contrary to its significant role in the global sulfur cycle and its biotechnological importance, the microbial fundamentals of acidophilic sulfur oxidation are only incompletely understood. Besides giving an overview of sulfur-oxidizing acidophiles, this review describes the so far known enzymatic reactions related to elemental sulfur oxidation in acidophilic bacteria and archaea. Although generally similar reactions are employed in both prokaryotic groups, the stoichiometry of the key enzymes is different. Bacteria oxidize elemental sulfur by a sulfur dioxygenase to sulfite whereas in archaea, a sulfur oxygenase reductase is used forming equal amounts of sulfide and sulfite. In both cases, the activation mechanism of elemental sulfur is not known but highly reactive linear sulfur forms are assumed to be the actual substrate. Inhibition as well as promotion of these biochemical steps is highly relevant in bioleaching operations. An efficient oxidation can prevent the formation of passivating sulfur layers. In other cases, a specific inhibition of sulfur biooxidation may be beneficial for reducing cooling and neutralization costs. In conclusion, the demand for a better knowledge of the biochemistry of sulfur-oxidizing acidophiles is underlined. (Abstract Copyright [2007], Wiley Periodicals, Inc.)

  10. Ökologie methanotropher Bakterien: Räumliche Verteilung und Funktion methanotropher Bakterien in Feuchtgebieten.

    OpenAIRE

    Krause, Sascha

    2010-01-01

    Methane is the second most important greenhouse gas after CO2 exerting a radiative forcing about a third of that of CO2. Most of the atmospheric methane is released from biogenic sources such as landfills, natural wetlands and rice fields. Methane emission from these sources would be significantly higher without the activity of methanotrophs that oxidize the biogenically produced methane, thus reducing the methane emissions up to ...

  11. EMERGING TECHNOLOGY BULLETIN - METHANOTROPHIC BIOREACTOR SYSTEM - BIOTROL, INC.

    Science.gov (United States)

    BioTrol's Methanotrophic Bioreactor is an above-ground remedial system for water contaminated with halogenated volatile organic compounds, including trichloroethylene (ICE) and related chemicals. Its design features circumvent problems peculiar to treatment of this unique class o...

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

    Science.gov (United States)

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

    2016-01-01

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

  13. Gene loss and horizontal gene transfer contributed to the genome evolution of the extreme acidophile Ferrovum

    Directory of Open Access Journals (Sweden)

    Sophie Roxana Ullrich

    2016-05-01

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

  14. Diversity of methanotrophs in urea-fertilized tropical rice agroecosystem

    OpenAIRE

    Vishwakarma, Pranjali; Dubey, Suresh K.

    2010-01-01

    Laboratory experiments were conducted to study the population size, diversity and methane oxidation potential of methanotrophs in tropical rice agroecosystem under the influence of N-fertilizer. Results indicate that the diversity of methane oxidizing bacteria (MOB) is altered in fertilizer treated soils compared to untreated control. Nevertheless, Type I MOB still dominated in the fertilized soils whereas the diversity of Type II methanotrophs decreases. Control soils have higher MOB populat...

  15. Methanol Improves Methane Uptake in Starved Methanotrophic Microorganisms

    OpenAIRE

    Jensen, Sigmund; Priemé, Anders; Bakken, Lars

    1998-01-01

    Methanotrophs in enrichment cultures grew and sustained atmospheric methane oxidation when supplied with methanol. If they were not supplied with methanol or formate, their atmospheric methane oxidation came to a halt, but it was restored within hours in response to methanol or formate. Indigenous forest soil methanotrophs were also dependent on a supply of methanol upon reduced methane access but only when exposed to a methane-free atmosphere. Their immediate response to each methanol additi...

  16. The more, the merrier: heterotroph richness stimulates methanotrophic activity

    OpenAIRE

    Ho, Adrian; De Roy, Karen; Thas, Olivier; De Neve, Jan; Hoefman, Sven; Vandamme, Peter; Heylen, Kim; Boon, Nico

    2014-01-01

    Although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. Using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. Artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. We considered methane oxidation rate as a functional response variable. Our results showed a signifi...

  17. Aerobic methanotroph diversity in Sanjiang wetland, Northeast China.

    Science.gov (United States)

    Yun, Juanli; Zhang, Hongxun; Deng, Yongcui; Wang, Yanfen

    2015-04-01

    Aerobic methanotrophs present in wetlands can serve as a methane filter and thereby significantly reduce methane emissions. Sanjiang wetland is a major methane source and the second largest wetland in China, yet little is known about the characteristics of aerobic methanotrophs in this region. In the present study, we investigated the diversity and abundance of methanotrophs in marsh soils from Sanjiang wetland with three different types of vegetation by 16S ribosomal RNA (rRNA) and pmoA gene analysis. Quantitative polymerase chain reaction analysis revealed the highest number of pmoA gene copies in marsh soils vegetated with Carex lasiocarpa (10(9) g(-1) dry soil), followed by Carex meyeriana, and the least with Deyeuxia angustifolia (10(8) g(-1) dry soil). Consistent results were obtained using Sanger sequencing and pyrosequencing techniques, both indicating the codominance of Methylobacter and Methylocystis species in Sanjiang wetland. Other less abundant methanotrophy, including cultivated Methylomonas and Methylosinus genus, and uncultured clusters such as LP20 and JR-1, were also detected in the wetland. Methanotroph diversity was almost the same in three different vegetation covered soils, suggesting that vegetation types had very little influence on the methanotroph diversity. Our study gives an in-depth insight into the community composition of aerobic methanotrophs in the Sanjiang wetland. PMID:25351140

  18. Electroporation-Based Genetic Manipulation in Type I Methanotrophs.

    Science.gov (United States)

    Yan, Xin; Chu, Frances; Puri, Aaron W; Fu, Yanfen; Lidstrom, Mary E

    2016-04-01

    Methane is becoming a major candidate for a prominent carbon feedstock in the future, and the bioconversion of methane into valuable products has drawn increasing attention. To facilitate the use of methanotrophic organisms as industrial strains and accelerate our ability to metabolically engineer methanotrophs, simple and rapid genetic tools are needed. Electroporation is one such enabling tool, but to date it has not been successful in a group of methanotrophs of interest for the production of chemicals and fuels, the gammaproteobacterial (type I) methanotrophs. In this study, we developed electroporation techniques with a high transformation efficiency for three different type I methanotrophs: Methylomicrobium buryatense 5GB1C, Methylomonas sp. strain LW13, and Methylobacter tundripaludum 21/22. We further developed this technique in M. buryatense, a haloalkaliphilic aerobic methanotroph that demonstrates robust growth with a high carbon conversion efficiency and is well suited for industrial use for the bioconversion of methane. On the basis of the high transformation efficiency of M. buryatense, gene knockouts or integration of a foreign fragment into the chromosome can be easily achieved by direct electroporation of PCR-generated deletion or integration constructs. Moreover, site-specific recombination (FLP-FRT [FLP recombination target] recombination) and sacB counterselection systems were employed to perform marker-free manipulation, and two new antibiotics, zeocin and hygromycin, were validated to be antibiotic markers in this strain. Together, these tools facilitate the rapid genetic manipulation of M. buryatense and other type I methanotrophs, promoting the ability to perform fundamental research and industrial process development with these strains. PMID:26801578

  19. Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing

    OpenAIRE

    ChristineSharp; MatthewStott

    2012-01-01

    Genomic analysis of the methanotrophic verrucomicrobium “Methylacidiphilum infernorum” strain V4 has shown that most pathways conferring its methanotrophic lifestyle are similar to those found in proteobacterial methanotrophs. However, due to the large sequence divergence of its methane monooxygenase-encoding genes (pmo), ‘universal’ pmoA polymerase chain reaction (PCR) primers do not target these bacteria. Unlike proteobacterial methanotrophs, “Methylacidiphilum” fixes carbon autotrophically...

  20. Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing

    OpenAIRE

    Sharp, Christine E; Stott, Matthew B.; Dunfield, Peter F.

    2012-01-01

    Genomic analysis of the methanotrophic verrucomicrobium “Methylacidiphilum infernorum” strain V4 has shown that most pathways conferring its methanotrophic lifestyle are similar to those found in proteobacterial methanotrophs. However, due to the large sequence divergence of its methane monooxygenase-encoding genes (pmo), “universal” pmoA polymerase chain reaction (PCR) primers do not target these bacteria. Unlike proteobacterial methanotrophs, “Methylacidiphilum” fixes carbon autotrophically...

  1. Variation in methanotroph-related proxies in peat deposits from Misten Bog, Hautes-Fagnes, Belgium

    OpenAIRE

    van Winden, Julia F.; Talbot, Helen M.; De Vleeschouwer, François; Reichart, Gert-Jan; Sinninghe Damsté, Jaap S.

    2012-01-01

    Methane emissions from peat bogs are strongly reduced by aerobic methane oxidising bacteria (methanotrophs) living in association with Sphagnum spp. Field studies and laboratory experiments have revealed that, with increasing water level and temperature, methanotrophic activity increases. To gain a better understanding of how longer term changes in methanotrophic activity are reflected in methanotroph biomarkers, a peat record (0–100 cm) from the Hautes-Fagnes (Belgium) encompassing the past ...

  2. Enrichment of mesophilic acidophiles from the Underground Copper Mine Bor

    Directory of Open Access Journals (Sweden)

    Conić Vesna T.

    2009-01-01

    Full Text Available In this work, autotrophic growth of mesophilic acidophiles from the Underground Copper Mine Bor was performed. Two selected solution samples collected from the 'Tilva Roš' ore body were prepared in a 9K nutrient medium (Silverman and Lundgren, 1959. The first sample TR k-16 was obtained during the hole drilling of the ore body, and the second TR k-31 from the drainage channel. Two samples of 9K media (Silverman and Lundgren, 1959 were inoculated with two selected solution samples from the underground mine Tilva Roš. Inoculated culture media were incubated without prior autoclaving in the period of 6 days at a temperature of 28 ?C with purging air through the system with enough oxygen and carbon dioxide. Oxidation rate of ferrous ions in the first 3 days of incubation was 14.8 and 10.7 wt.% Fe2+/day, the next 3 days 17.3 and 13.6 and for the total period of 6 days 98.3 and 74.8 wt.% for the first and second sample, respectively, i.e. 100 wt.% with initial percentage of ferrous ion in each medium. After centrifugation of enriched samples of culture media at 3000 rpm for 5 min, a plenty of mesophilic acidophiles were determined by microscopic method. According to Karavaiko [6], in the processes of incubition for 9K nutrient solution cells number reach a value of 108 cells/cm3.

  3. Aerobic Methanotrophs in Natural and Agricultural Soils of European Russia

    Directory of Open Access Journals (Sweden)

    Irina Kravchenko

    2013-07-01

    Full Text Available Human activities such as land management and global warming have great impact on the environment. Among changes associated with the global warming, rising methane emission is a serious concern. Therefore, we assessed methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight soil types (both unmanaged and agricultural distributed across the European part of Russia. Using a culture-independent approach targeting pmoA gene, we provide the first baseline data on the diversity of methanotrophs inhabiting most typical soil types. The analysis of pmoA clone libraries showed that methanotrophic populations in unmanaged soils are less diverse than in agricultural areas. These clone sequences were placed in three groups of, so far, uncultured methanotrophs: USC-gamma, cluster I, and pmoA/amoA cluster, which are believed to be responsible for atmospheric methane oxidation in upland soils. Agricultural soils harbored methanotrophs related to genera Methylosinus, Methylocystis, Methylomicrobium, Methylobacter, and Methylocaldum. Despite higher numbers of detected molecular operational taxonomic units (MOTUs, managed soils showed decreased methane oxidation rates as observed in both in situ and laboratory experiments. Our results also suggest that soil restoration may have a positive effect on methane consumption by terrestrial ecosystems.

  4. Sulfidogenesis in low pH (3.8-4.2) media by a mixed population of acidophilic bacteria.

    Science.gov (United States)

    Kimura, Sakurako; Hallberg, Kevin B; Johnson, D Barrie

    2006-03-01

    A defined mixed bacterial culture was established which catalyzed dissimilatory sulfate reduction, using glycerol as electron donor, at pH 3.8-4.2. The bacterial consortium comprised a endospore-forming sulfate reducing bacterium (isolate M1) that had been isolated from acidic sediment in a geothermal area of Montserrat (West Indies) and which had 94% sequence identity (of its 16S rRNA gene) to the Gram-positive neutrophile Desulfosporosinus orientis, and a Gram-negative (non sulfate-reducing) acidophile (isolate PFBC) that shared 99% gene identity with Acidocella aromatica. Whilst M1 was an obligate anaerobe, isolate PFBC, as other Acidocella spp., only grew in pure culture in aerobic media. Analysis of microbial communities, using a combination of total bacterial counts and fluorescent in situ hybridization, confirmed that concurrent growth of both bacteria occurred during sulfidogenesis under strictly anoxic conditions in a pH-controlled fermenter. In pure culture, M1 oxidized glycerol incompletely, producing stoichiometric amounts of acetic acid. In mixed culture with PFBC, however, acetic acid was present only in small concentrations and its occurrence was transient. Since M1 did not oxidize acetic acid, it was inferred that this metabolite was catabolized by Acidocella PFBC which, unlike glycerol, was shown to support the growth of this acidophile under aerobic conditions. In fermenter cultures maintained at pH 3.8-4.2, sulfidogenesis resulted in the removal of soluble zinc (as solid phase ZnS) whilst ferrous iron remained in solution. Potential syntrophic interactions, involving hydrogen transfer between M1 and PFBC, are discussed, as is the potential of sulfidogenesis in acidic liquors for the selective recovery of heavy metals from wastewaters. PMID:16456614

  5. Methane oxidation and methanotrophs: resistance and resilience against model perturbations

    Science.gov (United States)

    Ho, A.; Frenzel, P.

    2009-04-01

    Biodiversity is claimed to be essential for ecosystem functioning. However, most experiments on biodiversity and ecosystem functioning (BEF) have been made on higher plants, while only few studies have dealt with microbial communities. Overall microbial diversity may be very high, and general functions like aerobic carbon mineralization are assumed to be supported by highly redundant communities. Therefore, we focused on methane oxidation, a microbial process of global importance mitigating methane emissions from wetland, rice fields, and landfills. We used a rice paddy as our model system, where >90% of potentially emitted methane may be oxidized in the oxic surface layer. This community is presumed to consist of 10-20 taxa more or less equivalent to species. We focused on the ability of methanotrophs to recover from a disturbance causing a significant die-off of all microbial populations. This was simulated by mixing native with sterile soil in two ratios (1:4 and 1:40). Microcosms were incubated and the temporal shift of the methanotrophic communities was followed by pmoA-based Terminal Restriction Length Polymorphism (T-RFLP), qPCR, and a pmoA-based diagnostic microarray. We consistently observed distinctive temporal shifts between Methylocystaceaea and Methylococcacea, a rapid population growth leading to the same or even higher cell numbers as in microcosms made from native soil alone, but no effect on the amount of methane oxidized. The ratio of different methanotrophs changed with treatment, while the number of taxa stayed nearly the same. Overall, methanotrophs showed a remarkable resilience compensating for die-offs. It has to be noted, however, that our experiment focused on methanotrophs adapted to and living at high methane fluxes. Quite different, methanotrophs living in upland soils do not mitigate methane emissions, but are the only biological sink to atmospheric methane. These microbes are severely substrate limited, and will be much more

  6. nifH Sequences and Nitrogen Fixation in Type I and Type II Methanotrophs

    OpenAIRE

    Auman, Ann J.; Speake, Catherine C.; Lidstrom, Mary E.

    2001-01-01

    Some methane-oxidizing bacteria (methanotrophs) are known to be capable of expressing nitrogenase and utilizing N2 as a nitrogen source. However, no sequences are available for nif genes in these strains, and the known nitrogen-fixing methanotrophs are confined mainly to a few genera. The purpose of this work was to assess the nitrogen-fixing capabilities of a variety of methanotroph strains. nifH gene fragments from four type I methanotrophs and seven type II methanotrophs were PCR amplified...

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

    Energy Technology Data Exchange (ETDEWEB)

    Bacelar-Nicolau, P.; Johnson, D.B. [Univ. of Wales, Bangor (United Kingdom). School of Biological Sciences

    1999-02-01

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

  8. Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus

    Directory of Open Access Journals (Sweden)

    Stefanie eMangold

    2011-02-01

    Full Text Available Given the challenges to life at low pH, an analysis of inorganic sulfur compound oxidation was initiated in the chemolithoautotrophic extremophile Acidithiobacillus caldus. A. caldus is able to metabolize elemental sulfur and a broad range of inorganic sulfur compounds. It has been implicated in the production of environmentally damaging acidic solutions as well as participating in industrial bioleaching operations where it forms part of microbial consortia used for the recovery of metal ions. Based upon the recently published A. caldus type strain genome sequence, a bioinformatic reconstruction of elemental sulfur and inorganic sulfur compound metabolism predicted genes included: sulfide quinone reductase (sqr, tetrathionate hydrolase (tth, two sox gene clusters potentially involved in thiosulfate oxidation (soxABXYZ, sulfur oxygenase reductase (sor, and various electron transport components. RNA transcript profiles by semi-quantitative reverse transcription PCR suggested up-regulation of sox genes in the presence of tetrathionate. Extensive gel based proteomic comparisons of total soluble and membrane enriched protein fractions during growth on elemental sulfur and tetrathionate identified differential protein levels from the two Sox clusters as well as several chaperone and stress proteins up-regulated in the presence of elemental sulfur. Proteomics results also suggested the involvement of heterodisulfide reductase (HdrABC in A. caldus inorganic sulfur compound metabolism. A putative new function of Hdr in acidophiles is discussed. Additional proteomic analysis evaluated protein expression differences between cells grown attached to solid, elemental sulfur versus planktonic cells. This study has provided insights into sulfur metabolism of this acidophilic chemolithotroph and gene expression during attachment to solid elemental sulfur.

  9. Methane as a resource: can the methanotrophs add value?

    Science.gov (United States)

    Strong, P J; Xie, S; Clarke, W P

    2015-04-01

    Methane is an abundant gas used in energy recovery systems, heating, and transport. Methanotrophs are bacteria capable of using methane as their sole carbon source. Although intensively researched, the myriad of potential biotechnological applications of methanotrophic bacteria has not been comprehensively discussed in a single review. Methanotrophs can generate single-cell protein, biopolymers, components for nanotechnology applications (surface layers), soluble metabolites (methanol, formaldehyde, organic acids, and ectoine), lipids (biodiesel and health supplements), growth media, and vitamin B12 using methane as their carbon source. They may be genetically engineered to produce new compounds such as carotenoids or farnesene. Some enzymes (dehydrogenases, oxidase, and catalase) are valuable products with high conversion efficiencies and can generate methanol or sequester CO2 as formic acid ex vivo. Live cultures can be used for bioremediation, chemical transformation (propene to propylene oxide), wastewater denitrification, as components of biosensors, or possibly for directly generating electricity. This review demonstrates the potential for methanotrophs and their consortia to generate value while using methane as a carbon source. While there are notable challenges using a low solubility gas as a carbon source, the massive methane resource, and the potential cost savings while sequestering a greenhouse gas, keeps interest piqued in these unique bacteria. PMID:25723373

  10. Aquatic plant surface as a niche for methanotrophs

    Directory of Open Access Journals (Sweden)

    Naoko eYoshida

    2014-02-01

    Full Text Available This study investigated the potential local CH4 sink in various plant parts as a boundary environment of CH4 emission and consumption. By comparing CH4 consumption activities in cultures inoculated with parts from 39 plant species, we observed significantly higher consumption of CH4 associated with aquatic plants than other emergent plant parts such as woody plant leaves, macrophytic marine algae, and sea grass. In situ activity of CH4 consumption by methanotrophs associated with different species of aquatic plants was in the range of 3.7 – 37 μmol⋅h-1⋅g-1 dry weight, which was ca 5.7-370 fold higher than epiphytic CH4 consumption in submerged parts of emergent plants. The qPCR-estimated copy numbers of the particulate methane monooxygenase-encoding gene pmoA were variable among the aquatic plants and ranged in the order of 105 to 107 copies⋅g-1 dry weight, which correlated with the observed CH4 consumption activities. Phylogenetic identification of methanotrophs on aquatic plants based on the pmoA sequence analysis revealed a predominance of diverse gammaproteobacterial type-I methanotrophs, including a phylotype of a possible plant-associated methanotroph with the closest identity (86-89% to Methylocaldum gracile.

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

    Science.gov (United States)

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

    2016-05-01

    Biosynthesis of silver nanoparticles (AgNPs) is an eco-friendly approach by using different biological sources; for example, plants and microorganisms such as bacteria, fungi, and actinobacteria. In this report, we present the biological synthesis of silver nanoparticles (AgNPs) by acidophilic actinomycetes SL19 and SL24 strains isolated from pine forest soil (pH Pseudomonas aeruginosa, and uropathogens such as Enterobacter, S. aureus, P. aeruginosa, K. pneumoniae, and E. coli. The lowest MIC (40 μg ml(-1) ) was demonstrated by AgNPs synthesized from SL24 against E. coli. However, the AgNPs of SL19 showed lowest MIC (70 μg ml(-1) ) against S. aureus. The activity of antibiotic was enhanced, when tested in combination with silver nanoparticles synthesized from both actinobacterial strains. PMID:27151174

  12. [The use of real-time PCR technology to assess the effectiveness of methods of DNA extraction from cultures of acidophilic chemolithotrophic microorganisms].

    Science.gov (United States)

    Rogatykh, S V; Dokshukina, A A; Khaĭnasova, T S; Muradov, S V; Kofiadi, I A

    2011-01-01

    Comparative evaluation of efficiency of several methods of DNA extraction from storage cultures of acidophilic chemolithotrophic microorganism communities isolated from sulfide ores of Shanuch ore deposit (Kamchatka peninsula) was conducted. DNA extraction methods in various combinations of physical (heating to 65-98 degrees C, grinding with SiO2 particles), enzymatic (treatment with lysozyme and proteinase K), and chemical (GuSCN, CTAB and KOH) treatments were tested. The evaluation of efficiency was performed using Real-time PCR. The best result was obtained for the combined method based on GuSCN lysis activity (lysis at 65 degrees C) followed by purification with phenol and chloroform.

  13. Enrichment and activity of methanotrophic microorganisms from municipal wastewater sludge.

    Science.gov (United States)

    Siniscalchi, Luciene Alves Batista; Vale, Isabel Campante; Dell'Isola, Jéssica; Chernicharo, Carlos Augusto; Calabria Araujo, Juliana

    2015-01-01

    In this study, methanotrophic microorganisms were enriched from a municipal wastewater sludge taken from an Upflow Anaerobic Sludge Blanket reactor. The enrichment was performed in a sequencing batch reactor (SBR) with an autotrophic medium containing nitrite and nitrate. The microbial community composition of the inoculum and of the enrichment culture after 100 days of SBR operation was investigated and compared with the help of data obtained from 454 pyrosequencing analyses. The nitrite and nitrate removal efficiencies were 68% and 53%, respectively, probably due to heterotrophic denitrification. Archaeal cells of the anaerobic methanotrophic Archaic (ANME)-I and ANME-II groups were detected by polymerase chain reaction throughout the whole cultivation period. Pyrosequencing analysis showed that community composition was different among the two samples analysed. The dominant phyla found in the inoculum were Synergistestes, Firmicutes and Euryarchaeota, while Planctomycetes, Verrucomicrobia, Chloroflexi and Proteobacteria prevailed in the enriched biomass. The cultivation conditions decreased Methanobacterium abundance from 8% to 1%, and enriched for methanotrophic bacteria such as Methylocaldum, Methylocistis and Methylosinus. Sequences of Methylocaldum sp. accounted for 2.5% of the total reads. The presence and high predominance of Verrucomicrobia in the enriched biomass suggested that other unknown methanotrophic species related to that phylum might also have occurred in the reactor. Anaerobic methane oxidation activity was measured for both samples, and showed that the activity of the enrichment culture was nearly three times higher than the activity of the inoculum. Taken together, these results showed that the inoculum type and cultivation conditions were properly suited for methanotrophic enrichment. PMID:25495866

  14. Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms

    Directory of Open Access Journals (Sweden)

    Mark eDopson

    2014-04-01

    Full Text Available All metals are toxic at high concentrations and consequently their intracellular concentrations must be regulated. Acidophilic microorganisms have an optimum growth pH < 3 and proliferate in natural and anthropogenic low pH environments. Some acidophiles are involved in the catalysis of sulfide mineral dissolution, resulting in high concentrations of metals in solution. Acidophiles are often described as highly metal resistant via mechanisms such as multiple and/or more efficient active resistance systems than are present in neutrophiles. However, this is not the case for all acidophiles and we contend that their growth in high metal concentrations is partially due to an intrinsic tolerance as a consequence of the environment in which they live. In this perspective, we highlight metal tolerance via complexation of free metals by sulfate ions and passive tolerance to metal influx via an internal positive cytoplasmic transmembrane potential. These tolerance mechanisms have been largely ignored in past studies of acidophile growth in the presence of metals and should be taken into account.

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

    Science.gov (United States)

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

    2016-01-01

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

  16. Monitoring Methanotrophic Bacteria in Hybrid Anaerobic-Aerobic Reactors with PCR and a Catabolic Gene Probe

    OpenAIRE

    Miguez, Carlos B; Shen, Chun F; Bourque, Denis; Guiot, Serge R; Groleau, Denis

    1999-01-01

    We attempted to mimic in small upflow anaerobic sludge bed (UASB) bioreactors the metabolic association found in nature between methanogens and methanotrophs. UASB bioreactors were inoculated with pure cultures of methanotrophs, and the bioreactors were operated by using continuous low-level oxygenation in order to favor growth and/or survival of methanotrophs. Unlike the reactors in other similar studies, the hybrid anaerobic-aerobic bioreactors which we used were operated synchronously, not...

  17. Preferential cultivation of type II methanotrophic bacteria from littoral sediments (Lake Constance)

    OpenAIRE

    Bussmann, Ingeborg; Pester, Michael; Brune, Andreas; Schink, Bernhard

    2004-01-01

    Most widely used medium for cultivation of methanotrophic bacteria from various environments is that proposed in 1970 by Whittenbury. In order to adapt and optimize medium for culturing of methanotrophs from freshwater sediment, media with varying concentrations of substrates, phosphate, nitrate, and other mineral salts were used to enumerate methanotrophs by the most probable number method. High concentrations (s1 mM) of magnesium and sulfate, and high concentrations of nitrate (s500 WM) sig...

  18. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure

    Science.gov (United States)

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M. B.; Bodelier, Paul L. E.

    2016-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency. PMID:26779148

  19. Recurrence and frequency of disturbance have cumulative effect on methanotrophic activity, abundance, and community structure.

    Directory of Open Access Journals (Sweden)

    Adrian eHo

    2016-01-01

    Full Text Available Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by two-fold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency.

  20. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure.

    Science.gov (United States)

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M B; Bodelier, Paul L E

    2015-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a 'tipping point' where activity no longer recovered if disturbance persists and increase in frequency.

  1. Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

    Science.gov (United States)

    Saidi-Mehrabad, Alireza; He, Zhiguo; Tamas, Ivica; Sharp, Christine E; Brady, Allyson L; Rochman, Fauziah F; Bodrossy, Levente; Abell, Guy CJ; Penner, Tara; Dong, Xiaoli; Sensen, Christoph W; Dunfield, Peter F

    2013-01-01

    We investigated methanotrophic bacteria in slightly alkaline surface water (pH 7.4–8.7) of oilsands tailings ponds in Fort McMurray, Canada. These large lakes (up to 10 km2) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. They are primarily anoxic and produce methane but have an aerobic surface layer. Aerobic methane oxidation was measured in the surface water at rates up to 152 nmol CH4 ml−1 water d−1. Microbial diversity was investigated via pyrotag sequencing of amplified 16S rRNA genes, as well as by analysis of methanotroph-specific pmoA genes using both pyrosequencing and microarray analysis. The predominantly detected methanotroph in surface waters at all sampling times was an uncultured species related to the gammaproteobacterial genus Methylocaldum, although a few other methanotrophs were also detected, including Methylomonas spp. Active species were identified via 13CH4 stable isotope probing (SIP) of DNA, combined with pyrotag sequencing and shotgun metagenomic sequencing of heavy 13C-DNA. The SIP-PCR results demonstrated that the Methylocaldum and Methylomonas spp. actively consumed methane in fresh tailings pond water. Metagenomic analysis of DNA from the heavy SIP fraction verified the PCR-based results and identified additional pmoA genes not detected via PCR. The metagenome indicated that the overall methylotrophic community possessed known pathways for formaldehyde oxidation, carbon fixation and detoxification of nitrogenous compounds but appeared to possess only particulate methane monooxygenase not soluble methane monooxygenase. PMID:23254511

  2. Aquatic plant surface as a niche for methanotrophs

    OpenAIRE

    YasuyoshiSakai; NaokoYoshida; AkioMurakami

    2014-01-01

    This study investigated the potential local CH4 sink in various plant parts as a boundary environment of CH4 emission and consumption. By comparing CH4 consumption activities in cultures inoculated with parts from 39 plant species, we observed significantly higher consumption of CH4 associated with aquatic plants than other emergent plant parts such as woody plant leaves, macrophytic marine algae, and sea grass. In situ activity of CH4 consumption by methanotrophs associated with different s...

  3. Aerobic Methanotrophs in Natural and Agricultural Soils of European Russia

    OpenAIRE

    Irina Kravchenko; Andrey Yurkov; Anna Kizilova

    2013-01-01

    Human activities such as land management and global warming have great impact on the environment. Among changes associated with the global warming, rising methane emission is a serious concern. Therefore, we assessed methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight soil types (both unmanaged and agricultural) distributed across the European part of Russia. Using a culture-independent approach targeting pmoA gene, we provide the first baseline data on the di...

  4. Detection of methanotrophic bacteria in environmental samples with the PCR.

    OpenAIRE

    McDonald, I R; Kenna, E M; Murrell, J.C.

    1995-01-01

    We designed PCR primers by using the DNA sequences of the soluble methane monooxygenase gene clusters of Methylosinus trichosporium OB3b and Methylococcus capsulatus (Bath), and these primers were found to be specific for four of the five structural genes in the soluble methane monooxygenase gene clusters of several methanotrophs. We also designed primers for the gram-negative methylotroph-specific methanol dehydrogenase gene moxF. The specificity of these primers was confirmed by hybridizing...

  5. Aquatic plant surface as a niche for methanotrophs

    OpenAIRE

    Yoshida, Naoko; Iguchi, Hiroyuki; Yurimoto, Hiroya; Murakami, Akio; Sakai, Yasuyoshi

    2014-01-01

    This study investigated the potential local CH4 sink in various plant parts as a boundary environment of CH4 emission and consumption. By comparing CH4 consumption activities in cultures inoculated with parts from 39 plant species, we observed significantly higher consumption of CH4 associated with aquatic plants than other emergent plant parts such as woody plant leaves, macrophytic marine algae, and sea grass. In situ activity of CH4 consumption by methanotrophs associated with different sp...

  6. Widespread methanotrophic primary production in lowland chalk rivers

    OpenAIRE

    Shelley, Felicity; Grey, Jonathan; Trimmer, Mark

    2014-01-01

    Methane is oversaturated relative to the atmosphere in many rivers, yet its cycling and fate is poorly understood. While photosynthesis is the dominant source of autotrophic carbon to rivers, chemosynthesis and particularly methane oxidation could provide alternative sources of primary production where the riverbed is heavily shaded or at depth beneath the sediment surface. Here, we highlight geographically widespread methanotrophic carbon fixation within the gravel riverbeds of over 30 chalk...

  7. Molekularbiologische Untersuchungen zu Funktion und Phylogenie methanotropher Bakterien

    OpenAIRE

    Ricke, Peter

    2005-01-01

    This work focuses on the characterisation of methanotrophic bacteria (MB) by the aid of moleculare and microbiological methods as well as by bioinformatical methods. The results obtain in the course of this study are reported cumulative. The following topics will be reported: 1) Experiments were conducted to determine if a novel pmoA-like gene (pmoA2) recently discovered in the methane-oxidizing bacterium Methylocystis strain SC2 ...

  8. Diversity and Activity of Methanotrophic Bacteria in Different Upland Soils

    OpenAIRE

    Knief, Claudia; Lipski, André; Dunfield, Peter F.

    2003-01-01

    Samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (MB). MB were identified on the basis of the detection and comparative sequence analysis of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. MB commonly detected in soils were closely related to Methylocaldum spp., Methylosinus spp., Methylocystis spp., or the “forest sequence cluste...

  9. Feasibility of atmospheric methane removal using methanotrophic biotrickling filters

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Sukhwan; Carey, Jeffrey N.; Semrau, Jeremy D. [Michigan Univ., Ann Arbor, MI (United States). Dept. of Civil and Environmental Engineering

    2009-07-15

    Methane is a potent greenhouse gas with a global warming potential {proportional_to}23 times that of carbon dioxide. Here, we describe the modeling of a biotrickling filtration system composed of methane-consuming bacteria, i.e., methanotrophs, to assess the utility of these systems in removing methane from the atmosphere. Model results indicate that assuming the global average atmospheric concentration of methane, 1.7 ppmv, methane removal is ineffective using these methanotrophic biofilters as the methane concentration is too low to enable cell survival. If the concentration is increased to 500-6,000 ppmv, however, similar to that found above landfills and in concentrated animal feeding operations (factory farms), 4.98-35.7 tons of methane can be removed per biofilter per year assuming biotrickling filters of typical size (3.66 m in diameter and 11.5 m in height). Using reported ranges of capital, operational, and maintenance costs, the cost of the equivalent ton of CO{sub 2} removal using these systems is $90-$910 ($2,070-$20,900 per ton of methane), depending on the influent concentration of methane and if heating is required. The use of methanotrophic biofilters for controlling methane emissions is technically feasible and, provided that either the costs of biofilter construction and operation are reduced or the value of CO{sub 2} credits is increased, can also be economically attractive. (orig.)

  10. Biological Methanol Production by a Type II Methanotroph Methylocystis bryophila.

    Science.gov (United States)

    Patel, Sanjay K S; Mardina, Primata; Kim, Sang-Yong; Lee, Jung-Kul; Kim, In-Won

    2016-04-28

    Methane (CH₄) is the most abundant component in natural gas. To reduce its harmful environmental effect as a greenhouse gas, CH₄ can be utilized as a low-cost feed for the synthesis of methanol by methanotrophs. In this study, several methanotrophs were examined for their ability to produce methanol from CH₄; including Methylocella silvestris, Methylocystis bryophila, Methyloferula stellata, and Methylomonas methanica. Among these methanotrophs, M. bryophila exhibited the highest methanol production. The optimum process parameters aided in significant enhancement of methanol production up to 4.63 mM. Maximum methanol production was observed at pH 6.8, 30°C, 175 rpm, 100 mM phosphate buffer, 50 mM MgCl₂ as a methanol dehydrogenase inhibitor, 50% CH₄ concentration, 24 h of incubation, and 9 mg of dry cell mass ml(-1) inoculum load, respectively. Optimization of the process parameters, screening of methanol dehydrogenase inhibitors, and supplementation with formate resulted in significant improvements in methanol production using M. bryophila. This report suggests, for the first time, the potential of using M. bryophila for industrial methanol production from CH₄. PMID:26838340

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

    Directory of Open Access Journals (Sweden)

    Sophie R Ullrich

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

  12. A novel acidophile community populating waste ore deposits at an acid mine drainage site

    Institute of Scientific and Technical Information of China (English)

    HAO Chun-bo; ZHANG Hong-xun; BAI Zhi-hui; HU Qing; ZHANG Bao-guo

    2007-01-01

    Waste ore samples (pH 3.0) were collected at an acid mine drainage site in Anhui, China. The present acidophilic microbial community in the waste ore was studied with 16S rRNA gene clone library and denaturing gradient gel electrophoresis (DGGE). Eighteen different clones were identified and affiliated with Actinobacteria, low G + C Gram-positives, Thermomicrobia, Acidobacteria, Proteobacteria, Candidate division TM7, and Planctomycetes. Phylogenetic analysis of 16S rRNA gene sequences revealed a diversity of acidophiles in the samples that were mostly novel. It is unexpected that the moderately thermophilic acidophiles were abundant in the acidic ecosystem and may play a great role in the generation of AMD. The result of DGGE was consistent with that of clone library analysis. These findings help in the better understanding of the generation mechanism of AMD and in developing a more efficient method to control AMD.

  13. Identification of hopanoid, sterol, and tetrahymanol production in the aerobic methanotroph Methylomicrobium alcaliphilum 20Z

    Science.gov (United States)

    Welander, P. V.; Summons, R. E.

    2013-12-01

    Correlating the occurrence of molecular biosignatures preserved in the rock record with specific microbial taxa is a compelling strategy for studying microbial life in the context of the Earth's distant past. Polycyclic triterpenoids, including the hopanes and steranes, comprise classes of biomarkers that are readily detected in a variety of ancient sediments and are clearly recognized as the diagenetic products of modern day bacterial hopanoids and eukaryotic sterols. Thus, based on the distribution of these lipids in extant microbes, the occurrence of their diagenetic products in the rock record is often utilized as evidence for the existence of specific bacterial and eukaryotic taxa in ancient ecosystems. However, questions have arisen about our understanding of the taxonomic distribution of many of these molecular biomarkers in extant microbes. This is prompting reassessments of the use of polycyclic triterpenoids as geological proxies for microbial taxa, especially in the light of the poorly defined issue of microbial diversity. Recently, significant effort has been put forth to better understand the biosynthesis, function, and regulation of these lipid molecules in a variety of modern organisms so that a more informed interpretation of their occurrence in the rock record can be reached. Here we report the unprecedented production of three different classes of polycyclic triterpenoid biomarker lipids in one bacterium. Methylomicrobium alcaliphilum 20Z, a member of the Gammaproteobacteria, is a halotolerant alkaliphilic aerobic methanotroph previously isolated from a moderately saline soda lake in Tuva (Central Asia). In this study, M. alcaliphilum is shown to produce C-3 methylated and unmethylated aminohopanoids commonly associated with other mesophilic aerobic methanotrophs. In addition, this organism is also able to produce 4,4-dimethyl sterols and surprisingly, the gammacerane triterpenoid tetrahymanol. Previously, tetrahymanol production has only been

  14. Acquisition of useful and high ability genes for acidophilic bacteria; Kosansei saikin ni takai noryoku wo fuyosuru idenshi no kakutoku

    Energy Technology Data Exchange (ETDEWEB)

    Senda, T.; Inoue, C.; Shinbori, Y. [Tohoku University, Sendai (Japan)

    1997-02-01

    This effort aims at the development of high-performance bacteria usable in bio-leaching in metal smelting by acquiring genes capable of realizing such. A method is used of choosing some isolated strains exhibiting high-performance traits and acquiring target genes therefrom by use of genetic engineering. Approximately 200 kinds in the aggregate of acidophilic bacteria are currently available for the study, including isolated iron-oxidizing and sulfur-oxidizing bacteria, standard species acquired for the study, and strains previously isolated by the laboratory. The bacteria are tested with respect to their Fe{sup 2+}-oxidizing rates, sulfur-oxidizing capabilities, and strength to withstand inhibiting substances (Ag{sup +}, Cl{sup -}, Mo{sup 6+}, etc.), which results in the nomination of 8 strains. The study planned to follow includes processes involving the extraction of chromosome DNAs from the 8 strains and their refinement, gene cloning by the Southern hybridization method, determination of their base sequences, determination of the difference between the strains in point of gene expression, and investigations of the relations that the results of these processes bear toward the said high-performance traits. Also under way is a study about the infuence-exerting factors revealed during the evaluation of the abilities of acidphlic bacteria. 2 refs., 2 tabs.

  15. Associations of Methanotrophs With the Roots and Rhizomes of Aquatic Vegetation

    Science.gov (United States)

    King, Gary M.

    1994-01-01

    Results of an in vitro assay revealed that root-associated methane consumption was a common attribute or diverse emergent wetland macrophytes from a variety of habitats. Maximum potential uptake rates (V(sub maxp)) varied between about 1 and 10 micro mol g/ (dry weight) h, with no obvious correlation between rate and gross morphological characteristics of the plants. The V(sub maxp) corresponded to about 2 x 10(exp 18) to 2 x 10(exp 9) methanotrophs g/ (dry weight), assuming that root-associated methanotrophs have cell-specific activities comparable to those of known isolates. V(sub maxp) varied seasonally for an aquatic grass, Calamogrostis canadensis, and for the cattail, Typha latifolia, with highest rates in late summer. V(sub maxp) was well correlated with ambient temperature for C. canadensis but weakly correlated for T. Wifolia. The seasonal changes in V(sub maxp), as well as inferences from apparent half-saturation constants for methane uptake (K(sub app); generally 3 to 6 micro M), indicated that oxygen availability might be more important than methane as a rate determinant. In addition, roots incubated under anoxic conditions showed little or no postanoxia aerobic methane consumption, indicating that root-associated metbanotrophic populations might not tolerate variable oxygen availability. Hybridization of oligodeoxynucleotide probes specific for group 1 or group 2 methylotrophs also varied seasonally. The group 2-specific probe consistently hybridized to a greater extent than the group 1 probe, and the relative amount of group 2 probe hybridization to C. canadensis root extracts was positively correlated with V(sub maxp).

  16. The Methanol Dehydrogenase Gene, mxaF, as a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments

    OpenAIRE

    Lau, Evan; Meredith C Fisher; Steudler, Paul A.; Cavanaugh, Colleen Marie

    2013-01-01

    The mxaF gene, coding for the large \\((\\alpha)\\) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mx...

  17. Comparison of Aerobic Methanotrophic Communities in Littoral and Profundal Sediments of Lake Constance by a Molecular Approach▿

    OpenAIRE

    Rahalkar, Monali; Schink, Bernhard

    2007-01-01

    Analysis of pmoA and 16S rRNA gene clone libraries of methanotrophic bacteria in Lake Constance revealed an overall dominance of type I methanotrophs in both littoral and profundal sediments. The sediments exhibited minor differences in their methanotrophic community structures. Type X methanotrophs made up a significant part of the clone libraries only in the profundal sediment and were also found only there as a prominent peak by T-RFLP analyses.

  18. Family- and Genus-Level 16S rRNA-Targeted Oligonucleotide Probes for Ecological Studies of Methanotrophic Bacteria

    OpenAIRE

    J. Gulledge; Ahmad, A; Steudler, P. A.; Pomerantz, W. J.; Cavanaugh, Colleen Marie

    2001-01-01

    Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signature...

  19. [Biosynthesis of secondary metabolites in methanotrophs: biochemical and genetic aspects (review)].

    Science.gov (United States)

    Khmelenina, V N; Rozova, N; But, C Yu; Mustakhimov, I I; Reshetnikov, A S; Beschastnyi, A P; Trotsenko, Yu A

    2015-01-01

    The review summarizes the data on the metabolic potential of methanotrophs as producers of biopolymers, alternative biofuel, bioprotectants, and other secondary metabolites. The work provides the examples of modern 'omic' technologies used for genetic engineering of efficient methanotrophic producers. PMID:26027349

  20. Effect of temperature on denitrifying methanotrophic activity of 'Candidatus Methylomirabilis oxyfera'

    NARCIS (Netherlands)

    Kampman, C.; Piai, L.; Hendrickx, T.L.G.; Temmink, B.G.; Zeeman, G.; Buisman, C.J.N.

    2014-01-01

    The activity of denitrifying methanotrophic bacteria at 11-30 degrees C was assessed in short-term experiments. The aim was to determine the feasibility of applying denitrifying methanotrophic bacteria in low-temperature anaerobic wastewater treatment. This study showed that biomass enriched at 21 d

  1. Acidophilic green alga Pseudochlorella sp. YKT1 accumulates high amount of lipid droplets under a nitrogen-depleted condition at a low-pH.

    Directory of Open Access Journals (Sweden)

    Shunsuke Hirooka

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

  2. Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing

    Directory of Open Access Journals (Sweden)

    Christine eSharp

    2012-08-01

    Full Text Available Genomic analysis of the methanotrophic verrucomicrobium Methylacidiphilum infernorum strain V4 has shown that most pathways conferring its methanotrophic lifestyle are similar to those found in proteobacterial methanotrophs. However, due to the large sequence divergence of its methane monooxygenase-encoding genes (pmo, ‘universal’ pmoA polymerase chain reaction (PCR primers do not target these bacteria. Unlike proteobacterial methanotrophs, Methylacidiphilum fixes carbon autotrophically, and uses methane only for energy generation. As a result, techniques used to detect methanotrophs in the environment such as 13CH4-stable isotope probing (SIP and pmoA-targeted PCR do not detect verrucomicrobial methanotrophs, and they may have been overlooked in previous environmental studies. We developed a modified SIP technique to identify active methanotrophic verrucomicrobia in the environment by labelling with 13CO2 and 13CH4, individually and in combination. Testing the protocol in M. infernorum strain V4 resulted in assimilation of 13CO2 but not 13CH4, verifying its autotrophic lifestyle. To specifically detect methanotrophs (as opposed to other autotrophs via 13CO2-SIP, a quantitative PCR (qPCR assay specific for verrucomicrobial-pmoA genes was developed and used in combination with SIP. Incubation of an acidic, high-temperature geothermal soil with 13CH4 + 12CO2 caused little shift in the density distribution of verrucomicrobial-pmoA genes relative to controls. However, labelling with 13CO2 in combination with 12CH4 or 13CH4 induced a strong shift in the distribution of verrucomicrobial-pmoA genes towards the heavy DNA fractions. The modified SIP technique demonstrated that the primary methanotrophs active in the soil were autotrophs and belonged to the Verrucomicrobia. This is the first demonstration of autotrophic, non-proteobacterial methanotrophy in situ, and provides a tool to detect verrucomicrobial methanotrophs in other ecosystems.

  3. Influence of elevated ozone concentration on methanotrophic bacterial communities in soil under field condition

    Science.gov (United States)

    Huang, Y. Z.; Zhong, M.

    2015-05-01

    The open top chamber (OTC) method was used in combination with real-time quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) techniques in the wheat field to study the influence of different levels of O3 concentrations (ambient air filtered by activated carbons, 40 ppb, 80 ppb and 120 ppb) on the quantity and community structure of methanotrophic bacteria. O3 stress can influence the potential methane oxidation rate (PMOR) and potential methane production rate (PMPR) in the farmland soil. O3 treatment of 40 ppb improved significantly the 16S rRNA gene copy number in the total methanotrophic bacteria pmoA, and type I and type II methanotrophic bacteria in the soil depth of 0-20 cm. When the O3 concentration reached 120 ppb, the 16S rRNA gene copy number in the total methanotrophic bacteria pmoA and type I methanotrophic bacteria decreased significantly as compared to the control treatment in 10-20 cm layer. The 16s rRNA gene copy number of total methanotrophic bacteria pmoA and type I and type II methanotrophic bacteria were influenced by different O3 concentration and soil depth. The T-RFLP analysis indicated that O3 stress influenced significantly the community structure of the methanotrophic bacteria in soil, causing potential threat to the diversity of methanotrophic bacteria. It seems to imply that the rise of O3 concentration could produce an impact on the carbon cycling and the methane emission of the wheat field soil by changing the community structure and diversity of methanotrophic bacteria, which then influences the global climate change.

  4. Spatial patterns of methane oxidation and methanotrophic diversity in landfill cover soils of southern China.

    Science.gov (United States)

    Chi, Zi-Fang; Lu, Wen-Jing; Wang, Hong-Tao

    2015-04-01

    Aerobic CH4 oxidation is an important CH4 sink in landfills. To investigate the distribution and community diversity of methanotrophs and link with soil characteristics and operational parameters (e.g., concentrations of O2, CH4), cover soil samples were collected at different locations and depths from the Mengzi semi-aerobic landfill (SAL) in Yunnan Province of southern China. Specific PCR followed by denaturing gradient gel electrophoresis and realtime PCR were used to examine methanotrophs in the landfill cover soils. The results showed that different locations did harbor distinct methanotroph communities. Methanotrophs were more abundant in areas near the venting pipes because of the higher O2 concentrations. The depth of 20-25 cm, where the ratio of the CH4 to O2 was within the range from 1.3 to 8.6, was more conducive to the growth of CH4-oxidizing bacteria. Type II methanotrophs dominated in all samples compared with Type I methanotrophs, as evidenced by the high ratio of Type II to Type I methanotrophic copy numbers (from 1.76 to 11.60). The total copy numbers of methanotrophs detected were similar to other ecosystems, although the CH4 concentration was much higher in SAL cover soil. Methylobacter and Methylocystis were the most abundant Type I and Type II methanotrophs genera, respectively, in the Mengzi SAL. The results suggested that SALs could provide a special environment with both high concentrations of CH4 and O2 for methanotrophs, especially around the vertical venting pipes. PMID:25341468

  5. Spatial patterns of methane oxidation and methanotrophic diversity in landfill cover soils of southern China.

    Science.gov (United States)

    Chi, Zi-Fang; Lu, Wen-Jing; Wang, Hong-Tao

    2015-04-01

    Aerobic CH4 oxidation is an important CH4 sink in landfills. To investigate the distribution and community diversity of methanotrophs and link with soil characteristics and operational parameters (e.g., concentrations of O2, CH4), cover soil samples were collected at different locations and depths from the Mengzi semi-aerobic landfill (SAL) in Yunnan Province of southern China. Specific PCR followed by denaturing gradient gel electrophoresis and realtime PCR were used to examine methanotrophs in the landfill cover soils. The results showed that different locations did harbor distinct methanotroph communities. Methanotrophs were more abundant in areas near the venting pipes because of the higher O2 concentrations. The depth of 20-25 cm, where the ratio of the CH4 to O2 was within the range from 1.3 to 8.6, was more conducive to the growth of CH4-oxidizing bacteria. Type II methanotrophs dominated in all samples compared with Type I methanotrophs, as evidenced by the high ratio of Type II to Type I methanotrophic copy numbers (from 1.76 to 11.60). The total copy numbers of methanotrophs detected were similar to other ecosystems, although the CH4 concentration was much higher in SAL cover soil. Methylobacter and Methylocystis were the most abundant Type I and Type II methanotrophs genera, respectively, in the Mengzi SAL. The results suggested that SALs could provide a special environment with both high concentrations of CH4 and O2 for methanotrophs, especially around the vertical venting pipes.

  6. Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

    OpenAIRE

    Saidi-Mehrabad, Alireza; He, Zhiguo; Tamas, Ivica; Sharp, Christine E; Brady, Allyson L.; Rochman, Fauziah F.; Bodrossy, Levente; Abell, Guy CJ; Penner, Tara; Dong, Xiaoli; Sensen, Christoph W.; Dunfield, Peter F.

    2012-01-01

    We investigated methanotrophic bacteria in slightly alkaline surface water (pH 7.4–8.7) of oilsands tailings ponds in Fort McMurray, Canada. These large lakes (up to 10 km2) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. They are primarily anoxic and produce methane but have an aerobic surface layer. Aerobic methane oxidation was measured in the surface water at rates up to 152 nmol CH4 ml−1 water d−1. Microbial diversity was investigated via py...

  7. Heavy metal resistance strategies of acidophilic bacteria and their acquisition: importance for biomining and bioremediation.

    Science.gov (United States)

    Navarro, Claudio A; von Bernath, Diego; Jerez, Carlos A

    2013-01-01

    Microbial solubilizing of metals in acid environments is successfully used in industrial bioleaching of ores or biomining to extract metals such as copper, gold, uranium and others. This is done mainly by acidophilic and other microorganisms that mobilize metals and generate acid mine drainage or AMD, causing serious environmental problems. However, bioremediation or removal of the toxic metals from contaminated soils can be achieved by using the specific properties of the acidophilic microorganisms interacting with these elements. These bacteria resist high levels of metals by using a few "canonical" systems such as active efflux or trapping of the metal ions by metal chaperones. Nonetheless, gene duplications, the presence of genomic islands, the existence of additional mechanisms such as passive instruments for pH and cation homeostasis in acidophiles and an inorganic polyphosphate-driven metal resistance mechanism have also been proposed. Horizontal gene transfer in environmental microorganisms present in natural ecosystems is considered to be an important mechanism in their adaptive evolution. This process is carried out by different mobile genetic elements, including genomic islands (GI), which increase the adaptability and versatility of the microorganism. This mini-review also describes the possible role of GIs in metal resistance of some environmental microorganisms of importance in biomining and bioremediation of metal polluted environments such as Thiomonas arsenitoxydans, a moderate acidophilic microorganism, Acidithiobacillus caldus and Acidithiobacillus ferrooxidans strains ATCC 23270 and ATCC 53993, all extreme acidophiles able to tolerate exceptionally high levels of heavy metals. Some of these bacteria contain variable numbers of GIs, most of which code for high numbers of genes related to metal resistance. In some cases there is an apparent correlation between the number of metal resistance genes and the metal tolerance of each of these

  8. Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum.

    Science.gov (United States)

    Oshkin, Igor Y; Belova, Svetlana E; Danilova, Olga V; Miroshnikov, Kirill K; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Liesack, Werner; Dedysh, Svetlana N

    2016-06-01

    Two isolates of aerobic methanotrophic bacteria, strains Sph1T and Sph2, were obtained from cold methane seeps in a floodplain of the river Mukhrinskaya, Irtysh basin, West Siberia. Another morphologically and phenotypically similar methanotroph, strain OZ2, was isolated from a sediment of a subarctic freshwater lake, Archangelsk region, northern Russia. Cells of these three strains were Gram-stain-negative, light-pink-pigmented, non-motile, encapsulated, large cocci that contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme and utilized only methane and methanol. Strains Sph1T, Sph2 and OZ2 were able to grow at a pH range of 4.0-8.9 (optimum at pH 6.0-7.0) and at temperatures between 2 and 36 °C. Although their temperature optimum was at 20-25 °C, these methanotrophs grew well at lower temperatures, down to 4 °C. The major cellular fatty acids were C16 : 1ω5c, C16 : 1ω6c, C16 : 1ω7c, C16 : 1ω8c, C16 : 0 and C14 : 0; the DNA G+C content was 51.4-51.9 mol%. Strains Sph1T, Sph2 and OZ2 displayed nearly identical (99.1-99.7 % similarity) 16S rRNA gene sequences and belonged to the family Methylococcaceae of the class Gammaproteobacteria. The most closely related organism was Methylovulum miyakonense HT12T (96.0-96.5 % 16S rRNA gene sequence similarity and 90 % pmoA sequence similarity). The novel isolates, however, differed from Methylovulum miyakonense HT12T by cell morphology, pigmentation, absence of soluble methane monooxygenase, more active growth at low temperatures, growth over a broader pH range and higher DNA G+C content. On the basis of these differences, we propose a novel species, Methylovulum psychrotolerans sp. nov., to accommodate these methanotrophs. Strain Sph1T (=LMG 29227T=VKM B-3018T) is the type strain. PMID:27031985

  9. Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker

    Directory of Open Access Journals (Sweden)

    Claudia eKnief

    2015-12-01

    Full Text Available Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and –independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing unknown methanotrophic bacteria. This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

  10. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

    Science.gov (United States)

    Knief, Claudia

    2015-01-01

    Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities. PMID:26696968

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

    Science.gov (United States)

    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

  12. Stability of Trifluoromethane in Forest Soils and Methanotrophic Cultures

    Science.gov (United States)

    King, Gary M.

    1997-01-01

    Trifluoromethane (TFM) has been reported as an endproduct of trifluoroacetate degradation under oxic conditions. Although other halomethanes, such as chloroform, methyl bromide, and methyl fluoride, inhibit methane oxidation or are degraded by methanotrophs, the fate of TFM is unknown. TFM had no affect on atmospheric methane consumption when added to forest soils at either 10 ppm or 10,000 ppm. No degradation of TFM was observed at either concentration for incubations of 6 days. Cultures of Methylobacter albus BG8 and Methylosinus trichosporium OB3b grown With and without added copper were also used to assay TFM degradation at 10 10000 ppm levels. TFM did not inhibit methane oxidation under any growth conditions, including those inducing expression of soluble methane monooxygenase, nor was it degraded at measurable rates. In contrast, parallel assays showed that both methyl fluoride and chloroform inhibited methane oxidation in M. trichosporium OB3b. Our results suggest that TFM may be relatively inert with respect to methanotrophic degradition. Although TFM has a negligible ozone depletion potential, it absorbs infrared radiation and has a relatively long atmospheric residence time. Thus, accumulation of TFM in the atmosphere as a consequence of the decomposition of hydrochlorofluorocarbons may have significant unpredicted climate impacts.

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

    Science.gov (United States)

    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

  14. Spatio-temporal Variation of Sediment Methanotrophic Microorganisms in a Large Eutrophic Lake.

    Science.gov (United States)

    Yang, Yuyin; Zhao, Qun; Cui, Yahui; Wang, Yilin; Xie, Shuguang; Liu, Yong

    2016-01-01

    Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the methane emission from lake ecosystems to the atmosphere. However, the distribution of methanotrophic community in shallow and eutrophic lake and its influential factors remain essentially unclear. The present study investigated sediment methanotrophic microorganisms at different sites in eutrophic freshwater Dianchi Lake (China) in two different seasons. The abundance, diversity, and structure of sediment methanotrophic community showed a profound spatial and seasonal variation. The pmoA gene copy number in lake sediments ranged from 8.71 ± 0.49 × 10(4) to 2.09 ± 0.03 × 10(7) copies per gram of dry sediment. Sediment methanotrophic communities were composed of Methylococcus and Methylobacter (type I methanotrophs) and Methylosinus (type II methanotrophs), while type I MOB usually outnumbered type II MOB. Moreover, ammonia nitrogen was found to be a potential determinant of methanotrophic community structure in Dianchi Lake. PMID:26318324

  15. Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate.

    Science.gov (United States)

    Leng, Lingqin; Chang, Jiali; Geng, Kan; Lu, Yahai; Ma, Ke

    2015-07-01

    Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil. PMID:25475784

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  18. 13C-DEPLETED MICROBIAL LIPIDS INDICATE SEASONAL METHANOTROPHIC ACTIVITY IN SHALLOW ESTUARINE SEDIMENTS

    Science.gov (United States)

    Compound specific isotope analysis was combined with phospholipid fatty acid (PLFA) analysis to identify methanotrophic activity in members of the sedimentary microbial community in the Altamaha and Savannah River estuaries in Georgia. 13C-depleted PLFAs indicate methane utilizat...

  19. Evaluation of a Fluorescent Lectin-Based Staining Technique for Some Acidophilic Mining Bacteria

    OpenAIRE

    Fife, Dee Jay; Bruhn, Debby F.; Miller, Karen S.; Stoner, Daphne L.

    2000-01-01

    A fluorescence-labeled wheat germ agglutinin staining technique (R. K. Sizemore et al., Appl. Environ. Microbiol. 56:2245–2247, 1990) was modified and found to be effective for staining gram-positive, acidophilic mining bacteria. Bacteria identified by others as being gram positive through 16S rRNA sequence analyses, yet clustering near the divergence of that group, stained weakly. Gram-negative bacteria did not stain. Background staining of environmental samples was negligible, and pyrite an...

  20. Novel Methanotrophs of the Family Methylococcaceae from Different Geographical Regions and Habitats

    OpenAIRE

    Tajul Islam; Øivind Larsen; Vigdis Torsvik; Lise Øvreås; Hovik Panosyan; Colin Murrell, J; Nils-Kåre Birkeland; Levente Bodrossy

    2015-01-01

    Terrestrial methane seeps and rice paddy fields are important ecosystems in the methane cycle. Methanotrophic bacteria in these ecosystems play a key role in reducing methane emission into the atmosphere. Here, we describe three novel methanotrophs, designated BRS-K6, GFS-K6 and AK-K6, which were recovered from three different habitats in contrasting geographic regions and ecosystems: waterlogged rice-field soil and methane seep pond sediments from Bangladesh; and warm spring sediments from A...

  1. Dry/Wet Cycles Change the Activity and Population Dynamics of Methanotrophs in Rice Field Soil

    OpenAIRE

    Ma, Ke; Conrad, Ralf; Lu, Yahai

    2013-01-01

    The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane ...

  2. Shifts in Identity and Activity of Methanotrophs in Arctic Lake Sediments in Response to Temperature Changes

    OpenAIRE

    He, Ruo; Wooller, Matthew J; Pohlman, John W.; Quensen, John; Tiedje, James M.; Leigh, Mary Beth

    2012-01-01

    Methane (CH4) flux to the atmosphere is mitigated via microbial CH4 oxidation in sediments and water. As arctic temperatures increase, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is important to predicting future CH4 emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), and pyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°...

  3. Soluble methane monooxygenase component B gene probe for identification of methanotrophs that rapidly degrade trichloroethylene.

    OpenAIRE

    Tsien, H C; Hanson, R S

    1992-01-01

    Restriction fragment length polymorphisms, Western blot (immunoblot) analysis, and fluorescence-labelled signature probes were used for the characterization of methanotrophic bacteria as well as for the identification of methanotrophs which contained the soluble methane monooxygenase (MMO) gene and were able to degrade trichloroethylene (TCE). The gene encoding a soluble MMO component B protein from Methylosinus trichosporium OB3b was cloned. It contained a 2.2-kb EcoRI fragment. With this cl...

  4. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure

    OpenAIRE

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M. B.; Bodelier, Paul L. E.

    2016-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here...

  5. Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8

    OpenAIRE

    Kits, K. Dimitri; Campbell, Dustin J.; Rosana, Albert R.; Stein, Lisa Y.

    2015-01-01

    Aerobic methane-oxidizing bacteria (MOB) are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic MOB and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated meth...

  6. Independent phylogenetic origins of methanotrophic and chemoautotrophic bacterial endosymbioses in marine bivalves

    OpenAIRE

    Distel, D L; Cavanaugh, Colleen Marie

    1994-01-01

    The discovery of bacterium-bivalve symbioses capable of utilizing methane as a carbon and energy source indicates that the endosymbionts of hydrothermal vent and cold seep bivalves are not restricted to sulfur-oxidizing chemoautotrophic bacteria but also include methanotrophic bacteria. The phylogenetic origin of methanotrophic endosymbionts and their relationship to known symbiotic and free-living bacteria, however, have remained unexplored. In situ localization and phylogenetic analysis of ...

  7. Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z

    OpenAIRE

    Vuilleumier, Stéphane; Khmelenina, Valentina N; Bringel, Françoise; Reshetnikov, Alexandr S.; Lajus, Aurélie; Mangenot, Sophie; Rouy, Zoé; Op Den Camp, Huub J M; Jetten, Mike S. M.; DiSpirito, Alan A.; Dunfield, Peter; Klotz, Martin G.; Semrau, Jeremy D.; Stein, Lisa Y.; Barbe, Valérie

    2012-01-01

    Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic...

  8. Methanotrophic bacteria and the impact of soil physical conditions on their activity

    OpenAIRE

    Rożej A.; Stępniewski W.

    2000-01-01

    Occurrence of methane in the soil is accompanied by the development of methanotrophic microorganisms with structural and functional adaptation to its oxidation. Methanotrophs, microaerophilic organisms which are widely spread in aerobic soils and sediments, oxidise methane to derive energy and carbon for biomass production. Thus, they play an important role in reducing methane emission from the soil to atmosphere. Several physico-chemical factors influence the rate of methane oxidation in the...

  9. Viable methanotrophic bacteria enriched from air and rain can oxidize methane at cloud-like conditions

    OpenAIRE

    Finster, Kai; Hansen, Bjarne Munk; Karlson, Ulrich Gosewinkel; Šantl Temkiv, Tina; Pašić, Lejla

    2015-01-01

    Atmospheric methane is degraded by both photooxidation and, in topsoils, by methanotrophic bacteria, but this may not totally account for the global sink of this greenhouse gas. Topsoils are a prominent source of airborne bacteria, which can degrade some organic atmospheric compounds at rates similar to photooxidation. Although airborne methanotrophs would have direct access to atmospheric methane, their presence and activity in the atmosphere has not been investigated so far. We enriched air...

  10. Identification of methanotrophic lipid biomarkers in cold-seep mussel gills: chemical and isotopic analysis.

    OpenAIRE

    Jahnke, L L; Summons, R E; Dowling, L M; Zahiralis, K D

    1995-01-01

    A lipid analysis of the tissues of a cold-seep mytilid mussel collected from the Louisiana slope of the Gulf of Mexico was used in conjunction with a compound-specific isotope analysis to demonstrate the presence of methanotrophic symbionts in the mussel gill tissue and to demonstrate the host's dependence on bacterially synthesized metabolic intermediates. The gill tissue contained large amounts of group-specific methanotrophic biomarkers, bacteriohopanoids, 4-methylsterols, lipopolysacchar...

  11. Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

    OpenAIRE

    Hoefman, Sven; van der Ha, David; Boon, Nico; Vandamme, Peter; de Vos, Paul; Heylen, Kim

    2014-01-01

    Background: The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed...

  12. Survival and Recovery of Methanotrophic Bacteria Starved under Oxic and Anoxic Conditions †

    OpenAIRE

    Roslev, Peter; King, Gary M.

    1994-01-01

    The effects of carbon deprivation on survival of methanotrophic bacteria were compared in cultures incubated in the presence and absence of oxygen in the starvation medium. Survival and recovery of the examined methanotrophs were generally highest for cultures starved under anoxic conditions as indicated by poststarvation measurements of methane oxidation, tetrazolium salt reduction, plate counts, and protein synthesis. Methylosinus trichosporium OB3b survived up to 6 weeks of carbon deprivat...

  13. Bioreactor performance parameters for an industrially-promising methanotroph Methylomicrobium buryatense 5GB1

    OpenAIRE

    Gilman, Alexey; Laurens, Lieve M.; Puri, Aaron W.; Chu, Frances; Philip T. Pienkos; Lidstrom, Mary E.

    2015-01-01

    Background Methane is a feedstock of interest for the future, both from natural gas and from renewable biogas sources. Methanotrophic bacteria have the potential to enable commercial methane bioconversion to value-added products such as fuels and chemicals. A strain of interest for such applications is Methylomicrobium buryatense 5GB1, due to its robust growth characteristics. However, to take advantage of the potential of this methanotroph, it is important to generate comprehensive bioreacto...

  14. Influence of light intensity on methanotrophic bacterial activity in Petit Saut Reservoir, French Guiana.

    Science.gov (United States)

    Dumestre, J F; Guézennec, J; Galy-Lacaux, C; Delmas, R; Richard, S; Labroue, L

    1999-02-01

    One year after impoundment in January 1994, methanotrophic bacteria in Petit Saut Reservoir (French Guiana) were active at the oxic-anoxic interface. This activity was revealed by the sudden extinction of diffusive methane emission (600 metric tons of CH4. day-1 for the whole lake surface area, i.e., 360 km2). Lifting of inhibition was suspected. After reviewing the potential inhibitors of this physiological guild (O2, NH4+, sulfides) and considering the similarities with nitrifiers, we suggest that sunlight influenced the methanotrophic bacteria. On the basis of phospholipid analysis, only a type II methanotrophic community was identified in the lake. Both growth and methanotrophic activity of an enriched culture, obtained in the laboratory, were largely inhibited by illumination over 150 microeinsteins. m-2. s-1. These results were confirmed on a pure culture of Methylosinus trichosporium OB3B. In situ conditions showed that water transparency was quite stable in 1994 and 1995 and that the oxycline moved steadily deeper until January 1995. Considering the mean illumination profile during this period, we showed that removal of methanotrophic growth inhibition could only occur below a 2-m depth. The oxycline reached this level in October 1994, allowing methanotrophic bacteria to develop and to consume the entire methane emission 4 months later.

  15. Methanotrophic community structure of aged refuse and its capability for methane bio-oxidation

    Institute of Scientific and Technical Information of China (English)

    Juan Mei; Li Wang; Dan Han; Youcai Zhao

    2011-01-01

    Aged refuse from waste landfills closed for eight years was examined and found to contain rich methanotrophs capable of biooxidation for methane.Specially, community structure and methane oxidation capability of methanotrophs in the aged refuse were studied.The amount of methanotrophs ranged 61.97×103-632.91×103 cells/g (in dry basis) in aged refuse from Shanghai Laogang Landfill.Type Ⅰ and Ⅱ methanotrophs were found in the aged refuse in the presence of sterilized sewage sludge and only TypeⅠ methanotrophs were detected in the presence of nitrate minimal salt medium (NMS).The clone sequences of the pmoA gene obtained from the aged refuse were similar to the pmoA gene of Methylobacter, Methylocaldum, and Methylocystis, and two clones were distinct with known genera of Type Ⅰ methanotrophs according to phylogenetic analysis.Aged refuse enriched with NMS was used for methane biological oxidation and over 93% conversions were obtained.

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

    Science.gov (United States)

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

    2016-01-01

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

  17. Assessing the Efficacy of the Aerobic Methanotrophic Biofilter in Methane Hydrate Environments

    Energy Technology Data Exchange (ETDEWEB)

    Valentine, David

    2012-09-30

    In October 2008 the University of California at Santa Barbara (UCSB) initiated investigations of water column methane oxidation in methane hydrate environments, through a project funded by the National Energy Technology Laboratory (NETL) entitled: assessing the efficacy of the aerobic methanotrophic biofilter in methane hydrate environments. This Final Report describes the scientific advances and discoveries made under this award as well as the importance of these discoveries in the broader context of the research area. Benthic microbial mats inhabit the sea floor in areas where reduced chemicals such as sulfide reach the more oxidizing water that overlies the sediment. We set out to investigate the role that methanotrophs play in such mats at locations where methane reaches the sea floor along with sulfide. Mats were sampled from several seep environments and multiple sets were grown in-situ at a hydrocarbon seep in the Santa Barbara Basin. Mats grown in-situ were returned to the laboratory and used to perform stable isotope probing experiments in which they were treated with 13C-enriched methane. The microbial community was analyzed, demonstrating that three or more microbial groups became enriched in methane?s carbon: methanotrophs that presumably utilize methane directly, methylotrophs that presumably consume methanol excreted by the methanotrophs, and sulfide oxidizers that presumably consume carbon dioxide released by the methanotrophs and methylotrophs. Methanotrophs reached high relative abundance in mats grown on methane, but other bacterial processes include sulfide oxidation appeared to dominate mats, indicating that methanotrophy is not a dominant process in sustaining these benthic mats, but rather a secondary function modulated by methane availability. Methane that escapes the sediment in the deep ocean typically dissolved into the overlying water where it is available to methanotrophic bacteria. We set out to better understand the efficacy of this

  18. Effects of Nitrogen Load on the Function and Diversity of Methanotrophs in the Littoral Wetland of a Boreal Lake

    OpenAIRE

    HenriMPSiljanen; LeventeBodrossy

    2012-01-01

    Methane is the second most abundant greenhouse gas in the atmosphere. A major part of the total methane emissions from lake ecosystems are emitted from littoral wetlands. Methane emissions are significantly reduced by methanotrophs as they use methane as the sole energy and carbon source. Function of methanotrophs can be either activated or suppressed by nitrogen. However, the effects of nitrogen on methanotrophs in littoral wetlands are unknown. Here we report how nitrogen loading in situ af...

  19. Quantitative Detection of Methanotrophs in Soil by Novel pmoA-Targeted Real-Time PCR Assays

    OpenAIRE

    Kolb, Steffen; Knief, Claudia; Stubner, Stephan; Conrad, Ralf

    2003-01-01

    Methane oxidation in soils is mostly accomplished by methanotrophic bacteria. Little is known about the abundance of methanotrophs in soils, since quantification by cultivation and microscopic techniques is cumbersome. Comparison of 16S ribosomal DNA and pmoA (α subunit of the particulate methane monooxygenase) phylogenetic trees showed good correlation and revealed five distinct groups of methanotrophs within the α and γ subclasses of Proteobacteria: the Methylococcus group, the Methylobacte...

  20. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments

    Science.gov (United States)

    He, Ruo; Wooller, Matthew J.; Pohlman, John W.; Quensen, John; Tiedje, James M.; Leigh, Mary Beth

    2012-01-01

    Methane (CH4) emitted from high-latitude lakes accounts for 2–6% of the global atmospheric CH4 budget. Methanotrophs in lake sediments and water columns mitigate the amount of CH4 that enters the atmosphere, yet their identity and activity in arctic and subarctic lakes are poorly understood. We used stable isotope probing (SIP), quantitative PCR (Q-PCR), pyrosequencing and enrichment cultures to determine the identity and diversity of active aerobic methanotrophs in the water columns and sediments (0–25 cm) from an arctic tundra lake (Lake Qalluuraq) on the north slope of Alaska and a subarctic taiga lake (Lake Killarney) in Alaska's interior. The water column CH4 oxidation potential for these shallow (~2m deep) lakes was greatest in hypoxic bottom water from the subarctic lake. The type II methanotroph, Methylocystis, was prevalent in enrichment cultures of planktonic methanotrophs from the water columns. In the sediments, type I methanotrophs (Methylobacter, Methylosoma and Methylomonas) at the sediment-water interface (0–1 cm) were most active in assimilating CH4, whereas the type I methanotroph Methylobacter and/or type II methanotroph Methylocystis contributed substantially to carbon acquisition in the deeper (15–20 cm) sediments. In addition to methanotrophs, an unexpectedly high abundance of methylotrophs also actively utilized CH4-derived carbon. This study provides new insight into the identity and activity of methanotrophs in the sediments and water from high-latitude lakes.

  1. Evaluation of in-situ methanotrophic bioremediation for contaminated groundwater, St. Joseph, Michigan. Final report, January 1989-December 1989

    International Nuclear Information System (INIS)

    A feasibility study of utilizing indigenous bacteria that use methane as a source of cell carbon and energy (methanotrophs) for in-situ bioremediation of groundwater contaminants at the St. Joseph site is summarized. The contaminants, compounds, can be biotransformed by methanotrophic bacteria, which are found in some locations of the site in adequate populations. The process involves stimulating the growth of native populations of methanotrophs by injecting water containing dissolved methane and oxygen into the aquifer. The stimulated population of methanotrophs in turn has the capability to degrade trichloroethylene, 1,2-cis-dichloroethylene, 1,2-trans-dichloroethylene, and vinyl chloride

  2. Characterization of methanotrophic bacterial populations in natural and agricultural aerobic soils of the European Russia

    Science.gov (United States)

    Kravchenko, Irina; Sukhacheva, Marina; Kizilova, Anna

    2014-05-01

    Atmospheric methane contributes to about 20% of the total radiative forcing by long-lived greenhouse gases, and microbial methane oxidation in upland soils is the only biological sink of methane. Microbial methane oxidation in aerated upland soils is estimated as 15 - 45 Tg yr-1 or 3-9% of the annual sink. Therefore there is need of extensive research to characterize methanotrophic activity in various ecosystems for possible application to reduce atmospheric methane fluxes and to minimize global climate change. The vast majority of known aerobic methanotrophs belongs to the Proteobacteria and placed in the families Methylococcaceae in the Gammaproteobacteria, and Methylocystaceae and Beijerinckiaceae in the Alphaproteobacteria. Known exceptions include the phylum Verrucomicrobia and uncultured methanotrophs such as Candidatus 'Methylomirabilis oxyfera' affiliated with the 'NC10' phylum. Plenty of studies of aerobic methane oxidation and key players of the process have been performed on various types of soils, and it was found that Methylocystis spp and uncultivated methanotrophs are abundant in upland soils. Two of the uncultured groups are upland soil cluster alphaproteobacteria (USCa) and gammaproteobacteria (USCg), as revealed by cultivation-independent surveys of pmoA diversity. Russia is extremely rich in soil types due to its vast territories, and most of these soils have never been investigated from the aspect of methanotrophy. This study addresses methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight types of natural aerobic soils, four of which also had been under agricultural use. Methane fluxes have been measured by in situ static chamber method and methane oxidation rates in soil samples - by radioisotope tracer (14CH4) technique. Changes in methanotroph diversity and abundance were assessed by cloning and Sanger sequencing, and quantitative real-time PCR of pmoA genes. Methanotrophic population of unmanaged soils turned

  3. Isolation and characterization of organisms growing with methane only

    International Nuclear Information System (INIS)

    More than 20 obligate methane utilizing bacteria were isolated from local soil following shake flask enrichment and continuous subculture technique isolation of methanotrophs proved to the difficult and slow. All isolates were gram negative, strictly aerobic, use methane as their sole carbon and energy source, unable to grow on nutrient media and can use nitrate as N source. Some isolates were motile. Few were able to utilize methanol. All the tested soil samples contained methane utilizing organisms. (author)

  4. Single cell activity reveals direct electron transfer in methanotrophic consortia

    Science.gov (United States)

    McGlynn, Shawn E.; Chadwick, Grayson L.; Kempes, Christopher P.; Orphan, Victoria J.

    2015-10-01

    Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.

  5. Sucrose metabolism in halotolerant methanotroph Methylomicrobium alcaliphilum 20Z.

    Science.gov (United States)

    But, Sergey Y; Khmelenina, Valentina N; Reshetnikov, Alexander S; Mustakhimov, Ildar I; Kalyuzhnaya, Marina G; Trotsenko, Yuri A

    2015-04-01

    Sucrose accumulation has been observed in some methylotrophic bacteria utilizing methane, methanol, or methylated amines as a carbon and energy source. In this work, we have investigated the biochemical pathways for sucrose metabolism in the model halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. The genes encoding sucrose-phosphate synthase (Sps), sucrose-phosphate phosphatase (Spp), fructokinase (FruK), and amylosucrase (Ams) were co-transcribed and displayed similar expression levels. Functional Spp and Ams were purified after heterologous expression in Escherichia coli. Recombinant Spp exhibited high affinity for sucrose-6-phosphate and stayed active at very high levels of sucrose (K i  = 1.0 ± 0.6 M). The recombinant amylosucrase obeyed the classical Michaelis-Menten kinetics in the reactions of sucrose hydrolysis and transglycosylation. As a result, the complete metabolic network for sucrose biosynthesis and re-utilization in the non-phototrophic organism was reconstructed for the first time. Comparative genomic studies revealed analogous gene clusters in various Proteobacteria, thus indicating that the ability to produce and metabolize sucrose is widespread among prokaryotes.

  6. Enhanced bioleaching on attachment of indigenous acidophilic bacteria to pyrite surface

    Science.gov (United States)

    Wi, D. W.; Cho, K. H.; Kim, B. J.; Choi, N. C.; Park, C. Y.

    2012-04-01

    In recent years, bioleaching has been widely applied on an industrial scale due to the advantages of low cost and environment friendliness. The direct contact mechanism of bioleaching assumes the action of a metal sulfide-attached cell oxidizing the mineral by an enzyme system with oxygen to sulfate and metal cations. Fundamental surface properties of sulfide particles and leaching-bacteria in bioleaching play the key role in the efficiency of this process. The aim of this work is to investigate of direct contact bioleaching mechanism on pyrite through attachment properties between indigenous acidophilic bacteria and pyrite surfaces. The bacteria were obtained from sulfur hot springs, Hatchobaru thermal electricity plant in Japan. And pyrite was collected from mine waste from Gwang-yang abandoned gold mines, Korea. In XRD analyses of the pyrite, x-ray diffracted d-value belong to pyrite was observed. The indigenous acidophilic bacteria grew well in a solution and over the course of incubation pH decreased and Eh increased. In relation to a bacterial growth-curve, the lag phase was hardly shown while the exponential phase was very fast. Bioleaching experiment result was showed that twenty days after the indigenous acidophilic bacteria were inoculated to a pyrite-leaching medium, the bacterial sample had a greater concentration of Fe and Zn than within the control sample. In SEM-EDS analyses, rod-shaped bacteria and round-shaped microbes were well attached to the surface of pyrite. The size of the rod-shaped bacteria ranged from 1.05~1.10 ? to 4.01~5.38 ?. Round-shaped microbes were more than 3.0 ? in diameter. Paired cells of rod-shaped bacteria were attached to the surface of pyrite linearly.

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

    Science.gov (United States)

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

    2014-02-01

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

  8. Aerobic Vinyl Chloride Metabolism in Groundwater Microcosms by Methanotrophic and Etheneotrophic Bacteria.

    Science.gov (United States)

    Findlay, Margaret; Smoler, Donna F; Fogel, Samuel; Mattes, Timothy E

    2016-04-01

    Vinyl chloride (VC) is a carcinogen generated in groundwater by reductive dechlorination of chloroethenes. Under aerobic conditions, etheneotrophs oxidize ethene and VC, while VC-assimilators can use VC as their sole source of carbon and energy. Methanotrophs utilize only methane but can oxidize ethene to epoxyethane and VC to chlorooxirane. Microcosms were constructed with groundwater from the Carver site in MA containing these three native microbial types. Methane, ethene, and VC were added to the microcosms singly or as mixtures. In the absence of VC, ethene degraded faster when methane was also present. We hypothesized that methanotroph oxidation of ethene to epoxyethane competed with their use of methane, and that epoxyethane stimulated the activity of starved etheneotrophs by inducing the enzyme alkene monooxygenase. We then developed separate enrichment cultures of Carver methanotrophs and etheneotrophs, and demonstrated that Carver methanotrophs can oxidize ethene to epoxyethane, and that starved Carver etheneotrophs exhibit significantly reduced lag time for ethene utilization when epoxyethane is added. In our groundwater microcosm tests, when all three substrates were present, the rate of VC removal was faster than with either methane or ethene alone, consistent with the idea that methanotrophs stimulate etheneotroph destruction of VC. PMID:26918370

  9. Top-down control of methanotrophs regulates methane concentrations in a small humic lake

    Science.gov (United States)

    Saarenheimo, Jatta; Devlin, Shawn; Syväranta, Jari; Tiirola, Marja; Jones, Roger

    2014-05-01

    Many boreal lakes are known to be significant sources of methane (CH4), as methane production in anaerobic layers of boreal stratified lakes often exceeds oxidation of methane by methanotrophs, leading to methane fluxes to the atmosphere. In order to investigate whether trophic interactions control methanotrophy via regulation of bacterial community dynamics, we experimentally divided a small, humic, and fishless lake with high zooplankton abundance into two treatment basins. We then established either a) equal biomass of juvenile (12 cm) European perch (Perca fluviatilis) or b) adult fish and no fish in the two basins. We hypothesized that differences in predator presence and size would result in cascading trophic interactions, altering the abundance of zooplankton (Daphnia sp.) which are known to graze methanotrophic bacteria. Concurrently with zooplankton abundance and methane concentration measurements, methanotrophic bacterial abundance was assessed by quantitative PCR by targeting specific functional genes (pmoA). Fish presence, regardless of size, exerted high grazing pressure on zooplankton dramatically reducing their biomass. This shift in zooplankton density resulted in corresponding changes in methanotrophic bacterial abundance. We found a clear difference between epilimnetic methane concentrations for each treatment during the experiment, whereas the hypolimnetic methane concentrations showed no differences. The observed variation in epilimnetic methane concentrations was clearly linked to methanotrophic abundance/activity, which, in turn, was regulated by Daphnia biomass. This illustrates that cascading trophic interactions can be important regulators of methane concentration in stratified humic lakes and that previously unrelated ecological properties, fish abundance and atmospheric greenhouse gas concentrations, appear to be linked.

  10. Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8

    Science.gov (United States)

    Kits, K. Dimitri; Campbell, Dustin J.; Rosana, Albert R.; Stein, Lisa Y.

    2015-01-01

    Aerobic methane-oxidizing bacteria (MOB) are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic MOB and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated methanotrophs; however, the physiological pathways that allow some strains to transform nitrite, expression of gene inventories, as well as the electron sources that support this activity remain largely uncharacterized. Here we show that Methylomicrobium album strain BG8 utilizes methane, methanol, formaldehyde, formate, ethane, ethanol, and ammonia to support denitrification activity under hypoxia only in the presence of nitrite. We also demonstrate that transcript abundance of putative denitrification genes, nirS and one of two norB genes, increased in response to nitrite. Furthermore, we found that transcript abundance of pxmA, encoding the alpha subunit of a putative copper-containing monooxygenase, increased in response to both nitrite and hypoxia. Our results suggest that expression of denitrification genes, found widely within genomes of aerobic methanotrophs, allow the coupling of substrate oxidation to the reduction of nitrogen oxide terminal electron acceptors under oxygen limitation. The present study expands current knowledge of the metabolic flexibility of methanotrophs by revealing that a diverse array of electron donors support nitrite reduction to nitrous oxide under hypoxia. PMID:26500622

  11. Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

    Science.gov (United States)

    Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

    2011-10-01

    Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. PMID:23761342

  12. Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8

    Directory of Open Access Journals (Sweden)

    K. Dimitri eKits

    2015-10-01

    Full Text Available Aerobic methane-oxidizing bacteria are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic methane-oxidizing bacteria and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated methanotrophs; however, the physiological pathways that allow some strains to transform nitrite, expression of gene inventories, as well as the electron sources that support this activity remain largely uncharacterized. Here we show that M. album strain BG8 utilizes methane, methanol, formaldehyde, formate, ethane, ethanol and ammonia to support denitrification activity under hypoxia only in the presence of nitrite. We also demonstrate that transcript abundance of putative denitrification genes, nirS and one of two norB genes, increased in response to nitrite. Furthermore, we found that transcript abundance of pxmA, encoding the alpha subunit of a putative copper-containing monooxygenase, increased in response to both nitrite and hypoxia. Our results suggest that expression of denitrification genes, found widely within genomes of aerobic methanotrophs, allow the coupling of substrate oxidation to the reduction of nitrogen oxide terminal electron acceptors under oxygen limitation. The present study expands current knowledge of the metabolic flexibility of methanotrophs by revealing that a diverse array of electron donors support nitrite reduction to nitrous oxide under hypoxia.

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

    Science.gov (United States)

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

    2008-05-01

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

  14. Transfer of IncP Plasmids to Extremely Acidophilic Thiobacillus thiooxidans

    OpenAIRE

    Jin, S. M.; Yan, W. M.; Wang, Z. N.

    1992-01-01

    The broad-host-range IncP plasmids RP4, R68.45, RP1::Tn501, and and pUB307 were transferred directly to extremely acidophilic Thiobacillus thiooxidans from Escherichia coli by conjugation at frequencies of 10-5 to 10-7 per recipient. The ability of T. thiooxidans to receive and express the antibiotic resistance markers was examined. The plasmid RP4 was transferred back to E. coli from T. thiooxidans at a frequency of 1.0 × 10-3 per recipient.

  15. Transfer of IncP Plasmids to Extremely Acidophilic Thiobacillus thiooxidans.

    Science.gov (United States)

    Jin, S M; Yan, W M; Wang, Z N

    1992-01-01

    The broad-host-range IncP plasmids RP4, R68.45, RP1::Tn501, and and pUB307 were transferred directly to extremely acidophilic Thiobacillus thiooxidans from Escherichia coli by conjugation at frequencies of 10 to 10 per recipient. The ability of T. thiooxidans to receive and express the antibiotic resistance markers was examined. The plasmid RP4 was transferred back to E. coli from T. thiooxidans at a frequency of 1.0 x 10 per recipient.

  16. Effects of nitrogen load on the function and diversity of methanotrophs in the littoral wetland of a boreal lake

    Directory of Open Access Journals (Sweden)

    Henri MP Siljanen

    2012-02-01

    Full Text Available Methane is the second most abundant greenhouse gas in the atmosphere. A major part of the total methane emissions from lake ecosystems are emitted from littoral wetlands. Methane emissions are significantly reduced by methanotrophs as they use methane as the sole energy and carbon source. Function of methanotrophs can be either activated or suppressed by nitrogen. However, the effects of nitrogen on methanotrophs in littoral wetlands are unknown. Here we report how nitrogen loading in situ affected the function and diversity of methanotrophs in a littoral wetland. Methanotrophic community composition and functional diversity were analyzed with particulate methane monooxygenase (pmoA gene targeted microarray. Nitrogen load had no effects on methane oxidation potential and methane fluxes. Nitrogen load activated pmoA gene transcription of type I (Methylobacter, Methylomonas and LW21-freshwater phylotypes methanotrophs, but decreased the relative abundance of type II (Methylocystis, Methylosinus trichosporium and Methylosinus phylotypes methanotrophs. Hence, the overall activity of a methanotroph community in littoral wetlands is unlikely to be affected by nitrogen leached from the catchment area.

  17. Sensitivity of methanotrophic community structure, abundance, and gene expression to CH4 and O2 in simulated landfill biocover soil

    International Nuclear Information System (INIS)

    Pressure on mitigating CH4 emission in landfill requires better understanding of methanotrophs in landfill biocovers. Most previous studies focused on CH4 as the sole substrate. This study aims to understand the sensitivity of methanotrophs to both substrates CH4 and O2 concentrations in landfill biocovers. The estimated CH4 oxidation rates (4.66–98.7 × 10−16 mol cell−1 h−1) were evidently higher than the previous reports, suggesting that activity of methanotrophs was enhanced with both the increasing of O2 and CH4 concentrations. Denaturing gradient gel electrophoresis based on the amplification of pmoA genes suggested that methanotrophs were more sensitive to CH4 than O2. Quantification of methanotrophs using pmoA- and mmoX-targeted real-time polymerase chain reaction showed that Mbac and Mcoc as well as Mcys groups were significantly dominant. Mbac group with pmoA gene transcription was dominant. Results indicate that CH4 mitigation would have higher potential by increasing O2 at appropriate CH4 concentrations. -- Highlights: • Both CH4 and O2 as substrates of methanotrophs is the first to be taken account. • Increasing either CH4 or O2 would enhance activity of methanotrophs. • Methanotrophs are more sensitive to CH4 than O2. • CH4 mitigation have higher potential by controlling O2 and CH4 concentrations. -- The present paper is the first to take account of both CH4 and O2 as substrates of methanotrophs and further investigated methanotrophic community in landfill covers

  18. Survival and Recovery of Methanotrophic Bacteria Starved Under Oxic and Anoxic Conditions

    Science.gov (United States)

    Roslev, Peter; King, Gary M.

    1994-01-01

    The effects of carbon deprivation on survival of methanotrophic bacteria were compared in cultures incubated in the presence and absence of oxygen in the starvation medium. Survival and recovery of the examined methanotrophs were generally highest for cultures starved under anoxic conditions as indicated by poststarvation measurements of methane oxidation, tetrazolium salt reduction, plate counts, and protein synthesis. Methylosinus trichosporium OB3b survived up to 6 weeks of carbon deprivation under anoxic conditions while maintaining a physiological state that allowed relatively rapid (hours) methane oxidation after substrate addition. A small fraction of cells starved under oxic and anoxic conditions (4 and 10%, respectively) survived more than 10 weeks but required several days for recovery on plates and in liquid medium. A non-spore-forming methanotroph, strain WP 12, displayed 36 to 118% of its initial methane oxidation capacity after 5 days of carbon deprivation. Oxidation rates varied with growth history prior to the experiments as well as with starvation conditions. Strain WP 12 starved under anoxic conditions showed up to 90% higher methane oxidation activity and 46% higher protein production after starvation than did cultures starved under oxic conditions. Only minor changes in biomass and niorpholow were seen for methanotrophic bacteria starved tinder anoxic conditions. In contrast, starvation under oxic conditions resulted in morphology changes and an initial 28 to 35% loss of cell protein. These data suggest that methanotrophic bacteria can survin,e carbon deprivation under anoxic conditions by using maintenance energy derived Solelyr from an anaerobic endogenous metabolism. This capability could partly explain a significant potential for methane oxidation in environments not continuously, supporting aerobic methanotrophic growth.

  19. Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes

    Science.gov (United States)

    He, Ruo; Wooller, Matthew J.; Pohlman, John W.; Quensen, John; Tiedje, James M.; Leigh, Mary Beth

    2012-01-01

    Methane (CH4) flux to the atmosphere is mitigated via microbial CH4 oxidation in sediments and water. As arctic temperaturesincrease, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is importantto predicting future CH4 emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), andpyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°C,and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH4 oxidation activitywas measured in microcosm incubations containing sediments at all temperatures, with the highest CH4 oxidation potential of37.5 mol g1 day1 in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and ofthe 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in 13C-labeled DNA obtained bySIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisitionfrom CH4 in the sediments. The identity and relative abundance of active methanotrophs differed with the incubation temperature.Methylotrophs were also abundant in the microbial community that derived carbon from CH4, especially in the deeper sediments(depth, 15 to 20 cm) at low temperatures (4°C and 10°C), and showed a good linear relationship (R0.82) with the relativeabundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophiccommunities in arctic lake sediments respond to temperature variations.

  20. Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity.

    Science.gov (United States)

    Cébron, Aurélie; Bodrossy, Levente; Stralis-Pavese, Nancy; Singer, Andrew C; Thompson, Ian P; Prosser, James I; Murrell, J Colin

    2007-02-01

    Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating 13C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient 13C into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of 13CH4 with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in non-amended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of 13CH4 was slow and some cross-feeding of 13C occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of 13CH4, resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of 13C into active methanotrophs while avoiding the cross-feeding of 13C.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, Debaraj [Mineral and Material Processing Division, Korea Institute of Geosciences and Mineral Resources, Daejeon 305-350 (Korea, Republic of); Department of Microbiology, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Kim, Dong J. [Mineral and Material Processing Division, Korea Institute of Geosciences and Mineral Resources, Daejeon 305-350 (Korea, Republic of)], E-mail: djkim@kigam.re.kr; Ralph, David E. [AJ Parker CRC for Hydrometallurgy, Murdoch University, South Street Murdoch, Perth 6153 (Australia); Ahn, Jong G. [Mineral and Material Processing Division, Korea Institute of Geosciences and Mineral Resources, Daejeon 305-350 (Korea, Republic of); Rhee, Young H. [Department of Microbiology, Chungnam National University, Daejeon 305-764 (Korea, Republic of)

    2008-04-15

    Bioleaching of metals from hazardous spent hydro-processing catalysts was attempted in the second stage after growing the bacteria with sulfur in the first stage. The first stage involved transformation of elemental sulfur particles to sulfuric acid through an oxidation process by acidophilic bacteria. In the second stage, the acidic medium was utilized for the leaching process. Nickel, vanadium and molybdenum contained within spent catalyst were leached from the solid materials to liquid medium by the action of sulfuric acid that was produced by acidophilic leaching bacteria. Experiments were conducted varying the reaction time, amount of spent catalysts, amount of elemental sulfur and temperature. At 50 g/L spent catalyst concentration and 20 g/L elemental sulfur, 88.3% Ni, 46.3% Mo, and 94.8% V were recovered after 7 days. Chemical leaching with commercial sulfuric acid of the similar amount that produced by bacteria was compared. Thermodynamic parameters were calculated and the nature of reaction was found to be exothermic. Leaching kinetics of the metals was represented by different reaction kinetic equations, however, only diffusion controlled model showed the best correlation here. During the whole process Mo showed low dissolution because of substantiate precipitation with leach residues as MoO{sub 3}. Bioleach residues were characterized by EDX and XRD.

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

    International Nuclear Information System (INIS)

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

  3. Group-specific quantification of methanotrophs in landfill gas-purged laboratory biofilters by tyramide signal amplification-fluorescence in situ hybridization.

    Science.gov (United States)

    Wang, Hong; Einola, Juha; Heinonen, Mirja; Kulomaa, Markku; Rintala, Jukka

    2008-09-01

    The aim of this study was to quantitatively analyse methanotrophs in two laboratory landfill biofilters at different biofilter depths and at temperatures which mimicked the boreal climatic conditions. Both biofilters were dominated by type I methanotrophs. The biofilter depth profiles showed that type I methanotrophs occurred in the upper layer, where relatively high O(2) and low CH(4) concentrations were present, whereas type II methanotrophs were mostly distributed in the zone with high CH(4) and low O(2) concentrations. The number of type I methanotrophic cells declined when the temperature was raised from 15 degrees C to 23 degrees C, but increased when lowered to 5 degrees C. A slight decrease in type II methanotrophs was also observed when the temperature was raised from 15 degrees C to 23 degrees C, whereas cell numbers remained constant when lowered to 5 degrees C. The results indicated that low temperature conditions favored both type I and type II methanotrophs in the biofilters.

  4. 嗜酸糖苷水解酶研究进展%Research Progress on Acidophilic Glycoside Hydrolase

    Institute of Scientific and Technical Information of China (English)

    罗会颖; 姚斌; 范云六

    2013-01-01

    随着极端微生物及极端酶的广泛研究,嗜酸酶因其在极端酸性环境中具有高的酶活性和稳定性而倍受关注,并取得了较大的研究进展。嗜酸糖苷水解酶是嗜酸酶中最重要的一类,在生物能源、饲料、食品等工业中具有重要的应用前景。综述了重要嗜酸糖苷水解酶,包括嗜酸淀粉酶、嗜酸纤维素酶、嗜酸木聚糖酶和甘露聚糖酶在基因的挖掘、表达、分子改良嗜酸机制研究以及应用等方面国内外的研究进展,展望了嗜酸糖苷水解酶未来可能的研究方向和发展前景。%Extremophiles and enzymes from extremophiles are widely studied. Of them, acidophilic enzyme attracts much attention, due to its high activity and stability under extreme acidic conditions, and this research has made rapid progress. Acidophilic glycosyl hydrolase is one of the most important acidophilic enzymes, and has significant application prospect in bio-energy, animal feed, food and other industries. This paper reviewed the gene cloning, heterologous expression, molecular modification and acidophilic mechanisms of important acidophilic glycosyl hydrolases, including amylase, cellulase, xylanase, and mannanase. The research orientation and development prospects were also elucidated in this paper.

  5. [Depth Profiles of Methane Oxidation Kinetics and the Related Methanotrophic Community in a Simulated Landfill Cover].

    Science.gov (United States)

    Xing, Zhi-lin; Zhao, Tian-tao; Gao, Yan-hui; He, Zhi; Yang, Xu; Peng, Xu-ya

    2015-11-01

    Simulated landfill cover with real time online monitoring system was developed using cover soils. Then the system started and the concentrations of bio-gas in various depths were continuously monitored, and it was found that the system ran continually and stably after 2-3 h when methane flux changed. After that, the relationship between regularity of methane oxidation and methane flux in landfill cover was analyzed. The results indicated that concentration of oxygen decreased with increasing methane flux when the depth was deeper than 20 cm, and no obvious correlation between oxygen concentration in landfill cover surface and methane flux, however, methane oxidation rate showed positive correlation with methane flux in various depths (range of R2 was 0.851-0.999). Kinetics of CH4 oxidation in landfill cover was fitted by CH4 -O2 dual-substrate model (range of R2 was 0.902-0.955), the half-saturation constant K(m) increasing with depth was 0.157-0.729 in dynamic condition. Finally, methanotrophs community structure in original cover soil sample and that in simulated landfill cover were investigated by high-throughout sequencing technology, and the statistics indicated that the abundance and species of methanotrophs in simulated landfill cover significantly increased compared with those in original cover soil sample, and type I methanotrophs including Methylobacter and Methylophilaceae and type II methanotrophs Methylocystis were dominant species. PMID:26911022

  6. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing

    Science.gov (United States)

    He, Ruo; Wooller, Matthew J.; Pohlman, John W.; Catranis, Catharine; Quensen, John; Tiedje, James M.; Leigh, Mary Beth

    2012-01-01

    Arctic lakes are a significant source of the greenhouse gas methane (CH4), but the role that methane oxidizing bacteria (methanotrophs) play in limiting the overall CH4 flux is poorly understood. Here, we used stable isotope probing (SIP) techniques to identify the metabolically active aerobic methanotrophs in upper sediments (0–1 cm) from an arctic lake in northern Alaska sampled during ice-free summer conditions. The highest CH4 oxidation potential was observed in the upper sediment (0–1 cm depth) with 1.59 μmol g wet weight-1 day-1 compared with the deeper sediment samples (1–3 cm, 3–5 cm and 5–10 cm), which exhibited CH4 oxidation potentials below 0.4 μmol g wet weight-1 day-1. Both type I and type II methanotrophs were directly detected in the upper sediment total communities using targeted primer sets based on 16S rRNA genes. Sequencing of 16S rRNA genes and functional genes (pmoA and mxaF) in the 13C-DNA from the upper sediment indicated that type I methanotrophs, mainly Methylobacter, Methylosoma, Methylomonas and Methylovulum miyakonense, dominated the assimilation of CH4. Methylotrophs, including the genera Methylophilus and/or Methylotenera, were also abundant in the 13CDNA. Our results show that a diverse microbial consortium acquired carbon from CH4 in the sediments of this arctic lake.

  7. Effects of Ammonium and Nitrite on Growth and Competitive Fitness of Cultivated Methanotrophic Bacteria▿

    OpenAIRE

    Nyerges, Györgyi; Han, Suk-Kyun; Stein, Lisa Y.

    2010-01-01

    The effects of nitrite and ammonium on cultivated methanotrophic bacteria were investigated. Methylomicrobium album ATCC 33003 outcompeted Methylocystis sp. strain ATCC 49242 in cultures with high nitrite levels, whereas cultures with high ammonium levels allowed Methylocystis sp. to compete more easily. M. album pure cultures and cocultures consumed nitrite and produced nitrous oxide, suggesting a connection between denitrification and nitrite tolerance.

  8. Draft Genome Sequence of the Methanotrophic Gammaproteobacterium Methyloglobulus morosus DSM 22980 Strain KoM1

    OpenAIRE

    Poehlein, Anja; Daniel, Rolf

    2013-01-01

    Here, we report the draft genome sequence of the methanotrophic gammaproteobacterium Methyloglobulus morosus DSM 22980 strain KoM1, which is proposed to be the type species for the novel genus Methyloglobulus. The genome (4.143 Mb) consists of a single circular chromosome and harbors genes for 2-aminoethylphosphonate (ciliatine) biosynthesis.

  9. Methanotrophic production of copolymer, poly(hydroxybutyrate-co-hydroxyvalerate), with high hydroxyvalerate content

    Science.gov (United States)

    Type II methanotrophic bacteria are a promising production platform for PHA biopolymers. These bacteria are known to produce pure poly-3-hydroxybutyrate homopolymer. We describe the production of a wide range of PHB-co-HV co-polymers by the co-feeding of methane and valerate. The ratio of HB to HV m...

  10. Ammonium addition inhibits 13C-methane incorporation into methanotroph membrane lipids in a freshwater sediment

    NARCIS (Netherlands)

    Nold, S.C.; Boschker, H.T.S.; Pel, R.; Laanbroek, H.J.

    1999-01-01

    To investigate the effect of ammonium addition on the species composition and activity of freshwater methane oxidizing bacteria, intact sediment cores were labeled with 13CH4 and incubated under ambient and elevated ammonium concentrations. After 7 days, methanotroph activity was assessed by quantif

  11. THE EFFECT OF DISTURBANCE ON THE STABILITY AND FUNCTION OF METHANOTROPHS UNDER DIFFERENT ENERGY FLOWS

    NARCIS (Netherlands)

    Krause, S.; Frenzel, P.

    2010-01-01

    Methane is next to water vapor and carbon dioxide the third most important greenhouse gas. The largest single sources are natural wetlands and wetland rice fields. In wetland rice fields, aerobic methanotrophs play a key role oxidizing methane before it is released to the atmosphere. However, it has

  12. Methanotrophic Communities in Brazilian Ferralsols from Naturally Forested, Afforested, and Agricultural Sites▿ †

    OpenAIRE

    Dörr, Nicole; Glaser, Bruno; Kolb, Steffen

    2009-01-01

    Conversion of forests to farmland permanently lowers atmospheric methane consumption due to unresolved reasons. Alphaproteobacterial methanotrophs were predominant in forested soils and gammaproteobacterial species were predominant in farmland soils of subtropical ferralsols in Brazil. The capability of atmospheric methane consumption was obliterated in farmland soils, suggesting a shift from oligotrophic to copiotrophic species.

  13. Aerobic methanotrophic communities at the Red Sea brine-seawater interface

    KAUST Repository

    Abdallah, Rehab Z.

    2014-09-23

    Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H and Siam R (2014) Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Front. Microbiol. 5:487. doi: 10.3389/fmicb.2014.00487

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

    Science.gov (United States)

    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

  15. Test Plan for Methanotrophic Bioreactor at Savannah River Site-TNX

    International Nuclear Information System (INIS)

    The primary purpose of this project is to demonstrate the feasibility and practicality of operating a methanotrophic mobile trickle filter bioreactor (MMB) unit to effectively reduce or eliminate trichloroethylene (TCE) and associated hydrocarbons from contaminated groundwater. The two-column trickle filter system can process 1.67 gallons per minute (gpm) of contaminated groundwater. During this project, the pilot system will evaluate, optimize, and demonstrate methanotrophic treatment technology (MTT). The mobile system will receive a 1--4% methane to air mixture for stimulating the methanotrophic TCE degrading bacteria, thereby increasing the rates of degradation of these contaminants. This project will also evaluate the efficacy of different bacteria for degrading TCE for use in the system at the laboratory-scale sample groundwater monitoring wells at TNX and set up the system for continued operation. The trickle filter system may be used to inexpensively treat other small-scale organic waste streams at SRS after the initial start-up. The MTT was demonstrated as an effective and efficient method of degrading TCE in the laboratory and during a field-scale in situ demonstration for degrading TCE in a groundwater plume at SRS. The methanotrophic bacteria increase significantly in population numbers and in the production of methane monooxygenase (MMO), an extremely powerful oxidizer. MMO was demonstrated as effective in oxidizing TCE and other recalcitrant compounds in laboratory studies. In the presence of MMO, TCE is oxidized to TCE-epoxide, which breaks down spontaneously into simple, easily degraded, daughter compounds. The system will receive a 1--4% methane to air mixture, which will effectively grow and maintain the methanotrophic bacteria that will degrade TCE. This demonstration will have broad applications to bioremediating contaminated groundwater systems where in situ bioremediation is not practical

  16. Test Plan for Methanotrophic Bioreactor at Savannah River Site-TNX

    Energy Technology Data Exchange (ETDEWEB)

    Berry, C.J.

    1994-10-04

    The primary purpose of this project is to demonstrate the feasibility and practicality of operating a methanotrophic mobile trickle filter bioreactor (MMB) unit to effectively reduce or eliminate trichloroethylene (TCE) and associated hydrocarbons from contaminated groundwater. The two-column trickle filter system can process 1.67 gallons per minute (gpm) of contaminated groundwater. During this project, the pilot system will evaluate, optimize, and demonstrate methanotrophic treatment technology (MTT). The mobile system will receive a 1--4% methane to air mixture for stimulating the methanotrophic TCE degrading bacteria, thereby increasing the rates of degradation of these contaminants. This project will also evaluate the efficacy of different bacteria for degrading TCE for use in the system at the laboratory-scale sample groundwater monitoring wells at TNX and set up the system for continued operation. The trickle filter system may be used to inexpensively treat other small-scale organic waste streams at SRS after the initial start-up. The MTT was demonstrated as an effective and efficient method of degrading TCE in the laboratory and during a field-scale in situ demonstration for degrading TCE in a groundwater plume at SRS. The methanotrophic bacteria increase significantly in population numbers and in the production of methane monooxygenase (MMO), an extremely powerful oxidizer. MMO was demonstrated as effective in oxidizing TCE and other recalcitrant compounds in laboratory studies. In the presence of MMO, TCE is oxidized to TCE-epoxide, which breaks down spontaneously into simple, easily degraded, daughter compounds. The system will receive a 1--4% methane to air mixture, which will effectively grow and maintain the methanotrophic bacteria that will degrade TCE. This demonstration will have broad applications to bioremediating contaminated groundwater systems where in situ bioremediation is not practical.

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

    Energy Technology Data Exchange (ETDEWEB)

    Frank F. Roberto

    2008-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Elena Tamburini

    2015-08-01

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

  19. Low energy emulsion-based fermentation enabling accelerated methane mass transfer and growth of poly(3-hydroxybutyrate)-accumulating methanotrophs.

    Science.gov (United States)

    Myung, Jaewook; Kim, Minkyu; Pan, Ming; Criddle, Craig S; Tang, Sindy K Y

    2016-05-01

    Methane is a low-cost feedstock for the production of polyhydroxyalkanoate biopolymers, but methanotroph fermentations are limited by the low solubility of methane in water. To enhance mass transfer of methane to water, vigorous mixing or agitation is typically used, which inevitably increases power demand and operational costs. This work presents a method for accelerating methane mass transfer without agitation by growing methanotrophs in water-in-oil emulsions, where the oil has a higher solubility for methane than water does. In systems without agitation, the growth rate of methanotrophs in emulsions is five to six times that of methanotrophs in the medium-alone incubations. Within seven days, cells within the emulsions accumulate up to 67 times more P3HB than cells in the medium-alone incubations. This is achieved due to the increased interfacial area of the aqueous phase, and accelerated methane diffusion through the oil phase. PMID:26896714

  20. Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol

    OpenAIRE

    Vorobev, Alexey; Jagadevan, Sheeja; Jain, Sunit; Anantharaman, Karthik; Dick, Gregory J.; Vuilleumier, Stéphane; Semrau, Jeremy D.

    2014-01-01

    A minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotroph Methylocystis sp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathwa...

  1. Characterization of Root-Associated Methanotrophs from Three Freshwater Macrophytes: Pontederia cordata, Sparganium eurycarpum, and Sagittaria latifolia†

    OpenAIRE

    Calhoun, A.; King, G. M.

    1998-01-01

    Root-associated methanotrophic bacteria were enriched from three common aquatic macrophytes: Pontederia cordata, Sparganium eurycarpum, and Sagittaria latifolia. At least seven distinct taxa belonging to groups I and II were identified and presumptively assigned to the genera Methylosinus, Methylocystis, Methylomonas, and Methylococcus. Four of these strains appeared to be novel on the basis of partial 16S ribosomal DNA sequence analysis. The root-methanotroph association did not appear to be...

  2. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments

    OpenAIRE

    He, Ruo; Wooller, Matthew J; Pohlman, John W.; Quensen, John; Tiedje, James M.; Leigh, Mary Beth

    2012-01-01

    Methane (CH4) emitted from high-latitude lakes accounts for 2–6% of the global atmospheric CH4 budget. Methanotrophs in lake sediments and water columns mitigate the amount of CH4 that enters the atmosphere, yet their identity and activity in arctic and subarctic lakes are poorly understood. We used stable isotope probing (SIP), quantitative PCR (Q-PCR), pyrosequencing and enrichment cultures to determine the identity and diversity of active aerobic methanotrophs in the water columns and sedi...

  3. Estimating High-Affinity Methanotrophic Bacterial Biomass, Growth, and Turnover in Soil by Phospholipid Fatty Acid 13C Labeling

    OpenAIRE

    Maxfield, P. J.; E. R. C. Hornibrook; Evershed, R. P.

    2006-01-01

    A time series phospholipid fatty acid (PLFA) 13C-labeling study was undertaken to determine methanotrophic taxon, calculate methanotrophic biomass, and assess carbon recycling in an upland brown earth soil from Bronydd Mawr (Wales, United Kingdom). Laboratory incubations of soils were performed at ambient CH4 concentrations using synthetic air containing 2 parts per million of volume of 13CH4. Flowthrough chambers maintained a stable CH4 concentration throughout the 11-week incubation. Soils ...

  4. Methanotrophic activity and diversity in different Sphagnum magellanicum dominated habitats in the southernmost peat bogs of Patagonia

    OpenAIRE

    N. Kip; Fritz, C.; Langelaan, E. S.; Pan, Y.; L. Bodrossy; Pancotto, V.; M. S. M. Jetten; Smolders, A.J.P.; Camp, H. J. M.

    2012-01-01

    Sphagnum peatlands are important ecosystems in the methane cycle. Methanotrophs living inside the dead hyaline cells or on the Sphagnum mosses are able to act as a methane filter and thereby reduce methane emissions. We investigated in situ methane concentrations and the corresponding activity and diversity of methanotrophs in different Sphagnum dominated bog microhabitats. In contrast to the Northern Hemisphere peat ecosystems the temperate South American peat bogs are domi...

  5. Stable-Carbon-Isotope Composition of Fatty Acids in Hydrothermal Vent Mussels Containing Methanotrophic and Thiotrophic Bacterial Endosymbionts

    OpenAIRE

    Pond, David W; Bell, Michael V; Dixon, David R.; Fallick, Anthony E.; Segonzac, Michel; Sargent, John R.

    1998-01-01

    Fatty acid biomarker analysis coupled with gas chromatography-isotope ratio mass spectrometry was used to confirm the presence of methanotrophic and thiotrophic bacterial endosymbionts in the tissues of a hydrothermal vent mussel (Bathymodiolus sp.), collected from the Menez Gwen vent field on the mid-Atlantic ridge. Monounsaturated (n-8) fatty acids, which are diagnostic of methanotrophic bacteria, were detected in all three types of tissues examined (gill, posterior adductor, and mantle), a...

  6. Effect of methanogenic substrates on anaerobic oxidation of methane and sulfate reduction by an anaerobic methanotrophic enrichment

    OpenAIRE

    Meulepas, R.J.W.; Jagersma, C.G.; Khadem, A.F.; Buisman, C.J.N.; Stams, A.J.M.; Lens, P. N. L.

    2010-01-01

    Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) is assumed to be a syntrophic process, in which methanotrophic archaea produce an interspecies electron carrier (IEC), which is subsequently utilized by sulfate-reducing bacteria. In this paper, six methanogenic substrates are tested as candidate-IECs by assessing their effect on AOM and SR by an anaerobic methanotrophic enrichment. The presence of acetate, formate or hydrogen enhanced SR, but did not inhibit AOM, nor did ...

  7. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study

    OpenAIRE

    Matsen, Janet B.; Song eYang; Stein, Lisa Y.; Beck, David A. C.; Marina G. Kalyuzhanaya

    2013-01-01

    Methane-utilizing bacteria (methanotrophs) are important in both environmental and biotechnological applications, due to their ability to convert methane to multicarbon compounds. However, systems-level studies of methane metabolism have not been carried out in methanotrophs. In this work we have integrated genomic and transcriptomic information to provide an overview of central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methano...

  8. Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic Study

    OpenAIRE

    Matsen, Janet B.; Yang, Song; Stein, Lisa Y.; Beck, David; Marina G. Kalyuzhnaya

    2013-01-01

    Methane utilizing bacteria (methanotrophs) are important in both environmental and biotechnological applications, due to their ability to convert methane to multicarbon compounds. However, systems-level studies of methane metabolism have not been carried out in methanotrophs. In this work we have integrated genomic and transcriptomic information to provide an overview of central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methano...

  9. A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

    Directory of Open Access Journals (Sweden)

    Haverkamp Thomas HA

    2011-10-01

    Full Text Available Abstract Background Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where oxygen is available aerobic methanotrophs take part in methane oxidation. In this study, we used metagenomics to characterize the taxonomic and metabolic potential for methane oxidation at the Tonya seep in the Coal Oil Point area, California. Two metagenomes from different sediment depth horizons (0-4 cm and 10-15 cm below sea floor were sequenced by 454 technology. The metagenomes were analysed to characterize the distribution of aerobic and anaerobic methanotrophic taxa at the two sediment depths. To gain insight into the metabolic potential the metagenomes were searched for marker genes associated with methane oxidation. Results Blast searches followed by taxonomic binning in MEGAN revealed aerobic methanotrophs of the genus Methylococcus to be overrepresented in the 0-4 cm metagenome compared to the 10-15 cm metagenome. In the 10-15 cm metagenome, ANME of the ANME-1 clade, were identified as the most abundant methanotrophic taxon with 8.6% of the reads. Searches for particulate methane monooxygenase (pmoA and methyl-coenzyme M reductase (mcrA, marker genes for aerobic and anaerobic oxidation of methane respectively, identified pmoA in the 0-4 cm metagenome as Methylococcaceae related. The mcrA reads from the 10-15 cm horizon were all classified as originating from the ANME-1 clade. Conclusions Most of the taxa detected were present in both metagenomes and differences in community structure and corresponding metabolic potential between the two samples were mainly

  10. Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog.

    Science.gov (United States)

    Esson, Kaitlin C; Lin, Xueju; Kumaresan, Deepak; Chanton, Jeffrey P; Murrell, J Colin; Kostka, Joel E

    2016-04-15

    The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil(-1)day(-1) Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4%in situto 25 to 36% after 8 to 14 days. Phylogenetic analysis of the(13)C-enriched DNA fractions revealed that the active methanotrophs were dominated by the generaMethylocystis(type II;Alphaproteobacteria),Methylomonas, andMethylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed forpmoAin surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNApmoAamplicons from field samples confirmed that the dominant active methanotrophs wereMethylocystisandMethylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the generaMethylomonasandMethylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems. PMID:26873322

  11. Gene Identification and Substrate Regulation Provide Insights into Sulfur Accumulation during Bioleaching with the Psychrotolerant Acidophile Acidithiobacillus ferrivorans

    OpenAIRE

    Liljeqvist, Maria; Rzhepishevska, Olena I.; Dopson, Mark

    2013-01-01

    The psychrotolerant acidophile Acidithiobacillus ferrivorans has been identified from cold environments and has been shown to use ferrous iron and inorganic sulfur compounds as its energy sources. A bioinformatic evaluation presented in this study suggested that Acidithiobacillus ferrivorans utilized a ferrous iron oxidation pathway similar to that of the related species Acidithiobacillus ferrooxidans. However, the inorganic sulfur oxidation pathway was less clear, since the Acidithiobacillus...

  12. A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation.

    Science.gov (United States)

    Strong, P J; Kalyuzhnaya, M; Silverman, J; Clarke, W P

    2016-09-01

    Methane, a carbon source for methanotrophic bacteria, is the principal component of natural gas and is produced during anaerobic digestion of organic matter (biogas). Methanotrophs are a viable source of single cell protein (feed supplement) and can produce various products, since they accumulate osmolytes (e.g. ectoine, sucrose), phospholipids (potential biofuels) and biopolymers (polyhydroxybutyrate, glycogen), among others. Other cell components, such as surface layers, metal chelating proteins (methanobactin), enzymes (methane monooxygenase) or heterologous proteins hold promise as future products. Here, scenarios are presented where ectoine, polyhydroxybutyrate or protein G are synthesised as the primary product, in conjunction with a variety of ancillary products that could enhance process viability. Single or dual-stage processes and volumetric requirements for bioreactors are discussed, in terms of an annual biomass output of 1000 tonnesyear(-1). Product yields are discussed in relation to methane and oxygen consumption and organic waste generation. PMID:27146469

  13. Density-dependent enhancement of methane oxidation activity and growth of Methylocystis sp. by a non-methanotrophic bacterium Sphingopyxis sp

    OpenAIRE

    So-Yeon Jeong; Kyung-Suk Cho; Tae Gwan Kim

    2014-01-01

    Methanotrophs are a biological resource as they degrade the greenhouse gas methane and various organic contaminants. Several non-methanotrophic bacteria have shown potential to stimulate growth of methanotrophs when co-cultured, and however, the ecology is largely unknown. Effects of Sphingopyxis sp. NM1 on methanotrophic activity and growth of Methylocystis sp. M6 were investigated in this study. M6 and NM1 were mixed at mixing ratios of 9:1, 1:1, and 1:9 (v/v), using cell suspensions of 7.5...

  14. Methanotrophic and Methanogenic Communities in Swiss Alpine Fens Dominated by Carex rostrata and Eriophorum angustifolium.

    Science.gov (United States)

    Cheema, Simrita; Zeyer, Josef; Henneberger, Ruth

    2015-09-01

    Vascular plants play a key role in controlling CH4 emissions from natural wetlands, because they influence CH4 production, oxidation, and transport to the atmosphere. Here we investigated differences in the abundance and composition of methanotrophic and methanogenic communities in three Swiss alpine fens dominated by different vascular plant species under natural conditions. The sampling locations either were situated at geographically distinct sites with different physicochemical properties but the same dominant plant species (Carex rostrata) or were located within the same site, showing comparable physicochemical pore water properties, but had different plant species (C. rostrata or Eriophorum angustifolium). All three locations were permanently submerged and showed high levels of CH4 emissions (80.3 to 184.4 mg CH4 m(-2) day(-1)). Soil samples were collected from three different depths with different pore water CH4 and O2 concentrations and were analyzed for pmoA and mcrA gene and transcript abundance and community composition, as well as soil structure. The dominant plant species appeared to have a significant influence on the composition of the active methanotrophic communities (transcript level), while the methanogenic communities differed significantly only at the gene level. Yet no plant species-specific microbial taxa were discerned. Moreover, for all communities, differences in composition were more pronounced with the site (i.e., with different physicochemical properties) than with the plant species. Moreover, depth significantly influenced the composition of the active methanotrophic communities. Differences in abundance were generally low, and active methanotrophs and methanogens coexisted at all three locations and depths independently of CH4 and O2 concentrations or plant species. PMID:26092454

  15. Fate of 2,2,2-trichloroacetaldehyde (chloral hydrate) produced during trichloroethylene oxidation by methanotrophs.

    OpenAIRE

    Newman, L M; Wackett, L P

    1991-01-01

    Four different methanotrophs expressing soluble methane monooxygenase produced 2,2,2-trichloroacetaldehyde, or chloral hydrate, a controlled substance, during the oxidation of trichloroethylene. Chloral hydrate concentrations decreased in these cultures between 1 h and 24 h of incubation. Chloral hydrate was shown to be biologically transformed to trichloroethanol and trichloroacetic acid by Methylosinus trichosporium OB3b. At elevated pH and temperature, chloral hydrate readily decomposed an...

  16. Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin

    OpenAIRE

    Tavormina, Patricia L; Ussler, William; Orphan, Victoria J

    2008-01-01

    Methane vents are of significant geochemical and ecological importance. Notable progress has been made towards understanding anaerobic methane oxidation in marine sediments, however, the diversity and distribution of aerobic methanotrophs in the water column are poorly characterized. Both environments play an essential role in regulating methane release from the oceans to the atmosphere. In this study, the diversity of particulate methane monooxygenase (pmoA) and 16S rRNA genes from two metha...

  17. Molecular ecology and biogeography of methanotrophic bacteria in wetland rice fields

    OpenAIRE

    Lüke, Claudia

    2010-01-01

    Methanotrophic bacteria perform a central function in our climate system representing the only biogenic sink for the greenhouse gas methane. In wetland rice fields, they function as bio-filters preventing methane produced in anoxic layers escaping into the atmosphere, attenuating the potential methane emission by up to 90%. Despite intensive studies in the past, molecular approaches have barely started to explore the full diversit...

  18. Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria▿

    OpenAIRE

    Singh, Brajesh K.; Tate, Kevin R.; Kolipaka, Gokul; Hedley, Carolyn B.; Macdonald, Catriona A.; Millard, Peter; Murrell, J. Colin

    2007-01-01

    We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (Pinus radiata) forests and one shrubland (mainly Kunzea ericoides var. ericoides) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of ...

  19. Diversity and methane oxidation of active epibiotic methanotrophs on live Shinkaia crosnieri

    OpenAIRE

    Watsuji, Tomo-o; Yamamoto, Asami; Takaki, Yoshihiro; Ueda, Kenji; Kawagucci, Shinsuke; Takai, Ken

    2014-01-01

    Shinkaia crosnieri is a galatheid crab that predominantly dwells in deep-sea hydrothermal systems in the Okinawa Trough, Japan. In this study, the phylogenetic diversity of active methanotrophs in the epibiotic microbial community on the setae of S. crosnieri was characterized by reverse transcription-polymerase chain reaction (RT-PCR) of a functional gene (pmoA) encoding a subunit of particulate methane monooxygenase. Phylogenetic analysis of pmoA transcript sequences revealed that the activ...

  20. Trichloroethylene biodegradation by mesophilic and psychrophilic ammonia oxidizers and methanotrophs in groundwater microcosms.

    OpenAIRE

    Moran, B N; Hickey, W J

    1997-01-01

    This study investigated the efficiency of methane and ammonium for stimulating trichloroethylene (TCE) biodegradation in groundwater microcosms (flasks and batch exchange columns) at a psychrophilic temperature (12 degrees C) typical of shallow aquifers in the northern United States or a mesophilic temperature (24 degrees C) representative of most laboratory experiments. After 140 days, TCE biodegradation rates by ammonia oxidizers and methanotrophs in mesophilic flask microcosms were similar...

  1. Growth and Methane Oxidation Rates of Anaerobic Methanotrophic Archaea in a Continuous-Flow Bioreactor

    OpenAIRE

    Peter R. Girguis; Orphan, Victoria J; Hallam, Steven J.; DeLong, Edward F

    2003-01-01

    Anaerobic methanotrophic archaea have recently been identified in anoxic marine sediments, but have not yet been recovered in pure culture. Physiological studies on freshly collected samples containing archaea and their sulfate-reducing syntrophic partners have been conducted, but sample availability and viability can limit the scope of these experiments. To better study microbial anaerobic methane oxidation, we developed a novel continuous-flow anaerobic methane incubation system (AMIS) that...

  2. Methanotrophic and Methanogenic Communities in Swiss Alpine Fens Dominated by Carex rostrata and Eriophorum angustifolium

    OpenAIRE

    Cheema, Simrita; Zeyer, Josef; Henneberger, Ruth

    2015-01-01

    Vascular plants play a key role in controlling CH4 emissions from natural wetlands, because they influence CH4 production, oxidation, and transport to the atmosphere. Here we investigated differences in the abundance and composition of methanotrophic and methanogenic communities in three Swiss alpine fens dominated by different vascular plant species under natural conditions. The sampling locations either were situated at geographically distinct sites with different physicochemical properties...

  3. Response of methanotrophic communities to afforestation and reforestation in New Zealand

    OpenAIRE

    Nazaries, Loïc; Tate, Kevin R.; Ross, Des J; Singh, Jagrati; Dando, John; Saggar, Surinder; Baggs, Elizabeth M; Millard, Peter; Murrell, J. Colin; Singh, Brajesh K.

    2011-01-01

    Methanotrophs use methane (CH4) as a carbon source. They are particularly active in temperate forest soils. However, the rate of change of CH4 oxidation in soil with afforestation or reforestation is poorly understood. Here, soil CH4 oxidation was examined in New Zealand volcanic soils under regenerating native forests following burning, and in a mature native forest. Results were compared with data for pasture to pine land-use change at nearby sites. We show that following soil disturbance, ...

  4. Assimilation of Inorganic Nitrogen by Marine Invertebrates and Their Chemoautotrophic and Methanotrophic Symbionts

    OpenAIRE

    Lee, Raymond W; Childress, James J.

    1994-01-01

    Symbioses between marine invertebrates and their chemoautotrophic and methanotrophic symbionts are now known to exist in a variety of habitats where reduced chemical species are present. The utilization of chemical energy and reliance on C1 compounds by these symbioses are well documented. Much less is known about their metabolism of nitrogen. Earlier work has shown that the tissues of organisms in these associations are depleted of 15N compared with those of other marine organisms, indicatin...

  5. Influence of Light Intensity on Methanotrophic Bacterial Activity in Petit Saut Reservoir, French Guiana

    OpenAIRE

    Dumestre, J. F.; Guézennec, J.; Galy-Lacaux, C; Delmas, R.; Richard, S.; Labroue, L.

    1999-01-01

    One year after impoundment in January 1994, methanotrophic bacteria in Petit Saut Reservoir (French Guiana) were active at the oxic-anoxic interface. This activity was revealed by the sudden extinction of diffusive methane emission (600 metric tons of CH4 · day−1 for the whole lake surface area, i.e., 360 km2). Lifting of inhibition was suspected. After reviewing the potential inhibitors of this physiological guild (O2, NH4+, sulfides) and considering the similarities with nitrifiers, we sugg...

  6. Secretion of Bioplastic Polymers from Methanotrophic Bacteria Grown using Natural Gas

    OpenAIRE

    Nielsen, Chad L.; Miller, Charles D

    2016-01-01

    Biodegradable bioplastics show promise as a replacement for traditional plastics. Cost of production due to the cost of feedstocks and separation/purification processes are the main obstacles to widespread use of bioplastics. The possibility of reducing these costs through using methane gas as a feedstock and genetically transforming a methanotrophic bacterium to secrete bioplastics was investigated through experimentation. The bacteria are a promising option for bioplastic production.

  7. Methanotrophic microbial communities associated with bubble plumes above gas seeps in the Black Sea

    OpenAIRE

    Carsten J Schubert; Durisch-Kaiser, Edith; Holzner, Christian P.; Klauser, Lucia; Wehrli, Bernhard; Schmale, Oliver; Greinert, Jens; McGinnis, Daniel Frank; De Batist, Marc; Kipfer, Rolf

    2006-01-01

    Bubbles evolving from active gas seeps can be traced by hydroacoustic imaging up to 1000 m high in the Black Sea water column. Although methane concentrations are not distinguishable between the water column above the deep seep and reference sites, atmospheric noble gas measurements clearly show the constant input of gases (mainly methane) via seepage into the Black Sea. Archaea (ANME-1, ANME-2) and methanotrophic bacteria detected with specific 16S rRNA-targeted oligonucleotide probes are re...

  8. A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

    OpenAIRE

    Haverkamp Thomas HA; Håvelsrud Othilde; Kristensen Tom; Jakobsen Kjetill S; Rike Anne

    2011-01-01

    Background Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME) living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where ...

  9. Activity and Diversity of Methanotrophic Bacteria at Methane Seeps in Eastern Lake Constance Sediments ▿

    OpenAIRE

    Deutzmann, Jörg; Wörner, Susanne; Schink, Bernhard

    2011-01-01

    The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal ...

  10. Potential of pmoA Amplicon Pyrosequencing for Methanotroph Diversity Studies ▿†

    OpenAIRE

    Lüke, Claudia; Frenzel, Peter

    2011-01-01

    We analyzed the potential of pmoA amplicon pyrosequencing compared to that of Sanger sequencing with paddy soils as a model environment. We defined operational taxonomic unit (OTU) cutoff values of 7% and 18%, reflecting methanotrophic species and major phylogenetic pmoA lineages, respectively. Major lineages were already well covered by clone libraries; nevertheless, pyrosequencing provided a higher level of diversity at the species level.

  11. Molecular Analysis of the pmo (Particulate Methane Monooxygenase) Operons from Two Type II Methanotrophs

    OpenAIRE

    Gilbert, Bettina; McDonald, Ian R.; Finch, Ruth; Stafford, Graham P.; Nielsen, Allan K.; Murrell, J. Colin

    2000-01-01

    The particulate methane monooxygenase gene clusters, pmoCAB, from two representative type II methanotrophs of the α-Proteobacteria, Methylosinus trichosporium OB3b and Methylocystis sp. strain M, have been cloned and sequenced. Primer extension experiments revealed that the pmo cluster is probably transcribed from a single transcriptional start site located 300 bp upstream of the start of the first gene, pmoC, for Methylocystis sp. strain M. Immediately upstream of the putative start site, co...

  12. XoxF-Type Methanol Dehydrogenase from the Anaerobic Methanotroph “Candidatus Methylomirabilis oxyfera”

    OpenAIRE

    Wu, Ming L.; Wessels, Hans J. C. T.; Pol, Arjan; Op den Camp, Huub J. M.; Mike S.M. Jetten; van Niftrik, Laura; Keltjens, Jan T.

    2014-01-01

    “Candidatus Methylomirabilis oxyfera” is a newly discovered anaerobic methanotroph that, surprisingly, oxidizes methane through an aerobic methane oxidation pathway. The second step in this aerobic pathway is the oxidation of methanol. In Gram-negative bacteria, the reaction is catalyzed by pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH). The genome of “Ca. Methylomirabilis oxyfera” putatively encodes three different MDHs that are localized in one large gene cluster: one...

  13. Response of methanotrophic communities to afforestation and reforestation in New Zealand.

    Science.gov (United States)

    Nazaries, Loïc; Tate, Kevin R; Ross, Des J; Singh, Jagrati; Dando, John; Saggar, Surinder; Baggs, Elizabeth M; Millard, Peter; Murrell, J Colin; Singh, Brajesh K

    2011-11-01

    Methanotrophs use methane (CH(4)) as a carbon source. They are particularly active in temperate forest soils. However, the rate of change of CH(4) oxidation in soil with afforestation or reforestation is poorly understood. Here, soil CH(4) oxidation was examined in New Zealand volcanic soils under regenerating native forests following burning, and in a mature native forest. Results were compared with data for pasture to pine land-use change at nearby sites. We show that following soil disturbance, as little as 47 years may be needed for development of a stable methanotrophic community similar to that in the undisturbed native forest soil. Corresponding soil CH(4)-oxidation rates in the regenerating forest soil have the potential to reach those of the mature forest, but climo-edaphic fators appear limiting. The observed changes in CH(4)-oxidation rate were directly linked to a prior shift in methanotrophic communities, which suggests microbial control of the terrestrial CH(4) flux and identifies the need to account for this response to afforestation and reforestation in global prediction of CH(4) emission.

  14. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root?

    Science.gov (United States)

    Minamisawa, Kiwamu; Imaizumi-Anraku, Haruko; Bao, Zhihua; Shinoda, Ryo; Okubo, Takashi; Ikeda, Seishi

    2016-01-01

    The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation). PMID:26960961

  15. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root?

    Science.gov (United States)

    Minamisawa, Kiwamu; Imaizumi-Anraku, Haruko; Bao, Zhihua; Shinoda, Ryo; Okubo, Takashi; Ikeda, Seishi

    2016-03-26

    The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane-nitrogen (CH4-N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of (15)N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation). PMID:26960961

  16. Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils

    Science.gov (United States)

    Cai, Yuanfeng; Zheng, Yan; Bodelier, Paul L. E.; Conrad, Ralf; Jia, Zhongjun

    2016-06-01

    Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ~1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this `high-affinity' methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane.

  17. Evaluation and update of cutoff values for methanotrophic pmoA gene sequences.

    Science.gov (United States)

    Wen, Xi; Yang, Sizhong; Liebner, Susanne

    2016-09-01

    The functional pmoA gene is frequently used to probe the diversity and phylogeny of methane-oxidizing bacteria (MOB) in various environments. Here, we compared the similarities between the pmoA gene and the corresponding 16S rRNA gene sequences of 77 described species covering gamma- and alphaproteobacterial methanotrophs (type I and type II MOB, respectively) as well as methanotrophs from the phylum Verrucomicrobia. We updated and established the weighted mean pmoA gene cutoff values on the nucleotide level at 86, 82, and 71 % corresponding to the 97, 95, and 90 % similarity of the 16S rRNA gene. Based on these cutoffs, the functional gene fragments can be entirely processed at the nucleotide level throughout software platforms such as Mothur or QIIME which provide a user-friendly and command-based alternative to amino acid-based pipelines. Type II methanotrophs are less divergent than type I both with regard to ribosomal and functional gene sequence similarity and GC content. We suggest that this agrees with the theory of different life strategies proposed for type I and type II MOB. PMID:27098810

  18. COMETABOLIC TRANSFORMATION OF MONO- AND DICHLOROBIPHENYLS AND CHLOROHYDROXYBIPHENYLS BY METHANOTROPHIC GROUNDWATER ISOLATES. (R825689C094)

    Science.gov (United States)

    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...

  19. Optimization of Methanotrophic Growth and Production of Poly(3-Hydroxybutyrate) in a High-Throughput Microbioreactor System.

    Science.gov (United States)

    Sundstrom, Eric R; Criddle, Craig S

    2015-07-01

    Production of poly(3-hydroxybutyrate) (P3HB) from methane has economic and environmental advantages over production by agricultural feedstock. Identification of high-productivity strains and optimal growth conditions is critical to efficient conversion of methane to polymer. Current culture conditions, including serum bottles, shake flasks, and agar plates, are labor-intensive and therefore insufficient for systematic screening and isolation. Gas chromatography, the standard method for analysis of P3HB content in bacterial biomass, is also incompatible with high-throughput screening. Growth in aerated microtiter plates coupled with a 96-well Nile red flow-cytometric assay creates an integrated microbioreactor system for high-throughput growth and analysis of P3HB-producing methanotrophic cultures, eliminating the need for individual manipulation of experimental replicates. This system was tested in practice to conduct medium optimization for P3HB production in pure cultures of Methylocystis parvus OBBP. Optimization gave insight into unexpected interactions: for example, low calcium concentrations significantly enhanced P3HB production under nitrogen-limited conditions. Optimization of calcium and copper concentrations in the growth medium increased final P3HB content from 18.1% to 49.4% and P3HB concentration from 0.69 g/liter to 3.43 g/liter while reducing doubling time from 10.6 h to 8.6 h. The ability to culture and analyze thousands of replicates with high mass transfer in completely mixed culture promises to streamline medium optimization and allow the detection and isolation of highly productive strains. Applications for this system are numerous, encompassing analysis of biofuels and other lipid inclusions, as well as analysis of heterotrophic and photosynthetic systems. PMID:25956771

  20. In-Situ Quantification of Methanotrophic Activity in a Landfill Cover Soil Using Gas Push-Pull Tests

    Science.gov (United States)

    Gomez, K. E.; Gonzalez-Gil, G.; Schroth, M. H.; Zeyer, J.

    2007-12-01

    Landfills are both a major anthropogenic source and a sink for the greenhouse gas CH4. Methanogenic bacteria produce CH4 during the anaerobic digestion of landfill waste, whereas, methanotrophic bacteria consume CH4 as it is transported through a landfill cover soil. Methanotrophs are thought to be ubiquitous in soils, but typically exist in large numbers at oxic/anoxic interfaces, close to anaerobic methane sources but exposed to oxygen required for metabolism. Accurate in-situ quantification of the sink strength of methanotrophs in landfill cover soils is needed for global carbon balances and for local emissions mitigation strategies. We measured in-situ CH4 concentrations at 30, 60, and 100 cm depth at 18 evenly spaced locations across a landfill cover soil. Furthermore, we performed Gas Push-Pull Tests (GPPTs) to estimate in-situ rates of methanotrophic activity in the cover soil. The GPPT is a gas-tracer test in which a gas mixture containing CH4, O2, and non-reactive tracer gases is injected (pushed) into the soil followed by extraction (pull) from the same location. Quantification of CH4 oxidation rates is based upon comparison of the breakthrough curves of CH4 and tracer gases. We present the results of a series of GPPTs conducted at two locations in the cover soil to assess the feasibility and reproducibility of this technique to quantify methanotrophic activity. Additional GPPTs were performed with a methanotrophic inhibitor in the injection gas mixture to confirm the appropriate choice of tracers to quantify CH4 oxidation. Estimated CH4 oxidation rate constants indicate that the cover soil contains a highly active methanotrophic community.

  1. Effect of trichloroethylene and tetrachloroethylene on methane oxidation and community structure of methanotrophic consortium.

    Science.gov (United States)

    Choi, Sun-Ah; Lee, Eun-Hee; Cho, Kyung-Suk

    2013-01-01

    The methane oxidation rate and community structure of a methanotrophic consortium were analyzed to determine the effects of trichloroethylene (TCE) and tetrachloroethylene (PCE) on methane oxidation. The maximum methane oxidation rate (Vmax ) of the consortium was 326.8 μmol·g-dry biomass(-1)·h(-1), and it had a half-saturation constant (Km ) of 143.8 μM. The addition of TCE or PCE resulted in decreased methane oxidation rates, which were decreased from 101.73 to 5.47-24.64 μmol·g-dry biomass(-1)·h(-1) with an increase in the TCE-to-methane ratio, and to 61.95-67.43 μmol·g-dry biomass(-1)·h(-1) with an increase in the PCE-to-methane ratio. TCE and PCE were non-competitive inhibitors for methane oxidation, and their inhibition constants (Ki ) were 33.4 and 132.0 μM, respectively. When the methanotrophic community was analyzed based on pmoA using quantitative real-time PCR (qRT-PCR), the pmoA gene copy numbers were shown to decrease from 7.3 ± 0.7 × 10(8) to 2.1-5.0 × 10(7) pmoA gene copy number · g-dry biomass(-1) with an increase in the TCE-to-methane ratio and to 2.5-7.0 × 10(7) pmoA gene copy number · g-dry biomass(-1) with an increase in the PCE-to-methane ratio. Community analysis by microarray demonstrated that Methylocystis (type II methanotrophs) were the most abundant in the methanotrophic community composition in the presence of TCE. These results suggest that toxic effects caused by TCE and PCE change not only methane oxidation rates but also the community structure of the methanotrophic consortium.

  2. Aerobic methanotrophs drive the formation of a seasonal anoxic benthic nepheloid layer in monomictic Lake Lugano

    Science.gov (United States)

    Blees, Jan; Niemann, Helge; Wenk, Christine B.; Zopfi, Jacob; Schubert, Carsten J.; Jenzer, Joël S.; Veronesi, Mauro L.; Lehmann, Moritz F.

    2014-05-01

    In the southern basin of Lake Lugano, thermal stratification of the water column during summer and autumn leads to a lack of exchange between surface and deep water masses, and consequently to seasonal bottom water anoxia, associated with high methane concentrations. With the onset of bottom water anoxia, a dense layer of high particulate matter concentration - a so-called benthic nepheloid layer (BNL) - develops in the bottom waters. A sharp redox gradient marks the upper boundary of the BNL. At its maximum, the BNL extends 15 - 30 m from the sediment into the water column. We investigated the identity of the BNL and key environmental factors controlling its formation in the framework of a seasonal study. Compound specific C-isotope measurements and Fluorescence In Situ Hybridisation (FISH) of suspended particulate organic matter, radioactive tracer based measurements of methane oxidation, as well as investigation of geochemical water column parameters were performed in spring and autumn. Our analyses revealed that the microbial biomass within the BNL is dominated by methanotrophic bacteria. Aerobic methane oxidation (MOx) was restricted to a narrow zone at the top of the BNL, reaching maximum rates of up to 1.8 μM/day. The rates of MOx activity effectively consumed most (>99%) of the uprising methane, leading to the formation of a sharp CH4 concentration gradient and a strongly suppressed kinetic isotope effect (ɛ = -2.8o). CH4 oxidation was limited by the diffusive supply of O2 from the upper hypolimnion, implying that methanotrophy is the primary driver of the seasonal expansion of the anoxic bottom water volume, and explaining the vertical migration of the BNL in response to its own O2 consumption. The bulk organic matter extracted from the BNL was strongly depleted in 13C (δ13C methanotrophic. The cell size of methanotrophs was significantly larger than of other microbial cells, and an independent approach to quantify the contribution of methanotroph

  3. Above- and below-ground methane fluxes and methanotrophic activity in a landfill-cover soil

    International Nuclear Information System (INIS)

    Highlights: ► We quantify above- and below-ground CH4 fluxes in a landfill-cover soil. ► We link methanotrophic activity to estimates of CH4 loading from the waste body. ► Methane loading and emissions are highly variable in space and time. ► Eddy covariance measurements yield largest estimates of CH4 emissions. ► Potential methanotrophic activity is high at a location with substantial CH4 loading. - Abstract: Landfills are a major anthropogenic source of the greenhouse gas methane (CH4). However, much of the CH4 produced during the anaerobic degradation of organic waste is consumed by methanotrophic microorganisms during passage through the landfill-cover soil. On a section of a closed landfill near Liestal, Switzerland, we performed experiments to compare CH4 fluxes obtained by different methods at or above the cover-soil surface with below-ground fluxes, and to link methanotrophic activity to estimates of CH4 ingress (loading) from the waste body at selected locations. Fluxes of CH4 into or out of the cover soil were quantified by eddy-covariance and static flux-chamber measurements. In addition, CH4 concentrations at the soil surface were monitored using a field-portable FID detector. Near-surface CH4 fluxes and CH4 loading were estimated from soil–gas concentration profiles in conjunction with radon measurements, and gas push–pull tests (GPPTs) were performed to quantify rates of microbial CH4 oxidation. Eddy-covariance measurements yielded by far the largest and probably most representative estimates of overall CH4 emissions from the test section (daily mean up to ∼91,500 μmol m−2 d−1), whereas flux-chamber measurements and CH4 concentration profiles indicated that at the majority of locations the cover soil was a net sink for atmospheric CH4 (uptake up to −380 μmol m−2 d−1) during the experimental period. Methane concentration profiles also indicated strong variability in CH4 loading over short distances in the cover soil, while

  4. An Atypical Acidophil Cell Line Tumor Showing Focal Differentiation Toward Both Growth Hormone and Prolactin Cells.

    Science.gov (United States)

    Naritaka, Heiji; Kameya, Toru; Sato, Yuichi; Furuhata, Shigeru; Okui, Junichi; Kamiguchi, Yuji; Otani, Mitsuhiro; Toya, Shigeo

    1995-01-01

    We report a case of giant pituitary adenoma in a child. Computerized tomography (CT) scan revealed a suprasellar extension tumor mass with hydrocephalus. There was no clinical evidence of acromegaly, gigantism, and other hormonal symptoms. Endocrinologic studies showed within normal value of serum growth hormone (GH: 4.2 ng/mL) and slightly increased levels of prolactin (PRL: 78 ng/mL) and other pituitary hormone values were within normal range. On suppression test by bromocryptin, both GH and PRL levels were reduced. Histopathological findings revealed that the tumor consisted of predominantly chromophobic and partly eosinophilic adenoma cells. Immunohistochemical staining detected GH and PRL in a small number of distinctly different adenoma cells, respectively. Nonradioactive in situ hybridization (ISH) also showed GH and PRL mRNA expression in identical immunopositive cells. Electron microscopy (EM) demonstrated adenoma cells with moderate or small numbers of two types of dense granules and without fibrous body which are characteristic of sparsely granulated GH-cell adenomas. The adenoma does not fit into any classification but may be an atypical acidophil cell line tumor showing focal differentiation toward both GH and PRL cells. PMID:12114745

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

    Science.gov (United States)

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

    2011-12-01

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

  6. Effect of adaptation and pulp density on bioleaching of mine waste using indigenous acidophilic bacteria

    Science.gov (United States)

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

    2011-12-01

    Adaptation to environment is a natural phenomena that takes place in many animals, plants and microorganisms. These adapted organisms achieve stronger applicability than unadapted organisms after habitation in a specific environment for a long time. In the biohydrometallurgical industry, adaptation to special environment conditions by selective culturing is the most popular method for improving bioleaching activity of strains-although that is time consuming. This study investigated the influence of the bioleaching efficiency of mine waste under batch experimental conditions (adaptation and pulp density) using the indigenous acidophilic bacteria collected from acid mine drainage in Go-seong and Yeon-hwa, Korea. We conducted the batch experiments at the influences of parameters, such as the adaptation of bacteria and pulp density of the mine waste. In the adaptation case, the value of pH in 1'st adaptation bacteria sample exhibited lower than in 2'nd adaptation bacteria sample. And the content of both Cu and Zn at 1'st adaptation bacteria sample appeared lower than at 2'nd adaptation bacteria sample. In the SEM analysis, the rod-shaped bacteria with 1μm in length were observed on the filter paper (pore size - 0.45μm). The results of pulp density experiments revealed that the content of both Cu and Zn increased with increasing pulp density, since the increment of pulp density resulted in the enhancement of bioleaching capacity.

  7. Biodiversity and interactions of acidophiles: Key to understanding and optimizing microbial processing of ores and concentrates

    Institute of Scientific and Technical Information of China (English)

    D.B.JOHNSON

    2008-01-01

    Mining companies have become increasingly aware of the potential of microbiological approaches for recovering base and precious metals from low-grade ores,and for remediating acidic,metal-rich wastewaters that drain from both operating and abandoned mine sites.Biological systems offer a number of environmental and (sometimes) economical advantages over conventional approaches,such as pyrometallurgy,though their application is not appropriate in every situation.Mineral processing using micro-organisms has been exploited for extracting gold,copper,uranium and cobalt,and current developments are targeting other base metals.Recently,there has been a great increase in our knowledge and understanding of both the diversity of the microbiology of biomining environments,and of how the microorganisms interact with each other.The results from laboratory experiments which have simulated both stirred tank and heap bioreactor systems have shown that microbial consortia are more robust than pure cultures of mineral-oxidizing acidophiles,and also tend to be more effective at bioleaching and bio-oxidizing ores and concentrates.The paper presented a concise review of the nature and interactions of microbial consortia that are involved in the oxidation of sulfide minerals,and how these might be adapted to meet future challenges in biomining operations.

  8. Evidence of cell surface iron speciation of acidophilic iron-oxidizing microorganisms in indirect bioleaching process.

    Science.gov (United States)

    Nie, Zhen-yuan; Liu, Hong-chang; Xia, Jin-lan; Yang, Yi; Zhen, Xiang-jun; Zhang, Li-Juan; Qiu, Guan-zhou

    2016-02-01

    While indirect model has been widely accepted in bioleaching, but the evidence of cell surface iron speciation has not been reported. In the present work the iron speciation on the cell surfaces of four typically acidophilic iron-oxidizing microorganism (mesophilic Acidithiobacillus ferrooxidans ATCC 23270, moderately thermophilic Leptospirillum ferriphilum YSK and Sulfobacillus thermosulfidooxidans St, and extremely thermophilic Acidianus manzaensis YN25) grown on different energy substrates (chalcopyrite, pyrite, ferrous sulfate and elemental sulfur (S(0))) were studied in situ firstly by using synchrotron-based micro- X-ray fluorescence analysis and X-ray absorption near-edge structure spectroscopy. Results showed that the cells grown on iron-containing substrates had apparently higher surface iron content than the cells grown on S(0). Both ferrous iron and ferric iron were detected on the cell surface of all tested AIOMs, and the Fe(II)/Fe(III) ratios of the same microorganism were affected by different energy substrates. The iron distribution and bonding state of single cell of A. manzaensis were then studied in situ by scanning transmission soft X-ray microscopy based on dual-energy contrast analysis and stack analysis. Results showed that the iron species distributed evenly on the cell surface and bonded with amino, carboxyl and hydroxyl groups. PMID:26645388

  9. Isolation of amoebic-bacterial consortia capable of degrading trichloroethylene

    International Nuclear Information System (INIS)

    Groundwater from a waste disposal site contaminated with chlorinated alkenes was examined for the presence of amoebic-bacterial consortia capable of degrading the suspected carcinogen, trichloroethylene (TCE). Consortia were readily isolated from all of four test wells. They contained free-living amoebae, and heterotrophic and methylotrophic bacteria. Electron microscopic examination showed bacteria localized throughout the amoebic cytoplasm and an abundance of hyphomicrobium, but not Type I methanotrophs. The presence of Type II methanotrophs was indirectly indicated by lipid analysis of one consortium. The consortia have been passaged for over two years on mineral salts media in a methane atmosphere, which would not be expected to maintain the heterotrophs or amoebae separately. The methanotrophic bacteria apparently provided a stable nutrient source, allowing the persistence of the various genera. By use of 14C-radiotracer techniques, the degradation of TCE by the consortia was observed with 14C eventuating predominantly in CO2 and water-soluble products. In a more detailed examination of one consortia, the amoebae and heterotrohic components did not degrade TCE, while a mixed culture of heterotrophs and methanotrophs did degrade TCE, suggesting the latter component was the primary cause for the consortium's ability to degrade TCE. Amoebic-bacterial consortia may play a role in stabilizing and preserving methylotrophic bacteria in hostile environments

  10. Methanotrophic activity and diversity in different Sphagnum magellanicum dominated habitats in the southernmost peat bogs of Patagonia

    Directory of Open Access Journals (Sweden)

    M. S. M. Jetten

    2011-09-01

    Full Text Available Sphagnum peatlands are important ecosystems in the methane cycle. Methanotrophs living in and on the Sphagnum mosses are able to act as a methane filter and thereby reduce methane emissions. We investigated in situ methane concentrations and the corresponding activity and diversity of methanotrophs in different Sphagnum dominated bog microhabitats. In contrast to the Northern Hemisphere peat ecosystems the temperate South American peat bogs are dominated by one moss species; Sphagnum magellanicum. This permitted a species-independent comparison of the different bog microhabitats. Potential methane oxidizing activity was found in all Sphagnum mosses sampled and a positive correlation was found between activity and in situ methane concentrations. Substantial methane oxidation activity (23 μmol CH4 gDW−1 day−1 was found in pool mosses and could be correlated with higher in situ methane concentrations (>35 μmol CH4 l−1 pore water. Little methanotrophic activity (4 gDW−1 day−1 was observed in living Sphagnum mosses from lawns and hummocks. Methane oxidation activity was relatively high (>4 μmol CH4 gDW−1 day−1 in Sphagnum litter situated at depths around the water levels and rich in methane. The total bacterial community was studied using 16S rRNA gene sequencing and the methanotrophic communities were studied using a pmoA microarray and a complementary pmoA clone library. The methanotrophic diversity was similar in the different habitats of this study and surprisingly comparable to the methanotrophic diversity found in peat mosses from the Northern Hemisphere. The pmoA microarray data indicated that both alpha- and gammaproteobacterial methanotrophs were present in all Sphagnum mosses, even in those mosses with a low initial methane oxidation activity. Prolonged incubation of Sphagnum mosses from lawn and hummock with methane revealed that the methanotrophic community present was viable and showed an increased activity within 15

  11. The relative contribution of methanotrophs to microbial communities and carbon cycling in soil overlying a coal-bed methane seep

    Science.gov (United States)

    Mills, Christopher T.; Slater, Gregory F.; Dias, Robert F.; Carr, Stephanie A.; Reddy, Christopher M.; Schmidt, Raleigh; Mandernack, Kevin W.

    2013-01-01

    Seepage of coal-bed methane (CBM) through soils is a potential source of atmospheric CH4 and also a likely source of ancient (i.e. 14C-dead) carbon to soil microbial communities. Natural abundance 13C and 14C compositions of bacterial membrane phospholipid fatty acids (PLFAs) and soil gas CO2 and CH4 were used to assess the incorporation of CBM-derived carbon into methanotrophs and other members of the soil microbial community. Concentrations of type I and type II methanotroph PLFA biomarkers (16:1ω8c and 18:1ω8c, respectively) were elevated in CBM-impacted soils compared with a control site. Comparison of PLFA and 16s rDNA data suggested type I and II methanotroph populations were well estimated and overestimated by their PLFA biomarkers, respectively. The δ13C values of PLFAs common in type I and II methanotrophs were as negative as −67‰ and consistent with the assimilation of CBM. PLFAs more indicative of nonmethanotrophic bacteria had δ13C values that were intermediate indicating assimilation of both plant- and CBM-derived carbon. Δ14C values of select PLFAs (−351 to −936‰) indicated similar patterns of CBM assimilation by methanotrophs and nonmethanotrophs and were used to estimate that 35–91% of carbon assimilated by nonmethanotrophs was derived from CBM depending on time of sampling and soil depth.

  12. Effects of granular activated carbon on methane removal performance and methanotrophic community of a lab-scale bioreactor.

    Science.gov (United States)

    Lee, Eun-Hee; Choi, Sun-Ah; Yi, Taewoo; Kim, Tae Gwan; Lee, Sang-Don; Cho, Kyung-Suk

    2015-01-01

    Two identical lab-scale bioreactor systems were operated to examine the effects of granular activated carbon (GAC) on methane removal performance and methanotrophic community. Both bioreactor systems removed methane completely at a CH4 loading rate of 71.2 g-CH4·d(-1) for 17 days. However, the methane removal efficiency declined to 88% in the bioreactor without GAC, while the bioreactor amended with GAC showed greater methane removal efficiency of 97% at a CH4 loading rate of 107.5 g-CH4·d(-1). Although quantitative real-time PCR showed that methanotrophic populations were similar levels of 5-10 × 10(8) pmoA gene copy number·VSS(-1) in both systems, GAC addition changed the methanotrophic community composition of the bioreactor systems. Microarray assay revealed that GAC enhanced the type I methanotrophic genera including Methylobacter, Methylomicrobium, and Methylomonas of the system, which suggests that GAC probably provided a favorable environment for type I methanotrophs. These results indicated that GAC is a promising support material in bioreactor systems for CH4 mitigation.

  13. High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA

    Directory of Open Access Journals (Sweden)

    Evan Lau

    2015-04-01

    Full Text Available Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i organic horizon of forest soil; (ii surface peat; and (iii submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units, 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. Methylacidiphilum-like methanotrophs were not detected. Proteobacterial methanotrophic bacteria constitute <2% of microbiota in these environments, with the Methylocystaceae one to two orders of magnitude more abundant than the Methylococcaceae in all environments sampled. The Methylococcaceae are also less diverse in forest soil compared to the other two habitats. Nonmetric multidimensional scaling analyses indicated that the majority of methanotrophs from the Methylococcaceae and Methylocystaceae tend to occur in one habitat only (peat or Sphagnum moss or co-occurred in both Sphagnum moss and peat. This study provides insights into the structure of methanotrophic communities in relationship to habitat type, and suggests that peat and Sphagnum moss can influence methanotroph community structure and biogeography.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kurogi, T.; Linh, N. T. T.; Kuroki, T.; Yamada, T. [Department of Environmental and Life Science, Toyohashi University of Technology, Toyohashi 441-8580 (Japan); Hiraishi, A. [Department of Environmental and Life Science, Toyohashi University of Technology, Toyohashi 441-8580, Japan and Electronics-inspired Interdisciplinary Institute (EIIRIS), Toyohashi University of Technology, Toyohashi 441-8580 (Japan)

    2014-02-20

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

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

    Directory of Open Access Journals (Sweden)

    Francisco Navarro

    2016-10-01

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

  16. Rare bacteriohopanepolyols as markers for an autotrophic, intra-aerobic methanotroph

    Science.gov (United States)

    Kool, Dorien M.; Talbot, Helen M.; Rush, Darci; Ettwig, Katharina; Sinninghe Damsté, Jaap S.

    2014-07-01

    Bacteriohopanepolyols (BHPs) and their diagenetic products, hopanoids, are of great interest for their potential as biomarker lipids in both present day environments as well as in the geological record. Specific structural features such as methylation of the A-ring, and number and type of functional groups of C35 BHPs have been held characteristic for certain groups of organisms. Here we investigated the potential presence of BHPs in the unusual anaerobic methanotroph Methylomirabilis oxyfera and another Methylomirabilis sp. Although M. oxyfera thrives in anoxic settings, it uses internally produced molecular oxygen (from nitrite) for the oxidation of methane. We found that Methylomirabilis spp. synthesizes bacteriohopanehexol (BHP-hexol), -pentol, and -tetrol, and 3-methyl derivatives of each as major BHPs. None of the C-35 amino-BHPs that are more commonly observed in methanotrophs were detected. Our findings provide the first ever account of a 3-methyl-BHP-hexol, and only the second known source organism for BHP-hexol after Alicyclobacillus acidoterrestris. As the genes required for C3-methylation seem to be exclusively present in microorganisms with an aerobic metabolism, the abundant presence of 3-methyl-BHPs in Methylomirabilis spp. denotes for the first time the potential production of 3-methyl hopanoids in anoxic environments. Furthermore, with 13C-labeling experiments we show that M. oxyfera does not assimilate methane-carbon, but rather C from bicarbonate/CO2, into its BHPs. This implies that methanotroph-derived hopanoids do not necessarily exhibit a strongly depleted carbon isotopic signature, which is commonly anticipated with methanotrophy. This may have implications for the interpretation of the presence of hopanoids and their isotopic signature in the paleorecord.

  17. Identification of Methanotrophic Lipid Biomarkers in Cold-Seep Mussel Gills: Chemical and Isotopic Analysis

    Science.gov (United States)

    Jahnke, Linda L.; Summons, Roger E.; Dowling, Lesley M.; Zahiralis, Karen D.

    1995-01-01

    A lipid analysis of the tissues of a cold-seep mytilid mussel collected from the Louisiana slope of the Gulf of Mexico was used in conjunction with a compound-specific isotope analysis to demonstrate the presence of methanotrophic symbionts in the mussel gill tissue and to demonstrate the host's dependence on bacterially synthesized metabolic intermediates. The gill tissue contained large amounts of group-specific methanotrophic biomarkers, bacteriohopanoids, 4-methylsterols, lipopolysaccharide-associated hydroxy fatty acids, and type I-specific 16:1 fatty acid isomers with bond positions at delta-8, delta-10, and delta-ll. Only small amounts of these compounds were detected in the mantle or other tissues of the host animal. A variety of cholesterol and 4-methylsterol isomers were identified as both free and steryl esters, and the sterol double bond positions suggested that the major bacterially derived gill sterol(11.0% 4(alpha)-methyl-cholesta-8(14), 24-dien-3(beta)-ol) was converted to host cholesterol (64.2% of the gill sterol was cholest-5-en-3(beta)-ol). The stable carbon isotope values for gill and mantle preparations were, respectively, -59.0 and -60.4 per thousand for total tissue, -60.6 and -62.4 per thousand for total lipids, -60.2 and -63.9 per thousand for phospholipid fatty acids, and -71.8 and -73.8 per thousand for sterols. These stable carbon isotope values revealed that the relative fractionation pattern was similar to the patterns obtained in pure culture experiments with methanotrophic bacteria further supporting the conversion of the bacterial methyl-sterol pool.

  18. Degradation of methyl bromide by methanotrophic bacteria in cell suspensions and soils

    Science.gov (United States)

    Oremland, R.S.; Miller, L.G.; Culbertson, C.W.; Connell, T.L.; Jahnke, L.

    1994-01-01

    Cell suspensions of Methylococcus capsulatus mineralized methyl bromide (MeBr), as evidenced by its removal from the gas phase, the quantitative recovery of Br- in the spent medium, and the production of 14CO2 from [14C]MeBr. Methyl fluoride (MeF) inhibited oxidation of methane as well as that of [14C]MeBr. The rate of MeBr consumption by cells varied inversely with the supply of methane, which suggested a competitive relationship between these two substrates. However, MeBr did not support growth of the methanotroph. In soils exposed to high levels (10,000 ppm) of MeBr, methane oxidation was completely inhibited. At this concentration, MeBr removal rates were equivalent in killed and live controls, which indicated a chemical rather than biological removal reaction. At lower concentrations (1,000 ppm) of MeBr, methanotrophs were active and MeBr consumption rates were 10-fold higher in live controls than in killed controls. Soils exposed to trace levels (10 ppm) of MeBr demonstrated complete consumption within 5 h of incubation, while controls inhibited with MeF or incubated without O2 had 50% lower removal rates. Aerobic soils oxidized [14C]MeBr to 14CO2, and MeF inhibited oxidation by 72%. Field experiments demonstrated slightly lower MeBr removal rates in chambers containing MeF than in chambers lacking MeF. Collectively, these results show that soil methanotrophic bacteria, as well as other microbes, can degrade MeBr present in the environment.

  19. Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris

    Science.gov (United States)

    Crombie, Andrew T.; Murrell, J. Colin

    2014-06-01

    The climate-active gas methane is generated both by biological processes and by thermogenic decomposition of fossil organic material, which forms methane and short-chain alkanes, principally ethane, propane and butane. In addition to natural sources, environments are exposed to anthropogenic inputs of all these gases from oil and gas extraction and distribution. The gases provide carbon and/or energy for a diverse range of microorganisms that can metabolize them in both anoxic and oxic zones. Aerobic methanotrophs, which can assimilate methane, have been considered to be entirely distinct from utilizers of short-chain alkanes, and studies of environments exposed to mixtures of methane and multi-carbon alkanes have assumed that disparate groups of microorganisms are responsible for the metabolism of these gases. Here we describe the mechanism by which a single bacterial strain, Methylocella silvestris, can use methane or propane as a carbon and energy source, documenting a methanotroph that can utilize a short-chain alkane as an alternative to methane. Furthermore, during growth on a mixture of these gases, efficient consumption of both gases occurred at the same time. Two soluble di-iron centre monooxygenase (SDIMO) gene clusters were identified and were found to be differentially expressed during bacterial growth on these gases, although both were required for efficient propane utilization. This report of a methanotroph expressing an additional SDIMO that seems to be uniquely involved in short-chain alkane metabolism suggests that such metabolic flexibility may be important in many environments where methane and short-chain alkanes co-occur.

  20. Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

    OpenAIRE

    Esson, Kaitlin C.; Lin, Xueju; Kumaresan, Deepak; Jeffrey P Chanton; Murrell, J. Colin; Kostka, Joel E.

    2016-01-01

    The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, Minnesota, USA. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing, expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14-17 μmol CH4 g dry wt soil-1 d-1. Within DNA-SIP incubations...

  1. Stable Isotope Probing Analysis of the Diversity and Activity of Methanotrophic Bacteria in Soils from the Canadian High Arctic ▿

    OpenAIRE

    Martineau, Christine; Whyte, Lyle G.; Greer, Charles W.

    2010-01-01

    The melting of permafrost and its potential impact on CH4 emissions are major concerns in the context of global warming. Methanotrophic bacteria have the capacity to mitigate CH4 emissions from melting permafrost. Here, we used quantitative PCR (qPCR), stable isotope probing (SIP) of DNA, denaturing gradient gel electrophoresis (DGGE) fingerprinting, and sequencing of the 16S rRNA and pmoA genes to study the activity and diversity of methanotrophic bacteria in active-layer soils from Ellesmer...

  2. Molecular Characterization of Functional and Phylogenetic Genes from Natural Populations of Methanotrophs in Lake Sediments

    OpenAIRE

    Costello, Andria M.; Lidstrom, Mary E.

    1999-01-01

    The 16S rRNA and pmoA genes from natural populations of methane-oxidizing bacteria (methanotrophs) were PCR amplified from total community DNA extracted from Lake Washington sediments obtained from the area where peak methane oxidation occurred. Clone libraries were constructed for each of the genes, and approximately 200 clones from each library were analyzed by using restriction fragment length polymorphism (RFLP) and the tetrameric restriction enzymes MspI, HaeIII, and HhaI. The PCR produc...

  3. Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils

    OpenAIRE

    Cai, Yuanfeng; Yan, Zheng; Bodelier, P. L. E.; Conrad, R.; Jia, Zhongjun

    2016-01-01

    Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ~1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this ‘high-affinity’ methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was ...

  4. Methane Oxidation and Molecular Characterization of Methanotrophs from a Former Mercury Mine Impoundment

    OpenAIRE

    Baesman, Shaun M.; Miller, Laurence G.; Wei, Jeremy H.; Yirang Cho; Matys, Emily D.; Summons, Roger E.; Welander, Paula V.; Oremland, Ronald S.

    2015-01-01

    The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO2 with some CH4 present. The δ13CH4 value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively 12C-enriched CO2 suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bot...

  5. Earthworm activity in a simulated landfill cover soil shifts the community composition of active methanotrophs

    OpenAIRE

    Kumaresan, Deepak; Héry, Marina; Bodrossy, Levente; Singer, Andrew C.; Stralis-Pavese, Nancy; Thompson, Ian P.; Murrell, J. Colin

    2011-01-01

    Landfills represent a major source of methane into the atmosphere. In a previous study, we demonstrated that earthworm activity in landfill cover soil can increase soil methane oxidation capacity (Héry et al., 2008). In this study, a simulated landfill cover soil mesocosm (1 m x 0.15 m) was used to observe the influence of earthworms (Eisenia veneta) on the active methanotroph community composition, by analyzing the expression of the pmoA gene, which is responsible for methane oxidation. mRN...

  6. Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygen

    OpenAIRE

    Bussmann, Ingeborg; Rahalkar, Monali; Schink, Bernhard

    2006-01-01

    In sediments, methane-oxidizing bacteria live in opposing gradients of methane and oxygen. In such a gradient system, the fluxes of methane and oxygen are controlled by diffusion and consumption rates, and the rate-limiting substrate is maintained at a minimum concentration at the layer of consumption. Opposing gradients of methane and oxygen were mimicked in a specific cultivation set-up in which growth of methanotrophic bacteria occurred as a sharp band at either c. 5 or 20mm below the air-...

  7. Effects of toxicity, aeration, and reductant supply on trichloroethylene transformation by a mixed methanotrophic culture.

    OpenAIRE

    Alvarez-Cohen, L; McCarty, P L

    1991-01-01

    The trichloroethylene (TCE) transformation rate and capacity of a mixed methanotrophic culture at room temperature were measured to determine the effects of time without methane (resting), use of an alternative energy source (formate), aeration, and toxicity of TCE and its transformation products. The initial specific TCE transformation rate of resting cells was 0.6 mg of TCE per mg of cells per day, and they had a finite TCE transformation capacity of 0.036 mg of TCE per mg of cells. Formate...

  8. Seasonal and spatial aspects of the eco-distribution of methanotrophic bacteria in floodplain soils

    Science.gov (United States)

    Bodelier, P. L. E.; Meima-Franke, M.; Kamst, M.; Bodrossy, L.; Stralis-Pavese, N.; Hefting, M. M.; Laanbroek, R.

    2009-04-01

    METHECO is the acronym of a consortium of research groups funded by the European Science foundation (ESF) within the EuroDIVERSITY program. The consortium investigates the role of microbial diversity in the dynamics and stability of global methane consumption. The consortium covers various habitats (i.e. Landfills, rice paddies, alpine meadows, littoral wetlands, forests, arctic wetlands, peat soils and river floodplains) and assesses the effects of natural environmental perturbation on the function structure relationship of methane-consuming microbial communities. Consortium members follow the same experimental and methodological scheme using DNA and RNA based techniques (i.e. pmoA-based cloning, DGGE, micro arrays, Real Time PCR, stable isotope probing). This paper presents the results obtained in a river floodplain along the river Rhine in the Netherlands, a habitat anticipated to be subjected to major changes in flooding regime due to climate change. Experiments were carried out to assess methanotrophic diversity, methane oxidation kinetics and spatial variability of function and structure of methane-oxidizing communities. Flooding events affected methane consumption negatively on short term. However, the long -term consequences of the flooding regime where the establishment of a distinct maximum methane consumption activity exactly in the part of the floodplain intermediate between permanently and irregularly flooded, where moisture and organic matter content were optimal for methane cycling. The methanotrophic community composition as analysed by pmoA micro array mirrored the result of the activity measurements, demonstrating that the communities differed clearly according to the flooding gradient. Diversity as assessed by micro array and activity components (initial consumption, Vmax, Vmax/Km) were positively correlated. QPCR analyses showed that main types of methanotrophic bacteria were differentially distributed throughout the flooding gradient. Type I

  9. Effect of Mineral Nutrients on the Kinetics of Methane Utilization by Methanotrophs

    DEFF Research Database (Denmark)

    Boiesen, Anette; Arvin, Erik; Broholm, Kim

    1993-01-01

    The effect of different mineral nutrients on the kinetics of methane biodegradation by a mixed culture of methanotrophic bacteria was studied. The substrate factors examined were ammonia, iron, copper, manganese, phosphate, and sulphide. The presence of iron in the growth medium had a strong effect...... on the yield coefficient. Yield coefficients up to 0.49 mg protein per mg methane were observed when iron was added at concentrations of 0.10-5.0 mg/l. Iron addition also increased the maximum methane utilization rate. The same effect was observed after addition of ammonium to a medium where nitrate...

  10. Nitrite- and Nitrate-Dependent Methanotrophs - Environmental Detection and Relevance in Freshwater Ecosystems

    Science.gov (United States)

    Ettwig, K. F.

    2014-12-01

    Humans continue to have an enormous impact on global C and N cycles. While a clear stimulation of methane emissions through human activities is evident, the role of also increasingly released nitrogenous compounds as electron acceptors for microbial methane oxidation is not well constrained. We have developed diverse methods for environmental detection of nitrate(NO3-)- and - predominantly - nitrite(NO2-)-dependent methanotrophs, which have been applied to several freshwater environments. In contrast to most metabolically flexible heterotrophic denitrifiers, the microorganisms responsible for methane-dependent nitrate/nitrite reduction seem to be specialized to use methane only, grow slowly and employ pathways different from each other and from model organisms, which necessitate new approaches for the assessment of their environmental relevance. Nitrite-dependent methane oxidation is carried out by bacteria of the NC10 phylum, whereas nitrate-dependent methane oxidizers are close relatives of methanogenic archaea and sulfate-dependent anaerobic methanotrophs (ANME-2). Laboratory enrichment cultures of the nitrite-reducing methanotroph Methylomirabilis oxyfera (NC10 phylum) have formed the basis for its genetic and physiological characterization and the development of several independent methods for its sensitive detection. M. oxyfera differs from all known microorganisms by encoding an incomplete denitrification pathway, in which the last 2 steps, the reduction of NO via N2O to N2, apparently is replaced by the dismutation of NO to N2 and O2. The intracellularly produced O2 is used for methane oxidation via a methane monooxygenase, analogously to the phylogenetically unrelated proteobacterial methanotrophs. But unlike in proteobacteria, C is not assimilated from methane, but rather CO2, with important consequences for the interpretation of environmental isotope labelling studies. In addition, M. oxyfera is characterized by a distinct PLFA profile, including

  11. The acidophilic microorganisms diversity present in lignite and pit coal from Paroseni, Halânga, Turceni mines

    Directory of Open Access Journals (Sweden)

    Carmen Madalina CISMASIU

    2009-11-01

    Full Text Available Pollution from coal combustion is the largest problem in the current use of coal and the biggest constraint on the increased use of coal. When these fossil fuels are combusted, sulphur-di-oxide is released into the atmosphere causing acid rains which dissolves buildings, kills forest. Knowing the physiological groups of microorganisms present in the coal samples has an ecological importance, completing the knowledge in the field of the microorganism’s ecology and a practical importance, being a source of new microorganisms with biotechnological potential. The microbial communities evidenced in such sites include both groups of chemolithotrophic microorganisms involved in the metals biosolubilization processes and groups of heterotrophic microorganisms involved in the processes of bioaccumulation or biofixation of metallic ions. In this context, this paper presents the study regarding the main physiological groups of microorganisms present in the pit coal and lignite samples after the industrial processing of coal. The results revealed that the microorganisms belonging to the following physiological groups: aerobic heterotrophic acidophilic bacteria, strictly anaerobic heterotrophic (sulphur-reducing, nitrifying bacteria (nitrite and nitrate bacteria, denitrifying bacteria and acidophilic chemolithotrophic bacteria on Fe2+, on S0 and on S2O3.

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

    Science.gov (United States)

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

    2012-12-01

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

  13. Effect of VOCs and methane in the biological oxidation of the ferrous ion by an acidophilic consortium.

    Science.gov (United States)

    Almenglo, F; Ramírez, M; Gómez, J M; Cantero, D; Revah, S; González-Sánchez, A

    2012-01-01

    During the elimination of H2S from biogas in an aqueous ferric sulphate solution, volatile organic compounds (VOCs) and methane are absorbed and may have an effect on the subsequent biological regeneration of ferric ion. This study was conducted to investigate the effect of maximum concentrations of methane and some VOCs found in biogas on the ferrous oxidation of an acidophilic microbial consortium (FO consortium). The presence and impact of heterotrophic microorganisms on the activity of the acidophilic consortium was also evaluated. No effect on the ferrous oxidation rate was found with gas concentrations of 1500 mg toluene m(-3), 1400 mg 2-butanol m(-3) or 1250 mg 1,2-dichloroethane m(-3), nor with methane at gas concentrations ranging from 15-25% (v/v). A tenfold increase in VOCs concentrations totally inhibited the microbial activity of the FO consortium and the heterotrophs. The presence of a heterotrophic fungus may promote the autotrophic growth of the FO consortium. PMID:22629626

  14. Thiol/Disulfide system plays a crucial role in redox protection in the acidophilic iron-oxidizing bacterium Leptospirillum ferriphilum.

    Directory of Open Access Journals (Sweden)

    Javiera Norambuena

    Full Text Available Thiol/disulfide systems are involved in the maintenance of the redox status of proteins and other molecules that contain thiol/disulfide groups. Leptospirillum ferriphilum DSM14647, an acidophilic bacterium that uses Fe(2+ as electron donor, and withstands very high concentrations of iron and other redox active metals, is a good model to study how acidophiles preserve the thiol/disulfide balance. We studied the composition of thiol/disulfide systems and their role in the oxidative stress response in this extremophile bacterium. Bioinformatic analysis using genomic data and enzymatic assays using protein extracts from cells grown under oxidative stress revealed that the major thiol/disulfide system from L. ferriphilum are a cytoplasmic thioredoxin system (composed by thioredoxins Trx and thioredoxin reductase TR, periplasmic thiol oxidation system (DsbA/DsbB and a c-type cytochrome maturation system (DsbD/DsbE. Upon exposure of L. ferriphilum to reactive oxygen species (ROS-generating compounds, transcriptional activation of the genes encoding Trxs and the TR enzyme, which results in an increase of the corresponding activity, was observed. Altogether these data suggest that the thioredoxin-based thiol/disulfide system plays an important role in redox protection of L. ferriphilum favoring the survival of this microorganism under extreme environmental oxidative conditions.

  15. In situ bioremediation of trichloroethylene-contaminated water by a resting-cell methanotrophic microbial filter

    International Nuclear Information System (INIS)

    The Lawrence Livermore National Laboratory is testing and developing an in situ microbial filter technology for remediating migrating subsurface plumes contaminated with low concentrations of trichloroethylene (TCE). Their current focus is the establishment of a replenishable bioactive zone (catalytic filter) along expanding plume boundaries by the Injection of a representative methanotrophic bacterium, Methylosinus trichosporium OB3b. We have successfully demonstrated this microbial filter strategy using emplaced, attached resting cells (no methane additions) in a 1.1-m flow-through test bed loaded with water-saturated sand. Two separate 24 h pulses of TCE (109 ppb and 85 ppb), one week apart, were pumped through the system at a flow velocity of 1.5 cm/h; no TCE (<0.5 ppb) was detected on the downstream side of the microbial filter. Subsequent excavation of the wet sand confirmed the existence of a TCE-bioactive zone 19 days after it had been created. An enhanced longevity of the cellular, soluble-form methane monooxygenase produced by this methanotroph Is a result of our laboratory bioreactor culturing conditions. Additional experiments with cells in sealed vials and emplaced in the 1.1-m test bed yielded a high resting-cell finite TCE biotransformation capacity of ∼ 0.25 mg per mg of bacteria; this is suitable for a planned sand-filled trench field demonstration at a Lawrence Livermore National Laboratory site

  16. Carbon Isotope Fractionations Associated with Methanotrophic Growth with the Soluble and Particulate Methane Monooxygenases

    Science.gov (United States)

    Jahnke, Linda L.; Summons, Roger E.; Chang, Sherwood (Technical Monitor)

    1996-01-01

    Growth experiments with the RuMP-type methanotroph, Methylococcus capsulatus (Bath), have demonstrated that biomass and lipid biomarkers are significantly depleted in C-13 compared to the substrate methane and that the extent of fractionation is dependent on whether cells express the soluble (s) or particulate (p) methane monooxygenase (MMO). The presence or absence of the characteristic sMMO subunits was monitored using SDS-polyacrylamide gels. In M. capsulatus grown with no Cu supplementation, the characteristic sMMO subunits were observed in the soluble fraction throughout the entire growth period and biomass was depleted in C-13 by approximately 14,700 relative to substrate methane. In cells grown with 5uM Cu, no sMMO bands were observed and a greater fractionation of approximately 27,700 in resultant biomass was obtained. Methanol growth experiments with M. capsulatus and with a RuMP methylotroph, Methylophilus methylotrophus, in which biomass measurements yielded depletions in C-13 of 9 and 5%(sub o), respectively, suggest that oxidation of methane is the major fractionation step. Growth of M. capsulatus at a low level of oxygen, approximately 0.5%, had no significant effect on carbon isotope fractionation by either sMMO or pMMO. These observations are significant for identification of molecular biomarkers; and methanotrophic contributions to carbon isotope composition in natural environments.

  17. In situ bioremediation of trichloroethylene-contaminated water by a resting-cell methanotrophic microbial filter

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, R T; Duba, A G; Durham, W B; Hanna, M L; Jackson, K J; Jovanovich, M C; Knapp, R B; Knezovich, J P; Shah, N N; Shonnard, D R; Wijesinghe, A M

    1992-10-01

    The Lawrence Livermore National Laboratory is testing and developing an in situ microbial filter technology for remediating migrating subsurface plumes contaminated with low concentrations of trichloroethylene (TCE). Their current focus is the establishment of a replenishable bioactive zone (catalytic filter) along expanding plume boundaries by the Injection of a representative methanotrophic bacterium, Methylosinus trichosporium OB3b. We have successfully demonstrated this microbial filter strategy using emplaced, attached resting cells (no methane additions) in a 1.1-m flow-through test bed loaded with water-saturated sand. Two separate 24 h pulses of TCE (109 ppb and 85 ppb), one week apart, were pumped through the system at a flow velocity of 1.5 cm/h; no TCE (<0.5 ppb) was detected on the downstream side of the microbial filter. Subsequent excavation of the wet sand confirmed the existence of a TCE-bioactive zone 19 days after it had been created. An enhanced longevity of the cellular, soluble-form methane monooxygenase produced by this methanotroph Is a result of our laboratory bioreactor culturing conditions. Additional experiments with cells in sealed vials and emplaced in the 1.1-m test bed yielded a high resting-cell finite TCE biotransformation capacity of [approximately] 0.25 mg per mg of bacteria; this is suitable for a planned sand-filled trench field demonstration at a Lawrence Livermore National Laboratory site.

  18. Construction of the astaxanthin biosynthetic pathway in a methanotrophic bacterium Methylomonas sp. strain 16a.

    Science.gov (United States)

    Ye, Rick W; Yao, Henry; Stead, Kristen; Wang, Tao; Tao, Luan; Cheng, Qiong; Sharpe, Pamela L; Suh, Wonchul; Nagel, Eva; Arcilla, Dennis; Dragotta, Dominic; Miller, Edward S

    2007-04-01

    Methylomonas sp. strain 16a is an obligate methanotrophic bacterium that uses methane or methanol as the sole carbon source. An effort was made to engineer this organism for astaxanthin production. Upon expressing the canthaxanthin gene cluster under the control of the native hps promoter in the chromosome, canthaxanthin was produced as the main carotenoid. Further conversion to astaxanthin was carried out by expressing different combinations of crtW and crtZ genes encoding the beta-carotenoid ketolase and hydroxylase. The carotenoid intermediate profile was influenced by the copy number of these two genes under the control of the hps promoter. Expression of two copies of crtZ and one copy of crtW led to the accumulation of a large amount of the mono-ketolated product adonixanthin. On the other hand, expression of two copies of crtW and one copy of crtZ resulted in the presence of non-hydroxylated carotenoid canthaxanthin and the mono-hydroxylated adonirubin. Production of astaxanthin as the predominant carotenoid was obtained in a strain containing two complete sets of carotenoid biosynthetic genes. This strain had an astaxanthin titer ranging from 1 to 2.4 mg g(-1) of dry cell biomass depending on the growth conditions. More than 90% of the total carotenoid was astaxanthin, of which the majority was in the form of E-isomer. This result indicates that it is possible to produce astaxanthin with desirable properties in methanotrophs through genetic engineering.

  19. Biosynthesis of poly-3-hydroxybutyrate with a high molecular weight by methanotroph from methane and methanol

    Institute of Scientific and Technical Information of China (English)

    Yingxin Zhang; Jiaying Xin; Linlin Chen; Hao Song; Chungu Xia

    2008-01-01

    Poly-3-hydroxybutyrate (PHB) can be produced by various species of bacteria. Among the possible carbon sources, both methane and methanol could be a suitable substrate for the production of PHB. Methane is cheap and plentiful not only as natural gas, but also as biogas. Methanol can also maintain methanotrophic activity in some conditions. The methanotrophic strain Methylosinus trichosporium IMV3011 can accumulate PHB with methane and methanol in a brief nonsterile process. Liquid methanol (0.1%) was added to improve the oxidization of methane. The studies were carried out using shake flasks. Cultivation was performed in two stages: a continuous growth phase and a PHB accumulation phase under the conditions short of essential nutrients (ammonium, nitrate, phosphorus, copper, iron (III), magnesium or ethylenediamine tetraacetate (EDTA)) in batch culture. It was found that the most suitable growth time for the cell is 144 h. Then an optimized culture condition for second stage was determined, in which the PHB concentration could be much increased to 0.6 g/L. In order to increase PHB content, citric acid was added as an inhibitor of tricarboxylic acid cycle (TCA). It was found that citric acid is favorable for the PHB accumulation, and the PHB yield was increased to 40% (w/w) from the initial yield of 12% (w/w) after nutrient deficiency cultivation. The PHB produced is of very high quality with molecular weight up to 1.5 ×106Da.

  20. Poly-3-hydroxybutyrate metabolism in the type II methanotroph Methylocystis parvus OBBP.

    Science.gov (United States)

    Pieja, Allison J; Sundstrom, Eric R; Criddle, Craig S

    2011-09-01

    Differences in carbon assimilation pathways and reducing power requirements among organisms are likely to affect the role of the storage polymer poly-3-hydroxybutyrate (PHB). Previous researchers have demonstrated that PHB functions as a sole growth substrate in aerobic cultures enriched on acetate during periods of carbon deficiency, but it is uncertain how C(1) metabolism affects the role of PHB. In the present study, the type II methanotroph Methylocystis parvus OBBP did not replicate using stored PHB in the absence of methane, even when all other nutrients were provided in excess. When PHB-rich cultures of M. parvus OBBP were deprived of carbon and nitrogen for 48 h, they did not utilize significant amounts of stored PHB, and neither cell concentrations nor concentrations of total suspended solids changed significantly. When methane and nitrogen both were present, PHB and methane were consumed simultaneously. Cells with PHB had significantly higher specific growth rates than cells lacking PHB. The addition of formate (a source of reducing power) to PHB-rich cells delayed PHB consumption, but the addition of glyoxylate (a source of C(2) units) did not. This and results from other researchers suggest that methanotrophic PHB metabolism is linked to the supply of reducing power as opposed to the supply of C(2) units for synthesis. PMID:21724874

  1. Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus.

    Science.gov (United States)

    Valdes, Jorge; Ossandon, Francisco; Quatrini, Raquel; Dopson, Mark; Holmes, David S

    2011-12-01

    Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and inorganic sulfur compounds. Here we present the draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the identification of genes for survival and colonization of extremely acidic environments.

  2. Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the Evolution of the Acidithiobacillus Genus

    OpenAIRE

    Valdes, Jorge; Ossandon, Francisco; Quatrini, Raquel; Dopson, Mark; Holmes, David S

    2011-01-01

    Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and inorganic sulfur compounds. Here we present the draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the identification of genes for survival and colonization of extremely acidic environments.

  3. EMERGING TECHNOLOGY SUMMARY: PILOT-SCALE DEMONSTRATION OF A TWO-STAGE METHANOTROPHIC BIOREACTOR FOR BIODEGRADATION OF TRICHLOROETHENE IN GROUNDWATER

    Science.gov (United States)

    BioTrol, Inc., developed a two-stage, methanotrophic, bioreactor system for remediation of water contaminated with trichloroethylene (TCE) and other chlorinated, volatile, aliphatic hydrocarbons. The first stage was a suspended-growth culture vessel with a bubbleless methane tran...

  4. Autotrophic Carbon Dioxide Fixation via the Calvin-Benson-Bassham Cycle by the Denitrifying Methanotroph "Candidatus Methylomirabilis oxyfera"

    NARCIS (Netherlands)

    Rasigraf, O.; Kool, D.M.; Jetten, M.S.M.; Ettwig, K.F.; Sinninghe Damsté, J.S.

    2014-01-01

    Methane is an important greenhouse gas and the most abundant hydrocarbon in the Earth's atmosphere. Methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. "Candidatus Methylomirabilis oxyfera" is a

  5. Contribution of Methanotrophic and Nitrifying Bacteria to CH4 and NH4+ Oxidation in the Rhizosphere of Rice Plants as Determined by New Methods of Discrimination

    OpenAIRE

    Bodelier, Paul L. E.; Frenzel, Peter

    1999-01-01

    Methanotrophic and nitrifying bacteria are both able to oxidize CH4 as well as NH4+. To date it is not possible to estimate the relative contribution of methanotrophs to nitrification and that of nitrifiers to CH4 oxidation and thus to assess their roles in N and C cycling in soils and sediments. This study presents new options for discrimination between the activities of methanotrophs and nitrifiers, based on the competitive inhibitor CH3F and on recovery after inhibition with C2H2. By using...

  6. Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field.

    Science.gov (United States)

    Bao, Zhihua; Shinoda, Ryo; Minamisawa, Kiwamu

    2016-01-01

    N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input. PMID:27587832

  7. Quantifying adhesion of acidophilic bioleaching bacteria to silica and pyrite by atomic force microscopy with a bacterial probe.

    Science.gov (United States)

    Diao, Mengxue; Taran, Elena; Mahler, Stephen; Nguyen, Tuan A H; Nguyen, Anh V

    2014-03-01

    The adhesion of acidophilic bacteria to mineral surfaces is an important phenomenon in bioleaching processes. In this study, functionalized colloidal probes covered by bioleaching bacterial cells (Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans) were developed and used to sense specific adhesion forces to a silica surface and a pyrite surface in various solutions. Experimentally, recorded retraction curves of A. thiooxidans revealed sawtooth features that were in good agreement with the wormlike chain model, while that of L. ferrooxidans exhibited stair-step separation. The magnitudes of adhesion forces and snap-off distances were strongly influenced by the ionic strength and pH. Macroscopic surface properties including hydrophobicity and surface potential for bacterial cells and substrata were measured by a sessile drop method and microelectrophoresis. The ATR-FTIR spectra indicated the presence of different types of biopolymers on two strains of bacteria.

  8. The Effect of Specific Conditions on Cu, Ni, Zn and Al Recovery from PCBS Waste Using Acidophilic Bacterial Strains

    Directory of Open Access Journals (Sweden)

    Mrážiková A.

    2016-03-01

    Full Text Available The objective of this work was to evaluate the influence of static, stirring and shaking conditions on copper, zinc, nickel and aluminium dissolution from printed circuit boards (PCBs using the mixed acidophilic bacterial culture of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. The results revealed that static conditions were the most effective in zinc and aluminium dissolution. Zinc was removed almost completely under static conditions, whereas maximum of nickel dissolution was reached under the stirring conditions. The highest copper recovery (36% was reached under stirring conditions. The shaking conditions appeared to be the least suitable. The relative importance of these systems for the bioleaching of copper and nickel decreased in the order: stirring, static conditions, shaking.

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

    Science.gov (United States)

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

    2007-11-01

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

  10. Aerobic methanotrophic communities at the Red Sea brine-seawater interface

    Directory of Open Access Journals (Sweden)

    Rehab Z. Abdallah

    2014-09-01

    Full Text Available The central rift of the Red Sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. Three of these pools, the Atlantis II, Kebrit and Discovery Deeps, are uniquely characterized by a high concentration of hydrocarbons. The brine-seawater interface, described as an anoxic-oxic (brine-seawater boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. The sequencing of 16S rRNA pyrotags revealed that these interfaces are characterized by high microbial community diversity. Signatures of aerobic methane-oxidizing bacteria were detected in the Atlantis II Interface (ATII-I and the Kebrit Deep Upper (KB-U and Lower (KB-L brine-seawater interfaces. Through phylogenetic analysis of pmoA, we further demonstrated that the ATII-I aerobic methanotroph community is highly diverse. We propose four ATII-I pmoA clusters. Most importantly, cluster 2 groups with marine methane seep methanotrophs, and cluster 4 represent a unique lineage of an uncultured bacterium with divergent alkane monooxygenases. Moreover, non-metric multidimensional scaling (NMDS based on the ordination of putative enzymes involved in methane metabolism showed that the Kebrit interface layers were distinct from the ATII-I and DD-I brine-seawater interfaces.

  11. Growth rate characteristics of acidophilic heterotrophic organisms from mine waste rock piles

    Science.gov (United States)

    Yacob, T. W.; Silverstein, J.; Jenkins, J.; Andre, B. J.; Rajaram, H.

    2010-12-01

    Autotrophic iron oxidizing bacteria play a key role in pyrite oxidation and generation of acid mine drainage AMD. Scarcity of organic substrates in many disturbed sites insures that IOB have sufficient oxygen and other nutrients for growth. It is proposed that addition of organic carbon substrate to waste rock piles will result in enrichment of heterotrophic microorganisms limiting the role of IOB in AMD generation. Previous researchers have used the acidophilic heterotroph Acidiphilium cryptum as a model to study the effects of organic substrate addition on the pyrite oxidation/AMD cycle. In order to develop a quantitative model of effects such as competition for oxygen, it is necessary to use growth and substrate consumption rate expressions, and one approach is to choose a model strain such as A. cryptum for kinetic studies. However we have found that the growth rate characteristics of A. cryptum may not provide an accurate model of the remediation effects of organic addition to subsurface mined sites. Fluorescent in-situ hybridization (FISH) assays of extracts of mine waste rock enriched with glucose and yeast extract did not produce countable numbers of cells in the Acidiphilium genus, with a detection limit of3 x 104 cells/gram rock, despite evidence of the presence of well established heterotrophic organisms. However, an MPN enrichment produced heterotrophic population estimates of 1x107 and 1x109 cells/gram rock. Growth rate studies of A. cryptum showed that cultures took 120 hours to degrade 50% of an initial glucose concentration of 2,000 mg/L. However a mixed culture enriched from mine waste rock consumed 100% of the same amount of glucose in 24 hours. Substrate consumption data for the mixed culture were fit to a Monod growth model: {dS}/{dt} = μ_{max}S {( {X_0}/{Y} + S_0 -S )}/{(K_s +S)} Kinetic parameters were estimated utilizing a non linear regression method coupled with an ODE solver. The maximum specific growth rate of the mixed population with

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

    Science.gov (United States)

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

    2015-03-01

    Aerobic denitrification is the main process for high N2O production in acid tea field soil. However, the biological mechanisms for the high emission are not fully understood. In this study, we examined N2O emission and denitrifier communities in 100-year-old tea soils with four pH levels (3.71, 5.11, 6.19, and 7.41) and four nitrate concentration (0, 50, 200, and 1000 mg kg(-1) of NO3 (-)-N) addition. Results showed the highest N2O emission (10.1 mg kg(-1) over 21 days) from the soil at pH 3.71 with 1000 mg kg(-1) NO3 (-) addition. The N2O reduction and denitrification enzyme activity in the acid soils (pH pH 7.41. Moreover, TRF 78 of nirS and TRF 187 of nosZ dominated in soils of pH 3.71, suggesting an important role of acidophilic denitrifiers in N2O production and reduction. CCA analysis also showed a negative correlation between the dominant denitrifier ecotypes (nirS TRF 78, nosZ TRF 187) and soil pH. The representative sequences were identical to those of cultivated denitrifiers from acidic soils via phylogenetic tree analysis. Our results showed that the acidophilic denitrifier adaptation to the acid environment results in high N2O emission in this highly acidic tea soil. PMID:25273518

  13. pmoA-based analysis of methanotrophs in a littoral lake sediment reveals a diverse and stable community in a dynamic environment

    OpenAIRE

    Pester, Michael; Friedrich, Michael W.; Schink, Bernhard; Brune, Andreas

    2004-01-01

    Diversity and community structure of aerobic methane-oxidizing bacteria in the littoral sediment of Lake Constance was investigated by cloning analysis and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the pmoA gene. Phylogenetic analysis revealed a high diversity of type I and type II methanotrophs in the oxygenated uppermost centimeter of the sediment. T-RFLP profiles indicated a high similarity between the active methanotrophic community in the oxic layer and...

  14. High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA

    OpenAIRE

    Evan Lau; Edward J. Nolan IV; Zachary W. Dillard; Ryan D. Dague; Amanda L. Semple; Wendi L. Wentzell

    2015-01-01

    Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiple...

  15. Influence of the Endogenous Storage Lipid Poly-β-Hydroxybutyrate on the Reducing Power Availability during Cometabolism of Trichloroethylene and Naphthalene by Resting Methanotrophic Mixed Cultures

    OpenAIRE

    Henrysson, Tomas; McCarty, Perry L.

    1993-01-01

    The role of the storage lipid poly-β-hydroxybutyrate (PHB) in trichloroethylene transformation by methanotrophic mixed cultures was investigated. Naphthalene oxidation rates were used to assay for soluble methane monooxygenase activity. The PHB content of methanotrophic cells grown in reactors varied diurnally as well as from day to day. A positive correlation between the amount of PHB in the cells and the naphthalene oxidation rate as well as between PHB and the trichloroethylene transformat...

  16. Microbial ecology on the microcosm level: Activity and population dynamics of methanotrophic bacteria during early succession in a flooded rice field soil

    Science.gov (United States)

    Krause, S.; Frenzel, P.

    2009-04-01

    Methane oxidizing bacteria (methanotrophs) play an important role in natural wetlands and rice fields preventing large amounts of methane from escaping into the atmosphere. The occurrence of both type I and type II methanotrophs in the soil surface layer has been demonstrated in many studies. However, there is no profound understanding which of them are responsible for the oxidizing activity and how they differ ecologically. Hence, a gradient microcosm system was applied simulating oxic-anoxic interfaces of water saturated soils to unravel population dynamics in early succession of methanotrophs in a flooded rice paddy. Additionally, environmental parameters were analyzed to link environment, populations, and their specific activity. We measured pmoA-based (particulate methane monooxygenase) terminal restriction fragment length polymorphism (T-RFLP) profiles both on transcription and population level. DNA T-RFLP patterns showed no major differences in the methanotrophic community structure remaining relatively constant over time. In contrast the active methanotrophic community structure as detected by pmoA mRNA T-RFLP analysis clearly demonstrated a distinct pattern from DNA T-RFLP profiles. While type II represented the most prominent group on the population level it seems to play a minor role on the transcription level. Furthermore there were no clear implications towards a link between soil parameters (e.g. NH4+ concentration) and methanotrophic community structure.

  17. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs.

    OpenAIRE

    McDonald, I R; Murrell, J.C.

    1997-01-01

    The methanol dehydrogenase gene mxaF, encoding the large subunit of the enzyme, was amplified from the DNA of a number of representative methanotrophs, methyletrophs, and environmental samples by PCR using primers designed from regions of conserved amino acid sequence identified by comparison of three known sequences of the large subunit of methanol dehydrogenase. The resulting 550-bp PCR products were cloned and sequenced. Analysis of the predicted amino acid sequences corresponding to these...

  18. Responses of methanotrophic activity, community and EPS production to CH4 and O2 concentrations in waste biocover soils.

    Science.gov (United States)

    Wei, Xiao-Meng; Su, Yao; Zhang, Hong-Tao; Chen, Min; He, Ruo

    2015-08-01

    Biocover soils are known to be a good alternative material to mitigate CH4 emissions from landfills to the atmosphere. In this study, 16 treatments with four O2 concentrations (∼0%, 5%, 10% and 21%) and four CH4 concentrations (i.e. 1%, 10%, 20% and 50%) were conducted to estimate extracellular polymeric substances (EPS) production, methanotrophic activity and community in response to CH4 and O2 concentrations in waste biocover soil (WBS). When the CH4 concentration was saturated for CH4 oxidation in the WBS, the continuous exposure of CH4 above the saturated concentrations could not obviously enhance CH4 oxidation activity. In the WBS, extracellular protein (ECP) production was negatively related with the tested CH4 concentrations, while both ECP and extracellular polysaccharides (ECPS) productions were positively related with the tested O2 concentrations. Cloning and terminal restriction fragment length polymorphism analyses showed that type I methanotrophs (Methylocaldum, Methylococcaceae, Methylomicrobium and Methylobacter) and type II methanotrophs (Methylosinus) dominated in the WBS. Among them, Methylocaldum and/or Methylococcaceae were sensitive to low O2 concentrations of ∼0%. Methylobacter had propensity to grow at low O2 concentrations of ∼0% and 5%, while Methylosinus preferred environments with high concentrations of CH4 (⩾10%) and O2 (21%). In the tested five environmental variables of ECPS, O2, EPS, CH4 and ECP, only ECPS and O2 concentrations had significant effect on the methanotrophic communities. These results suggested that O2 concentration in landfill covers should be paid more attention to optimize and sustain CH4 oxidation for mitigating CH4 emission from landfills. PMID:25921582

  19. Inhibition of Nitrifiers and Methanotrophs from an Agricultural Humisol by Allylsulfide and Its Implications for Environmental Studies

    OpenAIRE

    Neufeld, Josh D.; Knowles, Roger

    1999-01-01

    Allylsulfide, an inhibitor of ammonia monooxygenase, was tested to determine its ability to inhibit nitrification and methane oxidation in pure cultures, in agricultural humisol enrichment cultures, and in humisol slurries. We confirmed that allylsulfide is a differential inhibitor of cultures of nitrifiers and methanotrophs at concentrations of 1 and 200 μM, respectively, which result in 50% inhibition. However, although a nitrifying enrichment culture added to sterilized humisol was inhibit...

  20. Consumption of Methane and CO_2 by Methanotrophic Microbial Mats from Gas Seeps of the Anoxic Black Sea

    OpenAIRE

    Treude, Tina; Orphan, Victoria; Knittel, Katrin; Gieseke, Armin; House, Christopher H.; Boetius, Antje

    2007-01-01

    The deep anoxic shelf of the northwestern Black Sea has numerous gas seeps, which are populated by methanotrophic microbial mats in and above the seafloor. Above the seafloor, the mats can form tall reef-like structures composed of porous carbonate and microbial biomass. Here, we investigated the spatial patterns of CH_4 and CO_2 assimilation in relation to the distribution of ANME groups and their associated bacteria in mat samples obtained from the surface of a large reef structure. A combi...

  1. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

    OpenAIRE

    Knief, Claudia

    2015-01-01

    Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences ...

  2. Genomic reconstruction of an uncultured hydrothermal vent gammaproteobacterial methanotroph (family Methylothermaceae indicates multiple adaptations to oxygen limitation

    Directory of Open Access Journals (Sweden)

    Connor Tobias Skennerton

    2015-12-01

    Full Text Available Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals and housing unique, productive microbial and animal communities fueled by chemosynthesis. Methane is a common constituent of hydrothermal vent fluid and is frequently consumed at vent sites by methanotrophic bacteria that serve to control escape of this greenhouse gas into the atmosphere. Despite their ecological and geochemical importance, little is known about the ecophysiology of uncultured hydrothermal vent-associated methanotrophic bacteria. Using metagenomic binning techniques, we recovered and analyzed a near-complete genome from a novel gammaproteobacterial methanotroph (B42 associated with a white smoker chimney in the Southern Lau basin. B42 was the dominant methanotroph in the community, at ~80x coverage, with only four others detected in the metagenome, all on low coverage contigs (7x - 12x. Phylogenetic placement of B42 showed it is a member of the Methylothermaceae, a family currently represented by only one sequenced genome. Metabolic inferences based on the presence of known pathways in the genome showed that B42 possesses a branched respiratory chain with A- and B-family heme copper oxidases, cytochrome bd oxidase and a partial denitrification pathway. These genes could allow B42 to respire over a wide range of oxygen concentrations within the highly dynamic vent environment. Phylogenies of the denitrification genes revealed they are the result of separate horizontal gene transfer from other proteobacteria and suggest that denitrification is a selective advantage in conditions where extremely low oxygen concentrations require all oxygen to be used for methane activation.

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

    Science.gov (United States)

    Nancucheo, Ivan; Johnson, D Barrie

    2010-01-01

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

  4. Methane dynamics in an alpine fen: a field-based study on methanogenic and methanotrophic microbial communities.

    Science.gov (United States)

    Franchini, Alessandro G; Henneberger, Ruth; Aeppli, Meret; Zeyer, Josef

    2015-03-01

    Wetlands are important sources of the greenhouse gas methane (CH4). We provide an in situ study of CH4 dynamics in the permanently submerged soil of a Swiss alpine fen. Physico-chemical pore water analyses were combined with structural and microbiological analyses of soil cores at high vertical resolution down to 50 cm depth. Methanotrophs and methanogens were active throughout the depth profile, and highest abundance of active methanotrophs and methanogens [6.1 × 10(5) and 1.1 × 10(7) pmoA and mcrA transcripts (g soil)(-1), respectively] was detected in the uppermost 2 cm of the soil. Active methanotrophic communities in the near-surface zone, dominated by viable mosses, varied from the communities in the deeper zones, but further changes with depth were not pronounced. Apart from a distinct active methanogenic community in the uppermost sample, a decrease of acetoclastic Methanosaetaceae with depth was observed in concomitance with decreasing root surface area. Overall, root surface area correlated with mcrA transcript abundance and CH4 pore water concentrations, which peaked (137.1 μM) at 10 to 15 cm depth. Our results suggest that stimulation of methanogenesis by root exudates of vascular plants had a stronger influence on CH4 dynamics than stimulation of CH4 oxidation by O2 input. PMID:25789997

  5. Stable carbon isotope fractionation of trans-1,2-dichloroethylene during co-metabolic degradation by methanotrophic bacteria

    Science.gov (United States)

    Brungard, K.L.; Munakata-Marr, J.; Johnson, C.A.; Mandernack, K.W.

    2003-01-01

    Changes in the carbon isotope ratio (??13C) of trans-1,2-dichloroethylene (t-DCE) were measured during its co-metabolic degradation by Methylomonas methanica, a type I methanotroph, and Methylosinus trichosporium OB3b, a type II methanotroph. In closed-vessel incubation experiments with each bacterium, the residual t-DCE became progressively enriched in 13C, indicating isotopic fractionation. From these experiments, the biological fractionation during t-DCE co-metabolism, expressed as ??, was measured to be -3.5??? for the type I culture and -6.7??? for the type II culture. This fractionation effect and subsequent enrichment in the ??13C of the residual t-DCE can thus be applied to determine the extent of biodegradation of DCE by these organisms. Based on these results, isotopic fractionation clearly warrants further study, as measured changes in the ??13C values of chlorinated solvents could ultimately be used to monitor the extent of biodegradation in laboratory or field settings where co-metabolism by methanotrophs occurs. ?? 2002 Elsevier Science B.V. All rights reserved.

  6. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study

    Directory of Open Access Journals (Sweden)

    Janet B Matsen

    2013-04-01

    Full Text Available Methane-utilizing bacteria (methanotrophs are important in both environmental and biotechnological applications, due to their ability to convert methane to multicarbon compounds. However, systems-level studies of methane metabolism have not been carried out in methanotrophs. In this work we have integrated genomic and transcriptomic information to provide an overview of central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotroph. Particulate methane monooxygenase, PQQ-dependent methanol dehydrogenase, the H4MPT-pathway and NAD-dependent formate dehydrogenase are involved in methane oxidation to CO2. All genes essential for operation of the serine cycle, the ethylmalonyl-CoA (EMC pathway, and the citric acid (TCA cycle were expressed. PEP-pyruvate-oxaloacetate interconversions may have a function in regulation and balancing carbon between the serine cycle and the EMC pathway. A set of transaminases may contribute to carbon partitioning between the pathways. Metabolic pathways for acquisition and/or assimilation of nitrogen and iron are discussed.

  7. Use of an acidophilic yeast strain to enable the growth of leaching bacteria on solid media.

    Science.gov (United States)

    Ngom, Baba; Liang, Yili; Liu, Yi; Yin, Huaqun; Liu, Xueduan

    2015-03-01

    In this study, a Candida digboiensis strain was isolated from a heap leaching plant in Zambia and used in double-layer agar plate to efficiently isolate and purify leaching bacteria. Unlike Acidiphilium sp., the yeast strain was tetrathionate tolerant and could metabolize a great range of organic compounds including organic acids. These properties allowed the yeast strain to enable and fasten the growth of iron and sulfur oxidizers on double-layer agar plate. The isolates were identified as Acidithiobacillus ferrooxidans FOX1, Leptospirillun ferriphilum BN, and Acidithiobacillus thiooxidans ZMB. These three leaching bacteria were inhibited by organic acids such as acetic and propionic acids; however, their activities were enhanced by Candida digboiensis NB under dissolved organic matter stress.

  8. Activities of methionine-γ-lyase in the acidophilic archaeon “Ferroplasma acidarmanus” strain fer1

    Directory of Open Access Journals (Sweden)

    Khan MA

    2013-04-01

    Full Text Available M A Khan,1 Madeline M López-Muñoz,2 Charles W Kaspar,3 Kai F Hung1 1Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA; 2Department of Biology, Universidad de Puerto Rico, Mayaguez, Puerto Rico; 3Bacteriology Department, University of Wisconsin, Madison, WI, USA Abstract: Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1's ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine-γ-lyase (EC 4.4.1.11, an enzyme known to carry out α, γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5'-phosphate (PLP binding domain and a partially conserved catalytic domain in both putative sequences. Detection of PLP-dependent and L-methionine-dependent production of α-keto compounds and thiol groups in fer1 confirmed the presence of methionine-γ-lyase activity. Further, fer1 lysate was capable of processing related substrates, including D-methionine, L-cysteine, L-cystathionine, and L/D-homocysteine. When the two putative fer1 methionine-γ-lyase gene-coded proteins were expressed in Escherichia coli cells, one sequence demonstrated an ability to carry out α, γ-elimination activity, while the other exhibited γ-replacement activity. These fer1 methionine-γ-lyases also exhibited optimum pH, substrate specificity, and catalytic preferences that are different from methionine-γ-lyases from other organisms. These differences are discussed in the context of molecular phylogeny constructed using a maximum

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

    NARCIS (Netherlands)

    Casal, C.; Cuaresma, M.; Vega, J.M.; Vilchez, C.

    2011-01-01

    Coccomyxa acidophila is an extremophile eukaryotic microalga isolated from the Tinto River mining area in Huelva, Spain. Coccomyxa acidophila accumulates relevant amounts of b-carotene and lutein, well-known carotenoids with many biotechnological applications, especially in food and health-related i

  10. Two-liquid phase partitioning biotrickling filters for methane abatement: exploring the potential of hydrophobic methanotrophs.

    Science.gov (United States)

    Lebrero, Raquel; Hernández, Laura; Pérez, Rebeca; Estrada, José M; Muñoz, Raúl

    2015-03-15

    The potential of two-liquid phase biotrickling filters (BTFs) to overcome mass transfer limitations derived from the poor aqueous solubility of CH4 has been scarcely investigated to date. In this context, the abatement of diluted methane emissions in two-liquid phase BTFs was evaluated using two different inocula: a type II methanotrophs culture in BTF 1 and a hydrophobic microbial consortium capable of growing inside silicone oil in BTF 2. Both BTFs supported stable elimination capacities above 45 g m(-3) h(-1) regardless of the inoculum, whereas no improvement derived from the presence of hydrophobic microorganisms compared to the type II metanotrophs culture was observed. Interestingly, the addition of silicone oil mediated a reduced metabolites concentration in the recycling aqueous phase, thus decreasing the needs for mineral medium renewal. Moreover, a 78% similarity was recorded between the microbial communities enriched in both BTFs at the end of the experimental period in spite of the differences in the initial inoculum structure. The results obtained confirmed the superior performance of two-liquid phase BTFs for CH4 abatement compared with conventional biotrickling filters. PMID:25555135

  11. Solubility of methane in water and in a medium for the cultivation of methanotrophs bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Serra, Maria Celeste C. [Centro de Quimica Estrutural, IST, Av. Rovisco Pais, 1096 Lisbon (Portugal) and Centro de Investigacao em Engenharia Quimica e Biotecnologia, ISEL, Av. Conselheiro Emidio Navarro, 1950-062 Lisbon (Portugal)]. E-mail: mcserra@deq.isel.ipl.pt; Pessoa, F.L.P. [DEQ/EQ/UFRJ CT, Bl E, Sl 209, Ilha do Fundao, Rio de Janeiro 21949/900 (Brazil)]. E-mail: fernando.pessoa@pesquisador.cnpq.br; Palavra, A.M.F. [Centro de Quimica Estrutural, IST, Av. Rovisco Pais, 1096 Lisbon (Portugal)]. E-mail: amfpalavra@popsrv.ist.utl.pt

    2006-12-15

    Solubility of methane in water and in an aqueous growth medium for the cultivation of methanotrophs bacteria was determined over the temperature range 293.15 to 323.15 K and at atmospheric pressure. The measurements were carried out in a Ben-Naim/Baer type apparatus with a precision of about {+-}0.3%. The experimental results were determined using accurate thermodynamic relations. The mole fractions of the dissolved gas at the gas partial pressure of 101.325 kPa, the Henry coefficients at the water vapour pressure and the Ostwald coefficients at infinite dilution were obtained. A comparison between the solubility of methane in water and those observed in fermentation medium over the temperature range of 298.15 to 308.15 K has shown that this gas is about {+-}2.3% more soluble in water. The temperature dependence of the mole fractions of methane was also determined using the Clarke-Glew-Weiss equation and the thermodynamic quantities, Gibbs energy, enthalpy and entropy changes, associated with the dissolution process were calculated. Furthermore, the experimental Henry coefficients for methane in water are compared with those calculated by the scaled particle theory. The estimated Henry coefficients are about {+-}4% lower than the experimental ones.

  12. Solubility of methane in water and in a medium for the cultivation of methanotrophs bacteria

    International Nuclear Information System (INIS)

    Solubility of methane in water and in an aqueous growth medium for the cultivation of methanotrophs bacteria was determined over the temperature range 293.15 to 323.15 K and at atmospheric pressure. The measurements were carried out in a Ben-Naim/Baer type apparatus with a precision of about ±0.3%. The experimental results were determined using accurate thermodynamic relations. The mole fractions of the dissolved gas at the gas partial pressure of 101.325 kPa, the Henry coefficients at the water vapour pressure and the Ostwald coefficients at infinite dilution were obtained. A comparison between the solubility of methane in water and those observed in fermentation medium over the temperature range of 298.15 to 308.15 K has shown that this gas is about ±2.3% more soluble in water. The temperature dependence of the mole fractions of methane was also determined using the Clarke-Glew-Weiss equation and the thermodynamic quantities, Gibbs energy, enthalpy and entropy changes, associated with the dissolution process were calculated. Furthermore, the experimental Henry coefficients for methane in water are compared with those calculated by the scaled particle theory. The estimated Henry coefficients are about ±4% lower than the experimental ones

  13. Methane turnover and methanotrophic communities in arctic aquatic ecosystems of the Lena Delta, Northeast Siberia.

    Science.gov (United States)

    Osudar, Roman; Liebner, Susanne; Alawi, Mashal; Yang, Sizhong; Bussmann, Ingeborg; Wagner, Dirk

    2016-08-01

    Large amounts of organic carbon are stored in Arctic permafrost environments, and microbial activity can potentially mineralize this carbon into methane, a potent greenhouse gas. In this study, we assessed the methane budget, the bacterial methane oxidation (MOX) and the underlying environmental controls of arctic lake systems, which represent substantial sources of methane. Five lake systems located on Samoylov Island (Lena Delta, Siberia) and the connected river sites were analyzed using radiotracers to estimate the MOX rates, and molecular biology methods to characterize the abundance and the community composition of methane-oxidizing bacteria (MOB). In contrast to the river, the lake systems had high variation in the methane concentrations, the abundance and composition of the MOB communities, and consequently, the MOX rates. The highest methane concentrations and the highest MOX rates were detected in the lake outlets and in a lake complex in a flood plain area. Though, in all aquatic systems, we detected both, Type I and II MOB, in lake systems, we observed a higher diversity including MOB, typical of the soil environments. The inoculation of soil MOB into the aquatic systems, resulting from permafrost thawing, might be an additional factor controlling the MOB community composition and potentially methanotrophic capacity. PMID:27230921

  14. Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics

    Science.gov (United States)

    Mosier, Annika C.; Justice, Nicholas B.; Bowen, Benjamin P.; Baran, Richard; Thomas, Brian C.; Northen, Trent R.; Banfield, Jillian F.

    2013-01-01

    ABSTRACT Microorganisms grow under a remarkable range of extreme conditions. Environmental transcriptomic and proteomic studies have highlighted metabolic pathways active in extremophilic communities. However, metabolites directly linked to their physiology are less well defined because metabolomics methods lag behind other omics technologies due to a wide range of experimental complexities often associated with the environmental matrix. We identified key metabolites associated with acidophilic and metal-tolerant microorganisms using stable isotope labeling coupled with untargeted, high-resolution mass spectrometry. We observed >3,500 metabolic features in biofilms growing in pH ~0.9 acid mine drainage solutions containing millimolar concentrations of iron, sulfate, zinc, copper, and arsenic. Stable isotope labeling improved chemical formula prediction by >50% for larger metabolites (>250 atomic mass units), many of which were unrepresented in metabolic databases and may represent novel compounds. Taurine and hydroxyectoine were identified and likely provide protection from osmotic stress in the biofilms. Community genomic, transcriptomic, and proteomic data implicate fungi in taurine metabolism. Leptospirillum group II bacteria decrease production of ectoine and hydroxyectoine as biofilms mature, suggesting that biofilm structure provides some resistance to high metal and proton concentrations. The combination of taurine, ectoine, and hydroxyectoine may also constitute a sulfur, nitrogen, and carbon currency in the communities. PMID:23481603

  15. Thermo-acidophillic biohydrogen production from rice bran de-oiled wastewater by Selectively enriched mixed culture

    Directory of Open Access Journals (Sweden)

    D.Sivaramakrishna, D.Sreekanth, V.Himabindu, M.Lakshmi Narasu

    2010-07-01

    Full Text Available The present study focuses on the biohydrogen production in an anaerobic batch reactor operated at thermophillic (570C and acidophilic conditions (pH 6 with rice bran de-oiled wastewater (RBOW as substrate. The hydrogen generating mixed microflora was enriched from slaughter house sludge (SHS through acid treatment (pH 3-4, for 24h coupled with heat treatment (1h at 1000C to eliminate non-spore forming bacteria and to inhibit the growth of methanogenic bacteria (MB prior to inoculation in the reactor. The hydrogen production rate was maximum at 570C (1861±14ml/L-WW/d compared to 370C (651±30ml/L-ww/d. The Hydrogen yield increased with temperature from 1.1 to 2.2 molH2/mol of substrate respectively. The optimum pH range for hydrogen production in this system was observed in between 5.5 to 6. Acid-forming pathway with butyric acid as a major metabolite dominated the metabolic flow during the hydrogen production.

  16. Thermo-acidophillic biohydrogen production from rice bran de-oiled wastewater by Selectively enriched mixed culture

    Energy Technology Data Exchange (ETDEWEB)

    Sivaramakrishna, D.; Sreekanth, D.; Himabindu, V. [Centre for Environment, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally Hyderabad-500 085 (India); Narasu, M. Lakshmi [Centre for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally Hyderabad-500 085 (India)

    2010-07-01

    The present study focuses on the biohydrogen production in an anaerobic batch reactor operated at thermophillic (570C) and acidophilic conditions (pH 6) with rice bran de-oiled wastewater (RBOW) as substrate. The hydrogen generating mixed microflora was enriched from slaughter house sludge (SHS) through acid treatment (pH 3-4, for 24h) coupled with heat treatment (1h at 1000C) to eliminate non-spore forming bacteria and to inhibit the growth of methanogenic bacteria (MB) prior to inoculation in the reactor. The hydrogen production rate was maximum at 570C (1861 +- 14ml/L-WW/d) compared to 370C (651 +- 30ml/L-ww/d). The Hydrogen yield increased with temperature from 1.1 to 2.2 molH2/mol of substrate respectively. The optimum pH range for hydrogen production in this system was observed in between 5.5 to 6. Acid-forming pathway with butyric acid as a major metabolite dominated the metabolic flow during the hydrogen production.

  17. Density-dependent enhancement of methane oxidation activity and growth of Methylocystis sp. by a non-methanotrophic bacterium Sphingopyxis sp

    Directory of Open Access Journals (Sweden)

    So-Yeon Jeong

    2014-12-01

    Full Text Available Methanotrophs are a biological resource as they degrade the greenhouse gas methane and various organic contaminants. Several non-methanotrophic bacteria have shown potential to stimulate growth of methanotrophs when co-cultured, and however, the ecology is largely unknown. Effects of Sphingopyxis sp. NM1 on methanotrophic activity and growth of Methylocystis sp. M6 were investigated in this study. M6 and NM1 were mixed at mixing ratios of 9:1, 1:1, and 1:9 (v/v, using cell suspensions of 7.5 × 1011 cells L−1. Methane oxidation of M6 was monitored, and M6 population was estimated using fluorescence in situ hybridization (FISH. Real-time PCR was applied to quantify rRNA and expression of transcripts for three enzymes involved in the methane oxidation pathway. NM1 had a positive effect on M6 growth at a 1:9 ratio (p < 0.05, while no significant effects were observed at 9:1 and 1:1 ratios. NM1 enhanced the methane oxidation 1.34-fold at the 1:9 ratio. NM1 increased the population density and relative rRNA level of M6 by 2.4-fold and 5.4-fold at the 1:9 ratio, indicating that NM1 stimulated the population growth of M6. NM1 increased the relative transcriptional expression of all mRNA targets only at the 1:9 ratio. These results demonstrated that NM1 enhanced the methanotrophic activity and growth of M6, which was dependent on the proportion of NM1 present in the culture. This stimulation can be used as management and enhancement strategies for methanotrophic biotechnological processes.

  18. High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

    Directory of Open Access Journals (Sweden)

    Hyo Jung eLee

    2015-06-01

    Full Text Available The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at the 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30–200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface, we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae that are likely physiologically

  19. Soluble Methane Monooxygenase Gene Clusters from Trichloroethylene-Degrading Methylomonas sp. Strains and Detection of Methanotrophs during In Situ Bioremediation

    OpenAIRE

    Shigematsu, Toru; Hanada, Satoshi; Eguchi, Masahiro; Kamagata, Yoichi; Kanagawa, Takahiro; Kurane, Ryuichiro

    1999-01-01

    The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from Methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gen...

  20. Identification of the Functionally Active Methanotroph Population in a Peat Soil Microcosm by Stable-Isotope Probing

    OpenAIRE

    Morris, Samantha A.; Radajewski, Stefan; Willison, Toby W.; Murrell, J. Colin

    2002-01-01

    The active population of low-affinity methanotrophs in a peat soil microcosm was characterized by stable-isotope probing. “Heavy” 13C-labeled DNA, produced after microbial growth on 13CH4, was separated from naturally abundant 12C-DNA by cesium chloride density gradient centrifugation and used as a template for the PCR. Amplification products of 16S rRNA genes and pmoA, mxaF, and mmoX, which encode key enzymes in the CH4 oxidation pathway, were analyzed. Sequences related to extant type I and...

  1. Physiology, biochemistry, and specific inhibitors of CH4, NH4+, and CO oxidation by methanotrophs and nitrifiers.

    OpenAIRE

    Bédard, C; Knowles, R

    1989-01-01

    Ammonia oxidizers (family Nitrobacteraceae) and methanotrophs (family Methylococcaceae) oxidize CO and CH4 to CO2 and NH4+ to NO2-. However, the relative contributions of the two groups of organisms to the metabolism of CO, CH4, and NH4+ in various environments are not known. In the ammonia oxidizers, ammonia monooxygenase, the enzyme responsible for the conversion of NH4+ to NH2OH, also catalyzes the oxidation of CH4 to CH3OH. Ammonia monooxygenase also mediates the transformation of CH3OH t...

  2. Molecular characterization of a deep-sea methanotrophic mussel symbiont that carries a RuBisCO gene

    OpenAIRE

    Elsaied, Hosam Easa; Kaneko, Ryo; Naganuma, Takeshi

    2006-01-01

    In our previous investigation on the genes of 1,5-bisphosphate carboxylase/oxygenase (RuBisCO; EC 4.1.1.39) in deep-sea chemoautotrophic and methanotrophic endosymbioses, the gene encoding the large subunit of RuBisCO form I (cbbL) had been detected in the gill of a mussel belonging to the genus Bathymodiolus from a western Pacific back-arc hydrothermal vent. This study further revealed the symbiont source of the RuBisCO cbbL gene along with the genes of 16S ribosomal RNA (16S rDNA), particul...

  3. Changes in methane oxidation activity and methanotrophic community composition in saline alkaline soils.

    Science.gov (United States)

    Serrano-Silva, Nancy; Valenzuela-Encinas, César; Marsch, Rodolfo; Dendooven, Luc; Alcántara-Hernández, Rocio J

    2014-05-01

    The soil of the former Lake Texcoco is a saline alkaline environment where anthropogenic drainage in some areas has reduced salt content and pH. Potential methane (CH4) consumption rates were measured in three soils of the former Lake Texcoco with different electrolytic conductivity (EC) and pH, i.e. Tex-S1 a >18 years drained soil (EC 0.7 dS m(-1), pH 8.5), Tex-S2 drained for ~10 years (EC 9.0 dS m(-1), pH 10.3) and the undrained Tex-S3 (EC 84.8 dS m(-1), pH 10.3). An arable soil from Alcholoya (EC 0.7 dS m(-1), pH 6.7), located nearby Lake Texcoco was used as control. Methane oxidation in the soil Tex-S1 (lowest EC and pH) was similar to that in the arable soil from Alcholoya (32.5 and 34.7 mg CH4 kg(-1) dry soil day(-1), respectively). Meanwhile, in soils Tex-S2 and Tex-S3, the potential CH4 oxidation rates were only 15.0 and 12.8 mg CH4 kg(-1) dry soil day(-1), respectively. Differences in CH4 oxidation were also related to changes in the methane-oxidizing communities in these soils. Sequence analysis of pmoA gene showed that soils differed in the identity and number of methanotrophic phylotypes. The Alcholoya soil and Tex-S1 contained phylotypes grouped within the upland soil cluster gamma and the Jasper Ridge, California JR-2 clade. In soil Tex-S3, a phylotype related to Methylomicrobium alcaliphilum was detected.

  4. Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems

    Directory of Open Access Journals (Sweden)

    Sophie eCrevecoeur

    2015-03-01

    Full Text Available Permafrost thawing leads to the formation of thermokarst ponds that potentially emit CO2 and CH4 to the atmosphere. In the Nunavik subarctic region (northern Quebec, Canada, these numerous, shallow ponds become well stratified during summer. This creates a physico-chemical gradient of temperature and oxygen, with an upper oxic layer and a bottom low-oxygen or anoxic layer. Our objective was to determine the influence of stratification and related limnological and landscape properties on the community structure of potentially active bacteria in these waters. Samples for RNA analysis were taken from ponds in three contrasting valleys across a gradient of permafrost degradation. A total of 1296 operational taxonomic units were identified by high-throughput amplicon sequencing, targeting bacterial 16S rRNA that was reverse transcribed to cDNA. β-proteobacteria were the dominant group in all ponds, with highest representation by the genera Variovorax and Polynucleobacter. Methanotrophs were also among the most abundant sequences at most sites. They accounted for up to 27 % of the total sequences (median of 4.9 % for all samples, indicating the importance of methane as a bacterial energy source in these waters. Both oxygenic (cyanobacteria and anoxygenic (Chlorobi phototrophs were also well represented, the latter in the low oxygen bottom waters. Ordination analyses showed that the communities clustered according to valley and depth, with significant effects attributed to dissolved oxygen, pH, dissolved organic carbon and total suspended solids. These results indicate that the bacterial assemblages of permafrost thaw ponds are filtered by environmental gradients, and are complex consortia of functionally diverse taxa that likely affect the composition as well as magnitude of greenhouse gas emissions from these abundant waters.

  5. Analysis of methanogenic and methanotrophic activity at the western margin of the Greenland Ice Sheet

    Science.gov (United States)

    Broemsen, E. L.; Webster, K. D.; Dieser, M.; Pratt, L. M.; Christner, B. C.

    2012-12-01

    Anoxic conditions in environments beneath the world's glaciers and ice sheets provide plausible habitats supporting the microbial production of methane. Recent reports of potential methane sources beneath the Greenland Ice Sheet (GrIS) suggest in situ production by an active community of methanogens. Beneath the GrIS, microbially derived methane can be dissolved in subglacial water, and during periods of melting, can exchange with the atmosphere at sites of subglacial discharge. Transfer of methane from subglacial fluids to the atmosphere could be a significant climate factor, but few data are available to make such assessments. The specific aim of this study was to characterize the composition and activity of methanogens and methanotrophs present in samples of subglacial outflow at the ice sheet margin near Kangerlussuaq, Greenland. Subglaical water was collected twice-weekly over a nine week period (mid July to mid September of 2012) and the dissolved methane concentration in the samples was determined via gas chromatography. Extracted RNA and DNA from the subglacial water was analyzed by analysis of 16s rRNA and rRNA genes present in the subglacial assemblages. From the molecular results we infer the presence of active methanogens related to the order Methanosarcinales. Further, locally elevated concentrations of atmospheric methane as high as 1.92 ± 0.03 ppmv, were detected in the ice tunnel of the subglacial outflow using open-path laser spectrometry. From these data we estimate rates of methane release at the ice sheet margin during the summer melt months at this geographical location. The results provide a context for addressing the impact that deglaciation will have on the release of greenhouse gases from ice sheets on a warming Earth.

  6. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    Energy Technology Data Exchange (ETDEWEB)

    Kampman, Christel, E-mail: christel.kampman@wur.nl [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Hendrickx, Tim L.G. [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Luesken, Francisca A.; Alen, Theo A. van; Op den Camp, Huub J.M.; Jetten, Mike S.M. [Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Zeeman, Grietje; Buisman, Cees J.N.; Temmink, Hardy [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands)

    2012-08-15

    Highlights: Black-Right-Pointing-Pointer A new concept for low-temperature anaerobic sewage treatment is proposed. Black-Right-Pointing-Pointer In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. Black-Right-Pointing-Pointer The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. Black-Right-Pointing-Pointer The volumetric consumption rate has to be increased by an order of magnitude for practical application. Black-Right-Pointing-Pointer Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to 'Candidatus Methylomirabilis oxyfera' were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO{sub 2}{sup -}-N/L d (using synthetic medium) and 37.8 mg NO{sub 2}{sup -}-N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass

  7. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    International Nuclear Information System (INIS)

    Highlights: ► A new concept for low-temperature anaerobic sewage treatment is proposed. ► In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. ► The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. ► The volumetric consumption rate has to be increased by an order of magnitude for practical application. ► Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to ‘Candidatus Methylomirabilis oxyfera’ were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO2−-N/L d (using synthetic medium) and 37.8 mg NO2−-N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass retention.

  8. Effect of methanogenic substrates on anaerobic oxidation of methane and sulfate reduction by an anaerobic methanotrophic enrichment.

    KAUST Repository

    Meulepas, Roel J W

    2010-05-06

    Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) is assumed to be a syntrophic process, in which methanotrophic archaea produce an interspecies electron carrier (IEC), which is subsequently utilized by sulfate-reducing bacteria. In this paper, six methanogenic substrates are tested as candidate-IECs by assessing their effect on AOM and SR by an anaerobic methanotrophic enrichment. The presence of acetate, formate or hydrogen enhanced SR, but did not inhibit AOM, nor did these substrates trigger methanogenesis. Carbon monoxide also enhanced SR but slightly inhibited AOM. Methanol did not enhance SR nor did it inhibit AOM, and methanethiol inhibited both SR and AOM completely. Subsequently, it was calculated at which candidate-IEC concentrations no more Gibbs free energy can be conserved from their production from methane at the applied conditions. These concentrations were at least 1,000 times lower can the final candidate-IEC concentration in the bulk liquid. Therefore, the tested candidate-IECs could not have been produced from methane during the incubations. Hence, acetate, formate, methanol, carbon monoxide, and hydrogen can be excluded as sole IEC in AOM coupled to SR. Methanethiol did inhibit AOM and can therefore not be excluded as IEC by this study.

  9. Acidithiobacillus ferriphilus sp. nov., a facultatively anaerobic iron- and sulfur-metabolizing extreme acidophile.

    Science.gov (United States)

    Falagán, Carmen; Johnson, D Barrie

    2016-01-01

    The genus Acidithiobacillus includes three species that conserve energy from the oxidation of ferrous iron, as well as reduced sulfur, to support their growth. Previous work, based on multi-locus sequence analysis, identified a fourth group of iron- and sulfur-oxidizing acidithiobacilli as a potential distinct species. Eleven strains of 'Group IV' acidithiobacilli, isolated from different global locations, have been studied. These were all shown to be obligate chemolithotrophs, growing aerobically by coupling the oxidation of ferrous iron or reduced sulfur (but not hydrogen) to molecular oxygen, or anaerobically by the oxidation of reduced sulfur coupled to ferric iron reduction. All strains were mesophilic, although some were also psychrotolerant. Strain variation was also noted in terms of tolerance to extremely low pH and to elevated concentrations of transition metals. One strain was noted to display far greater tolerance to chloride than reported for other iron-oxidizing acidithiobacilli. All of the strains were able to catalyse the oxidative dissolution of pyrite and, on the basis of some of the combined traits of some of the strains examined, it is proposed that these may have niche roles in commercial mineral bioprocessing operations, such as for low temperature bioleaching of polysulfide ores in brackish waters. The name Acidithiobacillus ferriphilus sp. nov. is proposed to accommodate the strains described, with the type strain being M20T ( = DSM 100412T = JCM 30830T). PMID:26498321

  10. Nitrogen removal from wastewater by anaerobic methane-driven denitrification in a lab-scale reactor: heterotrophic denitrifiers associated with denitrifying methanotrophs.

    Science.gov (United States)

    He, Zhanfei; Wang, Jiaqi; Zhang, Xu; Cai, Chaoyang; Geng, Sha; Zheng, Ping; Xu, Xinhua; Hu, Baolan

    2015-12-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) is a newly discovered bioprocess that reduces nitrite to dinitrogen with methane as electron donor, which has promising potential to remove nitrogen from wastewater. In this work, a lab-scale sequencing batch reactor (SBR) was operated for 609 days with methane as the sole external electron donor. In the SBR, nitrite in synthetic wastewater was removed continuously; the final volumetric nitrogen removal rate was 12.22±0.02 mg N L(-1) day(-1) and the percentage of nitrogen removal was 98.5 ± 0.2 %. Microbial community analysis indicated that denitrifying methanotrophs dominated (60-70 %) the population of the final sludge. Notably, activity testing and microbial analysis both suggested that heterotrophic denitrifiers existed in the reactor throughout the operation period. After 609 days, the activity testing indicated the nitrogen removal percentage of heterotrophic denitrification was 17 ± 2 % and that of n-damo was 83 ± 2 %. A possible mutualism may be developed between the dominated denitrifying methanotrophs and the associated heterotrophs through cross-feed. Heterotrophs may live on the microbial products excreted by denitrifying methanotrophs and provide growth factors that are required by denitrifying methanotrophs. PMID:26342737

  11. Isolation and characterisation of mineral-oxidising "Acidibacillus" spp. from mine sites and geothermal environments in different global locations.

    Science.gov (United States)

    Holanda, Roseanne; Hedrich, Sabrina; Ňancucheo, Ivan; Oliveira, Guilherme; Grail, Barry M; Johnson, D Barrie

    2016-09-01

    Eight strains of acidophilic bacteria, isolated from mine-impacted and geothermal sites from different parts of the world, were shown to form a distinct clade (proposed genus "Acidibacillus") within the phylum Firmicutes, well separated from the acidophilic genera Sulfobacillus and Alicyclobacillus. Two of the strains (both isolated from sites in Yellowstone National Park, USA) were moderate thermophiles that oxidised both ferrous iron and elemental sulphur, while the other six were mesophiles that also oxidised ferrous iron, but not sulphur. All eight isolates reduced ferric iron to varying degrees. The two groups shared <95% similarity of their 16S rRNA genes and were therefore considered to be distinct species: "Acidibacillus sulfuroxidans" (moderately thermophilic isolates) and "Acidibacillus ferrooxidans" (mesophilic isolates). Both species were obligate heterotrophs; none of the eight strains grew in the absence of organic carbon. "Acidibacillus" spp. were generally highly tolerant of elevated concentrations of cationic transition metals, though "A. sulfuroxidans" strains were more sensitive to some (e.g. nickel and zinc) than those of "A. ferrooxidans". Initial annotation of the genomes of two strains of "A. ferrooxidans" revealed the presence of genes (cbbL) involved in the RuBisCO pathway for CO2 assimilation and iron oxidation (rus), though with relatively low sequence identities.

  12. Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on methanotroph abundance and methane uptake in a grazed pasture soil.

    Science.gov (United States)

    Dai, Yu; Di, Hong J; Cameron, Keith C; He, Ji-Zheng

    2013-12-01

    Methane-oxidizing bacteria (methanotrophs) in the soil are a unique group of methylotrophic bacteria that utilize methane (CH4) as their sole source of carbon and energy which limit the flux of methane to the atmosphere from soils and consume atmospheric methane. A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of methanotrophs and on methane flux in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100 kg N ha(-1) and animal urine at 300 and 600 kg N ha(-1). DCD was applied at 10 kg ha(-1). The results showed that both the DNA and selected mRNA copy numbers of the methanotroph pmoA gene were not affected by the application of urea, urine or DCD. The methanotroph DNA and mRNA pmoA gene copy numbers were low in this soil, below 7.13 × 10(3) g(-1) soil and 3.75 × 10(3) μg(-1) RNA, respectively. Daily CH4 flux varied slightly among different treatments during the experimental period, ranging from -12.89 g CH4 ha(-1) day(-1) to -0.83 g CH4 ha(-1) day(-1), but no significant treatment effect was found. This study suggests that the application of urea fertilizer, animal urine returns and the use of the nitrification inhibitor DCD do not significantly affect soil methanotroph abundance or daily CH4 fluxes in grazed grassland soils.

  13. Spatial Patterns of Soil Development, Methane Oxidation, and Methanotrophic Diversity along a Receding Glacier Forefield, Southeast Greenland

    DEFF Research Database (Denmark)

    Barcena, Teresa Gomez; Finster, Kai; Yde, Jacob Clement

    2011-01-01

    Increasing global annual temperature leads to massive loss of ice cover worldwide. Consequently, glaciers retreat and ice-covered areas become exposed. We report on a study from the Mittivakkat Gletscher forefield in Southeast Greenland with special focus on methanotrophy in relation to exposure...... time to the atmosphere. The Mittivakkat Gletscher has receded since the end of the Little Ice Age (LIA; about AD 1850) and has left behind a series of deposits of decreasing age concurrently with its recession. Soil samples from this chronosequence were examined in order to elucidate main soil...... methanotrophs were at very low abundance and diversity during glaciation probably due to anoxia at the ice-sediment interface and that colonization after deglaciation is not completed yet. More detailed studies are required to explain the causes of discrepancy between activity and presence of high...

  14. Carbon isotopic fractionation in lipids from methanotrophic bacteria: relevance for interpretation of the geochemical record of biomarkers

    Science.gov (United States)

    Summons, R. E.; Jahnke, L. L.; Roksandic, Z.

    1994-01-01

    Experiments with cultured aerobic methane oxidising bacteria confirm that their biomarker lipids will be significantly depleted in 13C compared to the substrate. The methanotrophic bacteria Methylococcus capsulatus and Methylomonas methanica, grown on methane and using the RuMP cycle for carbon assimilation, show maximum 13C fractionation of approximately 30% in the resultant biomass. In M. capsulatus, the maximum fractionation is observed in the earliest part of the exponential growth stage and decreases to approximately 16% as cells approach stationary phase. This change may be associated with a shift from the particulate form to the soluble form of the methane monooxygenase enzyme. Less than maximum fractionation is observed when cells are grown with reduced methane availability. Biomass of M. capsulatus grown on methanol was depleted by 9% compared to the substrate. Additional strong 13C fractionation takes place during polyisoprenoid biosynthesis in methanotrophs. The delta 13C values of individual hopanoid and steroid biomarkers produced by these organisms were as much as l0% more negative than total biomass. In individual cultures, squalene was 13C-enriched by as much as 14% compared to the triterpane skeleton of bacteriohopaneaminopentol. Much of the isotopic dispersion in lipid metabolites could be attributed to shifts in their relative abundances, combined with an overall reduction in fractionation during the growth cycle. In cells grown on methanol, where there was no apparent effect of growth stage on overall fractionation there were still significant isotopic differences between closely related lipids including a 5.3% difference between the hopane and 3 beta-methylhopane skeletons. Hopane and sterane polyisoprenoids were also 13C-depleted compared to fatty acids. These observations have significant implications for the interpretation of specific compound isotopic signatures now being measured for hydrocarbons and other lipids present in sediments and

  15. Genomic and physiological analysis of carbon storage in the verrucomicrobial methanotroph "Ca. Methylacidiphilum fumariolicum" SolV

    Directory of Open Access Journals (Sweden)

    Ahmad Fouad eKhadem

    2012-09-01

    Full Text Available Candidatus Methylacidiphilum fumariolicum SolV is a verrucomicrobial methanotroph that can grow in extremely acidic environments at high temperature. Strain SolV fixes carbon dioxide (CO2 via the Calvin-Benson-Bassham cycle with methane as energy source, a trait so far very unusual in methanotrophs. In this study, the ability of Ca. M. fumariolicum to store carbon was explored by genome analysis, physiological studies and electron microscopy. When cell cultures were depleted for nitrogen, glycogen storage was clearly observed in cytoplasmic storage vesicles by electron microscopy. After cessation of growth, the dry weight kept increasing and the bacteria were filled up almost entirely by glycogen. This was confirmed by biochemical analysis, which showed that glycogen accumulated to 36% of the total dry weight of the cells. When methane was removed from the culture, this glycogen was consumed within 47 days. During the period of glycogen consumption, the bacteria kept their viability high when compared to bacteria without glycogen (from cultures growing exponentially. The latter bacteria lost viability already after a few days when starved for methane. Analysis of the draft genome of Ca. M. fumariolicum SolV demonstrated that all known genes for glycogen storage and degradation were present and also transcribed. Phylogenetic analysis of these genes showed that they form a separate cluster with Ca. M. infernorum V4, and the most closely related other sequences only have an identity of 40%. This study presents the first physiological evidence of glycogen storage in the phylum Verrucomicrobia and indicates that carbon storage is important for survival at times of methane starvation.

  16. Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids.

    OpenAIRE

    Shrestha, Minita; Abraham, Wolf-Rainer; Shrestha, Pravin Malla; Noll, Matthias; Conrad, Ralf

    2008-01-01

    Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH(4) into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH(4) flux in the presence and absence of difluoromethane as a specific inhibitor for methane oxidation. Methane oxidation started on da...

  17. Résilience d'une prairie subalpine acidophile au chaulage et à la fertilisation de courte durée

    OpenAIRE

    Spiegelberger, T.; Deléglise, C.; DeDanieli, S.; Bernard-Brunet, C.

    2010-01-01

    / Une expérience de fertilisation a débuté en 1989 dans les Alpes françaises, sur une prairie acidophile située à 2000 m d'altitude, où de la chaux (« chaulage ») et des scories enrichies par chlorure de potassium (« fertilisation ») ont été apportés jusqu'en 1992. Depuis, aucun autre amendement n'a été appliqué. En 2007 nous avons revisité l'expérience et avons observé que le pH du sol était toujours sensiblement plus haut sur les placettes chaulées, alors que les concentrations du sol e...

  18. Characterization of bacteria acidophilic in samples of water coming into a region that suffers influence of uranium mine in Caldas (MG)

    International Nuclear Information System (INIS)

    The fundamental condition for the bioleaching of the uranium ore is the presence of metallic sulfide such as pyrite associated with the ore, which is found in the ore and in the waste at the Unidade de Tratamento de Minerio (UTM) of Pocos de Caldas, State of Minas Gerais, Brazil. The present study aims to determine the chemical and microbiological characteristics in effluents of uranium mining from the UTM and in Antas dam, which receives treated effluents from the UTM. Water samples were collected Pit Mine (CM), located within the UTM facilities and from site 41 (Antas dam) in July and October 2008. We verified low pH values in water samples from CM (3.7) in comparison to the ones found at site 41 (6.65). There was a higher medium density value of Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and heterotrophic acidophilic bacteria in water samples at site CM compared to the values recorded from samples at site 41. Medium values of Fe2+, uranium and zinc in samples from the site CM were higher than at site 41. The concentration of fluoride (68.5 mL-l) and manganese (2.34 mL-1) in water samples from site 41 were above the limits fixed for water bodies in Resolution CONAMA 357. The relative seasonal variation of some variables observed at site CM (low pH values, high densities of Acidithiobacillus sp. and heterotrophic acidophilic bacteria) shows that this site is one of the main sites of occurrence of acid mine drainage and action of bioleaching bacteria at UTM. (author)

  19. Characterization of bacteria acidophilic in samples of water coming into a region that suffers influence of uranium mine in Caldas (MG)

    Energy Technology Data Exchange (ETDEWEB)

    Campos, Michelle B.; Ferrari, Carla R.; Roque, Claudio V.; Ronqui, Leilane B.; Nascimento, Marcos R.L. do; Rodgher, Suzelei; Azevedo, Heliana [Laboratorio de Pocos de Caldas (LAPOC-CNEN/MG), MG (Brazil)], e-mail: michelle_borato@hotmail.com, e-mail: carlarolimferrari@yahoo.com.br, e-mail: cvroque@cnen.gov.br, e-mail: leilanebio@yahoo.com.br, e-mail: pmarcos@cnen.gov.br, e-mail: surodgher@uol.com.br, e-mail: hgomes@cnen.gov.br

    2009-07-01

    The fundamental condition for the bioleaching of the uranium ore is the presence of metallic sulfide such as pyrite associated with the ore, which is found in the ore and in the waste at the Unidade de Tratamento de Minerio (UTM) of Pocos de Caldas, State of Minas Gerais, Brazil. The present study aims to determine the chemical and microbiological characteristics in effluents of uranium mining from the UTM and in Antas dam, which receives treated effluents from the UTM. Water samples were collected Pit Mine (CM), located within the UTM facilities and from site 41 (Antas dam) in July and October 2008. We verified low pH values in water samples from CM (3.7) in comparison to the ones found at site 41 (6.65). There was a higher medium density value of Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and heterotrophic acidophilic bacteria in water samples at site CM compared to the values recorded from samples at site 41. Medium values of Fe{sup 2+}, uranium and zinc in samples from the site CM were higher than at site 41. The concentration of fluoride (68.5 mL{sup -l}) and manganese (2.34 mL{sup -1}) in water samples from site 41 were above the limits fixed for water bodies in Resolution CONAMA 357. The relative seasonal variation of some variables observed at site CM (low pH values, high densities of Acidithiobacillus sp. and heterotrophic acidophilic bacteria) shows that this site is one of the main sites of occurrence of acid mine drainage and action of bioleaching bacteria at UTM. (author)

  20. GLOBAL MOLECULAR ANALYSES OF METHANE METABOLISM IN METHANOTROPHIC ALPHAPROTEOBACTERIUM, METHYLOSINUS TRICHOSPORIUM OB3B.PART II. METABOLOMICS AND 13C-LABELING STUDY

    Directory of Open Access Journals (Sweden)

    Marina G. Kalyuzhanaya

    2013-04-01

    Full Text Available In this work we use metabolomics and 13C-labeling data to refine central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotrophic bacterium. We demonstrate here that similar to non-methane utilizing methylotrophic alphaproteobacteria the core metabolism of the microbe is represented by several tightly connected metabolic cycles, such as the serine pathway, the ethylmalonyl-CoA (EMC pathway, and the citric acid (TCA cycle. Both in silico estimations and stable isotope labeling experiments combined with single cell (NanoSIMS and bulk biomass analyses indicate that a significantly larger portion of the cell carbon (over 60% is derived from CO2 in this methanotroph. Our 13C-labeling studies revealed an unusual topology of the assimilatory network in which phosph(enolpyruvate/pyruvate interconversions are key metabolic switches. A set of additional pathways for carbon fixation are identified and discussed.

  1. High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

    OpenAIRE

    Lee, Hyo Jung; Jeong, Sang Eun; Kim, Pil Joo; Madsen, Eugene L.; Jeon, Che Ok

    2015-01-01

    The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations d...

  2. Patterns of ^(15)N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS

    OpenAIRE

    Orphan, Victoria J; Turk, Kendra A.; Green, Abigail M.; House, Christopher H.

    2009-01-01

    Methane release from the oceans is controlled in large part by syntrophic interactions between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (DSS), frequently found as organized consortia. An understanding of the specifics of this symbiotic relationship and the metabolic heterogeneity existing between and within individual methane-oxidizing aggregates is currently lacking. Here, we use the microanalytical method FISH-SIMS (fluorescence in situ hybridization-secondary i...

  3. Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-Labeling Study

    OpenAIRE

    Yang, Song; Matsen, Janet B.; Konopka, Michael; Green-Saxena, Abigail; Clubb, Justin; Sadilek, Martin; Orphan, Victoria J; Beck, David; Kalyuzhnaya, Marina G.

    2013-01-01

    In this work we use metabolomics and ^(13)C-labeling data to refine central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotrophic bacterium. We demonstrate here that similar to non-methane utilizing methylotrophic alphaproteobacteria the core metabolism of the microbe is represented by several tightly connected metabolic cycles, such as the serine pathway, the ethylmalonyl-CoA (EMC) pathway, and the citric acid (TCA) cycle. ...

  4. Influence of endogenous and exogenous electron donors and trichloroethylene oxidation toxicity on trichloroethylene oxidation by methanotrophic cultures from a groundwater aquifer.

    OpenAIRE

    Henry, S M; Grbić-Galić, D

    1991-01-01

    Trichloroethylene (TCE)-transforming aquifer methanotrophs were evaluated for the influence of TCE oxidation toxicity and the effect of reductant availability on TCE transformation rates during methane starvation. TCE oxidation at relatively low (6 mg liter-1) TCE concentrations significantly reduced subsequent methane utilization in mixed and pure cultures tested and reduced the number of viable cells in the pure culture Methylomonas sp. strain MM2 by an order of magnitude. Perchloroethylene...

  5. Ecophysiological Characteristics of Obligate Methanotrophic Bacteria and Methane Oxidation In Situ

    Science.gov (United States)

    King, Gary M.

    1993-01-01

    Most of the obligate methane-oxidizing bacteria (MOB) described to date are neutrophilic mesophiles that grow optimally in dilute media. Kinetic analyses generally indicate that bacterial methane uptake occurs by transport systems with a K(sub m) greater than l micronM. These and other properties of MOB are inconsistent with characteristics of methane oxidation in situ. The inconsistencies indicate a need for greater attention to the ecophysiological characteristics of isolates and the design of enrichment and isolation schemes which emphasize ecologically relevant parameters (e.g., low temperature, limited and diverse substrate availability, low water potential).

  6. Rapid assessment of methanotrophic capacity of compost-based materials considering the effects of air-filled porosity, water content and dissolved organic carbon.

    Science.gov (United States)

    Mancebo, Uriel; Hettiaratchi, J Patrick A

    2015-02-01

    Since the global warming potential of CH4 is 25 times that of CO2 on a 100-year time horizon, the development of methanotrophic applications for the conversion of CH4 to CO2 is emerging as an area of interest for researchers and practicing engineers. Compost exhibits most of the characteristics required for methanotroph growth media and has been used in several projects. This paper presents results from a study that was undertaken to assess the influence of physical and chemical characteristics of compost-based materials on the biological oxidation of CH4 when used in methane biofilters. The results showed that easily-measurable parameters, such as air filled porosity, water content and dissolved organic carbon, are correlated with maximum CH4 removal rates. The results obtained were used to develop an empirical relationship that could be regarded as a rapid assessment tool for the estimation of the performance of compost-based materials in engineered methanotrophic applications. PMID:25484123

  7. Methanotrophic activity in the water column above shallow gas flares west of Prins Karls Forland, Arctic Ocean

    Science.gov (United States)

    Gründger, Friederike; Svenning, Mette M.; Niemann, Helge; Silyakova, Anna; Serov, Pavel; Pavlov, Alexey K.; Granskog, Mats A.; Ferre, Bénédicte; Carroll, JoLynn

    2016-04-01

    Numerous gas flares, interpreted to be streams of methane bubbles, were discovered in shallow waters (average water depth about 90 m) on the continental shelf west of Prins Karls Forland (Western Svalbard) in the Arctic Ocean. Gas is released from the seabed to the water column and potentially transferred into the atmosphere where it acts as a potent greenhouse gas. In order to resolve the fate of dissolved methane in the water column, we carried out grid-pattern biogeochemical measurements in the study area of 30 x 15 km. Specifically, we measured concentrations of dissolved methane and microbial methane oxidation (MOx) rates at 8 water depths at 31 sampling stations and performed 16S rRNA sequencing analysis on selected samples to characterize the microbial community composition. Availability of dissolved methane is essential for the process of microbial methane oxidation. However, our measurements reveal that high concentrations of dissolved methane in the water column do not necessarily lead to high MOx rates. Our results indicated that the presence of marine methanotrophic biomass as well as dissolved organic matter is of larger importance for the process of microbial methane oxidation. For example, we found MOx hot spots with values up to 13 nmol l‑1 d‑1 at bottom water depth with dissolved methane concentrations less than 160 nmol l‑1. In contrast, at stations where bottom methane concentration values reached 640 nmol l‑1, MOx rates were less than 0.7 nmol l‑1 d‑1. To interpret observed interconnection between methane concentrations and MOx rates, we use vertical distributions of seawater temperature, salinity and properties of colored dissolved organic matter (CDOM). This information helps us characterize the oceanographic setting and circulation patterns in the area, which we believe has a major impact on the origin and distribution of methanotrophic microbial biomass and methane oxidation in methanerich bottom water. This study is part of the

  8. Effect of CH4/O2 ratio on fatty acid profile and polyhydroxybutyrate content in a heterotrophic-methanotrophic consortium.

    Science.gov (United States)

    Karthikeyan, Obulisamy P; Chidambarampadmavathy, Karthigeyan; Nadarajan, Saravanan; Lee, Patrick K H; Heimann, Kirsten

    2015-12-01

    Understanding the role of heterotrophic-methanotrophic (H-Meth) communities is important for improvement of methane (CH4) oxidation capacities (MOC) particularly in conjunction with bio-product development in industrial bio-filters. Initially, a H-Meth consortium was established and enriched from marine sediments and characterized by next generation sequencing of the 16s rDNA gene. The enriched consortium was subjected to 10-50% CH4 (i.e., 0.20-1.6 CH4/O2 ratios) to study the effects on MOCs, biomass growth, fatty acid profiles and biopolymer (e.g. polyhydroxybutyrate; PHB) content. Methylocystis, Methylophaga and Pseudoxanthomonas dominated the H-Meth consortium. Culture enrichment of the H-Meth consortium resulted in 15-20-folds higher MOC compared to seed sediments. Increasing CH4 concentration (and decreased O2 levels) yielded higher MOCs, but did not improve total fatty acid contents. PHB contents varied between 2.5% and 8.5% independently of CH4/O2 ratios. The results suggest that H-Meth consortia could potentially be used in industrial bio-filters for production of biopolymer/biofuel precursors from CH4. PMID:26247542

  9. A novel denitrifying methanotroph of the NC10 phylum and its microcolony

    Science.gov (United States)

    He, Zhanfei; Cai, Chaoyang; Wang, Jiaqi; Xu, Xinhua; Zheng, Ping; Jetten, Mike S. M.; Hu, Baolan

    2016-09-01

    The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies.

  10. A novel denitrifying methanotroph of the NC10 phylum and its microcolony.

    Science.gov (United States)

    He, Zhanfei; Cai, Chaoyang; Wang, Jiaqi; Xu, Xinhua; Zheng, Ping; Jetten, Mike S M; Hu, Baolan

    2016-01-01

    The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species 'Candidatus Methylomirabilis oxyfera' (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it 'Candidatus Methylomirabilis sinica' (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7-1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25-0.5 × 0.8-1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies. PMID:27582299

  11. The δ15N and δ18O values of N2O produced during the co-oxidation of ammonia by methanotrophic bacteria

    Science.gov (United States)

    Mandernack, Kevin W.; Mills, Christopher T.; Johnson, Craig A.; Rahn, Thomas; Kinney, Chad

    2009-01-01

    In order to determine if the δ15N and δ18O values of N2O produced during co-oxidation of NH4+ by methanotrophic (methane oxidizing) bacteria can be isotopically distinguished from N2O produced either by autotrophic nitrifying or denitrifying bacteria, we conducted laboratory incubation experiments with pure cultures of methanotrophic bacteria that were provided NH4Cl as an oxidation substrate. The N2O produced during NH4+ oxidation by methanotrophic bacteria showed nitrogen isotope fractionation between NH4+ and N2O (εN2O–NH4+) of − 48 and − 55‰ for Methylomonas methanica and Methylosinus trichosporium, OB3b respectively. These large fractionations are similar to those previously measured for autotrophic nitrifying bacteria and consistent with N2O formation by multiple rate limiting steps that include NH4+oxidation by the methane monooxygenase enzyme and reduction of NO2− to N2O. Consequently, N2O formed by NH4+ oxidation via methanotrophic or autotrophic nitrifying bacteria might generally be characterized by lower δ15NN2O values than that formed by denitrificaiton, although this also depends on the variability of δ15N of available nitrogen sources (e.g., NH4+, NO3−, NO2−). Additional incubations with M. trichosporium OB3b at high and low CH4 conditions in waters of different δ18O values revealed that 19–27% of the oxygen in N2O was derived from O2 with the remainder from water. The biochemical mechanisms that could explain this amount of O2 incorporation are discussed. The δ18O of N2O formed under high CH4 conditions was ~ + 15‰ more positive than that formed under lower CH4 conditions. This enrichment resulted in part from the incorporation of O2 into N2O that was enriched in 18O due to an isotope fractionation effect of − 16.1 ± 2.0‰ and − 17.5 ± 5.4‰ associated with O2 consumption during the high and low methane concentration incubations, respectively. Therefore, N2O formed by NH4+

  12. Influence of water chemistry on the distribution of an acidophilic protozoan in an acid mine drainage system at the abandoned Green Valley coal mine, Indiana, USA

    Energy Technology Data Exchange (ETDEWEB)

    Brake, S.S.; Dannelly, H.K.; Connors, K.A.; Hasiotis, S.T. [Indiana State University, Terre Haute, IN (United States). Dept. of Geography Geology & Anthropology

    2001-07-01

    Euglena mutabilis, a benthic photosynthetic protozoan that intracellularly sequesters Fe, is variably abundant in the main effluent channel that contains acid mine drainage (AMD) discharging from the Green Valley coal mine site in western Indiana. Samples of effluent (pH 3.0-4.6) taken from the main channel and samples of contaminated stream water (pH 3.3 to 8.0) collected from an adjacent stream were analyzed to evaluate the influence of water chemistry on E. mutabilis distribution. E. mutabilis communities were restricted to areas containing unmixed effluent with the thickest (up to 3 mm) benthic communities residing in effluent containing high concentrations of total Fe (up to 12110 mg/l), SO{sub 4}(up to 2940 mg/l), Al (up to 1846 mg/l), and Cl (up to 629 mg/l). Communities were also present, but much less abundant, in areas with effluent containing lower concentrations of these same constituents. In effluent where SO{sub 4} was most highly concentrated, E. mutabilis was largely absent, suggesting that extremely high concentrations of SO{sub 4} may have an adverse effect on this potentially beneficial Fe-mediating, acidophilic protozoan.

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

    Science.gov (United States)

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

    2016-05-01

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

  14. Computer modeling of methanotrophic oxidation of hydrocarbons in the unsaturated zone from an enhanced oil recovery/sequestration project, Rangely, Colorado, USA

    International Nuclear Information System (INIS)

    Measurements of CH4 and CO2 concentrations in soil gas, and as exchange rates (fluxes) with the atmosphere were made over the Rangely oil field, Colorado, USA. The Rangely field has been operated as a large CO2 enhanced oil recovery (EOR) project since 1986, and may serve as a prototype for CO2 sequestration in depleted oil/gas fields. The first of this pair of papers reported on the details of the methodology and results of field measurements of these gases, including light alkanes. The interpretation was enhanced by the extensive use of 13C and some 14C measurements. The fluxes of both CH4 and CO2 to the atmosphere were estimated. This research has demonstrated and quantified the methanotrophic oxidation of microseeping CH4 in the unsaturated zone. Strong spatial variations were found and studied further by nested soil gas sampling in holes up to 9 m deep. Areas of microseepage were found, as well as areas where atmospheric CH4 was the only source for methanotrophic oxidation. Computer modeling was used to determine rate constants for the oxidation process. Strong seasonal differences exist in the rates of CH4 oxidation because of the semiarid and severe climate of Rangely. Rate constants of 1000 day-1 were determined. During the summer, the highest rates were near the surface, but shifted downward to about 2 m depth in the winter. Methanotrophic oxidation of CH4 in the unsaturated zone will be the most important component of amelioration of CH4 microseepage induced by overpressuring of the reservoir undergoing CO2 injection. These types of measurements and interpretation will be necessary in order to fully understand the environmental effects of CO2 sequestration in oil/gas fields

  15. Identification and Characterization of EctR1, a New Transcriptional Regulator of the Ectoine Biosynthesis Genes in the Halotolerant Methanotroph Methylomicrobium alcaliphilum 20Z▿ †

    OpenAIRE

    Mustakhimov, Ildar I.; Alexander S. Reshetnikov; Glukhov, Anatoly S.; Khmelenina, Valentina N.; Kalyuzhnaya, Marina G.; Trotsenko, Yuri A.

    2009-01-01

    Genes encoding key enzymes of the ectoine biosynthesis pathway in the halotolerant obligate methanotroph Methylomicrobium alcaliphilum 20Z have been shown to be organized into an ectABC-ask operon. Transcription of the ect operon is initiated from two promoters, ectAp1 and ectAp2 (ectAp1p2), similar to the σ70-dependent promoters of Escherichia coli. Upstream of the gene cluster, an open reading frame (ectR1) encoding a MarR-like transcriptional regulator was identified. Investigation of the ...

  16. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs.

    Science.gov (United States)

    Lesniewski, Ryan A; Jain, Sunit; Anantharaman, Karthik; Schloss, Patrick D; Dick, Gregory J

    2012-12-01

    Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3-4 times) and microbially mediated manganese oxidation rates (15-125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10-20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California.

  17. Complete genome sequence of Methylophilus sp. TWE2 isolated from methane oxidation enrichment culture of tap-water.

    Science.gov (United States)

    Xia, Fei; Zou, Bin; Shen, Cong; Zhu, Ting; Gao, Xin-Hua; Quan, Zhe-Xue

    2015-10-10

    The non-methane-utilizing methylotroph, Methylophilus sp. TWE2, was isolated from tap-water during the enrichment of methanotrophs with methane. The complete genome sequence of strain TWE2 showed that this bacterium may convert methanol to formaldehyde via catalysis of methanol dehydrogenase (MDH), after which formaldehyde would be assimilated to biomass through the ribulose monophosphate (RuMP) pathway or dissimilated via the tetrahydromethanopterin (H4MPT) pathway. The deficiency of glycolysis and the TCA cycle indicate that strain TWE2 may be an obligate methylotroph. This is the first complete genome sequence of the genus Methylophilus. PMID:26253961

  18. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    Science.gov (United States)

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2013-07-23

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  19. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2014-04-08

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  20. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Ward, Thomas E.

    2016-03-22

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  1. Evaluation of the influence of methane and copper concentration and methane mass transport on the community structure and biodegradation kinetics of methanotrophic cultures.

    Science.gov (United States)

    Cantera, Sara; Lebrero, Raquel; García-Encina, Pedro A; Muñoz, Raúl

    2016-04-15

    The environmental conditions during culture enrichment, which ultimately determine its maximum specific biodegradation rate (qmax) and affinity for the target pollutant (Ks), play a key role in the performance of bioreactors devoted to the treatment of methane emissions. This study assessed the influence of Cu(2+) and CH4 concentration and the effective CH4 supply rate during culture enrichment on the structure and biodegradation kinetics of methanotrophic communities. The results obtained demonstrated that an increase in Cu(2+) concentration from 0.05 to 25 μM increased the qmax and Ks of the communities enriched by a factor of ≈ 3, even if the Cu(2+) concentration did not seem to have an effect on the enzymatic "copper switch" and only pMMO was detected. In addition, high Cu(2+) concentrations supported lower diversity coefficients (Hs ≈ 1.5× lower) and apparently promoted the growth of more adapted methanotrophs such as Methylomonas. Despite no clear effect of CH4 concentration on the population structure or on the biodegradation kinetics of the communities enriched was recorded at the two low CH4 concentrations studied (1 and 8%), a higher agitation rate increased the qmax by a factor of ≈ 2.3 and Ks by a factor of ≈ 3.1. PMID:26866670

  2. Microbial community profiling of the Chinoike Jigoku ("Blood Pond Hell") hot spring in Beppu, Japan: isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1.

    Science.gov (United States)

    Masaki, Yusei; Tsutsumi, Katsutoshi; Hirano, Shin-Ichi; Okibe, Naoko

    2016-09-01

    Chinoike Jigoku ("Blood Pond Hell") is located in the hot spring town of Beppu on the southern island of Kyushu in Japan, and is the site of a red-colored acidic geothermal pond. This study aimed to investigate the microbial population composition in this extremely acidic environment and to isolate/characterize acidophilic microorganism with metal-reducing ability. Initially, PCR (using bacteria- and archaea-specific primers) of environmental DNA samples detected the presence of bacteria, but not archaea. This was followed by random sequencing analysis, confirming the presence of wide bacterial diversity at the site (123 clones derived from 18 bacterial and 1 archaeal genera), including those closely related to known autotrophic and heterotrophic acidophiles (Acidithiobacillus sp., Sulfobacillus sp., Alicyclobacillus sp.). Nevertheless, successive culture enrichment with Fe(III) under micro-aerobic conditions led to isolation of an unknown archaeal organism, Sulfolobus sp. GA1 (with 99.7% 16S rRNA gene sequence identity with Sulfolobus shibatae). Unlike many other known Sulfolobus spp., strain GA1 was shown to lack sulfur oxidation ability. Strain GA1 possessed only minor Fe(II) oxidation ability, but readily reduced Fe(III) during heterotrophic growth under micro-aerobic conditions. Strain GA1 was capable of reducing highly toxic Cr(VI) to less toxic/soluble Cr(III), demonstrating its potential utility in bioremediation of toxic metal species. PMID:27208660

  3. Microbial community profiling of the Chinoike Jigoku ("Blood Pond Hell") hot spring in Beppu, Japan: isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1.

    Science.gov (United States)

    Masaki, Yusei; Tsutsumi, Katsutoshi; Hirano, Shin-Ichi; Okibe, Naoko

    2016-09-01

    Chinoike Jigoku ("Blood Pond Hell") is located in the hot spring town of Beppu on the southern island of Kyushu in Japan, and is the site of a red-colored acidic geothermal pond. This study aimed to investigate the microbial population composition in this extremely acidic environment and to isolate/characterize acidophilic microorganism with metal-reducing ability. Initially, PCR (using bacteria- and archaea-specific primers) of environmental DNA samples detected the presence of bacteria, but not archaea. This was followed by random sequencing analysis, confirming the presence of wide bacterial diversity at the site (123 clones derived from 18 bacterial and 1 archaeal genera), including those closely related to known autotrophic and heterotrophic acidophiles (Acidithiobacillus sp., Sulfobacillus sp., Alicyclobacillus sp.). Nevertheless, successive culture enrichment with Fe(III) under micro-aerobic conditions led to isolation of an unknown archaeal organism, Sulfolobus sp. GA1 (with 99.7% 16S rRNA gene sequence identity with Sulfolobus shibatae). Unlike many other known Sulfolobus spp., strain GA1 was shown to lack sulfur oxidation ability. Strain GA1 possessed only minor Fe(II) oxidation ability, but readily reduced Fe(III) during heterotrophic growth under micro-aerobic conditions. Strain GA1 was capable of reducing highly toxic Cr(VI) to less toxic/soluble Cr(III), demonstrating its potential utility in bioremediation of toxic metal species.

  4. A new acidophilic endo-β-1,4-xylanase from Penicillium oxalicum: cloning, purification, and insights into the influence of metal ions on xylanase activity.

    Science.gov (United States)

    Liao, Hanpeng; Sun, Shaowei; Wang, Pan; Bi, Wenli; Tan, Shiyong; Wei, Zhong; Mei, Xinlan; Liu, Dongyang; Raza, Waseem; Shen, Qirong; Xu, Yangchun

    2014-07-01

    A new acidophilic xylanase (XYN11A) from Penicillium oxalicum GZ-2 has been purified, identified and characterized. Synchronized fluorescence spectroscopy was used for the first time to evaluate the influence of metal ions on xylanase activity. The purified enzyme was identified by MALDI TOF/TOF mass spectrometry, and its gene (xyn11A) was identified as an open reading frame of 706 bp with a 68 bp intron. This gene encodes a mature protein of 196 residues with a predicted molecular weight of 21.3 kDa that has the 100 % identity with the putative xylanase from the P. oxalicum 114-2. The enzyme shows a structure comprising a catalytic module family 10 (GH10) and no carbohydrate-binding module family. The specific activities were 150.2, 60.2, and 72.6 U/mg for beechwood xylan, birchwood xylan, and oat spelt xylan, respectively. XYN11A exhibited optimal activity at pH 4.0 and remarkable pH stability under extremely acidic condition (pH 3). The specific activity, K m and V max values were 150.2 U/mg, 30.7 mg/mL, and 403.9 μmol/min/mg for beechwood xylan, respectively. XYN11A is a endo-β-1,4-xylanase since it release xylobiose and xylotriose as the main products by hydrolyzing xylans. The activity of XYN11A was enhanced 155 % by 1 mM Fe(2+) ions, but was inhibited strongly by Fe(3+). The reason of enhancing the xylanase activity of XYN11A with 1 mM Fe(2+) treatment may be responsible for the change of microenvironment of tryptophan residues studied by synchronous fluorescence spectrophotometry. Inhibition of the xylanase activity by Fe(3+) was first time demonstrated to associate tryptophan fluorescence quenching. PMID:24818699

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

    Science.gov (United States)

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

    2016-01-01

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

  6. Acidophilic granulocytes in the gills of gilthead seabream Sparus aurata: evidence for their responses to a natural infection by a copepod ectoparasite.

    Science.gov (United States)

    Lui, Alice; Manera, Maurizio; Giari, Luisa; Mulero, Victoriano; Dezfuli, Bahram Sayyaf

    2013-09-01

    Immunohistochemical and ultrastructural studies were conducted on the gills of gilthead seabream, Sparus aurata L., naturally infected with the copepod ectoparasite Ergasilus lizae (Krøyer, 1863) in order to assess pathology and the host immune cell response. Gills of 56 gilthead seabream were screened for ectoparasites; 36 specimens (64.3%) harbored E. lizae. Intensity of infection was 32.7 ± 8.7 (mean ± SE). Pathological alterations to the gills of the host were more pronounced in close proximity to the copepod site of attachment. The parasite attached to the gills by means of its modified second antennae, occluded the arteries, provoked epithelial hyperplasia and hemorrhages and most often caused lamellar disruption. Numerous granular cells were encountered near the site of E. lizae attachment. In both infected and uninfected gills, the granular cells lay within the filaments and frequently occurred within the connective tissue inside and outside the blood vessels of the filaments. The type of granular cell was identified by immunohistochemical staining by using the monoclonal antibody G7 (mAb G7), which specifically recognizes acidophilic granulocytes (AGs) of S. aurata and with an anti-histamine antibody (as a marker for mast cells, MCs) on sections from 13 uninfected gills and 21 parasitized gills. The use of mAb G7 revealed that, in gills harboring copepods, the number of G7-positive cells (i.e., AGs; 32.9 ± 3.9, mean number of cells per 45,000 μm2 ± SE) was significantly higher than the density of the same cells in uninfected gills (15.3 ± 3.8; ANOVA, P < 0.05). Few histamine-positive granular cells (i.e., MCs) were found in the uninfected and parasitized gills. Here, we show, for the first time in S. aurata infected gills, that AGs rather than MCs are recruited and involved in the response to E. lizae infection in seabream. PMID:23644766

  7. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

    Science.gov (United States)

    Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

    The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

  8. Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy

    Directory of Open Access Journals (Sweden)

    S Emil Ruff

    2016-03-01

    Full Text Available The anaerobic oxidation of methane (AOM is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME and sulfate-reducing bacteria (SRB, and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic-carbon depleted permeable sands off the Island of Elba (Italy. We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3 and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise

  9. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

    Science.gov (United States)

    Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

    The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g(-1) day(-1) indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20-50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

  10. 缺氧嗜甲烷古菌研究进展%Advances in Research on Anaerobic Methanotrophs

    Institute of Scientific and Technical Information of China (English)

    李江; 刘晓风; 廖银章; 袁月祥; 闫志英

    2011-01-01

    The distribution, niche, form and metabolism charaleristics of anaerobic methanotrophs (ANME) are summarized, and the phylogenetic relationship between ANME and methanogenic archaea are discussed. Methane can be oxidized by syntrophism of ANME and sulfate-reducing bacteria under the oxygen deficit condition. ANME mainly distribute in deep-sea and cold-seep area, and generally associate sulfate-reducing bacteria to carry out anaerobic oxidation of methane by proposed "reverse methanogenesis" or "methylogenesis" pathways. Little is known about the niche of such archaea as there is no pure culture. The cells are coccoid or rod, often occuring as consortia or in long multicellular chains. ANME are phylogenetically related to methanogenic archaea and they have common characters. Fig 1, Tab 1, Ref 37%综述了缺氧嗜甲烷古菌的分布、生态位、形态与代谢特征的新发现,并讨论了其与产甲烷菌的关系.在无氧条件下,缺氧嗜甲烷古菌与硫酸盐还原菌互养,氧化甲烷气体以阻止其进入大气.缺氧嗜甲烷古菌主要分布于深海甲烷渗漏区和冷泉区域,在其他多种缺氧环境中也能发现,由于还未获得纯培养,对这类微生物的生态位知之甚少.其细胞呈球状、杆状,有时聚集成球状集合体或连接形成丝状体.缺氧甲烷氧化可能经过“反甲烷合成”、“甲基合成”等路径.嗜甲烷古菌与产甲烷菌有着较近的亲缘关系,并且存在许多相似点.图1表1参37

  11. Effects of Long-Term CO2 Enrichment on Soil-Atmosphere CH4 Fluxes and the Spatial Micro-Distribution of Methanotrophic Bacteria.

    Directory of Open Access Journals (Sweden)

    Saeed Karbin

    Full Text Available Effects of elevated atmospheric CO2 concentrations on plant growth and associated C cycling have intensively been studied, but less is known about effects on the fluxes of radiatively active trace gases other than CO2. Net soil-atmosphere CH4 fluxes are determined by the balance of soil microbially-driven methane (CH4 oxidation and methanogenesis, and both might change under elevated CO2.Here, we studied CH4 dynamics in a permanent grassland exposed to elevated CO2 for 14 years. Soil-atmosphere fluxes of CH4 were measured using large static chambers, over a period of four years. The ecosystem was a net sink for atmospheric CH4 for most of the time except summer to fall when net CH4 emissions occurred. We did not detect any elevated CO2 effects on CH4 fluxes, but emissions were difficult to quantify due to their discontinuous nature, most likely because of ebullition from the saturated zone. Potential methanotrophic activity, determined by incubation of fresh sieved soil under standardized conditions, also did not reveal any effect of the CO2 treatment. Finally, we determined the spatial micro-distribution of methanotrophic activity at less than 5× atmospheric (10 ppm and elevated (10000 ppm CH4 concentrations, using a novel auto-radiographic technique. These analyses indicated that domains of net CH4 assimilation were distributed throughout the analyzed top 15 cm of soils, with no dependence on CH4 concentration or CO2 treatment.Our investigations suggest that elevated CO2 exerts no or only minor effects on CH4 fluxes in the type of ecosystem we studied, at least as long as soil moisture differences are small or absent as was the case here. The autoradiographic analyses further indicate that the spatial niche of CH4 oxidation does not shift in response to CO2 enrichment or CH4 concentration, and that the same type of methanotrophs may oxidize CH4 from atmospheric and soil-internal sources.

  12. In vitro cholesterol-lowering properties of Lactobacillus plantarum AN6 isolated from aji-narezushi.

    Science.gov (United States)

    Kuda, T; Yazaki, T; Ono, M; Takahashi, H; Kimura, B

    2013-09-01

    Aji-narezushi is a traditional lactic acid-fermented fish. In this study, we screened for lactose-utilizing, acidophilic, bile-resistant and cholesterol-lowering lactic acid bacteria (LAB) from aji-narezushi for use as starter strains for fermented foods, as well as for use as probiotics. Of the 301 LAB isolates, 277 fermented lactose, and among these, 171 grew in de Man, Rogosa and Sharpe broth adjusted to pH 3·5. Thirty-four of the isolates were grown in a broth containing 3% (w/v) bile. All of the isolates were lactobacilli. Seven isolates that demonstrated cholesterol-lowering activity in ethanolic solution were selected. All of the isolates were identified as Lactobacillus plantarum. Lactobacillus plantarum AN6 showed the highest cholesterol-lowering activity. AN6 was more resistant to acid, salt and bile than the type strain NBRC15891(T). One-half of the cholesterol-lowering effect remained after boiling AN6 for 10 min. The Fourier transform infrared (FT-IR) analysis indicated that the content of cell wall polysaccharides in AN6 is higher than ones in the type strain. These results indicate that Lact. plantarum AN6 can be used as a profitable starter organism and probiotic.

  13. Methanotrophic N2-Fixation in Boreal Peatlands: Master Regulation of Newly Fixed N and Moderation of CH4 Fluxes to the Atmosphere

    Science.gov (United States)

    Schlesinger, M.; Fillingim, H. M.; Wieder, R. K.; Vile, M. A.

    2015-12-01

    Boreal peatlands are important to global carbon (C) and nitrogen (N) cycling. While they cover only 3-4% of the terrestrial surface, they account for 25-30% and 9-15% of the world's soil C and N, respectively. Globally, peatlands function as a net sink for atmospheric CO2, but also act as a net source of CH4. In peatlands of Alberta, Canada, rates of atmospheric N deposition are low: ~1 kg·ha-1·yr-1, however, NPP of Sphagnum mosses is surprisingly high. Sphagnum mosses are able to maintain high levels of NPP due to their symbiotic relationship with N2-fixing methanotrophs. Annually, rates of N2-fixation typically provide between 10-30 kg of newly fixed N per ha, while also oxidizing CH4. CH4 fluxes from boreal peatlands in Canada are typically quite low, however, fluxes also can be high during rare episodic ebullition events. CH4 accumulation and storage is substantial, especially at depth as CH4 concentrations in peat pore water typically exceed 1000 μM at 1-m below the peat surface. Given that CH4 fluxes are typically low, we wanted to examine the importance of CH4 oxidation in these same peats. We hypothesized that methanotrophic N2-fixation may be important not only in providing inputs of newly fixed N, but also in regulating CH4 emissions from peatlands. We measured concentrations of CH4 in peat porewaters, CH4 flux rates, CH4 oxidation rates, biological N2-fixation rates. Porewater CH4 concentrations were highest at depth and decreased to negligible amounts closer to the surface of the water table. CH4 flux rates were low and ranged from -2.6 to +8.7 μmol·m-2·min-1 (negative values indicate net CH4 consumption). In Sphagnum incubations, rates of CH4 oxidation (0.6-10.2 mmol·m-2·min-1) were ~2-3 orders of magnitude higher than CH4 flux rates. Additionally, N2-fixation rates in paired cores ranged from 11.7-63.3 kg·ha-1·yr-1; CH4 oxidation rates in these same units ranged from ~3.1-622 kg·CH4 oxidized ha-1·yr-1. Additionally, we confirmed that N2

  14. Molecular detection of diversity of methanogens and methanotrophs in natural wetland soil%自然湿地土壤产甲烷菌和甲烷氧化菌多样性的分子检测

    Institute of Scientific and Technical Information of China (English)

    佘晨兴; 仝川

    2011-01-01

    Methane is one of the most important greenhouse gases and plays an essential role in atmospheric chemistry. The largest single source of methane is natural wetlands , which have been suggested to contribute significantly to the interannual variability of global methane emissions. Methanogens and methanotrophs are the main functional microbial groups mediating methane cycles of natural wetlands. Biogenic methane is produced by methanogenic archaea or methanogens as the final step in anaerobic degradation of organic matter. However, only about half of the produced methane is emitted to the atmosphere , while the remainder is oxidized by a diverse group of bacteria referred to as methane oxidizing bacteria ( MOB) or methanotrophs. It is evident that the studies on the diversity of methanogens and methanotrophs can assist with revealing microbial-mediated methane cycles and the temporal-spatial heterogeneity of methane emission from natural wetlands. Traditional methods based on laboratory culture techniques have been proven inadequate to describe the vast microbial diversity, because those methods miss more than 99% of the organisms while enriching those thriving in cultures but not numerically or functionally important in the environment. Introduction of molecular methods independent of culture techniques has vastly improved the potential to describe microbial diversity. The 16S ribosomal RNA ( rRNA) gene is by far the most frequently used phylogenetic marker for studying microbial ecology and diversity in the environment. An additional approach includes the sequencing of functional genes that are unique to the physiology of the group of microorganisms studied. Methanogen and methanotroph communities have been characterized by employing the 16S rRNA gene or functional genes as molecular markers in different types of natural wetlands. The functional gene of methanogens is mcrA, which encodes subunits of Methyl-coenzyme M reductase; whilst the functional genes of

  15. Isolated dextrogastria

    Energy Technology Data Exchange (ETDEWEB)

    Cha, Kyung Soo; Kim, Soo Ryun; Lee, Yong Chul; Park, Soo Soung [Chung Ang University College of Medicine, Seoul (Korea, Republic of); Sim, Young Soo [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1982-06-15

    Isolated situs inversus of the stomach with otherwise normal position of the thoracic and abdominal viscera is an extremely rare anomaly occurring in two district forms. Majority of cases are associated with eventration of the diphragm and are reported as being confused with spontaneous pneumothorax or pyopneumothorax at base of the right lung. The right sided stomach may produce interesting and confusing changes in liver scan. We have experienced 2 cases of the isolated dextrogastria.

  16. Isolated dextrogastria

    International Nuclear Information System (INIS)

    Isolated situs inversus of the stomach with otherwise normal position of the thoracic and abdominal viscera is an extremely rare anomaly occurring in two district forms. Majority of cases are associated with eventration of the diphragm and are reported as being confused with spontaneous pneumothorax or pyopneumothorax at base of the right lung. The right sided stomach may produce interesting and confusing changes in liver scan. We have experienced 2 cases of the isolated dextrogastria

  17. Biooxidación de sulfuros mediante cepas nativas de acidófilos compatibles con Acidithiobacillus ferrooxidans y thiooxidans, mina de oro El Zancudo, (Titiribí, Colombia Sulphide bioxidation using native Acidithiobacillus ferrooxidans and thiooxidans, related acidophile strains from "El Zancudo" gold mine (Titiribí, Colombia

    Directory of Open Access Journals (Sweden)

    Márquez G. Marco A.

    2005-12-01

    Full Text Available El propósito de esta investigación fue evaluar a escala de laboratorio la acción de microorganismos acidófilos nativos compatibles con las especies Acidithiobacillus ferrooxidans y thiooxidans, aislados de la mina El Zancudo, Titiribí (Antioquia sobre la oxidación de sulfuros donde predominan la pirita y arsenopirita, variando las concentraciones de sustrato (8% y 16%, y el tamaño de partícula (75 um y 106 xm. Los resultados de las mediciones diarias de pH y potencial redox realizadas por un tiempo de 25 días, demuestran que hubo una actividad de oxidación eficiente y se llegó a valores de pH de 1,4 y potencial redox de 600 mV, además de encontrarse en solución niveles altos de alrededor de 20 g/L de As y 60 g/L de Fe. Por los análisis de DRX, FTIR y SEM/EDX, se evidencia la presencia de productos propios de la oxidación bacteriana, como jarosita y arsenatos de hierro, además de una corrosión inicial y avanzada en los granos de pirita y arsenopirita, respectivamente. Palabras clave: quimiolitotrofos, biolixiviación, pirita, arsenopirita, mineralogía aplicada.This investigation was aimed at a laboratory evaluation of the action of native Acidithiobacillus ferrooxidans-and thiooxidans-related acidophile micro-organism (isolated from El Zancudo gold mine in Titiribí, Colombia on the oxidation of sulphides, mainly consisting of pyrite and arsenopyrite; sulphide concentration varied from 8% to 16% and particle size from 75 um to 106 um. pH and redox potential measurement revealed efficient oxidation for each culture over a 25-day period, reaching 1,4 pH and 600 mV redox potential. 20 g/L As and 60 g/L Fe levels were reached in solution. XRD, FTIR and SEM/EDX analysis revealed the presence of bacterial oxidation products such as jarosite and iron arsenates, as well as low and high corrosion in pyrites and arsenopyrites, respectively. Key words: chemolithotrophics, bioleaching, pyrite, arsenopyrite, applied mineralogy.

  18. Research Progress on Methanotrophic Bacteria in Landfills and the Reduction of Methane Emission%垃圾填埋场甲烷氧化菌及甲烷减排的研究进展

    Institute of Scientific and Technical Information of China (English)

    王晓琳; 曹爱新; 周传斌; 赵恺凝; 赵国柱

    2016-01-01

    As the main source of anthropogenic methane emission,landfills globally produce 35-69 Tg methane per year. The technology of reducing the methane emission in landfills has become a hot topic at present. Methanotrophic bacteria decomposing methane are the important biological collection to reduce atmospheric methane emissions,which is of significance in keeping the balance of the methane concentration in the atmosphere. Starting from the taxonomy and characteristics of methanotrophic bacteria,and the mechanism of its oxidizing methane, we summarized the latest research progress on the methods of studying diversity,factors affecting the activities of methanotrophic bacteria in landfills,and applications of them in the biological reduction of methane emission. Based on the prior researches,the issues in current studies of methanotrophic bacteria are also discussed. We propose comprehensive measures of utilizing the complex microbial agents of methanotrophic bacteria in landfills,providing a new thought in the research and application of reducing methane emission in landfills.%垃圾填埋场是全球最重要的人为甲烷排放源之一,其全球年甲烷释放量为35-69 Tg,垃圾填埋场甲烷减排是目前全球温室气体研究的热点。甲烷氧化菌能够氧化分解甲烷,作为减少大气甲烷排放的重要生物汇,对保持大气中甲烷浓度的平衡具有重要意义。从甲烷氧化菌的类型及其特征、甲烷氧化机理着手,介绍了多样性研究方法、填埋场中甲烷氧化菌的活性影响因素及甲烷生物减排应用等最新研究进展。在综述前人研究的基础上,探讨了目前研究的不足,提出了利用甲烷氧化菌复合微生物菌剂等综合处理措施,旨为垃圾填埋场甲烷减排的研究和应用提供新的思路。

  19. Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil.

    Science.gov (United States)

    Okamura, Keiko; Hisada, Takayoshi; Kanbe, Toshio; Hiraishi, Akira

    2009-02-01

    A photoorganotrophic alphaproteobacterium designated strain G2-11(T) was isolated from submerged paddy soil. This bacterium had relatively large, oval to rod-shaped cells (2.0-3.0x3.0-10 microm). Cells were motile by means of single polar flagella. The color of phototrophically growing cultures was reddish-brown. The cell extract had absorption maxima at 375, 465, 492, 529, 592, 804, and 844 nm, indicating the presence of bacteriochlorophyll a and carotenoides of the spirilloxanthin series. Vesicular intracytoplasmic membranes were present. The main component of cellular fatty acids was C(18:1)omega7c. Ubiquinone-10 and rhodoquinone-10 were the major quinones. A 16S rRNA gene sequence analysis revealed that the isolate is closest to the acidophilic aerobic photosynthetic bacterium Acidisphaera rubrifaciens strain HS-AP3(T) (93.3% similarity). The G+C content of genomic DNA is 67.8 mol%. The name Rhodovastum atsumiense gen. nov., sp. nov. is proposed for the novel isolate. The type strain is strain G2-11(T) (=NBRC 104268(T)=KCTC 5708(T)).

  20. Isoler nu

    DEFF Research Database (Denmark)

    Andersen, N.E.; Ankerstjerne, P.; Jørgensen, B.;

    Omfattende vejledning, der angiver, hvordan energiforbruget i eksisterende huse kan nedbringes ved isolering, tætning og forbedring af varmeanlægget, og hvor meget det koster. Anvisningen indeholder detaljerede eksempler på efterisolering af ydervægge, tage, gulve og vinduer. Henvender sig til ej...

  1. 水稻土甲烷氧化菌对镉胁迫的响应%Response of methanotrophic community structure and oxidation potential to cadmium stress in a Chinese paddy soil

    Institute of Scientific and Technical Information of China (English)

    郑勇; 郑袁明; 贺纪正

    2012-01-01

    重金属污染影响土壤微生物群落结构与活性,间接影响土壤碳(如CO2、CH4)的生物地球化学循环和全球气候变化.甲烷氧化菌氧化消耗CH4,降低大气中CH4含量,在缓解由温室气体导致的全球温暖化方面起着重要作用.本研究通过短期土壤培养实验,比较研究了不同强度重金属镉(Cd)胁迫下,水稻土中甲烷氧化菌的多度、群落组成及其氧化CH4潜势的差异.结果表明,添加Cd含量越大,水稻土氧化CH4潜势越弱,甲烷氧化菌pmoA基因拷贝数显著减少;甲烷氧化菌多度与水稻土氧化CH4潜势之间存在显著正相关关系(P< 0.001).群落组成分析发现,在相对低含量Cd(1 mg·kg-1)条件下,有新的甲烷氧化菌菌属出现,而添加较高含量Cd (10 mg·kg-1)时甲烷氧化菌种类减少.总之,Cd胁迫降低水稻土中甲烷氧化菌多样性及其氧化CH4潜势,可能导致原位CH4消耗减少,从而增加稻田CH4排放.%Heavy metal contamination has strong effect on the soil microbial community and activities, and also affects the biogeochemical cycling of soil carbon (e.g. CO2 and CH4) and global climate change. Fortunately, methane-oxidizing bacteria (methanotrophs) can consume CH4 and therefore play a critical role in the mitigation of global warming. Here, a short-term, laboratory-based incubation experiment was conducted to examine the effects of cadmium (Cd) amendments on the abundance, community composition and oxidation potential of methanotrophs in a southern China paddy soil. The results showed that there were significantly lower methanotrophic oxidation potential and abundance in the treatment of Cd amendment of 10 mg·kg-1 (high-Cd) than those in the treatment of Cd amendment of 1 mg·kg-1 (low-Cd) dry weight soil and the Control. Correlation analyses indicated that the methanotrophic oxidation potentials were significantly positively correlated with the abundance of methanotrophs (P < 0.001). For the community in rice

  2. Long-term cultivation of a stable Methylocystis-dominated methanotrophic enrichment enabling tailored production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate).

    Science.gov (United States)

    Myung, Jaewook; Galega, Wakuna M; Van Nostrand, Joy D; Yuan, Tong; Zhou, Jizhong; Criddle, Craig S

    2015-12-01

    Methane (CH4) is a readily available feedstock for production of polyhydroxyalkanoates (PHAs). The structure and PHA production capacity of a Methylocystis-dominated methanotrophic enrichment was stable in long-term operation (>175 days) when grown exponentially under non-aseptic conditions in fill-and-draw batch cultures with ammonium as nitrogen source. Cells harvested in the draw step were incubated in the absence of nitrogen with various combinations of CH4 and valerate to assess capacity for synthesis of poly(3-hydroxybutyrate) (P3HB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). When fed CH4 alone, only P3HB was produced. When fed CH4 plus valerate, PHBV was synthesized. The mol% of 3-hydroxyvalerate (3HV) increased with added valerate. Oxidation of CH4 was required for valerate assimilation, and the fraction of CH4 oxidized increased with increased mol% 3 HV. By separating PHA accumulation from cell replication, tailored PHA-rich biomass can be generated by addition of co-substrate, while retaining a large inoculum for the next cycle of cell division. PMID:26454368

  3. Vertical profiles of community abundance and diversity of anaerobic methanotrophic archaea (ANME) and bacteria in a simple waste landfill in north China.

    Science.gov (United States)

    Dong, Jun; Ding, Linjie; Wang, Xu; Chi, Zifang; Lei, Jiansen

    2015-03-01

    Anaerobic methane oxidation (AMO) is considered to be an important sink of CH4 in habitats as marine sediments. But, few studies focused on AMO in landfills which may be an important sink of CH4 derived from waste fermentation. To show evidence of AMO and to uncover function anaerobic methanotroph (ANME) community in landfill, different age waste samples were collected in Jinqianpu landfill located in north China. Through high-throughput sequencing, Methanomicrobiales and Methanosarcinales archaea associated with ANME and reverse methanogenic archaea of Methanosarcina and Methanobacterium were detected. Sulfate-reducing bacteria (SRB) (Desulfobulbus and Desulfococcus) which could couple with ANME-conducting AMO were also found. But, the community structure of ANME had no significant difference with depths. From the results of investigation, we can come to a conclusion that sulfate-dependent anaerobic methane oxidation (SR-DAMO) would be the dominant AMO process in the landfill, while iron-dependent anaerobic methane oxidation (M/IR-DAMO) process was weak though concentration of ferric iron was large in the landfill. Denitrification-dependent anaerobic methane oxidation (NR-DAMO) was negative because of lack of nitrate and relevant function microorganisms in the landfill. Results also indicate that CH4 mitigation would have higher potential by increasing electron acceptor contents and promoting the growth of relevant function microorganisms. PMID:25561057

  4. A novel framework for quantifying past methane recycling by Sphagnum-methanotroph symbiosis using carbon and hydrogen isotope ratios of leaf wax biomarkers

    Science.gov (United States)

    Nichols, Jonathan E.; Isles, Peter D. F.; Peteet, Dorothy M.

    2014-05-01

    concentration of atmospheric methane is strongly linked to variations in Earth's climate. Currently, we can directly reconstruct the total atmospheric concentration of methane, but not individual terms of the methane cycle. Northern wetlands, dominated by Sphagnum, are an important contributor of atmospheric methane, and we seek to understand the methane cycle in these systems. We present a novel method for quantifying the proportion of carbon Sphagnum assimilates from its methanotrophic symbionts using stable isotope ratios of leaf-wax biomarkers. Carbon isotope ratios of Sphagnum compounds are determined by two competing influences, water content and the isotope ratio of source carbon. We disentangled these effects using a combined hydrogen and carbon isotope approach. We constrained Sphagnum water content using the contrast between the hydrogen isotope ratios of Sphagnum and vascular plant biomarkers. We then used Sphagnum water content to calculate the carbon isotope ratio of Sphagnum's carbon pool. Using a mass balance equation, we calculated the proportion of recycled methane contributed to the Sphagnum carbon pool, "PRM." We quantified PRM in peat monoliths from three microhabitats in the Mer Bleue peatland complex. Modern studies have shown that water table depth and vegetation have strong influences on the peatland methane cycle on instrumental time scales. With this new approach, δ13C of Sphagnum compounds are now a useful tool for investigating the relationships among hydrology, vegetation, and methanotrophy in Sphagnum peatlands over the time scales of entire peatland sediment records, vital to our understanding of the global carbon cycle through the Late Glacial and Holocene.

  5. A Novel Framework for Quantifying past Methane Recycling by Sphagnum-Methanotroph Symbiosis Using Carbon and Hydrogen Isotope Ratios of Leaf Wax Biomarkers

    Science.gov (United States)

    Nichols, Jonathan E.; Isles, Peter D. F.; Peteet, Dorothy M.

    2014-01-01

    The concentration of atmospheric methane is strongly linked to variations in Earth's climate. Currently, we can directly reconstruct the total atmospheric concentration of methane, but not individual terms of the methane cycle. Northern wetlands, dominated by Sphagnum, are an important contributor of atmospheric methane, and we seek to understand the methane cycle in these systems. We present a novel method for quantifying the proportion of carbon Sphagnum assimilates from its methanotrophic symbionts using stable isotope ratios of leaf-wax biomarkers. Carbon isotope ratios of Sphagnum compounds are determined by two competing influences, water content and the isotope ratio of source carbon. We disentangled these effects using a combined hydrogen and carbon isotope approach. We constrained Sphagnum water content using the contrast between the hydrogen isotope ratios of Sphagnum and vascular plant biomarkers. We then used Sphagnum water content to calculate the carbon isotope ratio of Sphagnum's carbon pool. Using a mass balance equation, we calculated the proportion of recycled methane contributed to the Sphagnum carbon pool, 'PRM.' We quantified PRM in peat monoliths from three microhabitats in the Mer Bleue peatland complex. Modern studies have shown that water table depth and vegetation have strong influences on the peatland methane cycle on instrumental time scales. With this new approach, delta C-13 of Sphagnum compounds are now a useful tool for investigating the relationships among hydrology, vegetation, and methanotrophy in Sphagnum peatlands over the time scales of entire peatland sediment records, vital to our understanding of the global carbon cycle through the Late Glacial and Holocene.

  6. Vertical profiles of community abundance and diversity of anaerobic methanotrophic archaea (ANME) and bacteria in a simple waste landfill in north China.

    Science.gov (United States)

    Dong, Jun; Ding, Linjie; Wang, Xu; Chi, Zifang; Lei, Jiansen

    2015-03-01

    Anaerobic methane oxidation (AMO) is considered to be an important sink of CH4 in habitats as marine sediments. But, few studies focused on AMO in landfills which may be an important sink of CH4 derived from waste fermentation. To show evidence of AMO and to uncover function anaerobic methanotroph (ANME) community in landfill, different age waste samples were collected in Jinqianpu landfill located in north China. Through high-throughput sequencing, Methanomicrobiales and Methanosarcinales archaea associated with ANME and reverse methanogenic archaea of Methanosarcina and Methanobacterium were detected. Sulfate-reducing bacteria (SRB) (Desulfobulbus and Desulfococcus) which could couple with ANME-conducting AMO were also found. But, the community structure of ANME had no significant difference with depths. From the results of investigation, we can come to a conclusion that sulfate-dependent anaerobic methane oxidation (SR-DAMO) would be the dominant AMO process in the landfill, while iron-dependent anaerobic methane oxidation (M/IR-DAMO) process was weak though concentration of ferric iron was large in the landfill. Denitrification-dependent anaerobic methane oxidation (NR-DAMO) was negative because of lack of nitrate and relevant function microorganisms in the landfill. Results also indicate that CH4 mitigation would have higher potential by increasing electron acceptor contents and promoting the growth of relevant function microorganisms.

  7. Eksistentiel Isolation

    OpenAIRE

    Matikainen, Oliver Albert; Andersen, Kian Alexander; Thorup, Johannes Hoff; Slotsager, Christian Knud; Jensen, Mette Ingersholm; Bachmann, Zenia Gruhl; Razga, Pauline Marie

    2015-01-01

    This study examines whether or not isolation can lead to personal growth. In order to answer this question we distinguish between loneliness and aloneness. We explain the theory of existential psychotherapist Irvin D. Yalom and on the basis of this examination, we analyze a conducted interview through the theory. Based on the theory, interview and analysis, we discuss the validity of Yalom’s theory. Considering the examination, the analysis and the distinction between the two types of isolati...

  8. First Genome Data from Uncultured Upland Soil Cluster Alpha Methanotrophs Provide Further Evidence for a Close Phylogenetic Relationship to Methylocapsa acidiphila B2 and for High-Affinity Methanotrophy Involving Particulate Methane Monooxygenase

    OpenAIRE

    Ricke, Peter; Kube, Michael; Nakagawa, Satoshi; Erkel, Christoph; Reinhardt, Richard; Liesack, Werner

    2005-01-01

    Members of upland soil cluster alpha (USCα) are assumed to be methanotrophic bacteria (MB) adapted to the trace level of atmospheric methane. So far, these MB have eluded all cultivation attempts. While the 16S rRNA phylogeny of USCα members is still not known, phylogenies constructed for the active-site polypeptide (encoded by pmoA) of particulate methane monooxygenase (pMMO) placed USCα next to the alphaproteobacterial Methylocapsa acidiphila B2. To assess whether the pmoA tree reflects the...

  9. The protein ORF80 from the acidophilic and thermophilic archaeon Sulfolobus islandicus binds highly site-specifically to double-stranded DNA and represents a novel type of basic leucine zipper protein

    Science.gov (United States)

    Lipps, Georg; Ibanez, Pablo; Stroessenreuther, Thomas; Hekimian, Katya; Krauss, Gerhard

    2001-01-01

    The cryptic high copy number plasmid pRN1 from the thermophilic and acidophilic crenarchaeote Sulfolobus islandicus shares three conserved open reading frames with other S.islandicus plasmids. One of the open reading frames, namely orf80, encodes a 9.5 kDa protein that has no homology to any characterised protein. Recombinant ORF80 purified from Escherichia coli binds to double-stranded DNA in a sequence-specific manner as suggested by EMSA experiments and DNase I footprints. Two highly symmetrical binding sites separated by ∼60 bp were found upstream of the orf80 gene. Both binding sites contain two TTAA motifs as well as other conserved bases. Fluorescence measurements show that short duplex DNAs derived from a single binding site sequence are bound with submicromolar affinity and moderate cooperativity by ORF80. On DNA fragments carrying both binding sites, a rather large protein–DNA complex is formed in a highly cooperative manner. ORF80 contains an N-terminal leucine zipper motif and a highly basic domain at its C-terminus. Compared to all known basic leucine zipper proteins the order of the domains is reversed in ORF80. ORF80 may therefore constitute a new subclass of basic leucine zipper DNA-binding proteins. PMID:11812827

  10. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

    Science.gov (United States)

    Case, David H.

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  11. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

    Science.gov (United States)

    Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  12. Isolation of a strain of Acidithiobacillus caldus and its role in bioleaching of chalcopyrite

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Q.G.; Bo, F.; Bo, Z.H.; Xi, L.; Jian, G.; Fei, L.F.; Hua, C.X. [Central South University of Technology, Changsha (China)

    2007-09-15

    A moderately thermophilic and acidophilic sulfur-oxidizing bacterium named S-2, was isolated from coal heap drainage. The bacterium was motile, Gramnegative, rod-shaped, measured 0.4 to 0.6 by 1 to 2 gm, and grew optimally at 42-45{sup o}C and an initial pH of 2.5. The strain S-2 grew autotrophically by using elemental sulfur, sodium thiosulfate and potassium tetrathionate as energy sources. The strain did not use organic matter and inorganic minerals including ferrous sulfate, pyrite and chalcopyrite as energy sources. The morphological, biochemical, physiological characterization and analysis based on 16S rRNA gene sequence indicated that the strain S2 is most closely related to Acidithiobacillus caldus (> 99% similarity in gene sequence). The combination of the strain S-2 with Leptospirillum ferriphilum or Acidithiobacillus ferrooxidans in chalcopyrite bioleaching improved the copper-leaching efficiency. Scanning electron microscope (SEM) analysis revealed that the chalcopyrite surface in a mixed culture of Leptospirillum ferriphilum and Acidithiobacillus caldus was heavily etched. The energy dispersive X-ray (EDX) analysis indicated that Acidithiobacillus caldus has the potential role to enhance the recovery of copper from chalcopyrite by oxidizing the sulfur formed during the bioleaching progress.

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

    Science.gov (United States)

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

    2005-02-01

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

  14. Metabolic engineering in methanotrophic bacteria.

    Science.gov (United States)

    Kalyuzhnaya, Marina G; Puri, Aaron W; Lidstrom, Mary E

    2015-05-01

    Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems. PMID:25825038

  15. Metabolic engineering in methanotrophic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Kalyuzhnaya, MG; Puri, AW; Lidstrom, ME

    2015-05-01

    Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems. (C) 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  16. Understand Quarantine and Isolation

    Science.gov (United States)

    ... Social Media What CDC is Doing Blog: Public Health Matters What's New Preparation & Planning Emergency Preparedness and Response Understand Quarantine and Isolation Recommend on Facebook Tweet Share Compartir Isolation and quarantine help protect the public by ...

  17. Complete Genome Sequence of Beijerinckia indica subsp. indica▿

    OpenAIRE

    Tamas, Ivica; Dedysh, Svetlana N.; Liesack, Werner; Stott, Matthew B.; Alam, Maqsudul; Murrell, J. Colin; Dunfield, Peter F.

    2010-01-01

    Beijerinckia indica subsp. indica is an aerobic, acidophilic, exopolysaccharide-producing, N2-fixing soil bacterium. It is a generalist chemoorganotroph that is phylogenetically closely related to facultative and obligate methanotrophs of the genera Methylocella and Methylocapsa. Here we report the full genome sequence of this bacterium.

  18. Mutation and premating isolation.

    Science.gov (United States)

    Woodruff, R C; Thompson, J N

    2002-11-01

    While premating isolation might be traceable to different genetic mechanisms in different species, evidence supports the idea that as few as one or two genes may often be sufficient to initiate isolation. Thus, new mutation can theoretically play a key role in the process. But it has long been thought that a new isolation mutation would fail, because there would be no other individuals for the isolation-mutation-carrier to mate with. We now realize that premeiotic mutations are very common and will yield a cluster of progeny carrying the same new mutant allele. In this paper, we discuss the evidence for genetically simple premating isolation barriers and the role that clusters of an isolation mutation may play in initiating allopatric, and even sympatric, species divisions.

  19. Genetics Home Reference: isolated growth hormone deficiency

    Science.gov (United States)

    ... deficiency dwarfism, pituitary growth hormone deficiency dwarfism isolated GH deficiency isolated HGH deficiency isolated human growth hormone deficiency isolated somatotropin deficiency isolated somatotropin deficiency disorder ...

  20. Alternativ isolering i bygninger

    DEFF Research Database (Denmark)

    Andersen, T.; Skibstrup Eriksen, S.

    Denne SBI-meddelelse beskriver resultaterne af en undersøgelse af bygninger, hvor der er anvendt alternativ isolering. Undersøgelsen omfatter termografering og fugtmåling af udvendige bygningsdele isoleret med alternativ isolering. Endvidere rapporteres resultaterne af målinger af indholdet af tu...

  1. Community of thermoacidophilic and arsenic resistant microorganisms isolated from a deep profile of mine heaps.

    Science.gov (United States)

    Casas-Flores, S; Gómez-Rodríguez, E Y; García-Meza, J V

    2015-12-01

    Soluble arsenic (As) in acidic feed solution may inhibit the copper (Cu) bioleaching process within mine heaps. To clarify the effect of soluble arsenic on the live biomass and bioxidative activity in heaps, toxicological assays were performed using a synthetic feed solution given by a mine company. The microorganisms had previously been isolated from two heap samples at up to 66 m depth, and cultured using specific media for chemolithotrophic acidophiles (pH 1-2) and moderate thermophiles (48°C), for arsenic tolerance assay. The four media with the highest biomass were selected to assay As-resistance; one culture (Q63h) was chosen to assay biooxidative activity, using a heap sample that contained chalcopyrite and covellite. We found that 0.5 g/L of As does not affect living biomass or biooxidative activity on Cu sulfides, but it dissolves Cu, while As precipitates as arsenic acid (H3AsO4·½H2O). The arsenic tolerant community, as identified by 16S rDNA gene sequence analysis, was composed of three main metabolic groups: chemolithotrophs (Leptospirillum, Sulfobacillus); chemolithoheterotrophs and organoheterotrophs as Acidovorax temperans, Pseudomonas alcaligenes, P. mendocina and Sphingomonas spp. Leptospirillum spp. and S. thermosulfidooxidans were the dominant taxa in the Q63-66 cultures from the deepest sample of the oldest, highest-temperature heap. The results indicated arsenic resistance in the microbial community, therefore specific primers were used to amplify ars (arsenic resistance system), aio (arsenite oxidase), or arr (arsenate respiratory reduction) genes from total sample DNA. Presence of arsB genes in S. thermosulfidooxidans in the Q63-66 cultures permits H3AsO4-As(V) detoxification and strengthens the community's response to As. PMID:26283066

  2. Extremely Isolated Elliptical Galaxies

    Science.gov (United States)

    Fuse, Christopher R.; Marcum, P.; Fanelli, M.; Aars, C.

    2006-06-01

    Isolated galaxies provide a means of assessing the evolution of galactic systems. Extremely isolated galaxies define a zero-interaction baseline for comparative studies of galaxy evolution. We present results of a search for isolated elliptical galaxies (IEGs). We utilize the optical imaging data produced by the Sloan Digital Sky Survey (SDSS) to identify candidate galaxies from Release 1-4 of the SDSS. Candidate IEGs meet strict isolation criteria: Any IEG must be separated by at least 2.5 Mpc from any neighboring non-dwarf galaxy having a MV fainter than -16.5 mag. The candidate isolated systems have no non-dwarf neighbors within a distance such that we can insure that the IEGs have never interacted with another existing galaxy since formation.In order to increase the signal-to-noise ratio, we have used the SDSS images in the u,g,r filters to create combined sets of images for each IEG. The stacked images permit a more robust determination of the morphology of the candidate galaxies. Verification that these are spheroidal systems is achieved through a bulge/disk decomposition technique using standard surface photometry. Our preliminary sample of 51 isolated systems defines a complete volume-limited population of extremely isolated early-type galaxies within a distance of 72Mpc

  3. Alternativ isolering i bygninger

    DEFF Research Database (Denmark)

    Hansen, Ernst Jan de Place

    2001-01-01

    Resume af rapport om målinger på alternative isoleringsmaterialer i bygninger, udgivet af Statens Byggeforskningsinstitut (SBI meddelelse 128) under Energistyrelsens udviklingsprogram "Miljø- og arbejdsmiljøvenlig isolering"...

  4. Base isolation: Fresh insight

    Energy Technology Data Exchange (ETDEWEB)

    Shustov, V.

    1993-07-15

    The objective of the research is a further development of the engineering concept of seismic isolation. Neglecting the transient stage of seismic loading results in a widespread misjudgement: The force of resistance associated with velocity is mostly conceived as a source of damping vibrations, though it is an active force at the same time, during an earthquake type excitation. For very pliant systems such as base isolated structures with relatively low bearing stiffness and with artificially added heavy damping mechanism, the so called `damping`` force may occur even the main pushing force at an earthquake. Thus, one of the two basic pillars of the common seismic isolation philosophy, namely, the doctrine of usefulness and necessity of a strong damping mechanism, is turning out to be a self-deception, sometimes even jeopardizing the safety of structures and discrediting the very idea of seismic isolation. There is a way out: breaking with damping dependancy.

  5. Isolation of Human Eosinophils

    OpenAIRE

    Akuthota, Praveen; Shamri, Revital; Weller, Peter F.

    2012-01-01

    Highly purified eosinophils can be isolated from peripheral blood by negative selection using an antibody-based magnetic negative selection protocol. The basic protocol describes a sequential fractionation of peripheral blood in which CD16+ granulocytes are enriched first from whole blood, followed by isolation of eosinophils. This technique is easy to use, fast, and highly reproducible. Support protocols describe a staining methods that can be used to evaluate the purity of eosinophils and d...

  6. Isolated sleep paralysis

    OpenAIRE

    Sawant, Neena S.; Shubhangi R Parkar; Tambe, Ravindra

    2005-01-01

    Sleep paralysis (SP) is a cardinal symptom of narcolepsy. However, little is available in the literature about isolated sleep paralysis. This report discusses the case of a patient with isolated sleep paralysis who progressed from mild to severe SP over 8 years. He also restarted drinking alcohol to be able to fall asleep and allay his anxiety symptoms. The patient was taught relaxation techniques and he showed complete remission of the symptoms of SP on follow up after 8 months.

  7. Isolated Fallopian Tube Torsion

    Directory of Open Access Journals (Sweden)

    S. Kardakis

    2013-01-01

    Full Text Available Isolated torsion of the Fallopian tube is a rare gynecological cause of acute lower abdominal pain, and diagnosis is difficult. There are no pathognomonic symptoms; clinical, imaging, or laboratory findings. A preoperative ultrasound showing tubular adnexal masses of heterogeneous echogenicity with cystic component is often present. Diagnosis can rarely be made before operation, and laparoscopy is necessary to establish the diagnosis. Unfortunately, surgery often is performed too late for tube conservation. Isolated Fallopian tube torsion should be suspected in case of acute pelvic pain, and prompt intervention is necessary.

  8. Motion of isolated bodies

    Energy Technology Data Exchange (ETDEWEB)

    Choquet-Bruhat, Yvonne [Academie des Sciences, 23 Quai de Conti, 75270 Paris Cedex 06 (France); Friedrich, Helmut [Max-Planck-Institut fuer Gravitationsphysik, Am Muehlenberg 1, 14476 Golm (Germany)

    2006-10-21

    It is shown that sufficiently smooth initial data for the Einstein-dust or the Einstein-Maxwell-dust equations with non-negative density of compact support develop into solutions representing isolated bodies in the sense that the matter field has spatially compact support and is embedded in an exterior vacuum solution.

  9. Motion of Isolated bodies

    CERN Document Server

    Choquet-Bruhat, Y; Choquet-Bruhat, Yvonne; Friedrich, Helmut

    2006-01-01

    It is shown that sufficiently smooth initial data for the Einstein-dust or the Einstein-Maxwell-dust equations with non-negative density of compact support develop into solutions representing isolated bodies in the sense that the matter field has spatially compact support and is embedded in an exterior vacuum solution.

  10. Chiral fiber optical isolator

    Science.gov (United States)

    Kopp, Victor I.; Zhang, Guoyin; Zhang, Sheng; Genack, Azriel Z.; Neugroschl, Dan

    2009-02-01

    We propose an in-fiber chiral optical isolator based on chiral fiber polarizer technology and calculate its performance by incorporating the magnetic field into the scattering matrix. The design will be implemented in a special preform, which is passed through a miniature heat zone as it is drawn and twisted. The birefringence of the fiber is controlled by adjusted the diameter of a dual-core optical fiber. By adjusting the twist, the fiber can convert linear to circular polarization and reject one component of circular polarization. In the novel central portion of the isolator, the fiber diameter is large. The effective birefringence of the circular central core with high Verdet constant embedded in an outer core of slightly smaller index of refraction is small. The central potion is a non-reciprocal polarization converter which passes forward traveling left circularly polarized (LCP) light as LCP, while converting backward propagating LCP to right circularly polarized (RCP) light. Both polarizations of light traveling backwards are scattered out of the isolator. Since it is an all-glass structure, we anticipate that the isolator will be able to handle several watts of power and will be environmentally robust.

  11. Isolated fructose malabsorption.

    OpenAIRE

    Wales, J. K.; Primhak, R A; Rattenbury, J; Taylor, C J

    1990-01-01

    A patient with isolated fructose malabsorption presented with diarrhoea and colic during the first year of life and subsequently responded to a fructose free diet. Fructose malabsorption has been implicated in some cases of irritable bowel syndrome in adults and may also be an infrequently recognised cause of gastrointestinal symptoms in children.

  12. Isolated jejunal varices.

    Directory of Open Access Journals (Sweden)

    Bhagwat S

    1995-04-01

    Full Text Available Isolated jejunal varices are an uncommon manifestation of portal hypertension. A one and a half year old boy presented with recurrent, massive gastrointestinal bleeding from jejunal varices. The bleeding site was identified at exploratory laparotomy. Jejunal resection and anastomosis resulted in complete resolution of the bleeding and there has been no recurrent bleeding over an eight month follow-up period.

  13. Proteoglycan isolation and analysis

    DEFF Research Database (Denmark)

    Woods, A; Couchman, J R

    2001-01-01

    Proteoglycans can be difficult molecules to isolate and analyze due to large mass, charge, and tendency to aggregate or form macromolecular complexes. This unit describes detailed methods for purification of matrix, cell surface, and cytoskeleton-linked proteoglycans. Methods for analysis...

  14. Characterization of Methylocystis strain JTA1 isolated from aged refuse and its tolerance to chloroform

    Institute of Scientific and Technical Information of China (English)

    Tiantao Zhao; Lijie Zhang; Yunru Zhang; Zhilin Xing; Xuya Peng

    2013-01-01

    To accelerate the efficiency of methane biodegradation in landfills,a Gram-negative,rod-shaped,non-motile,non-spore-forming bacterium,JTA1,which can utilize methane as well as acetate,was isolated from the Laogang MSW landfills,Shanghai,China.Strain JTA1 was a member of genus Methylocystis on the basis of 16S rRNA and pmoA gene sequence similarity.The maximum specific cell growth rates (μmax=0.042 hr-1,R2=0.995) was derived through Boltzmann simulation,and the apparent half-saturation constants (Km(app) =7.08 mmol/L,R2 =0.982) was calculated according to Michaelis-Menton hyperbolic model,indicating that Methylocystis strain JTA1 had higher-affinity potential for methane oxidation than other reported methanotrophs.By way of adding the strain JTA1 culture,the methane consumption of aged refuse reached 115 mL,almost two times of control experiment.In addition,high tolerance of Methylocystis strain JTA1 to chloroform could facilitate the methane oxidation of aged refuse bio-covers.At the chloroform concentration of 50 mg/L,the methane-oxidation rate of bio-cover reached 0.114 mL/(day.g),much higher than the highest rate,0.0135 mL/(day.g),of reported bio-covers.In conclusion,strain JTA1 opens up a new possibility for environmental biotechnology,such as soil or landfills bioremediation and wastewater decontamination.

  15. Method for isolating nucleic acids

    Science.gov (United States)

    Hurt, Jr., Richard Ashley; Elias, Dwayne A.

    2015-09-29

    The current disclosure provides methods and kits for isolating nucleic acid from an environmental sample. The current methods and compositions further provide methods for isolating nucleic acids by reducing adsorption of nucleic acids by charged ions and particles within an environmental sample. The methods of the current disclosure provide methods for isolating nucleic acids by releasing adsorbed nucleic acids from charged particles during the nucleic acid isolation process. The current disclosure facilitates the isolation of nucleic acids of sufficient quality and quantity to enable one of ordinary skill in the art to utilize or analyze the isolated nucleic acids for a wide variety of applications including, sequencing or species population analysis.

  16. Isolated lung perfusion.

    Science.gov (United States)

    Cypel, Marcelo; Keshavjee, Shaf

    2012-01-01

    Isolated lung perfusion (ILP) has been historically used as a method to study basic lung physiologic concepts using animal models. More recently, ILP has been applied in lung transplantation and thoracic oncology. In lung transplantation, ILP has been used to assess physiological integrity of donor lungs after the organ is removed from the donor. This procedure is called Ex vivo Lung Perfusion (EVLP), and it has also been proposed as a method for active treatment and repair of injured unsuitable donor organs ex vivo. In oncology, ILP is an attractive method to deliver high dose chemotherapy to treat pulmonary metastatic disease. Since the lung vasculature is isolated in vivo, this technique is called in vivo lung perfusion (IVLP). This review will focus on the rationale, technical aspects, experimental and clinical experience of EVLP and IVLP. A perspective on the future use of these techniques is described. PMID:22202033

  17. Ultrasonic thermometer isolation standoffs

    International Nuclear Information System (INIS)

    A method is provided for minimizing sticking of the transmission line to the protective sheath and preventing noise echoes from interfering with signal echoes in an improved high temperature ultrasonic thermometer which includes an ultrasonic transmission line surrounded by a protective sheath. Small isolation standoffs are mounted on the transmission line to minimize points of contact between the transmission line and the protective sheath, the isolation standoffs serving as discontinuities mounted on the transmission line at locations where a signal echo is desired or where an echo can be tolerated. Consequently any noise echo generated by the sticking of the standoff to the protective sheath only adds to the amplitude of the echo generated at the standoff and does not interfere with the other signal echoes. 6 claims, 3 figures

  18. High voltage isolation transformer

    Science.gov (United States)

    Clatterbuck, C. H.; Ruitberg, A. P. (Inventor)

    1985-01-01

    A high voltage isolation transformer is provided with primary and secondary coils separated by discrete electrostatic shields from the surfaces of insulating spools on which the coils are wound. The electrostatic shields are formed by coatings of a compound with a low electrical conductivity which completely encase the coils and adhere to the surfaces of the insulating spools adjacent to the coils. Coatings of the compound also line axial bores of the spools, thereby forming electrostatic shields separating the spools from legs of a ferromagnetic core extending through the bores. The transformer is able to isolate a high constant potential applied to one of its coils, without the occurrence of sparking or corona, by coupling the coatings, lining the axial bores to the ferromagnetic core and by coupling one terminal of each coil to the respective coating encasing the coil.

  19. Electron isolation at ATLAS

    International Nuclear Information System (INIS)

    The ATLAS experiment at the Large Hadron Collider (LHC) will face the challenge of efficiently selecting interesting candidate events in pp collisions at 14 TeV centre-of-mass energy, whilst rejecting the enormous number of background events. Many of these interesting candidate events have isolated leptons in the final state, like for example events with a gauge boson or SUSY. On top of the standard ATLAS electron identification an isolation criterion has been developed using a likelihood as multivariate approach with several discriminating variables. The likelihood is constructed by selecting electrons from Z decays for the signal and for the background electrons from b quark jets. Results for the example of the associated Higgs boson production with top quarks and subsequent decay into a pair of W bosons are presented. In addition first results of a likelihood to discriminate against jets are given and a possible extension for muons is discussed

  20. Brown Fat Cell Isolation

    OpenAIRE

    sprotocols

    2014-01-01

    Author: C.R. Kahn ### 1.) ISOLATION AND PRIMARY CULTURE OF BROWN FAT PREADIPOCYTES ### Rationale: To prepare primary brown preadipocytes for immortalization: useful for metabolic studies from knockout mice. This consists of the following five protocols. References: Fasshauer, M., J. Klein, K M. Kriauciunas, K. Ueki, M.Benito, and C.R. Kahn. 2001. Essential role of insulin substrate 1 in differentiation of brown adipocytes. *Mol Cell Biol* 21: 319-329. Fasshauer, M....

  1. Napoleon in isolation

    OpenAIRE

    Calegari, Danny

    1999-01-01

    Napoleon's theorem in elementary geometry describes how certain linear operations on plane polygons of arbitrary shape always produce regular polygons. More generally, certain triangulations of a polygon that tiles R^2 admit deformations which keep fixed the symmetry group of the tiling. This gives rise to isolation phenomena in cusped hyperbolic 3-manifolds, where hyperbolic Dehn surgeries on some collection of cusps leaves the geometric structure at some other collection of cusps unchanged.

  2. Isolated unilateral disk edema

    OpenAIRE

    Varner P

    2011-01-01

    Paul VarnerJohn J Pershing VAMC, Poplar Bluff, MO, USAAbstract: Isolated unilateral disk edema is a familiar clinical presentation with myriad associations. Related, non-consensus terminology is a barrier to understanding a common pathogenesis. Mechanisms for the development of disk edema are reviewed, and a new framework for clinical differentiation of medical associations is presented.Keywords: disk edema, axoplasmic flow, clinical multiplier, optic neuritis, ischemic optic neuropathy, papi...

  3. Isolated Pulmonary Valve Endocarditis

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Hatamizadeh

    2009-06-01

    Full Text Available Infective endocarditis is one of the most severe complications of parenteral drug abuse. The outstanding clinical feature of infective endocarditis in intravenous drug abusers is the high incidence of right-sided valve infection, and the tricuspid valve is involved in 60% to 70% of the cases. We herein report a case of isolated pulmonic valve infective endocarditis with a native pulmonary valve.

  4. Mechanical beam isolator

    International Nuclear Information System (INIS)

    Back-reflections from a target, lenses, etc. can gain energy passing backwards through a laser just like the main beam gains energy passing forwards. Unless something blocks these back-reflections early in their path, they can seriously damage the laser. A Mechanical Beam Isolator is a device that blocks back-reflections early, relatively inexpensively, and without introducing aberrations to the laser beam

  5. Beyond Insulation and Isolation

    DEFF Research Database (Denmark)

    Højlund, Marie Koldkjær

    2016-01-01

    insulation and isolation strategies to reduce measurable and perceptual noise levels. However, these strategies are unsuited to support the need to feel as an integral part of the shared hospital environment. This article suggests that the gap is intimately linked to a reductionist framework underlying the......Most research on the acoustic environment in the Western modern hospital identifies raised noise levels as the main causal explanation for the ranking of noise as critical stressors for patients, relatives and staffs. Therefore the most widely used strategies to tackle the problem in practice are...

  6. NORMOLIPEMIC ISOLATED XANTHOMA

    Directory of Open Access Journals (Sweden)

    Gowri Sankar

    2013-10-01

    Full Text Available ABSTRACT: Xanthomas are often a manifestation of underlying lipid abnormalities.A 17 - year - old female presented to our hospital with pain and swelling over t he left knee joint.Routine investigations and lipid profile were normal. Dermatological examination and Psychiatric examination were done and found to be normal. Histopathology from the lesion revealed macrophages and Touton type of giant cells. We present a case of normolipemic isolated xanthoma, which not only is an an uncommon occurrence but also needs a regular follow up because a high association with reticuloendothelial malignancies has also been reported.

  7. Diabetes in Population Isolates

    DEFF Research Database (Denmark)

    Grarup, Niels; Moltke, Ida; Albrechtsen, Anders;

    2016-01-01

    Type 2 diabetes (T2D) is an increasing health problem worldwide with particularly high occurrence in specific subpopulations and ancestry groups. The high prevalence of T2D is caused both by changes in lifestyle and genetic predisposition. A large number of studies have sought to identify...... on glucose-stimulated plasma glucose, serum insulin levels, and T2D. The variant defines a specific subtype of non-autoimmune diabetes characterized by decreased post-prandial glucose uptake and muscular insulin resistance. These and other recent findings in population isolates illustrate the value...

  8. Isolation of RNP granules

    DEFF Research Database (Denmark)

    Jønson, Lars; Nielsen, Finn Cilius; Christiansen, Jan

    2011-01-01

    be regarded as a supramolecular assembly of RNA and protein, probably representing several overlapping post-transcriptional operons. The present protocol describes how RNP granules may be isolated by the transgenic expression of a 3X FLAG version of an RNA-binding protein under tetracycline control...... via the tetracycline receptor/operator complex. In this way, inclusion of an appropriate tetracycline concentration ensures expression of the tagged version at the endogenous level, and the 3X FLAG tag is a convenient "handle" for the subsequent immunoprecipitation by immobilized anti-FLAG antibody....

  9. Journey from isolation

    Directory of Open Access Journals (Sweden)

    Wim A. Dreyer

    2011-06-01

    Full Text Available Since the Ottawa Consultation in 1982, the relationship between the Nederduitsch Hervormde Kerk van Afrika (NHKA and the World Alliance of Reformed Churches (WARC was nonexistent. In the NHKA it became progressively clear that it would be impossible to travel the road of faith alone. This article examined the factors which contributed to the growing isolation of the NHKA, especially nationalism, a particularistic ecclesiology and the rejection of Apartheid by international ecumenical bodies. It also reflected on efforts of the NHKA to return to the international ecumenical movement.

  10. How isolated is Antarctica?

    Science.gov (United States)

    Clarke, Andrew; Barnes, David K A; Hodgson, Dominic A

    2005-01-01

    The traditional view of Antarctica and the surrounding Southern Ocean as an isolated system is now being challenged by the recent discovery at the Antarctic Peninsula of adult spider crabs Hyas areneus from the North Atlantic and of larvae of subpolar marine invertebrates. These observations question whether the well described biogeographical similarities between the benthic fauna of the Antarctic Peninsula and the Magellan region of South America result from history (the two regions were once contiguous), or from a previously unrecognized low level of faunal exchange. Such exchange might be influenced by regional climate change, and also exacerbated by changes in human impact. PMID:16701330

  11. Schizosaccharomyces isolation method

    Directory of Open Access Journals (Sweden)

    Benito Santiago

    2014-01-01

    Full Text Available This study discusses the optimization of a selective and differential medium which would facilitate the isolation of Schizosaccharomyces (a genus with a low incidence compared to other microorganisms to select individuals from this genus for industrial purposes, especially in light of the recent recommendation of the use of yeasts from this genus in the wine industry by the International Organisation of Vine and Wine, or to detect the presence of such yeasts, for those many authors who consider them food spoilers. To this end, we studied various selective differential agents based on the main physiological characteristics of these species, such as their high resistances to high concentrations of sugar, sulfur dioxide, sorbic acid, benzoic acid, acetic acid or malo ethanolic fermentation. This selective medium is based on the genus resistance to the antibiotic actidione and its high resistance to inhibitory agents such as benzoic acid. Malic acid was used as a differential factor due to the ability of this genus to metabolise it to ethanol, which allows detecting of the degradation of this compound. Lastly, the medium was successfully used to isolate strains of Schizosaccharomyces pombe from honey and honeycombs.

  12. Effects of soil fumigants on methanotrophic activity

    Science.gov (United States)

    Negative impacts on methane (CH4) oxidation capacity have already been observed for a variety of agronomic practices, but effect of soil fumigation on CH4 oxidation has not been investigated. Fumigation is a common practice in agricultural crop and nursery seedling protection. Soils from various agr...

  13. Patients experience of source isolation

    DEFF Research Database (Denmark)

    Johansen, Kamilla; Pedersen, Didde; Kragbak, Nina;

    2013-01-01

    to the patients, and it is important to gain insight in the patients perspectives of being isolated, to develop treatment and caring strategies that may reduce the negative side effects of isolation. Aim: To make a systematic literature review, and analyse the literature to describe the state of the art knowledge...... and older and articles were peer reviewed. 11 articles were included and analysed by means of systematic text condensation. Results: Five themes were found; (1) Insufficient information, (2) Quality of care, (3) Physical environment, (4) Importance of relatives and (5) Psychological consequence....... The design of the ward with a balance between source isolation and visual and communicative opening to the outside is important to reduce the negative impact from isolation. Keywords: literature review, isolation, source isolation, patients experiences, patients perspectives, depression, coping, information...

  14. Isolation and the parish ministry

    OpenAIRE

    Irvine, Andrew R.

    1989-01-01

    The purpose of this thesis was to examine the concept of isolation as it occurs within the profession of ministry. Isolation, for the purpose of this thesis, is defined social-psychologically. Within the field research isolation is considered as evidenced professionally, socially and spiritually. This study utilized as its sample base 200 hundred Church of Scotland ministers (15% of total population) which provided 159 usable responses to an extensive mail survey. The mai...

  15. A hybrid base isolation system

    Energy Technology Data Exchange (ETDEWEB)

    Hart, G.C. [Univ. of California, Los Angeles, CA (United States); Lobo, R.F.; Srinivasan, M. [Hart Consultant Group, Santa Monica, CA (United States); Asher, J.W. [kpff Engineers, Santa Monica, CA (United States)

    1995-12-01

    This paper proposes a new analysis procedure for hybrid base isolation buildings when considering the displacement response of a base isolated building to wind loads. The system is considered hybrid because of the presence of viscous dampers in the building above the isolator level. The proposed analysis approach incorporates a detailed site specific wind study combined with a dynamic nonlinear analysis of the building response.

  16. Isolated Pelvic Hyperthermochemotherapeutic Perfusion -An Experimental Study on Isolating Efficacy

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Hyperthermochemotherapeutic perfusion model through isolated pelvic vessels was developed to evaluate the leakage of hyperthermia and drugs (such as adriamycin) from the isolated pelvic circulation to systemic circulation and its associated side/toxic effects. The isolated pelvic circulation was perfused through a femoral artery catheter with hyperthermic (48 ℃ to 55 ℃) adriamycin solution (50 μg/ml) for 30 min. The efflux was drained through a femoral vein catheter. And the pelvic temperature was kept at the level of 43±0.5 ℃. The temperature of pelvic circulation was kept at 4 ℃ to 5 ℃ greater than the systemic/core temperature. The adriamycin concentration of pelvic efflux was 12 to 46 folds of that of systemic serum. The difference between them was very significant (P<0.001). As the perfusion pressure was increased, which kept lower than the mean systemic artery pressure, the leakage of the adriamycin from the isolated pelvic circulation to systemic circulation was increased, but there was no significant difference between them (P>0.05). During isolated perfusion, the systemic blood dynamics remained stable and there were no organic injuries on the important organs. It was suggested that the isolating efficacy of the modality of isolated pelvic hyperthermochemotherapeutic perfusion through vessels was rather high. The hyperthermia and drugs could be effectively limited in the isolated pelvic region with minor side effects on the systemic circulation and important organs.

  17. Catalogues of isolated galaxies, isolated pairs, and isolated triplets in the local Universe

    CERN Document Server

    Argudo-Fernández, M; Bergond, G; Puertas, S Duarte; Carmona, E Ramos; Sabater, J; Lorenzo, M Fernández; Espada, D; Sulentic, J; Ruiz, J E; Leon, S

    2015-01-01

    The construction of catalogues of galaxies and the posterior study of galaxy properties in relation to their environment, have been hampered by the scarce redshift information. The new 3-dimensional (3D) surveys permits to distinguish small, faint, physically bound satellites from a background projected galaxy population, giving a more comprehensive 3D picture of the surroundings. We aim to provide representative samples of isolated galaxies, isolated pairs, and isolated triplets for testing galaxy evolution and secular processes in low density regions of the local Universe, as well as to characterise their local and large-scale environments. We use spectroscopic data from the SDSS to automatically and homogeneously compile catalogues of 3,702 isolated galaxies, 1,240 isolated pairs, and 315 isolated triplets in the local Universe. To quantify the effects of their local and large-scale environments, we compute the projected density and the tidal strength for the brightest galaxy in each sample. We find eviden...

  18. Seismic isolation for Advanced LIGO

    CERN Document Server

    Abbott, R; Allen, G; Cowley, S; Daw, E; Debra, D; Giaime, J; Hammond, G; Hammond, M; Hardham, C; How, J; Hua, W; Johnson, W; Lantz, B; Mason, K; Mittleman, R; Nichol, J; Richman, S; Rollins, J; Shoemaker, D; Stapfer, G; Stebbins, R

    2002-01-01

    The baseline design concept for a seismic isolation component of the proposed 'Advanced LIGO' detector upgrade has been developed with proof-of-principle experiments and computer models. It consists of a two-stage in-vacuum active isolation platform that is supported by an external hydraulic actuation stage. Construction is underway for prototype testing of a full-scale preliminary design.

  19. Improved Active Vibration Isolation Systems

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The control force, feedback gain, and actuator stroke of several active vibration isolation systems were analyzed based on a single-layer active vibration isolation system. The analysis shows that the feedback gain and actuator stroke cannot be selected independently and the active isolation system design must make a compromise between the feedback gain and actuator stroke. The performance of active isolation systems can be improved by the joint vibration reduction using an active vibration isolation system with an adaptive dynamic vibration absorber. The results show that the joint vibration reduction method can successfully avoid the compromise between the feedback gain and actuator stroke. The control force and the object vibration amplitude are also greatly reduced.

  20. Isolation of rat adrenocortical mitochondria

    International Nuclear Information System (INIS)

    Highlights: ► A method for isolation of adrenocortical mitochondria from the adrenal gland of rats is described. ► The purified isolated mitochondria show excellent morphological integrity. ► The properties of oxidative phosphorylation are excellent. ► The method increases the opportunity of direct analysis of adrenal mitochondria from small animals. -- Abstract: This report describes a relatively simple and reliable method for isolating adrenocortical mitochondria from rats in good, reasonably pure yield. These organelles, which heretofore have been unobtainable in isolated form from small laboratory animals, are now readily accessible. A high degree of mitochondrial purity is shown by the electron micrographs, as well as the structural integrity of each mitochondrion. That these organelles have retained their functional integrity is shown by their high respiratory control ratios. In general, the biochemical performance of these adrenal cortical mitochondria closely mirrors that of typical hepatic or cardiac mitochondria.

  1. Isolation of methylglyoxal from liver.

    Science.gov (United States)

    Fodor, G; Mujumdar, R; Szent-Gyorgyi, A

    1978-01-01

    Acetaldehyde and methylglyoxal were shown to be present in liver bound to protein. They were isolated in the form of 2,4-dinitrophenylhydrazones and osazones, respectively. The NMR spectrum of pure methylglyoxal was recorded. PMID:279916

  2. Isolation of rat adrenocortical mitochondria

    Energy Technology Data Exchange (ETDEWEB)

    Solinas, Paola [Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 (United States); Department of Medicine, Center for Mitochondrial Disease, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 (United States); Fujioka, Hisashi [Electron Microscopy Facility, Department of Pharmacology, Center for Mitochondrial Disease, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 (United States); Tandler, Bernard [Department of Biological Sciences, School of Dental Medicine, Center for Mitochondrial Disease, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 (United States); Hoppel, Charles L., E-mail: charles.hoppel@case.edu [Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 (United States); Department of Medicine, Center for Mitochondrial Disease, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 (United States)

    2012-10-12

    Highlights: Black-Right-Pointing-Pointer A method for isolation of adrenocortical mitochondria from the adrenal gland of rats is described. Black-Right-Pointing-Pointer The purified isolated mitochondria show excellent morphological integrity. Black-Right-Pointing-Pointer The properties of oxidative phosphorylation are excellent. Black-Right-Pointing-Pointer The method increases the opportunity of direct analysis of adrenal mitochondria from small animals. -- Abstract: This report describes a relatively simple and reliable method for isolating adrenocortical mitochondria from rats in good, reasonably pure yield. These organelles, which heretofore have been unobtainable in isolated form from small laboratory animals, are now readily accessible. A high degree of mitochondrial purity is shown by the electron micrographs, as well as the structural integrity of each mitochondrion. That these organelles have retained their functional integrity is shown by their high respiratory control ratios. In general, the biochemical performance of these adrenal cortical mitochondria closely mirrors that of typical hepatic or cardiac mitochondria.

  3. Isolated tubercles of some Palaeoscolecida

    NARCIS (Netherlands)

    Boogaard, van den M.

    1989-01-01

    Tubercles of Palaeoscolex? tenensis Kraft & Mergl, 1989 found as isolated phosphatic microfossils in Ordovician limestones are described. The probability that the phosphatic microfossils assigned to the genera Hadimopanella Gedik, 1977 and Milaculum Müller, 1973 represent tubercles of palaeoscolecid

  4. Missed isolated posterior malleolar fractures

    OpenAIRE

    Ozler, Turhan; Guven, Melih; Onal, Ayberk; Ulucay, Cagatay; Beyzadeoglu, Tahsin; Altintas, Faik

    2014-01-01

    Objective:The aim of this study was to evaluate the injury mechanism and clinical and radiological results of the patients with isolated posterior malleolar fracture.Methods: Seven patients (5 male, 2 female; mean age: 32 years; range: 23-40) with a missed isolated posterior malleolar fracture were included in the study. All patients had initially been examined for an ankle sprain in the emergency room, where the initial plain radiographs did not show any abnormality. Due to the long lasting ...

  5. Pneumothorax complicating isolated clavicle fracture.

    Science.gov (United States)

    Hani, Redouane; Ennaciri, Badr; Jeddi, Idriss; El Bardouni, Ahmed; Mahfoud, Mustapha; Berrada, Mohamed Saleh

    2015-01-01

    Isolated clavicle fractures are among the commonest of traumatic fractures in the emergency department. Complications of isolated clavicle fractures are rare. Pneumothorax has been described as a complication of a fractured clavicle only rarely in English literature. In all the reported cases, the pneumothorax was treated by a thoracostomy and the clavicle fracture was treated conservatively. In our case, the pneumothorax required a chest drain insertion and the clavicle fracture was treated surgically with good result.

  6. Base isolation of fluid containers

    Energy Technology Data Exchange (ETDEWEB)

    Kim, S. [Cygna Group Inc./ICF Kaiser International, Oakland, CA (United States)

    1995-12-01

    Fluid containers often constitute critical internal equipment in power plants. However, due to possible structure-equipment interaction effect they are particularly vulnerable during strong earthquake events. An effective technique for protecting fluid containers is base isolation. By deflecting the possible seismic input energy into the superstructure, base isolation can substantially reduce seismic demand on the containers, making it more cost effective than equivalent conventional design.

  7. Base isolation of fluid containers

    International Nuclear Information System (INIS)

    Fluid containers often constitute critical internal equipment in power plants. However, due to possible structure-equipment interaction effect they are particularly vulnerable during strong earthquake events. An effective technique for protecting fluid containers is base isolation. By deflecting the possible seismic input energy into the superstructure, base isolation can substantially reduce seismic demand on the containers, making it more cost effective than equivalent conventional design

  8. So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites.

    Science.gov (United States)

    Gagliano, A L; Tagliavia, M; D'Alessandro, W; Franzetti, A; Parello, F; Quatrini, P

    2016-03-01

    This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4 (+) concentration. At the same time, abundant availability of NH4 (+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils. PMID:26560641

  9. So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites.

    Science.gov (United States)

    Gagliano, A L; Tagliavia, M; D'Alessandro, W; Franzetti, A; Parello, F; Quatrini, P

    2016-03-01

    This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.

  10. Geomorphology of Minnesota - Isolated Landform Structures

    Data.gov (United States)

    Minnesota Department of Natural Resources — Geomorphology of Minnesota - Isolated Landform Structures are essentially cartographic arcs representing isolated glacial features that were mapped in conjunction...

  11. Isolation and identification of local Bacillus isolates for xylanase biosynthesis.

    Directory of Open Access Journals (Sweden)

    Hassan Ammoneh

    2014-04-01

    Full Text Available Bacillus species are attractive industrial organisms due to their rapid growth rates leading to a short fermentation cycle and for their capacity to secrete important enzymes and proteins such as xylanase into the extracellular medium. Considering the industrial importance of xylanase, in this current study, Bacillus spp. were isolated from different soils and were screened for their xylanase production.Bacillus isolates used in this study were obtained from a national screening program carried out during 2006-2007 in which soil samples that covered areas throughout the interior of Syria were collected. The prepared inoculum from each of Bacillus isolates was aliquoted onto xylan agar plates, incubated at 30°C for 72 h and screened for xylanase synthesis.Xylanolytic isolates were selected depending on the clear zones of xylan hydrolysis. Fifteen isolates having the highest clearing zone were determined and grown in a solid state fermentation. Of the 15 isolates, three bacilli namely SY30A, SY185C and SY190E that showed maximum xylanase production, were identified using the 16S rDNA sequencing method. According to 16S rDNA gene sequence data, the closest phylogenetic neighbor for SY30A was Bacillus pumilus and for SY185C and SY190E isolates was Bacillus subtilis. Optimal pH and temperature for xylanase activity was 7.0 and 55ºC for SY30A and 6.0 and 60ºC for SY185C and SY190E, respectively. Under these conditions, the following activities were found to be around 1157 ± 58, 916 ± 46 and 794 ± 39 (U/g for SY30A, SY185C and SY190E, respectivly.Selected local Bacillus isolates were found to be a potential source of xylanase which was proven to be quite suitable for multiple biotechnological applications. These isolates might after extensive optimization steps be an alternative to commercially available strains.

  12. Catalogues of isolated galaxies, isolated pairs, and isolated triplets in the local Universe

    Science.gov (United States)

    Argudo-Fernández, M.; Verley, S.; Bergond, G.; Duarte Puertas, S.; Ramos Carmona, E.; Sabater, J.; Fernández Lorenzo, M.; Espada, D.; Sulentic, J.; Ruiz, J. E.; Leon, S.

    2015-06-01

    Context. The construction of catalogues of galaxies and the a posteriori study of galaxy properties in relation to their environment have been hampered by scarce redshift information. The new 3-dimensional (3D) surveys permit small, faint, physically bound satellites to be distinguished from a background-projected galaxy population, giving a more comprehensive 3D picture of the surroundings. Aims: We aim to provide representative samples of isolated galaxies, isolated pairs, and isolated triplets for testing galaxy evolution and secular processes in low density regions of the local Universe, as well as to characterise their local and large-scale environments. Methods: We used spectroscopic data from the tenth data release of the Sloan Digital Sky Survey (SDSS-DR10) to automatically and homogeneously compile catalogues of 3702 isolated galaxies, 1240 isolated pairs, and 315 isolated triplets in the local Universe (z ≤ 0.080). To quantify the effects of their local and large-scale environments, we computed the projected density and the tidal strength for the brightest galaxy in each sample. Results: We find evidence of isolated pairs and isolated triplets that are physically bound at projected separations up to d ≤ 450 kpc with radial velocity difference Δν ≤ 160 km s-1, where the effect of the companion typically accounts for more than 98% of the total tidal strength affecting the central galaxy. For galaxies in the catalogues, we provide their positions, redshifts, and degrees of relation with their physical and large-scale environments. The catalogues are publicly available to the scientific community. Conclusions: For isolated galaxies, isolated pairs, and isolated triplets, there is no difference in their degree of interaction with the large-scale structure (up to 5 Mpc), which may suggest that they have a common origin in their formation and evolution. We find that most of them belong to the outer parts of filaments, walls, and clusters, and generally

  13. Isolation of isoprene degrading bacteria from soils, development of isoA gene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing.

    Science.gov (United States)

    El Khawand, Myriam; Crombie, Andrew T; Johnston, Antonia; Vavlline, Dmitrii V; McAuliffe, Joseph C; Latone, Jacob A; Primak, Yuliya A; Lee, Sang-Kyu; Whited, Gregg M; McGenity, Terry J; Murrell, J Colin

    2016-09-01

    Emissions of biogenic volatile organic compounds (bVOCs), are an important element in the global carbon cycle, accounting for a significant proportion of fixed carbon. They contribute directly and indirectly to global warming and climate change and have a major effect on atmospheric chemistry. Plants emit isoprene to the atmosphere in similar quantities to emissions of methane from all sources and each accounts for approximately one third of total VOCs. Although methanotrophs, capable of growth on methane, have been intensively studied, we know little of isoprene biodegradation. Here, we report the isolation of two isoprene-degrading strains from the terrestrial environment and describe the design and testing of polymerase chain reaction (PCR) primers targeting isoA, the gene encoding the active-site component of the conserved isoprene monooxygenase, which are capable of retrieving isoA sequences from isoprene-enriched environmental samples. Stable isotope probing experiments, using biosynthesized (13) C-labelled isoprene, identified the active isoprene-degrading bacteria in soil. This study identifies novel isoprene-degrading strains using both culture-dependent and, for the first time, culture-independent methods and provides the tools and foundations for continued investigation of the biogeography and molecular ecology of isoprene-degrading bacteria. PMID:27102583

  14. Perceived social isolation and cognition.

    Science.gov (United States)

    Cacioppo, John T; Hawkley, Louise C

    2009-10-01

    Social species, from Drosophila melanogaster to Homo sapiens, fare poorly when isolated. Homo sapiens, an irrepressibly meaning-making species, are, in normal circumstances, dramatically affected by perceived social isolation. Research indicates that perceived social isolation (i.e. loneliness) is a risk factor for, and may contribute to, poorer overall cognitive performance, faster cognitive decline, poorer executive functioning, increased negativity and depressive cognition, heightened sensitivity to social threats, a confirmatory bias in social cognition that is self-protective and paradoxically self-defeating, heightened anthropomorphism and contagion that threatens social cohesion. These differences in attention and cognition impact on emotions, decisions, behaviors and interpersonal interactions that can contribute to the association between loneliness and cognitive decline and between loneliness and morbidity more generally. PMID:19726219

  15. VIBRATION ISOLATION SYSTEM PROBABILITY ANALYSIS

    Directory of Open Access Journals (Sweden)

    Smirnov Vladimir Alexandrovich

    2012-10-01

    Full Text Available The article deals with the probability analysis for a vibration isolation system of high-precision equipment, which is extremely sensitive to low-frequency oscillations even of submicron amplitude. The external sources of low-frequency vibrations may include the natural city background or internal low-frequency sources inside buildings (pedestrian activity, HVAC. Taking Gauss distribution into account, the author estimates the probability of the relative displacement of the isolated mass being still lower than the vibration criteria. This problem is being solved in the three dimensional space, evolved by the system parameters, including damping and natural frequency. According to this probability distribution, the chance of exceeding the vibration criteria for a vibration isolation system is evaluated. Optimal system parameters - damping and natural frequency - are being developed, thus the possibility of exceeding vibration criteria VC-E and VC-D is assumed to be less than 0.04.

  16. Bacteria isolated from amoebae/bacteria consortium

    Science.gov (United States)

    Tyndall, Richard L.

    1995-01-01

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  17. Is an isolated cleft lip an isolated anomaly?

    NARCIS (Netherlands)

    Deelder, J. D.; Breugem, C. C.; de Vries, Iris; de Bruin, M.; van der Molen, A. B. Mink; van der Horst, C. M. A. M.

    2011-01-01

    Introduction: It is well known that patients with cleft lip/palate or cleft palate can have associated anomalies. However, there is a relative paucity of information about the possible anomalies associated with an isolated cleft lip. A recent study (Vallino et al., 2008) showed that children with cl

  18. Active Fault Isolation in MIMO Systems

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Poulsen, Niels Kjølstad

    2014-01-01

    isolation is based directly on the input/output s ignals applied for the fault detection. It is guaranteed that the fault group includes the fault that had occurred in the system. The second step is individual fault isolation in the fault group . Both types of isolation are obtained by applying dedicated......Active fault isolation of parametric faults in closed-loop MIMO system s are considered in this paper. The fault isolation consists of two steps. T he first step is group- wise fault isolation. Here, a group of faults is isolated from other pos sible faults in the system. The group-wise fault...

  19. Isolated complete corpus callosal agenesis

    Directory of Open Access Journals (Sweden)

    Jaiganesh S, Venkateshwaran A, Naresh Kumar C, Rajasekhar KV

    2014-11-01

    Full Text Available Isolated complete corpus callosal agenesis is a rare entity. Usually this condition will be an associated finding in other syndromes. 3 month old male child came with complaints of deformed foot on both sides, not having a social smile and neck holding. Patient referred to the Radiology department for MRI brain which showed complete absence of corpus callosum, widely separated and parallely placed lateral ventricles, colpocephaly, high riding of 3rd ventricle and absence of cingulate gyrus and radial arrangement of gyri along the interhemispheric fissure. Hence it was reported as isolated complete corpus callosal agenesis and this article describes the Embryogenesis, anatomy, developmental anomalies and its clinical manifestations & prognosis.

  20. [Isolated giant hydatid in kidney].

    Science.gov (United States)

    Ozgör, Faruk; Erbin, Akif; Berberoğlu, Ahmet Yalçın; Binbay, Murat; Sarılar, Omer; Müslümanoğlu, Ahmet Yaser

    2014-06-01

    Cyst hydatid of the kidney is parasitic condition caused by Echinococcus granulosus and identified in many countries, especially associated with sheep farming. Echinococcal larvae enter the bloodstream using the digestive system and invade any organs in the human body. The urinary system is the third most common area affected by parasitic infection after liver and lungs, but isolated renal involvement is a very rare situation, even in endemic areas. İn our case, we aimed to report a 57-year-old female patient with an 18-centimeter isolated renal cyst hydatid treated by retroperitoneal nephrectomy. The diagnosis was based on imaging findings and confirmed by histopathologically.