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Sample records for aerobic methanotrophic bacteria

  1. Methanotrophic bacteria.

    PubMed Central

    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 formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene. PMID:8801441

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

    PubMed Central

    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

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

    PubMed

    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.

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

    PubMed Central

    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 sequentially. Here, emphasis was placed on monitoring various methanotrophic populations by using classical methods and also a PCR amplification assay based on the mmoX gene fragment of the soluble methane monooxygenase (sMMO). The following results were obtained: (i) under the conditions used, Methylosinus sporium appeared to survive better than Methylosinus trichosporium; (ii) the PCR method which we used could detect as few as about 2,000 sMMO gene-containing methanotrophs per g (wet weight) of granular sludge; (iii) inoculation of the bioreactors with pure cultures of methanotrophs contributed greatly to increases in the sMMO-containing population (although the sMMO-containing population decreased gradually with time, at the end of an experiment it was always at least 2 logs larger than the initial population before inoculation); (iv) in general, there was a good correlation between populations with the sMMO gene and populations that exhibited sMMO activity; and (v) inoculation with sMMO-positive cultures helped increase significantly the proportion of sMMO-positive methanotrophs in reactors, even after several weeks of operation under various regimes. At some point, anaerobic-aerobic bioreactors like those described here might be used for biodegradation of various chlorinated pollutants. PMID:9925557

  5. [Methanotrophic bacteria of acid sphagnum bogs].

    PubMed

    Dedysh, S N

    2002-01-01

    Acid sphagnum bogs cover a considerable part of the territory of Russia and are an important natural source of biogenic methane, which is formed in their anaerobic layers. A considerable portion of this methane is consumed in the aerobic part of the bog profile by acidophilic methanotrophic bacteria, which comprise the methane filter of sphagnum bogs and decrease CH4 emission to the atmosphere. For a long time, these bacteria escaped isolation, which became possible only after the elucidation of the optimal conditions of their functioning in situ: pH 4.5 to 5.5; temperature, from 15 to 20 degrees C; and low salt concentration in the solution. Reproduction of these conditions and rejection of earlier used media with a high content of biogenic elements allowed methanotrophic bacteria of two new genera and species--Methylocella palustris and Methylocapsa acidophila--to be isolated from the peat of sphagnum bogs of the northern part of European Russia and West Siberia. These bacteria are well adapted to the conditions in cold, acid, oligotrophic sphagnum bogs. They grow in a pH range of 4.2-7.5 with an optimum at 5.0-5.5, prefer moderate temperatures (15-25 degrees C) and media with a low content of mineral salts (200-500 mg/l), and are capable of active nitrogen fixation. Design of fluorescently labeled 16S rRNA-targeted oligonucleotide probes for the detection of Methylocella palustris and Methylocapsa acidophila and their application to the analysis of sphagnum peat samples showed that these bacteria represent dominant populations of methanotrophs with a density of 10(5)-10(6) cells/g peat. In addition to Methylocella and Methylocapsa populations, one more abundant population of methanotrophs was revealed (10(6) cells/g peat), which were phylogenetically close to the genus Methylocystis.

  6. Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

    PubMed Central

    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

  7. Metabolic engineering in methanotrophic bacteria

    SciTech Connect

    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.

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

    NASA Astrophysics Data System (ADS)

    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

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

    NASA Astrophysics Data System (ADS)

    van Winden, Julia F.; Talbot, Helen M.; Kip, Nardy; Reichart, Gert-Jan; Pol, Arjan; McNamara, Niall P.; Jetten, Mike S. M.; Op den Camp, Huub J. M.; Sinninghe Damsté, Jaap 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 extreme acidophilic verrucomicrobial methanotroph. A type I Methylovulum-like strain (M200) contains a remarkable combination of BHPs, including a complete suite of mono-unsaturated aminobacteriohopanepentol, -tetrol and -triol. The Methylomonas-like strain (M5) mainly produces aminobacteriohopanepentol, characteristic for type I methanotrophs, and the Methylosinus-like strain (29) contains both aminobacteriohopanetetrol and aminobacteriohopanetriol, typical for a type II methanotroph. The type II methanotroph Methylocella palustris and the verrucomicrobial Methylacidiphilum fumariolicum strain SolV primarily produce aminotriol, which is also produced by many other bacteria. In Sphagnum mosses and underlying peat from a peat bog from Moorhouse, UK, the only detectable BHPs indicative of methanotrophs are aminobacteriohopanepentol (aminopentol) and aminobacteriohopanetetrol (aminotetrol), although both are relatively low in abundance compared to other BHPs. Aminopentol serves as a marker for type I methanotrophs, while aminotetrol may reflect the presence of both type I and type II methanotrophs. The similar quantities of aminotetrol and aminopentol indicate that the methanotrophic community in Sphagnum peat probably consist of a combination of both type I and type II methanotrophs, which is in line with previously published pmoA-based micro-array results.

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

    SciTech Connect

    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

  11. Methanotrophic bacteria and facilitated transport of pollutants in aquifer material

    SciTech Connect

    Jenkins, M.B.; Chen, Jyh-Herng; Kadner, D.J.; Lion, L.W. )

    1994-10-01

    In-situ stimulation of methanotrophic bacteria has been considered for aquifer remediation. Experimental results 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 removal of other environmental contaminants such as polynuclear aromatic hydrocarbons and transition metals in aquifer material. Three methanotrophic bacteria were used in the experiments: Methylomonas albus BG8, Methylosinus trichosporium OB3b, and Methylocystis parvus OBBP. The distribution coefficients for Cd with extraceullular polymers were of the same order as that obtained with the aquifer sand, indicating polymers from the methanotrophic bacteria could act to increase the transport of Cd in a porous medium. Polymer from BG8 significantly reduced the apparent distribution coefficient for Cd with an aquifer sand. [[sup 14]C]phenanthrene also sorbed to extracellular polymer and to washed, suspended methanotrophic cells. The exopolymer of BG8 and OBBP significantly reduced the apparent distribution coefficient (K[sub d]) for phenanthrene with aquifer sand. The distribution coefficients for phenanthrene with the methanotrophic cells were an order of magnitude greater than those previously reported for other heterotrophic bacteria. Cells of the methanotrophs also significantly reduced the apparent K[sub d] for phenanthrene with an aquifer sand. The three strains of methanotrophs displayed mobility in a column of packed sand, and strain OBBP reduced the retardation coefficient of phenanthrene with an aquifer sand by 27%. These data indicate that both extracellular polymer and mobile cells of methanotrophic bacteria display a capacity to facilitate the mobility of pollutant metals and polynuclear aromatic hydrocarbons in aquifer material. 48 refs., 3 figs., 4 tabs.

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

    USGS Publications Warehouse

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed Central

    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 morphology were seen for methanotrophic bacteria starved under 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 survive carbon deprivation under anoxic conditions by using maintenance energy derived solely from an anaerobic endogenous metabolism. This capability could partly explain a significant potential for methane oxidation in environments not continuously supporting aerobic methanotrophic growth. PMID:16349336

  15. Aerobic Anoxygenic Phototrophic Bacteria

    PubMed Central

    Yurkov, Vladimir V.; Beatty, J. Thomas

    1998-01-01

    The aerobic anoxygenic phototrophic bacteria are a relatively recently discovered bacterial group. Although taxonomically and phylogenetically heterogeneous, these bacteria share the following distinguishing features: the presence of bacteriochlorophyll a incorporated into reaction center and light-harvesting complexes, low levels of the photosynthetic unit in cells, an abundance of carotenoids, a strong inhibition by light of bacteriochlorophyll synthesis, and the inability to grow photosynthetically under anaerobic conditions. Aerobic anoxygenic phototrophic bacteria are classified in two marine (Erythrobacter and Roseobacter) and six freshwater (Acidiphilium, Erythromicrobium, Erythromonas, Porphyrobacter, Roseococcus, and Sandaracinobacter) genera, which phylogenetically belong to the α-1, α-3, and α-4 subclasses of the class Proteobacteria. Despite this phylogenetic information, the evolution and ancestry of their photosynthetic properties are unclear. We discuss several current proposals for the evolutionary origin of aerobic phototrophic bacteria. The closest phylogenetic relatives of aerobic phototrophic bacteria include facultatively anaerobic purple nonsulfur phototrophic bacteria. Since these two bacterial groups share many properties, yet have significant differences, we compare and contrast their physiology, with an emphasis on morphology and photosynthetic and other metabolic processes. PMID:9729607

  16. Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity.

    PubMed

    Wasmund, Kenneth; Kurtböke, D Ipek; Burns, Kathryn A; Bourne, David G

    2009-05-01

    This study examined the diversity of Bacteria, Archaea and in particular aerobic methanotrophs associated with a shallow (84 m) methane seep in the tropical Timor Sea, Australia. Seepage of thermogenic methane was associated with a large carbonate hardground covered in coarse carbonate-rich sediments and various benthic organisms such as solitary corals. The diversity of Bacteria and Archaea was studied by analysis of cloned 16S rRNA genes, while aerobic methanotrophic bacteria were quantified using real-time PCR targeting the alpha-subunit of particulate methane monooxygenase (pmoA) genes and diversity was studied by analysis of cloned pmoA genes. Phylogenetic analysis of bacterial and archaeal 16S rRNA genes revealed diverse and mostly novel phylotypes related to sequences previously recovered from marine sediments. A small number of bacterial 16S rRNA gene sequences were related to aerobic methanotrophs distantly related to the genera Methylococcus and Methylocaldum. Real-time PCR targeting pmoA genes showed that the highest numbers of methanotrophs were present in surface sediments associated with the seep area. Phylogenetic analysis of pmoA sequences revealed that all phylotypes were novel and fell into two large clusters comprised of only marine sequences distantly related to the genera Methylococcus and Methylocaldum that were clearly divergent from terrestrial phylotypes. This study provides evidence for the existence of a novel microbial diversity and diverse aerobic methanotrophs that appear to constitute marine specialized lineages.

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

    PubMed Central

    Abdallah, Rehab Z.; Adel, Mustafa; Ouf, Amged; Sayed, Ahmed; Ghazy, Mohamed A.; Alam, Intikhab; Essack, Magbubah; Lafi, Feras F.; Bajic, Vladimir B.; El-Dorry, Hamza; Siam, Rania

    2014-01-01

    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. PMID:25295031

  18. Aerobic methane oxidation and methanotroph community composition during seasonal stratification in Mono Lake, California (USA).

    PubMed

    Carini, Stephen; Bano, Nasreen; LeCleir, Gary; Joye, Samantha B

    2005-08-01

    Patterns of aerobic methane (CH4) oxidation and associated methanotroph community composition were investigated during the development of seasonal stratification in Mono Lake, California (USA). CH4 oxidation rates were measured using a tritiated CH4 radiotracer technique. Fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and sequence analysis were used to characterize methanotroph community composition. A temporally shifting zone of elevated CH4 oxidation (59-123 nM day(-1)) was consistently associated with a suboxycline, microaerophilic zone that migrated upwards in the water column as stratification progressed. FISH analysis revealed stable numbers of type I (4.1-9.3 x 10(5) cells ml(-1)) and type II (1.4-3.4 x 10(5) cells ml(-1)) methanotrophs over depth and over time. Denaturing gradient gel electrophoresis and sequence analysis indicated slight shifts in methanotroph community composition despite stable absolute cell numbers. Variable CH4 oxidation rates in the presence of a relatively stable methanotroph population suggested that zones of high CH4 oxidation resulted from an increase in activity of a subset of the existing methanotroph population. These results challenge existing paradigms suggesting that zones of elevated CH4 oxidation activity result from the accumulation of methanotrophic biomass and illustrate that type II methanotrophs may be an important component of the methanotroph population in saline and/or alkaline pelagic environments.

  19. Complete genome sequence of Methylocystis sp. strain SC2, an aerobic methanotroph with high-affinity methane oxidation potential.

    PubMed

    Dam, Bomba; Dam, Somasri; Kube, Michael; Reinhardt, Richard; Liesack, Werner

    2012-11-01

    Methylocystis sp. strain SC2 is an aerobic type II methanotroph isolated from a highly polluted aquifer in Germany. A specific trait of the SC2 strain is the expression of two isozymes of particulate methane monooxygenase with different methane oxidation kinetics. Here we report the complete genome sequence of this methanotroph that contains not only a circular chromosome but also two large plasmids.

  20. Clay enhancement of methane, low molecular weight hydrocarbon and halocarbon conversion by methanotrophic bacteria

    DOEpatents

    Apel, William A.; Dugan, Patrick R.

    1995-04-04

    An apparatus and method for increasing the rate of oxidation of toxic vapors by methanotrophic bacteria. The toxic vapors of interest are methane and trichloroethylene. The apparatus includes a gas phase bioreactor within a closed loop pumping system or a single pass system. The methanotrophic bacteria include Methylomonas methanica, Methylosinus trichosporium, and uncharacterized environmental enrichments.

  1. Clay enhancement of methane, low molecular weight hydrocarbon and halocarbon conversion by methanotrophic bacteria

    DOEpatents

    Apel, William A.; Dugan, Patrick R.

    1995-01-01

    An apparatus and method for increasing the rate of oxidation of toxic vapors by methanotrophic bacteria. The toxic vapors of interest are methane and trichloroethylene. The apparatus includes a gas phase bioreactor within a closed loop pumping system or a single pass system. The methanotrophic bacteria include Methylomonas methanica, Methylosinus trichosporium, and uncharacterized environmental enrichments.

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

    PubMed

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

    2008-07-01

    Methane vents are of significant geochemical and ecological importance. Notable progress has been made toward 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 methane vent environments along the California continental margin was characterized. The pmoA phylotypes recovered from methane-rich sediments and the overlying water column differed. Sediments harbored the greatest number of unique pmoA phylotypes broadly affiliated with the Methylococcaceae family, whereas planktonic pmoA phylotypes formed three clades that were distinct from the sediment-hosted methanotrophs and distantly related to established methanotrophic clades. Water column-associated phylotypes were highly similar between field sites, suggesting that planktonic methanotroph diversity is controlled primarily by environmental factors rather than geographical proximity. Analysis of 16S rRNA genes from methane-rich waters did not readily recover known methanotrophic lineages, with only a few phylotypes demonstrating distant relatedness to Methylococcus. The development of new pmo primers increased the recovery of monooxygenase genes from the water column and led to the discovery of a highly diverged monooxygenase sequence which is phylogenetically intermediate to Amo and pMMO. This sequence potentiates insight into the amo/pmo superfamily. Together, these findings lend perspective into the diversity and segregation of aerobic methanotrophs within different methane-rich habitats in the marine environment.

  3. Effect of afforestation and reforestation of pastures on the activity and population dynamics of methanotrophic bacteria.

    PubMed

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

    2007-08-01

    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 phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C18 PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C16 PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (pmoA) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to Methylococcus capsulatus) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.

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

    PubMed

    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.

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

    USGS Publications Warehouse

    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.

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

    USGS Publications Warehouse

    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.

  7. Oxidation of methane in biotrickling filters inoculated with methanotrophic bacteria.

    PubMed

    Cáceres, Manuel; Dorado, Antonio D; Gentina, Juan C; Aroca, Germán

    2016-07-01

    The oxidation of methane (CH4) using biofilters has been proposed as an alternative to mitigate anthropogenic greenhouse gas emissions with a low concentration of CH4 that cannot be used as a source of energy. However, conventional biofilters utilize organic packing materials that have a short lifespan, clogging problems, and are commonly inoculated with non-specific microorganisms leading to unpredictable CH4 elimination capacities (EC) and removal efficiencies (RE). The main objective of this work was to characterize the oxidation of CH4 in two biotrickling filters (BTFs) packed with polyethylene rings and inoculated with two methanotrophic bacteria, Methylomicrobium album and Methylocystis sp., in order to determine EC and CO2 production (pCO2) when using a specific inoculum. The repeatability of the results in both BTFs was determined when they operated at the same inlet load of CH4. A dynamic mathematical model that describes the CH4 abatement in the BTFs was developed and validated using mass transfer and kinetic parameters estimated independently. The results showed that EC and pCO2 of the BTFs are not identical but very similar for all the conditions tested. The use of specific inoculum has shown a faster startup and higher EC per unit area (0.019 gCH4 m(-2) h(-1)) in comparison to most of the previous studies at the same CH4 load rate (23.2 gCH4 m(-3) h(-1)). Global mass balance showed that the maximum reduction of CO2 equivalents was 98.5 gCO2eq m(-3) h(-1). The developed model satisfactorily described CH4 abatement in BTFs for a wide range of conditions.

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

    PubMed Central

    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 endophytic methanotrophs from Sphagnum sp. were initiated in NMS medium, a most widely used medium for cultivation of methanotrophic bacteria from various environments proposed in 1970 by Whittenbury. Incubation was carried out at 10, 20, 30, and 37°C with vigorous shaking on a shaker (180 rpm). The source of carbon and energy for endophytes were methane at the concentration range between 1-20%. It appeared that the consortium of endophytic bacteria grew only at the temperature of 20 and 30°C. During the culture of endophytes, the measurements of gas concentration showed a steady loss of methane and oxygen, as well as accumulation of carbon dioxide as a CH4 oxidation product. The use of FISH has made characterization of endophytic consortia possible. It turned out that the population of endophytes consists of type I and II methanotrophs as well as associated non-methanotrophic bacteria. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged up to 4,7 μMCH4 per ml of the population of endophytes per day. PMID:25401064

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

    NASA Astrophysics Data System (ADS)

    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.

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

    DOEpatents

    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.

  11. Clay enhancement of methane, low molecular weight hydrocarbon and halocarbon conversion by methanotrophic bacteria

    SciTech Connect

    Apel, W.A.; Dugan, P.R.

    1991-12-31

    The invention described in this report relates to a combined system of an apparatus and a method of increasing the rates of oxidation of gases and hazardous vapors by methanotrophic and other bacteria. The gases of interest are methane and trichlorethylene and other hazardous vapors. In a preferred embodiment, the oxidation rate of methane is improved by the addition of clays, e.g., kaolin, sometimes called ``China clay.``

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

    PubMed Central

    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 Ellesmere Island in the Canadian high Arctic. Results showed that most of the soils had the capacity to oxidize CH4 at 4°C and at room temperature (RT), but the oxidation rates were greater at RT than at 4°C and were significantly enhanced by nutrient amendment. The DGGE banding patterns associated with active methanotrophic bacterial populations were also different depending on the temperature of incubation and the addition of nutrients. Sequencing of the 16S rRNA and pmoA genes indicated a low diversity of the active methanotrophic bacteria, with all methanotroph 16S rRNA and pmoA gene sequences being related to type I methanotrophs from Methylobacter and Methylosarcina. The dominance of type I methanotrophs over type II methanotrophs in the native soil samples was confirmed by qPCR of the 16S rRNA gene with primers specific for these two groups of bacteria. The 16S rRNA and pmoA gene sequences related to those of Methylobacter tundripaludum were found in all soils, regardless of the incubation conditions, and they might therefore play a role in CH4 degradation in situ. This work is providing new information supporting the potential importance of Methylobacter spp. in Arctic soils found in previous studies and contributes to the limited body of knowledge on methanotrophic activity and diversity in this extreme environment. PMID:20622133

  13. Carbon isotopic fractionation in lipids from methanotrophic bacteria: relevance for interpretation of the geochemical record of biomarkers

    NASA Technical Reports Server (NTRS)

    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

  14. [Methanotrophic bacteria in cold seeps of the floodplains of northern rivers].

    PubMed

    Belova, S É; Oshkin, I Iu; Glagolev, M V; Lapshina, E D; Maksiutov, Sh Sh; Dedysh, S N

    2013-01-01

    Small mud volcanoes (cold seeps), which are common in the floodplains of northern rivers, are a potentially important, although poorly studied sources of atmospheric methane. Field research on the cold seeps of the Mukhrina River (Khanty-Mansiysk Autonomous okrug, Russia) revealed methane fluxes from these structures to be orders of magnitude higher than from equivalent areas of the mid-taiga bogs. Microbial communities developing around the seeps were formed under conditions of high methane concentrations, low temperatures (3-5 degrees C), and near-neutral pH. Molecular identification of methane-oxidizing bacteria from this community by analysis of the pmoA gene encoding particulate methane monooxygenase revealed both type I and type II methanotrophs (classes Gammaproteobacteria and Alphaproteobacteria, respectively), with predomination of type I methanotrophs. Among the latter, microorganisms related to Methylobacterpsychrophilus and Methylobacter tundripaludum, Crenothrix polyspora (a stagnant water dweller), and a number of methanotrophs belonging to unknown taxa were detected. Growth characteristics of two isolates were determined. Methylobactersp. CMS7 exhibited active growth at 4-10 degrees C, while Methylocystis sp. SB12 grew better at 20 degrees C. Experimental results confirmed the major role ofmethanotrophic gammaproteobacteria in controlling the methane emission from cold river seeps.

  15. Diversity and phylogeny of the ectoine biosynthesis genes in aerobic, moderately halophilic methylotrophic bacteria.

    PubMed

    Reshetnikov, Alexander S; Khmelenina, Valentina N; Mustakhimov, Ildar I; Kalyuzhnaya, Marina; Lidstrom, Mary; Trotsenko, Yuri A

    2011-11-01

    The genes of ectoine biosynthesis pathway were identified in six species of aerobic, slightly halophilic bacteria utilizing methane, methanol or methylamine. Two types of ectoine gene cluster organization were revealed in the methylotrophs. The gene cluster ectABC coding for diaminobutyric acid (DABA) acetyltransferase (EctA), DABA aminotransferase (EctB) and ectoine synthase (EctC) was found in methanotrophs Methylobacter marinus 7C and Methylomicrobium kenyense AMO1(T). In methanotroph Methylomicrobium alcaliphilum ML1, methanol-utilizers Methylophaga thalassica 33146(T) , Methylophaga alcalica M8 and methylamine-utilizer Methylarcula marina h1(T), the genes forming the ectABC-ask operon are preceded by ectR, encoding a putative transcriptional regulatory protein EctR. Phylogenetic relationships of the Ect proteins do not correlate with phylogenetic affiliation of the strains, thus implying that the ability of methylotrophs to produce ectoine is most likely the result of a horizontal transfer event.

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

    NASA Astrophysics Data System (ADS)

    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

  17. The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems.

    PubMed

    Rush, Darci; Osborne, Kate A; Birgel, Daniel; Kappler, Andreas; Hirayama, Hisako; Peckmann, Jörn; Poulton, Simon W; Nickel, Julia C; Mangelsdorf, Kai; Kalyuzhnaya, Marina; Sidgwick, Frances R; Talbot, Helen M

    2016-01-01

    Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today. AMO bacteria are known to synthesise bacteriohopanepolyol (BHP) lipids. Preliminary evidence pointed towards 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being a characteristic biomarker for Type I methanotrophs. Here, the BHP compositions were examined for species of the recently described novel Type I methanotroph bacterial genera Methylomarinum and Methylomarinovum, as well as for a novel species of a Type I Methylomicrobium. Aminopentol was the most abundant BHP only in Methylomarinovum caldicuralii, while Methylomicrobium did not produce aminopentol at all. In addition to the expected regular aminotriol and aminotetrol BHPs, novel structures tentatively identified as methylcarbamate lipids related to C-35 amino-BHPs (MC-BHPs) were found to be synthesised in significant amounts by some AMO cultures. Subsequently, sediments and authigenic carbonates from methane-influenced marine environments were analysed. Most samples also did not contain significant amounts of aminopentol, indicating that aminopentol is not a useful biomarker for marine aerobic methanotophic bacteria. However, the BHP composition of the marine samples do point toward the novel MC-BHPs components being potential new biomarkers for AMO.

  18. The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems

    PubMed Central

    Birgel, Daniel; Kappler, Andreas; Hirayama, Hisako; Peckmann, Jörn; Poulton, Simon W.; Nickel, Julia C.; Mangelsdorf, Kai; Kalyuzhnaya, Marina; Sidgwick, Frances R.; Talbot, Helen M.

    2016-01-01

    Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today. AMO bacteria are known to synthesise bacteriohopanepolyol (BHP) lipids. Preliminary evidence pointed towards 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being a characteristic biomarker for Type I methanotrophs. Here, the BHP compositions were examined for species of the recently described novel Type I methanotroph bacterial genera Methylomarinum and Methylomarinovum, as well as for a novel species of a Type I Methylomicrobium. Aminopentol was the most abundant BHP only in Methylomarinovum caldicuralii, while Methylomicrobium did not produce aminopentol at all. In addition to the expected regular aminotriol and aminotetrol BHPs, novel structures tentatively identified as methylcarbamate lipids related to C-35 amino-BHPs (MC-BHPs) were found to be synthesised in significant amounts by some AMO cultures. Subsequently, sediments and authigenic carbonates from methane-influenced marine environments were analysed. Most samples also did not contain significant amounts of aminopentol, indicating that aminopentol is not a useful biomarker for marine aerobic methanotophic bacteria. However, the BHP composition of the marine samples do point toward the novel MC-BHPs components being potential new biomarkers for AMO. PMID:27824887

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Biology of Moderately Halophilic Aerobic Bacteria

    PubMed Central

    Ventosa, Antonio; Nieto, Joaquín J.; Oren, Aharon

    1998-01-01

    The moderately halophilic heterotrophic aerobic bacteria form a diverse group of microorganisms. The property of halophilism is widespread within the bacterial domain. Bacterial halophiles are abundant in environments such as salt lakes, saline soils, and salted food products. Most species keep their intracellular ionic concentrations at low levels while synthesizing or accumulating organic solutes to provide osmotic equilibrium of the cytoplasm with the surrounding medium. Complex mechanisms of adjustment of the intracellular environments and the properties of the cytoplasmic membrane enable rapid adaptation to changes in the salt concentration of the environment. Approaches to the study of genetic processes have recently been developed for several moderate halophiles, opening the way toward an understanding of haloadaptation at the molecular level. The new information obtained is also expected to contribute to the development of novel biotechnological uses for these organisms. PMID:9618450

  1. Genomic insights into the metabolic potential and interactions between marine methanotrophic ANME archaea and associated bacteria

    NASA Astrophysics Data System (ADS)

    Orphan, V. J.; Skennerton, C.; Chadwick, G.; Haroon, F.; Tyson, G. W.; Leu, A.; Hatzenpichler, R.; Woyke, T.; Malmstrom, R.; Yu, H.; Scheller, S.

    2015-12-01

    Cooperative metabolic interactions between multiple groups of methanotrophic 'ANME' archaea and sulfate-reducing bacteria represent the primary sink for methane within continental margin sediments. These syntrophic associations are frequently observed as structured multi-celled consortia in methane seeps, often comprising a substantial proportion of the microbial biomass within near seafloor seep sediments. Since their discovery nearly 15 years ago, a number of distinct ANME groups and multiple sulfate-reducing bacterial partners have been described from seep environments worldwide. Attempts to reconstruct the genomes of some ANME organisms have been reported, however the ecological physiology and metabolic interactions of distinct ANME lineages and their bacterial partners remains poorly understood. Here, we used a fluorescence azide-alkyne click chemistry technique known as BONCAT combined with FAC sorting to examine patterns in microbial membership and the genomes of single, metabolically active ANME-bacterial consortia recovered from methane seep sediments. This targeted consortia-level sequencing approach revealed significant diversity in the ANME-bacterial associations in situ as well as insights into the potential syntrophic mechanisms underpinning these enigmatic methane-fueled partnerships.

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

    PubMed Central

    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

  3. Methanotrophic bacteria associated to rice roots: the cultivar effect assessed by T-RFLP and microarray analysis.

    PubMed

    Lüke, Claudia; Bodrossy, Levente; Lupotto, Elisabetta; Frenzel, Peter

    2011-10-01

    Rice plants play a key role in regulating methane emissions from paddy fields by affecting both underlying processes: methane production and oxidation. Specific differences were reported for methane oxidation rates; however, studies on the bacterial communities involved are rare. Here, we analysed the methanotrophic community on the roots of 18 different rice cultivars by pmoA-based terminal restriction fragment length polymorphism (T-RFLP) and microarray analysis. Both techniques showed comparable and consistent results revealing a high diversity dominated by type II and type Ib methanotrophs. pmoA microarrays have been successfully used to study methane-oxidizing bacteria in various environments. However, the microarray's full potential resolving community structure has not been exploited yet. Here, we provide an example on how to include this information into multivariate statistics. The analysis revealed a rice cultivar effect on the methanotroph community composition that could be affiliated to the plant genotype. This effect became only significant by including the specific phylogenetic resolution provided by the microarray into the statistical analysis.

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

    NASA Astrophysics Data System (ADS)

    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

  5. Autonomous application of quantitative PCR in the deep sea: in situ surveys of aerobic methanotrophs using the deep-sea environmental sample processor.

    PubMed

    Ussler, William; Preston, Christina; Tavormina, Patricia; Pargett, Doug; Jensen, Scott; Roman, Brent; Marin, Roman; Shah, Sunita R; Girguis, Peter R; Birch, James M; Orphan, Victoria; Scholin, Christopher

    2013-08-20

    Recent advances in ocean observing systems and genomic technologies have led to the development of the deep-sea environmental sample processor (D-ESP). The D-ESP filters particulates from seawater at depths up to 4000 m and applies a variety of molecular assays to the particulates, including quantitative PCR (qPCR), to identify particular organisms and genes in situ. Preserved samples enable laboratory-based validation of in situ results and expanded studies of genomic diversity and gene expression. Tests of the D-ESP at a methane-rich mound in the Santa Monica Basin centered on detection of 16S rRNA and particulate methane monooxygenase (pmoA) genes for two putative aerobic methanotrophs. Comparison of in situ qPCR results with laboratory-based assays of preserved samples demonstrates the D-ESP generated high-quality qPCR data while operating autonomously on the seafloor. Levels of 16S rRNA and pmoA cDNA detected in preserved samples are consistent with an active community of aerobic methanotrophs near the methane-rich mound. These findings are substantiated at low methane sites off Point Conception and in Monterey Bay where target genes are at or below detection limits. Successful deployment of the D-ESP is a major step toward developing autonomous systems to facilitate a wide range of marine microbiological investigations.

  6. High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

    PubMed Central

    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 decreased sharply to below detection limits at 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 active in situ. PMID

  7. Variable carbon isotope fractionation expressed by aerobic CH 4-oxidizing bacteria

    NASA Astrophysics Data System (ADS)

    Templeton, Alexis S.; Chu, Kung-Hui; Alvarez-Cohen, Lisa; Conrad, Mark E.

    2006-04-01

    Carbon isotope fractionation factors reported for aerobic bacterial oxidation of CH 4(α) range from 1.003 to 1.039. In a series of experiments designed to monitor changes in the carbon isotopic fractionation of CH 4 by Type I and Type II methanotrophic bacteria, we found that the magnitude of fractionation was largely due to the first oxidation step catalyzed by methane monooxygenase (MMO). The most important factor that modulates the (α) is the fraction of the total CH 4 oxidized per unit time, which strongly correlates to the cell density of the growth cultures under constant flow conditions. At cell densities of less than 0.1 g/L, fractionation factors greater than 1.03 were observed, whereas at cell densities greater than 0.5 g/L the fractionation factors decreased to as low as 1.002. At low cell densities, low concentrations of MMO limit the amount of CH 4 oxidized, while at higher cell densities, the overall rates of CH 4 oxidation increase sufficiently that diffusion of CH 4 from the gaseous to dissolved state and into the cells is likely the rate-determining step. Thus, the residual CH 4 is more fractionated at low cell densities, when only a small fraction of the total CH 4 has been oxidized, than at high cell densities, when up to 40% of the influent CH 4 has been utilized. Therefore, since Rayleigh distillation behavior is not observed, δ 13C values of the residual CH 4 cannot be used to infer the amount oxidized in either laboratory or field-studies. The measured (α) was the same for both Type I and Type II methanotrophs expressing particulate or soluble MMO. However, large differences in the δ 13C values of biomass produced by the two types of methanotrophs were observed. Methylosinus trichosporium OB3b (Type II) produced biomass with δ 13C values about 15‰ higher than the dissimilated CO 2, whereas Methylomonas methanica (Type I) produced biomass with δ 13C values only about 6‰ higher than the CO 2. These effects were independent of the

  8. Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants.

    PubMed

    Stępniewska, Zofia; Goraj, Weronika; Kuźniar, Agnieszka; Łopacka, Natalia; Małysza, Magdalena

    2017-03-09

    Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland). Methanotrophic bacteria were isolated from plants by adding sterile fragments of different parts of plants (roots and stems) to agar mineral medium (nitrate mineral salts (NMS)) and incubated at different methane values (1-20% CH4). Single colonies were streaked on new NMS agar media and, after incubation, transferred to liquid NMS medium. Bacterial growth dynamics in the culture solution was studied by optical density-OD600 and methane consumption. Changes in the methane concentration during incubation were controlled by the gas chromatography technique. Characterization of methanotrophs was made by fluorescence in situ hybridization (FISH) with Mg705 and Mg84 for type I methanotrophs and Ma450 for type II methanotrophs. Identification of endophytes was performed after 16S ribosomal RNA (rRNA) and mmoX gene amplification. Our study confirmed the presence of both types of methanotrophic bacteria (types I and II) with the predominance of type I methanotrophs. Among cultivable methanotrophs, there were different strains of the genus Methylomonas and Methylosinus. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged from 0.463 ± 0.067 to 5.928 ± 0.169 μmol/L CH4/mL/day.

  9. The aerobic activity of metronidazole against anaerobic bacteria.

    PubMed

    Dione, Niokhor; Khelaifia, Saber; Lagier, Jean-Christophe; Raoult, Didier

    2015-05-01

    Recently, the aerobic growth of strictly anaerobic bacteria was demonstrated using antioxidants. Metronidazole is frequently used to treat infections caused by anaerobic bacteria; however, to date its antibacterial activity was only tested in anaerobic conditions. Here we aerobically tested using antioxidants the in vitro activities of metronidazole, gentamicin, doxycycline and imipenem against 10 common anaerobic and aerobic bacteria. In vitro susceptibility testing was performed by the disk diffusion method, and minimum inhibitory concentrations (MICs) were determined by Etest. Aerobic culture of the bacteria was performed at 37°C using Schaedler agar medium supplemented with 1mg/mL ascorbic acid and 0.1mg/mL glutathione; the pH was adjusted to 7.2 by 10M KOH. Growth of anaerobic bacteria cultured aerobically using antioxidants was inhibited by metronidazole after 72h of incubation at 37°C, with a mean inhibition diameter of 37.76mm and an MIC of 1μg/mL; however, strains remained non-sensitive to gentamicin. No growth inhibition of aerobic bacteria was observed after 24h of incubation at 37°C with metronidazole; however, inhibition was observed with doxycycline and imipenem used as controls. These results indicate that bacterial sensitivity to metronidazole is not related to the oxygen tension but is a result of the sensitivity of the micro-organism. In future, both culture and antibiotic susceptibility testing of strictly anaerobic bacteria will be performed in an aerobic atmosphere using antioxidants in clinical microbiology laboratories.

  10. Stereospecificity and physiology of co-oxidative production of chemicals by methanotrophic bacteria. [Methane monooxygenase:a2

    SciTech Connect

    Kelley, R.L.; Hoefer, D.E.; Conrad, J.R.; Srivastava, V.J.; Akin, C.

    1991-01-01

    Methanotrophic bacteria can use methane as a sole source of carbon and energy. The enzyme responsible for the oxidation of methane in these organisms, methane monooxygenase, is also able to biotransform a number of substrates into industrially important chemicals. One such example is the oxidation of propylene to propylene oxide. Several strains of mesophilic and thermophilic methanotrophs have been tested for their ability to produce propylene oxide with formate, methanol, and methane as the co-oxidative substrates. Cultures in the late stationary phase were found to be more productive than exponentially growing cultures. Methane did not inhibit propylene epoxidation on low-density cultures; in fact, the yields of propylene oxide were greater when both methane and propylene were present than when only propylene was present. In higher-density cultures, however, methane did appear to inhibit oxidation of propylene. The effects of several culture parameters such as pH, temperature, and concentration of micronutrients on propylene oxide production ad steroespecificity were determined. Propylene oxide production was proportional to the amount of cell loading up to 14 g/L. Unwashed cells produced more propylene oxide than washed cells. The long- and short-term inhibitory effects of propylene oxide on the methanotrophic strains were also investigated. A tolerance of up to 1 M propylene oxide was observed, and the maximum inhibitory effect was seen within 30 minute. The steroespecificity for propylene oxide production and oxidation of 3-methylcyclohexene was determined for several strains. Methylosinus trichosporium (OB3b), particularly a cell-free extract of this strain, had the greatest steroespecificity. 13 refs., 12 figs., 3 tabs.

  11. Project Summary. IN-SITU AQUIFER RESTORATION OF CHLORINATED ALIPHATICS BY METHANOTROPHIC BACTERIA

    EPA Science Inventory

    This project evaluated the potential of an innovative approach to aquifer restoration: enhanced in-situ biotransformation of chlorinated aliphatic solvents by a bacterial community grown on methane under aerobic conditions. The target chlorinated compounds were trichloroethene (...

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

    PubMed

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

    2012-01-01

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

  13. Revisiting methanotrophic communities in sewage treatment plants.

    PubMed

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

    2013-04-01

    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.

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

    PubMed Central

    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

  15. Biodegradation of Asphalt Cement-20 by Aerobic Bacteria

    PubMed Central

    Pendrys, John P.

    1989-01-01

    Seven gram-negative, aerobic bacteria were isolated from a mixed culture enriched for asphalt-degrading bacteria. The predominant genera of these isolates were Pseudomonas, Acinetobacter, Alcaligenes, Flavimonas, and Flavobacterium. The mixed culture preferentially degraded the saturate and naphthene aromatic fractions of asphalt cement-20. A residue remained on the surface which was resistant to biodegradation and protected the underlying asphalt from biodegradation. The most potent asphalt-degrading bacterium, Acinetobacter calcoaceticus NAV2, excretes an emulsifier which is capable of emulsifying the saturate and naphthene aromatic fractions of asphalt cement-20. This emulsifier is not denatured by phenol. PMID:16347928

  16. 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.

    PubMed

    Lau, Evan; Iv, Edward J Nolan; Dillard, Zachary W; Dague, Ryan D; Semple, Amanda L; Wentzell, Wendi L

    2015-04-02

    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.

  17. 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

    PubMed Central

    Lau, Evan; Nolan, Edward J.; Dillard, Zachary W.; Dague, Ryan D.; Semple, Amanda L.; Wentzell, Wendi L.

    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 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. PMID:27682082

  18. Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation.

    PubMed

    Koch, Hanna; Galushko, Alexander; Albertsen, Mads; Schintlmeister, Arno; Gruber-Dorninger, Christiane; Lücker, Sebastian; Pelletier, Eric; Le Paslier, Denis; Spieck, Eva; Richter, Andreas; Nielsen, Per H; Wagner, Michael; Daims, Holger

    2014-08-29

    The bacterial oxidation of nitrite to nitrate is a key process of the biogeochemical nitrogen cycle. Nitrite-oxidizing bacteria are considered a highly specialized functional group, which depends on the supply of nitrite from other microorganisms and whose distribution strictly correlates with nitrification in the environment and in wastewater treatment plants. On the basis of genomics, physiological experiments, and single-cell analyses, we show that Nitrospira moscoviensis, which represents a widely distributed lineage of nitrite-oxidizing bacteria, has the genetic inventory to utilize hydrogen (H2) as an alternative energy source for aerobic respiration and grows on H2 without nitrite. CO2 fixation occurred with H2 as the sole electron donor. Our results demonstrate a chemolithoautotrophic lifestyle of nitrite-oxidizing bacteria outside the nitrogen cycle, suggesting greater ecological flexibility than previously assumed.

  19. The δ15N and δ18O values of N2O produced during the co-oxidation of ammonia by methanotrophic bacteria

    USGS Publications Warehouse

    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+

  20. Ecophysiological Characteristics of Obligate Methanotrophic Bacteria and Methane Oxidation In Situ

    NASA Technical Reports Server (NTRS)

    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).

  1. Aerobic sulfur-oxidizing bacteria: Environmental selection and diversification

    NASA Technical Reports Server (NTRS)

    Caldwell, D.

    1985-01-01

    Sulfur-oxidizing bacteria oxidize reduced inorganic compounds to sulfuric acid. Lithotrophic sulfur oxidizer use the energy obtained from oxidation for microbial growth. Heterotrophic sulfur oxidizers obtain energy from the oxidation of organic compounds. In sulfur-oxidizing mixotrophs energy are derived either from the oxidation of inorganic or organic compounds. Sulfur-oxidizing bacteria are usually located within the sulfide/oxygen interfaces of springs, sediments, soil microenvironments, and the hypolimnion. Colonization of the interface is necessary since sulfide auto-oxidizes and because both oxygen and sulfide are needed for growth. The environmental stresses associated with the colonization of these interfaces resulted in the evolution of morphologically diverse and unique aerobic sulfur oxidizers.

  2. Aerobic salivary bacteria in wild and captive Komodo dragons.

    PubMed

    Montgomery, Joel M; Gillespie, Don; Sastrawan, Putra; Fredeking, Terry M; Stewart, George L

    2002-07-01

    During the months of November 1996, August 1997, and March 1998, saliva and plasma samples were collected for isolation of aerobic bacteria from 26 wild and 13 captive Komodo dragons (Varanus komodoensis). Twenty-eight Gram-negative and 29 Gram-positive species of bacteria were isolated from the saliva of the 39 Komodo dragons. A greater number of wild than captive dragons were positive for both Gram-negative and Gram-positive bacteria. The average number of bacterial species within the saliva of wild dragons was 46% greater than for captive dragons. While Escherichia coli was the most common bacterium isolated from the saliva of wild dragons, this species was not present in captive dragons. The most common bacteria isolated from the saliva of captive dragons were Staphylococcus capitis and Staphylococcus capitis and Staphylococcus caseolyticus, neither of which were found in wild dragons. High mortality was seen among mice injected with saliva from wild dragons and the only bacterium isolated from the blood of dying mice was Pasteurella multocida. A competitive inhibition enzyme-linked immunosorbent assay revealed the presence of anti-Pasteurella antibody in the plasma of Komodo dragons. Four species of bacteria isolated from dragon saliva showed resistance to one or more of 16 antimicrobics tested. The wide variety of bacteria demonstrated in the saliva of the Komodo dragon in this study, at least one species of which was highly lethal in mice and 54 species of which are known pathogens, support the observation that wounds inflicted by this animal are often associated with sepsis and subsequent bacteremia in prey animals.

  3. Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS.

    PubMed

    Orphan, Victoria J; Turk, Kendra A; Green, Abigail M; House, Christopher H

    2009-07-01

    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 ion mass spectrometry) to describe the physiological traits and anabolic activity of individual methanotrophic consortia, specifically tracking (15)N-labelled protein synthesis to examine the effects of organization and size on the metabolic activity of the syntrophic partners. Patterns of (15)N distribution within individual aggregates showed enhanced (15)N assimilation in ANME-2 cells relative to the co-associated DSS revealing a decoupling in anabolic activity between the partners. Protein synthesis in ANME-2 cells was sustained throughout the core of individual ANME-2/DSS consortia ranging in size range from 4 to 20 μm. This indicates that metabolic activity of the methane-oxidizing archaea is not limited to, or noticeably enhanced at the ANME-2/DSS boundary. Overall, the metabolic activity of both syntrophic partners within consortia was greater than activity measured in representatives of the ANME-2 and DSS observed alone, with smaller ANME-2/DSS aggregates displaying a tendency for greater (15)N uptake and doubling times ranging from 3 to 5 months. The combination of (15)N-labelling and FISH-SIMS provides an important perspective on the extent of heterogeneity within methanotrophic aggregates and may aid in constraining predictive models of activity and growth by these syntrophic consortia.

  4. Stable carbon isotope fractionation of trans-1,2-dichloroethylene during co-metabolic degradation by methanotrophic bacteria

    USGS Publications Warehouse

    Brungard, Karen L.; Munakata-Marr, Junko; Johnson, Craig A.; Mandernack, Kevin W.

    2003-01-01

    Changes in the carbon isotope ratio (δ13C) 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 ε, was measured to be -3.50/00 for the type I culture and -6.70/00 for the type II culture. This fractionation effect and subsequent enrichment in the δ13C 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 δ13C 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.

  5. Evaluation of the petrifilm aerobic count plate for enumeration of aerobic marine bacteria from seawater and Caulerpa lentillifera.

    PubMed

    Kudaka, Jun; Horii, Toru; Tamanaha, Koji; Itokazu, Kiyomasa; Nakamura, Masaji; Taira, Katsuya; Nidaira, Minoru; Okano, Sho; Kitahara, Akio

    2010-08-01

    The enumeration and evaluation of the activity of marine bacteria are important in the food industry. However, detection of marine bacteria in seawater or seafood has not been easy. The Petrifilm aerobic count plate (ACP) is a ready-to-use alternative to the traditional enumeration media used for bacteria associated with food. The purpose of this study was to evaluate the usefulness of a simple detection and enumeration method utilizing the Petrifilm ACP for enumeration of aerobic marine bacteria from seawater and an edible seaweed, Caulerpa lentillifera. The efficiency of enumeration of total aerobic marine bacteria on Petrifilm ACP was compared with that using the spread plate method on marine agar with 80 seawater and 64 C. lentillifera samples. With sterile seawater as the diluent, a close correlation was observed between the method utilizing Petrifilm ACP and that utilizing the conventional marine agar (r=0.98 for seawater and 0.91 for C. lentillifera). The Petrifilm ACP method was simpler and less time-consuming than the conventional method. These results indicate that Petrifilm ACP is a suitable alternative to conventional marine agar for enumeration of marine microorganisms in seawater and C. lentillifera samples.

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

    PubMed Central

    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

  7. Effect of selected monoterpenes on methane oxidation, denitrification, and aerobic metabolism by bacteria in pure culture.

    PubMed

    Amaral, J A; Ekins, A; Richards, S R; Knowles, R

    1998-02-01

    Selected monoterpenes inhibited methane oxidation by methanotrophs (Methylosinus trichosporium OB3b, Methylobacter luteus), denitrification by environmental isolates, and aerobic metabolism by several heterotrophic pure cultures. Inhibition occurred to various extents and was transient. Complete inhibition of methane oxidation by Methylosinus trichosporium OB3b with 1.1 mM (-)-alpha-pinene lasted for more than 2 days with a culture of optical density of 0.05 before activity resumed. Inhibition was greater under conditions under which particulate methane monooxygenase was expressed. No apparent consumption or conversion of monoterpenes by methanotrophs was detected by gas chromatography, and the reason that transient inhibition occurs is not clear. Aerobic metabolism by several heterotrophs was much less sensitive than methanotrophy was; Escherichia coli (optical density, 0.01), for example, was not affected by up to 7.3 mM (-)-alpha-pinene. The degree of inhibition was monoterpene and species dependent. Denitrification by isolates from a polluted sediment was not inhibited by 3.7 mM (-)-alpha-pinene, gamma-terpinene, or beta-myrcene, whereas 50 to 100% inhibition was observed for isolates from a temperate swamp soil. The inhibitory effect of monoterpenes on methane oxidation was greatest with unsaturated, cyclic hydrocarbon forms [e.g., (-)-alpha-pinene, (S)-(-)-limonene, (R)-(+)-limonene, and gamma-terpinene]. Lower levels of inhibition occurred with oxide and alcohol derivatives [(R)-(+)-limonene oxide, alpha-pinene oxide, linalool, alpha-terpineol] and a noncyclic hydrocarbon (beta-myrcene). Isomers of pinene inhibited activity to different extents. Given their natural sources, monoterpenes may be significant factors affecting bacterial activities in nature.

  8. Antibiotic Susceptibility Pattern of Aerobic and Anaerobic Bacteria Isolated From Surgical Site Infection of Hospitalized Patients

    PubMed Central

    Akhi, Mohammad Taghi; Ghotaslou, Reza; Beheshtirouy, Samad; Asgharzadeh, Mohammad; Pirzadeh, Tahereh; Asghari, Babak; Alizadeh, Naser; Toloue Ostadgavahi, Ali; Sorayaei Somesaraei, Vida; Memar, Mohammad Yousef

    2015-01-01

    Background: Surgical Site Infections (SSIs) are infections of incision or deep tissue at operation sites. These infections prolong hospitalization, delay wound healing, and increase the overall cost and morbidity. Objectives: This study aimed to investigate anaerobic and aerobic bacteria prevalence in surgical site infections and determinate antibiotic susceptibility pattern in these isolates. Materials and Methods: One hundred SSIs specimens were obtained by needle aspiration from purulent material in depth of infected site. These specimens were cultured and incubated in both aerobic and anaerobic condition. For detection of antibiotic susceptibility pattern in aerobic and anaerobic bacteria, we used disk diffusion, agar dilution, and E-test methods. Results: A total of 194 bacterial strains were isolated from 100 samples of surgical sites. Predominant aerobic and facultative anaerobic bacteria isolated from these specimens were the members of Enterobacteriaceae family (66, 34.03%) followed by Pseudomonas aeruginosa (26, 13.4%), Staphylococcus aureus (24, 12.37%), Acinetobacter spp. (18, 9.28%), Enterococcus spp. (16, 8.24%), coagulase negative Staphylococcus spp. (14, 7.22%) and nonhemolytic streptococci (2, 1.03%). Bacteroides fragilis (26, 13.4%), and Clostridium perfringens (2, 1.03%) were isolated as anaerobic bacteria. The most resistant bacteria among anaerobic isolates were B. fragilis. All Gram-positive isolates were susceptible to vancomycin and linezolid while most of Enterobacteriaceae showed sensitivity to imipenem. Conclusions: Most SSIs specimens were polymicrobial and predominant anaerobic isolate was B. fragilis. Isolated aerobic and anaerobic strains showed high level of resistance to antibiotics. PMID:26421133

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

    PubMed Central

    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 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 due to abundance

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

    PubMed

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

    2015-06-23

    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 δ(13)CH₄ value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively (12)C-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

    PubMed Central

    Baesman, Shaun M.; 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. PMID:27682090

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

    USGS Publications Warehouse

    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.

  13. Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri

    PubMed Central

    McDonald, Michael J.; Galafassi, Silvia; Compagno, Concetta; Piškur, Jure

    2017-01-01

    The Crabtree positive yeasts, such as Saccharomyces cerevisiae, prefer fermentation to respiration, even under fully aerobic conditions. The selective pressures that drove the evolution of this trait remain controversial because of the low ATP yield of fermentation compared to respiration. Here we propagate experimental populations of the weak-Crabtree yeast Lachancea kluyveri, in competitive co-culture with bacteria. We find that L. kluyveri adapts by producing quantities of ethanol lethal to bacteria and evolves several of the defining characteristics of Crabtree positive yeasts. We use precise quantitative analysis to show that the rate advantage of fermentation over aerobic respiration is insufficient to provide an overall growth advantage. Thus, the rapid consumption of glucose and the utilization of ethanol are essential for the success of the aerobic fermentation strategy. These results corroborate that selection derived from competition with bacteria could have provided the impetus for the evolution of the Crabtree positive trait. PMID:28282411

  14. Abundance and salt tolerance of obligately aerobic, phototrophic bacteria in a marine microbial mat

    NASA Astrophysics Data System (ADS)

    Yurkov, Vladimir V.; Van Gemerden, Hans

    Data have been collected on the abundance of obligately aerobic, bacteriochlorophyll- a-containing bacteria in a marine microbial mat on the West Frisian Island of Texel, The Netherlands. Plate counts on media rich in organic matter revealed average numbers of 3 ∗10 5·cm -3 sediment in the top 10 mm of the mat; the number of purple non-sulphur bacteria was of the same magnitude. Due to the relatively small dimensions of obligately aerobic anoxygenic phototrophic bacteria and purple non-sulphur bacteria, compared to those of purple sulphur bacteria, the contributions of either of the two former groups to the biomass of Bchl- a-containing organisms was approximately 3%. The specific Bchl- a-content of the isolated obligately aerobic phototrophs was very low (0.8 to 1.0 μg·mg -1 protein) compared to that of purple non-sulphur bacteria (16 to 20 μg·mg -1 protein), and purple sulphur bacteria (27 to 30 μg·mg -1). As a consequence, the relative contribution to the total Bchl a concentration of the two former groups (0.1% and 2.1%, respectively) was negligible, compared to that of the purple sulphur bacteria (97.8%). Salinities <50 had little effect on growth rate and yield of isolates; at salinities between 50 and 100 the doubling time increased progressively with a concomitant decrease in yield; no growth occurred at salinities > 140.

  15. Vertical profiles of community abundance and diversity of anaerobic methanotrophic archaea (ANME) and bacteria in a simple waste landfill in north China.

    PubMed

    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.

  16. Comparison of dry medium culture plates for mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet products.

    PubMed

    Park, Junghyun; Kim, Myunghee

    2013-12-01

    This study was performed to compare the performance of Sanita-Kun dry medium culture plate with those of traditional culture medium and Petrifilm dry medium culture plate for the enumeration of the mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet. Mesophilic aerobic bacteria were comparatively evaluated in milk, ice cream, ham, and codfish fillet using Sanita-Kun aerobic count (SAC), Petrifilm aerobic count (PAC), and traditional plate count agar (PCA) media. According to the results, all methods showed high correlations of 0.989~1.000 and no significant differences were observed for enumerating the mesophilic aerobic bacteria in the tested food products. SAC method was easier to perform and count colonies efficiently as compared to the PCA and PAC methods. Therefore, we concluded that the SAC method offers an acceptable alternative to the PCA and PAC methods for counting the mesophilic aerobic bacteria in milk, ice cream, ham, and codfish fillet products.

  17. Unusual novel n-4 polyunsaturated fatty acids in cold-seep mussels (Bathymodiolus japonicus and Bathymodiolus platifrons), originating from symbiotic methanotrophic bacteria.

    PubMed

    Saito, Hiroaki

    2008-07-25

    Novel fatty acids originated from the two cold-seep mussels Bathymodiolus japonicus and Bathymodiolus platifrons, which host methane-oxidizing bacteria, were determined by using gas chromatography-mass spectrometry analysis of the 4,4-dimethyloxazoline derivatives. The major polyunsaturated fatty acids (PUFAs) in the two mussels belong to unusual n-4 and n-7 methylene interrupted PUFAs, such as 18:3 n-7,10,13 (Delta5,8,11-18:3), 18:4 n-4,7,10,13 (Delta5,8,11,14-18:4), 20:3n-7,10,13 (Delta7,10,13-20:3), 20:4n-4,7,10,13 (Delta7,10,13,16-20:4), and 21:4n-7,10,13,16 (Delta5,8,11,14-20:4). The similarity of fatty acids in the two Bathymodiolus species produced by the symbiotic bacteria, indicate occurrence of highly homologous mussel symbionts. In contrast to the lipids of shallow-water mussel Mytilus galloprovincialis, which contains photosynthetic n-3 PUFAs, the two Bathymodiolus mussels were lacking in docosahexaenoic acid and icosapentaenoic acid even though they are marine animals. These findings suggest the Bathymodiolus species survive independently of photosynthetic products, similar to the Calyptogena clams, which house sulfur-oxidizing bacteria and whose lipid contains n-4 non-methylene interrupted PUFAs (20:3n-4,7,15 (Delta5,13,16-20:3), 20:4n-1,4,7,15 (Delta5,13,16,19-20:4), and 21:3n-4,7,16 (Delta5,14,17-20:3)). The similarity in n-4 fatty acids between the mussels and the clam suggests that these bivalves depend on analogous n-4 family PUFAs and that the n-4 PUFA family is a characteristic of all vent bivalves depending on geothermal energy. The differences of the n-4 PUFAs between the mussels and the clam suggest a generic specificity of symbiotic bacteria and differences in lipid physiology between thiotrophic and methanotrophic symbionts. Such a highly diversified variety of n-4 family PUFAs in the mussels and the clam under different environments presumably increase the great potential of the chemosynthetic bacteria.

  18. Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review.

    PubMed

    Zhu, Jing; Wang, Qian; Yuan, Mengdong; Tan, Giin-Yu Amy; Sun, Faqian; Wang, Cheng; Wu, Weixiang; Lee, Po-Heng

    2016-03-01

    Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking

  19. Genetic Tools for the Industrially Promising Methanotroph Methylomicrobium buryatense

    SciTech Connect

    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.

  20. Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia.

    PubMed

    Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

    2014-10-01

    In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

  1. Hydrogen evolution by strictly aerobic hydrogen bacteria under anaerobic conditions.

    PubMed

    Kuhn, M; Steinbüchel, A; Schlegel, H G

    1984-08-01

    When strains and mutants of the strictly aerobic hydrogen-oxidizing bacterium Alcaligenes eutrophus are grown heterotrophically on gluconate or fructose and are subsequently exposed to anaerobic conditions in the presence of the organic substrates, molecular hydrogen is evolved. Hydrogen evolution started immediately after the suspension was flushed with nitrogen, reached maximum rates of 70 to 100 mumol of H2 per h per g of protein, and continued with slowly decreasing rates for at least 18 h. The addition of oxygen to an H2-evolving culture, as well as the addition of nitrate to cells (which had formed the dissimilatory nitrate reductase system during the preceding growth), caused immediate cessation of hydrogen evolution. Formate is not the source of H2 evolution. The rates of H2 evolution with formate as the substrate were lower than those with gluconate. The formate hydrogenlyase system was not detectable in intact cells or crude cell extracts. Rather the cytoplasmic, NAD-reducing hydrogenase is involved by catalyzing the release of excessive reducing equivalents under anaerobic conditions in the absence of suitable electron acceptors. This conclusion is based on the following experimental results. H2 is formed only by cells which had synthesized the hydrogenases during growth. Mutants lacking the membrane-bound hydrogenase were still able to evolve H2. Mutants lacking the NAD-reducing or both hydrogenases were unable to evolve H2.

  2. Aerobic biodegradation of propylene glycol by soil bacteria.

    PubMed

    Toscano, Giuseppe; Cavalca, Lucia; Letizia Colarieti, M; Scelza, Rosalia; Scotti, Riccardo; Rao, Maria A; Andreoni, Vincenza; Ciccazzo, Sonia; Greco, Guido

    2013-09-01

    Propylene glycol (PG) is a main component of aircraft deicing fluids and its extensive use in Northern airports is a source of soil and groundwater contamination. Bacterial consortia able to grow on PG as sole carbon and energy source were selected from soil samples taken along the runways of Oslo Airport Gardermoen site (Norway). DGGE analysis of enrichment cultures showed that PG-degrading populations were mainly composed by Pseudomonas species, although Bacteroidetes were found, as well. Nineteen bacterial strains, able to grow on PG as sole carbon and energy source, were isolated and identified as different Pseudomonas species. Maximum specific growth rate of mixed cultures in the absence of nutrient limitation was 0.014 h(-1) at 4 °C. Substrate C:N:P molar ratios calculated on the basis of measured growth yields are in good agreement with the suggested values for biostimulation reported in literature. Therefore, the addition of nutrients is suggested as a suitable technique to sustain PG aerobic degradation at the maximum rate by autochthonous microorganisms of unsaturated soil profile.

  3. Diversity of methanotroph communities in a basalt aquifer.

    PubMed

    Newby, D T; Reed, D W; Petzke, L M; Igoe, A L; Delwiche, M E; Roberto, F F; McKinley, J P; Whiticar, M J; Colwell, F S

    2004-06-01

    Methanotrophic bacteria play an important role in global cycling of carbon and co-metabolism of contaminants. Methanotrophs from pristine regions of the Snake River Plain Aquifer (SRPA; Idaho, USA) were studied in order to gain insight into the native groundwater communities' genetic potential to carry out TCE co-metabolism. Wells were selected that were proximal to a TCE plume believed to be undergoing natural attenuation. Methane concentrations ranged from 1 to >1000 nM. Carbon isotope ratios and diversity data together suggest that the SRPA contains active communities of methanotrophs that oxidize microbially produced methane. Microorganisms removed from groundwater by filtration were used as inocula for enrichments or frozen immediately and DNA was subsequently extracted for molecular characterization. Primers that specifically target methanotroph 16S rRNA genes or genes that code for subunits of soluble or particulate methane monooxygenase, mmoX and pmoA, respectively, were used to characterize the indigenous methanotrophs via PCR, cloning, RFLP analysis, and sequencing. Type I methanotroph clones aligned with Methylomonas, Methylocaldum, and Methylobacter sequences and a distinct 16S rRNA phylogenetic lineage grouped near Methylobacter. The majority of clone sequences in type II methanotroph 16S rRNA, pmoA, and mmoX gene libraries grouped closely with sequences in the Methylocystis genus. A subset of the type II methanotroph clones from the aquifer had sequences that aligned most closely to Methylosinus trichosporium OB3b and Methylocystis spp., known TCE-co-metabolizing methanotrophs.

  4. Autotrophic carbon dioxide fixation via the Calvin-Benson-Bassham cycle by the denitrifying methanotroph "Candidatus Methylomirabilis oxyfera".

    PubMed

    Rasigraf, Olivia; Kool, Dorien M; Jetten, Mike S M; Sinninghe Damsté, Jaap S; Ettwig, Katharina F

    2014-04-01

    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 recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase reaction. Previous genome analysis has suggested that, like the verrucomicrobial methanotrophs, "Ca. Methylomirabilis oxyfera" encodes and transcribes genes for the Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. Here we provide multiple independent lines of evidence for autotrophic carbon dioxide fixation by "Ca. Methylomirabilis oxyfera" via the CBB cycle. The activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), a key enzyme of the CBB cycle, in cell extracts from an "Ca. Methylomirabilis oxyfera" enrichment culture was shown to account for up to 10% of the total methane oxidation activity. Labeling studies with whole cells in batch incubations supplied with either (13)CH4 or [(13)C]bicarbonate revealed that "Ca. Methylomirabilis oxyfera" biomass and lipids became significantly more enriched in (13)C after incubation with (13)C-labeled bicarbonate (and unlabeled methane) than after incubation with (13)C-labeled methane (and unlabeled bicarbonate), providing evidence for autotrophic carbon dioxide fixation. Besides this experimental approach, detailed genomic and transcriptomic analysis demonstrated an operational CBB cycle in "Ca. Methylomirabilis oxyfera." Altogether, these results show that the CBB cycle is active and plays a major role in carbon assimilation by "Ca. Methylomirabilis oxyfera" bacteria. Our results suggest that autotrophy might be more widespread among methanotrophs than was previously assumed and implies that a methanotrophic

  5. Testing for aerobic heterotrophic bacteria allows no prediction of contamination with potentially pathogenic bacteria in the output water of dental chair units

    PubMed Central

    Bristela, Margit; Skolka, Astrid; Schmid-Schwap, Martina; Piehslinger, Eva; Indra, Alexander; Wewalka, Günther; Stauffer, Fritz

    2012-01-01

    Background: Currently, to our knowledge, quality of output water of dental chair units is not covered by specific regulations in the European Union, and national recommendations are heterogeneous. In Germany, water used in dental chair units must follow drinking water quality. In the United States of America, testing for aerobic heterotrophic bacteria is recommended. The present study was performed to evaluate whether the counts of aerobic heterotrophic bacteria correlate with the presence of potentially pathogenic bacteria such as Legionella spp. or Pseudomonas aeruginosa. Methods: 71 samples were collected from 26 dental chair units with integrated disinfection device and 31 samples from 15 outlets of the water distribution pipework within the department were examined. Samples were tested for aerobic heterotrophic bacteria at 35°C and 22°C using different culture media and for Legionella spp. and for Pseudomonas aeruginosa. Additionally, strains of Legionella pneumophila serogroup 1 were typed with monoclonal antibodies and representative samples of Legionella pneumophila serogroup 1 were typed by sequence based typing. Results: Our results showed a correlation between different agars for aerobic heterotrophic bacteria but no correlation for the count of aerobic heterotrophic bacteria and the presence of Legionella spp. or Pseudomonas aeruginosa. Conclusion: Testing for aerobic heterotrophic bacteria in output water or water distribution pipework within the departments alone is without any value for predicting whether the water is contaminated with potentially pathogenic bacteria like Legionella spp. or Pseudomonas aeruginosa. PMID:22558046

  6. Evaluation of Petrifilm method for enumerating aerobic bacteria in Crottin goat cheese.

    PubMed

    de Sousa, G B; Tamagnini, L M; González, R D; Budde, C E

    2005-01-01

    The Petrifilm Aerobic Count Plate (ACP) developed by 3M laboratories, is a ready-to-use culture medium system, useful for the enumeration of aerobic bacteria in food. Petrifilm was compared with a standard method in several different food products with satisfactory results. However, many studies showed that bacterial counts in Petrifilm were significantly lower than those obtained with conventional methods in fermented food. The purpose of this study was to compare the Petrifilm method for enumerating aerobic bacteria with a conventional method (PCA) in Crottin goat's cheese. Thirty samples were used for the colony count. The mean count and standard deviation were 7.18 +/- 1.17 log CFU g(-1) on PCA and 7.11 +/- 1.05 log CFU g(-1) on Petrifilm. Analysis of variance revealed no significant differences between both methods (t = 1.33, P = 0.193). The Pearson correlation coefficient (0.971, P = 0.0001) indicated a strong linear relationship between the Petrifilm and the standard method. The results showed that Petrifilm is suitable and a convenient alternative to this standard method for the enumeration of aerobic flora in goat soft cheese.

  7. Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre. Revised

    NASA Technical Reports Server (NTRS)

    Cottrell, Matthew T.; Mannino, Antonio; Kirchman, David L.

    2005-01-01

    The abundance of aerobic anoxygenic phototrophic (AM) bacteria, cyanobacteria and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic but only 5% or less in the Pacific. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than Prochlorococcus and 10-folder higher than Synechococcus. In contrast, Prochlorococcus outnumbered AAP bacteria 5- to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. Concentrations of bacteriochlorophyll a (BChl a) were low (approx.1%) compared to chlorophyll a. Although the BChl a content of AAP bacteria per cell was typically 20- to 250-fold lower than the divinyl-chlorophyll a content of Prochlorococcus, in shelf break water the pigment content of AAP bacteria approached that of Prochlorococcus. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP genera (Erythrobacter and Roseobacter spp.). The distribution of AAP bacteria in the water column, which was similar in the Atlantic and the Pacific, was consistent with phototrophy.

  8. Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki

    PubMed Central

    Sharp, Christine E.; Smirnova, Angela V.; Kalyuzhnaya, Marina G.; Bringel, Françoise; Hirayama, Hisako; Jetten, Mike S. M.; Khmelenina, Valentina N.; Klotz, Martin G.; Knief, Claudia; Kyrpides, Nikos; Op den Camp, Huub J. M.; Reshetnikov, Alexander S.; Sakai, Yasuyoshi; Shapiro, Nicole; Trotsenko, Yuri A.; Vuilleumier, Stéphane; Woyke, Tanja

    2015-01-01

    Methylohalobius crimeensis strain 10Ki is a moderately halophilic aerobic methanotroph isolated from a hypersaline lake in the Crimean Peninsula, Ukraine. This organism has the highest salt tolerance of any cultured methanotroph. Here, we present a draft genome sequence of this bacterium. PMID:26067976

  9. Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan

    PubMed Central

    Hirose, Setsuko; Matsuura, Katsumi; Haruta, Shin

    2016-01-01

    The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms. PMID:27453124

  10. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

    SciTech Connect

    Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

    2016-04-18

    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 ofDeltaproteobacteriadiversity. 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. In addition, 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

  11. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

    DOE PAGES

    Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

    2016-04-18

    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 ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » 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. In addition, 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

  12. Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

    PubMed Central

    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

  13. High abundances of aerobic anoxygenic photosynthetic bacteria in the South Pacific Ocean.

    PubMed

    Lami, Raphaël; Cottrell, Matthew T; Ras, Joséphine; Ulloa, Osvaldo; Obernosterer, Ingrid; Claustre, Hervé; Kirchman, David L; Lebaron, Philippe

    2007-07-01

    Little is known about the abundance, distribution, and ecology of aerobic anoxygenic phototrophic (AAP) bacteria, particularly in oligotrophic environments, which represent 60% of the ocean. We investigated the abundance of AAP bacteria across the South Pacific Ocean, including the center of the gyre, the most oligotrophic water body of the world ocean. AAP bacteria, Prochlorococcus, and total prokaryotic abundances, as well as bacteriochlorophyll a (BChl a) and divinyl-chlorophyll a concentrations, were measured at several depths in the photic zone along a gradient of oligotrophic conditions. The abundances of AAP bacteria and Prochlorococcus were high, together accounting for up to 58% of the total prokaryotic community. The abundance of AAP bacteria alone was up to 1.94 x 10(5) cells ml(-1) and as high as 24% of the overall community. These measurements were consistent with the high BChl a concentrations (up to 3.32 x 10(-3) microg liter(-1)) found at all stations. However, the BChl a content per AAP bacterial cell was low, suggesting that AAP bacteria are mostly heterotrophic organisms. Interestingly, the biovolume and therefore biomass of AAP bacteria was on average twofold higher than that of other prokaryotic cells. This study demonstrates that AAP bacteria can be abundant in various oligotrophic conditions, including the most oligotrophic regime of the world ocean, and can account for a large part of the bacterioplanktonic carbon stock.

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

    PubMed Central

    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

  15. Binary Interactions of Antagonistic Bacteria with Candida albicans Under Aerobic and Anaerobic Conditions.

    PubMed

    Benadé, Eliska; Stone, Wendy; Mouton, Marnel; Postma, Ferdinand; Wilsenach, Jac; Botha, Alfred

    2016-04-01

    We used both aerobic and anaerobic liquid co-cultures, prepared with Luria Bertani broth, to study the effect of bacteria on the survival of Candida albicans in the external environment, away from an animal host. The bacteria were represented by Aeromonas hydrophila, Bacillus cereus, Bacillus subtilis, Clostridium, Enterobacter, Klebsiella pneumoniae, Kluyvera ascorbata and Serratia marcescens. Under aerobic conditions, the yeast's growth was inhibited in the presence of bacterial growth; however, under anaerobic conditions, yeast and bacterial growth in co-cultures was similar to that observed for pure cultures. Subsequent assays revealed that the majority of bacterial strains aerobically produced extracellular hydrolytic enzymes capable of yeast cell wall hydrolysis, including chitinases and mannan-degrading enzymes. In contrast, except for the A. hydrophila strain, these enzymes were not detected in anaerobic bacterial cultures, nor was the antimicrobial compound prodigiosin found in anaerobic cultures of S. marcescens. When we suspended C. albicans cells in crude extracellular enzyme preparations from K. pneumoniae and S. marcescens, we detected no negative effect on yeast viability. However, we found that these preparations enhance the toxicity of prodigiosin towards the yeast, especially in combination with mannan-degrading enzymes. Analyses of the chitin and mannan content of yeast cell walls revealed that less chitin was produced under anaerobic than aerobic conditions; however, the levels of mannan, known for its low permeability, remained the same. The latter phenomenon, as well as reduced production of the bacterial enzymes and prodigiosin, may contribute to anaerobic growth and survival of C. albicans in the presence of bacteria.

  16. Survival of anaerobic and aerobic bacteria in a nonsupportive gassed transport system.

    PubMed Central

    Chow, A W; Cunningham, P J; Guze, L B

    1976-01-01

    Survival of anaerobic and aerobic bacteria in a commercially available, non-supportive, gassed (oxygen-free) transport container (Anaport) was evaluated quantitatively. Saline-suspended obligate anaerobes survived significantly better in the gassed container in aerobic control tubes (P less than 0.025, t test), and counts were virtually unchanged after 8 h of holding. Similarly, initial counts and relative proportions of a mixture of Bacteroides fragilis and Staphylococcus aureus were maintained for 72 h. The value of the gassed transport system was less apparent when microorganisms were suspended in nutrient broth. The major advantage of the gassed transport system appears to be for holding of specimens collected by saline irrigation. PMID:1254710

  17. Recovery of anaerobic, facultative, and aerobic bacteria from clinical specimens in three anaerobic transport systems.

    PubMed

    Helstad, A G; Kimball, J L; Maki, D G

    1977-06-01

    With aspirated specimens from clinical infections, we evaluated the recovery of anaerobic, aerobic, and facultative bacteria in three widely used transport systems: (i) aspirated fluid in a gassed-out tube (FGT), (ii) swab in modified Cary and Blair transport medium (SCB), and (iii) swab in a gassed-out tube (SGT). Transport tubes were held at 25 degrees C and semiquantitatively sampled at 0, 2, 24, and 48 h. Twenty-five clinical specimens yielded 75 anaerobic strains and 43 isolates of facultative and 3 of aerobic bacteria. Only one anaerobic isolate was not recovered in the first 24 h, and then, only in the SGT. At 48 h, 73 anaerobic strains (97%) were recovered in the FGT, 69 (92%) in the SCB, and 64 (85%) in the SGT. Two problems hindered the recovery of anaerobes in the SCB and SGT systems: first die-off of organisms, as evidenced by a decrease in colony-forming units of 20 strains (27%) in the SCB and 25 strains (33%) in the SGT, as compared with 7 strains (9%) in the FGT, over 48 h; and second, overgrowth of facultative bacteria, more frequent with SCB and SGT. The FGT method was clearly superior at 48 h to the SCB and SGT systems in this study and is recommended as the preferred method for transporting specimens for anaerobic culture.

  18. Aerobic Mercury-resistant bacteria alter Mercury speciation and retention in the Tagus Estuary (Portugal).

    PubMed

    Figueiredo, Neusa L; Canário, João; O'Driscoll, Nelson J; Duarte, Aida; Carvalho, Cristina

    2016-02-01

    Aerobic mercury-resistant bacteria were isolated from the sediments of two highly mercury-polluted areas of the Tagus Estuary (Barreiro and Cala do Norte) and one natural reserve area (Alcochete) in order to test their capacity to transform mercury. Bacterial species were identified using 16S rRNA amplification and sequencing techniques and the results indicate the prevalence of Bacillus sp. Resistance patterns to mercurial compounds were established by the determination of minimal inhibitory concentrations. Representative Hg-resistant bacteria were further tested for transformation pathways (reduction, volatilization and methylation) in cultures containing mercury chloride. Bacterial Hg-methylation was carried out by Vibrio fluvialis, Bacillus megaterium and Serratia marcescens that transformed 2-8% of total mercury into methylmercury in 48h. In addition, most of the HgR bacterial isolates showed Hg(2+)-reduction andHg(0)-volatilization resulting 6-50% mercury loss from the culture media. In summary, the results obtained under controlled laboratory conditions indicate that aerobic Hg-resistant bacteria from the Tagus Estuary significantly affect both the methylation and reduction of mercury and may have a dual face by providing a pathway for pollution dispersion while forming methylmercury, which is highly toxic for living organisms.

  19. The effect of bacteria, enzymes and inulin on fermentation and aerobic stability of corn silage

    PubMed Central

    Peymanfar, S; Kermanshahi, RK

    2012-01-01

    Background and Objectives Ensiling is a conservation method for forage crops. It is based on the fact that anaerobe lactic acid bacteria (LAB) convert watersoluble carbohydrates into organic acids. Therefore, pH decreases and the forage is preserved. The aim of this study was to isolate special kinds of lactic acid bacteria from silage and to study the effect of bacteria, inulin and enzymes as silage additives on the fermentation and aerobic stability of the silage. Materials and Methods The heterofermentative LAB were isolated from corn silages in Broujerd, Iran and biochemically characterized. Acid tolerance was studied by exposure to acidic PBS and growth in bile salt was measured by the spectrophotometric method. Results The results of molecular analysis using 16SrDNA sequences showed that the isolates belonged to Lactobacillus and Enterococcus genera. To enhance stability in acidic environment and against bile salts, microencapsulation with Alginate and Chitosan was used. The Lactobacillus plantarum strains were used as control. The inoculants (1 × 107 cfu/g) alone or in combination with inulin or in combination with enzymes were added to chopped forages and ensiled in 1.5-L anaerobic jars. Conclusion Combination of the isolates Lactobacillus and Enterococcus with inulin and enzymes can improve the aerobic stability of corn silage. PMID:23205249

  20. Phylogenetic and Kinetic Diversity of Aerobic Vinyl Chloride-Assimilating Bacteria from Contaminated Sites

    PubMed Central

    Coleman, Nicholas V.; Mattes, Timothy E.; Gossett, James M.; Spain, Jim C.

    2002-01-01

    Aerobic bacteria that grow on vinyl chloride (VC) have been isolated previously, but their diversity and distribution are largely unknown. It is also unclear whether such bacteria contribute to the natural attenuation of VC at chlorinated-ethene-contaminated sites. We detected aerobic VC biodegradation in 23 of 37 microcosms and enrichments inoculated with samples from various sites. Twelve different bacteria (11 Mycobacterium strains and 1 Nocardioides strain) capable of growth on VC as the sole carbon source were isolated, and 5 representative strains were examined further. All the isolates grew on ethene in addition to VC and contained VC-inducible ethene monooxygenase activity. The Mycobacterium strains (JS60, JS61, JS616, and JS617) all had similar growth yields (5.4 to 6.6 g of protein/mol), maximum specific growth rates (0.17 to 0.23 day−1), and maximum specific substrate utilization rates (9 to 16 nmol/min/mg of protein) with VC. The Nocardioides strain (JS614) had a higher growth yield (10.3 g of protein/mol), growth rate (0.71 day−1), and substrate utilization rate (43 nmol/min/mg of protein) with VC but was much more sensitive to VC starvation. Half-velocity constant (Ks) values for VC were between 0.5 and 3.2 μM, while Ks values for oxygen ranged from 0.03 to 0.3 mg/liter. Our results indicate that aerobic VC-degrading microorganisms (predominantly Mycobacterium strains) are widely distributed at sites contaminated with chlorinated solvents and are likely to be responsible for the natural attenuation of VC. PMID:12450841

  1. Protection of probiotic bacteria in a synbiotic matrix following aerobic storage at 4 °C.

    PubMed

    Chaluvadi, S; Hotchkiss, A T; Call, J E; Luchansky, J B; Phillips, J G; Liu, Ls; Yam, K L

    2012-09-01

    The survival of single strains of Bifidobacterium breve, Bifidobacterium longum, Lactobacillus acidophilus, and Lactobacillus reuteri was investigated in synbiotics that included 10 mg/ml of fructo-oligosaccharides, inulin and pectic-oligosaccharides in an alginate matrix under refrigerated (4 °C) aerobic storage conditions. When the matrices were cross-linked with calcium (45 mM), 102-103 cfu/ml of L. acidophilus and L. reuteri, and 0-103 cfu/ml of B. breve and B. longum survived refrigerated aerobic storage for 28 days. Following refrigerated storage, acetic (3-9 mM), butyric (0-2 mM), propionic (5-16 mM) and lactic acids (1-48 mM) were produced during the growth of probiotics in BHI broth at 37 °C, suggesting their metabolic activity after storage was stressed. When calcium cross-linking was not used in synbiotics, the matrix remained more gel-like after inoculation when compared to the calcium cross-linked matrix. At least 107 cfu/ml of probiotic bacteria survived after 21 days of storage within these gel-like alginate matrices. Significantly higher levels of B. breve, L. acidophilus and L. reuteri were obtained from the synbiotic matrices supplemented with fructo-oligosaccharides, inulin and pectic-oligosaccharides compared to alginate alone. B. longum survival was the same (~7 logs) in all gel-like synbiotic matrices. These results show that synbiotics protected probiotic bacteria and extended their shelf-life under refrigerated aerobic conditions. Synbiotics represent a viable delivery vehicle for health-promoting bacteria.

  2. Evaluation of the 3M™ Petrifilm™ Rapid Aerobic Count Plate for the Enumeration of Aerobic Bacteria: Collaborative Study, First Action 2015.13.

    PubMed

    Bird, Patrick; Flannery, Jonathan; Crowley, Erin; Agin, James; Goins, David; Jechorek, Robert

    2016-05-01

    The 3M™ Petrifilm™ Rapid Aerobic Count (RAC) Plate is a sample-ready culture medium system containing dual-sensor indicator technology for the rapid quantification of aerobic bacteria in food products. The 3M Petrifilm RAC Plate was compared to the U.S. Food and Drug Administration Bacteriological Analytical Manual (FDA BAM) Chapter 3 (Aerobic Plate Count) for the enumeration of aerobic bacteria in raw easy-peel shrimp and the Standard Methods for the Examination of Dairy Products (SMEDP) Chapter 6 (Standard Plate Count Method) for the enumeration of aerobic bacteria in pasteurized skim milk and instant nonfat dry milk (instant NFDM). The 3M Petrifilm RAC Plate was evaluated using a paired study design in a multilaboratory collaborative study following current AOAC validation guidelines. Three target contamination levels (low, 10-100 CFU/g; medium, 100-1000 CFU/g; and high 1000-10 000 CFU/g) were evaluated for naturally occurring aerobic microflora for each matrix. For raw easy-peel shrimp, duplicate 3M Petrifilm RAC Plates were enumerated after 24 ± 2 h incubation at both 32 and 35°C. Pasteurized skim milk 3M Petrifilm RAC Plates were enumerated after 24 ± 2 h incubation at 32°C, and instant NFDM 3M Petrifilm RAC Plates were enumerated after 48 ± 3 h incubation at 32°C. No statistical difference was observed between 3M Petrifilm RAC Plate and FDA BAM or SMEDP reference methods for each contamination level.

  3. Characteristics of alcohol dehydrogenases of certain aerobic bacteria representing human colonic flora.

    PubMed

    Nosova, T; Jousimies-Somer, H; Kaihovaara, P; Jokelainen, K; Heine, R; Salaspuro, M

    1997-05-01

    We have recently proposed the existence of a bacteriocolonic pathway for ethanol oxidation [i.e., ethanol is oxidized by alcohol dehydrogenases (ADHs) of intestinal bacteria resulting in high intracolonic levels of reactive and toxic acetaldehyde]. The aim of this in vitro study was to characterize further ADH activity of some aerobic bacteria, representing the normal human colonic flora. These bacteria were earlier shown to possess high cytosolic ADH activities (Escherichia coli IH 133369, Klebsiella pneumoniae IH 35385, Klebsiella oxytoca IH 35339, Pseudomonas aeruginosa IH 35342, and Hafnia alvei IH 53227). ADHs of the tested bacteria strongly preferred NAD as a cofactor. Marked ADH activities were found in all bacteria, even at low ethanol concentrations (1.5 mM) that may occur in the colon due to bacterial fermentation. The Km for ethanol varied from 29.9 mM for K. pneumoniae to 0.06 mM for Hafnia alvei. The inhibition of ADH by 4-methylpyrazole was found to be of the competitive type in 4 of 5 bacteria, and Ki varied from 18.26 +/- 3.3 mM for Escherichia coli to 0.47 +/- 0.13 mM for K. pneumoniae. At pH 7.4, ADH activity was significantly lower than at pH 9.6 in four bacterial strains. ADH of K. oxytoca, however, showed almost equal activities at neutral pH and at 9.6. In conclusion, NAD-linked alcohol dehydrogenases of aerobic colonic bacteria possess low apparent Km's for ethanol. Accordingly, they may oxidize moderate amounts of ethanol ingested during social drinking with nearly maximal velocity. This may result in the marked production of intracolonic acetaldehyde. Kinetic characteristics of the bacterial enzymes may enable some of them to produce acetaldehyde even from endogenous ethanol formed by other bacteria via alcoholic fermentation. The microbial ADHs were inhibited by 4-methylpyrazole by the same competitive inhibition as hepatic ADH, however, with nearly 1000 times lower susceptibility. Individual variations in human colonic flora may thus

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2011-08-15

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

  6. The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria.

    PubMed

    Ney, Blair; Ahmed, F Hafna; Carere, Carlo R; Biswas, Ambarish; Warden, Andrew C; Morales, Sergio E; Pandey, Gunjan; Watt, Stephen J; Oakeshott, John G; Taylor, Matthew C; Stott, Matthew B; Jackson, Colin J; Greening, Chris

    2017-01-01

    F420 is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds. Considered one of the rarest cofactors in biology, F420 is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria. In this work, we show that this cofactor is more widely distributed than previously reported. We detected the genes encoding all five known F420 biosynthesis enzymes (cofC, cofD, cofE, cofG and cofH) in at least 653 bacterial and 173 archaeal species, including members of the dominant soil phyla Proteobacteria, Chloroflexi and Firmicutes. Metagenome datamining validated that these genes were disproportionately abundant in aerated soils compared with other ecosystems. We confirmed through high-performance liquid chromatography analysis that aerobically grown stationary-phase cultures of three bacterial species, Paracoccus denitrificans, Oligotropha carboxidovorans and Thermomicrobium roseum, synthesized F420, with oligoglutamate sidechains of different lengths. To understand the evolution of F420 biosynthesis, we also analyzed the distribution, phylogeny and genetic organization of the cof genes. Our data suggest that although the Fo precursor to F420 originated in methanogens, F420 itself was first synthesized in an ancestral actinobacterium. F420 biosynthesis genes were then disseminated horizontally to archaea and other bacteria. Together, our findings suggest that the cofactor is more significant in aerobic bacterial metabolism and soil ecosystem composition than previously thought. The cofactor may confer several competitive advantages for aerobic soil bacteria by mediating their central metabolic processes and broadening the range of organic compounds they can synthesize, detoxify and mineralize.

  7. [Abundance and diversity of methanotrophic Gammaproteobacteria in northern wetlands].

    PubMed

    Danilova, O V; Dedysh, S N

    2014-01-01

    Numeric abundance, identity and pH preferences of methanotrophic Gammaproteobacteria (type I methanotrophs) inhabiting the northern acidic wetlands were studied. The rates of methane oxidation by peat samples from six-wetlands of European Northern Russia (pH 3.9-4.7) varied from 0.04 to 0.60 μg CH4 g(-1) peat h(-1). The number of cells revealed by hybridization with fluorochrome-labeled probes M84 + M705 specific for type I methanotrophs was 0.05-2.16 x 10(5) cells g(-1) dry peat, i.e. 0.4-12.5% of the total number of methanotrophs and 0.004-0.39% of the total number of bacteria. Analysis of the fragments of the pmoA gene encoding particulate methane monooxygenase revealed predominance of the genus Methylocystis (92% of the clones) in the studied sample of acidic peat, while the proportion of the pmoA sequences of type I methanotrophs was insignificant (8%). PCR amplification of the 16S rRNA gene fragments of type I methanotrophs with TypeIF-Type IR primers had low specificity, since only three sequences out of 53 analyzed belonged to methanotrophs and exhibited 93-99% similarity to those of Methylovulum, Methylomonas, and Methylobacter species. Isolates of type I methanotrophs obtained from peat (strains SH10 and 83A5) were identified as members of the species Methylomonaspaludis and Methylovulum miyakonense, respectively. Only Methylomonaspaludum SH10 was capable of growth in acidic media (pH range for growth 3.8-7.2 with the optimum at pH 5.8-6.2), while Methylovulum miyakonense 83A5 exhibited the typical growth characteristics of neutrophilic methanotrophs (pH range for growth 5.5-8.0 with the optimum at pH 6.5-7.5).

  8. Effects of Long-Term CO2 Enrichment on Soil-Atmosphere CH4 Fluxes and the Spatial Micro-Distribution of Methanotrophic Bacteria

    PubMed Central

    Karbin, Saeed; Guillet, Cécile; Kammann, Claudia I.; Niklaus, Pascal A.

    2015-01-01

    Background 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. Methods and Results 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. Conclusions 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. PMID:26147694

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

    PubMed Central

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

    2016-01-01

    Summary 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 M ethylobacter and M ethylomonas spp. and specifically a M ethylobacter 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 (M ethylocaldum), acidophiles (M ethylosoma) and haloalkaliphiles (M ethylomicrobium). 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

  10. Abundance of Common Aerobic Anoxygenic Phototrophic Bacteria in a Coastal Aquaculture Area

    PubMed Central

    Sato-Takabe, Yuki; Nakao, Hironori; Kataoka, Takafumi; Yokokawa, Taichi; Hamasaki, Koji; Ohta, Kohei; Suzuki, Satoru

    2016-01-01

    Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10–53% of the total bacterial assemblage. By examining pufM gene sequence, a common phylogenetic AAnPB species was found in all sampling sites through the year. The common species and other season-specific species were phylogenetically close to unculturable clones recorded in the Sargasso Sea and Pacific Ocean. The present study suggests that the common species may be a cosmopolitan species with worldwide distribution that is abundant not only in the oligotrophic open ocean but also in eutrophic aquaculture areas. PMID:28018324

  11. Summer community structure of aerobic anoxygenic phototrophic bacteria in the western Arctic Ocean.

    PubMed

    Boeuf, Dominique; Cottrell, Matthew T; Kirchman, David L; Lebaron, Philippe; Jeanthon, Christian

    2013-09-01

    Aerobic anoxygenic phototrophic (AAP) bacteria are found in a range of aquatic and terrestrial environments, potentially playing unique roles in biogeochemical cycles. Although known to occur in the Arctic Ocean, their ecology and the factors that govern their community structure and distribution in this extreme environment are poorly understood. Here, we examined summer AAP abundance and diversity in the North East Pacific and the Arctic Ocean with emphasis on the southern Beaufort Sea. AAP bacteria comprised up to 10 and 14% of the prokaryotic community in the bottom nepheloid layer and surface waters of the Mackenzie plume, respectively. However, relative AAP abundances were low in offshore waters. Environmental pufM clone libraries revealed that AAP bacteria in the Alphaproteobacteria and Betaproteobacteria classes dominated in offshore and in river-influenced surface waters, respectively. The most frequent AAP group was a new uncultivated betaproteobacterial clade whose abundance decreased along the salinity gradient of the Mackenzie plume even though its photosynthetic genes were actively expressed in offshore waters. Our data indicate that AAP bacterial assemblages represented a mixture of freshwater and marine taxa mostly restricted to the Arctic Ocean and highlight the substantial influence of riverine inputs on their distribution in coastal environments.

  12. Characterisation of aerobically grown non-spore-forming bacteria from paper mill pulps containing recycled fibres.

    PubMed

    Suihko, Maija-Liisa; Skyttä, Eija

    2009-01-01

    A total of 179 non-spore-forming bacteria aerobically growing on Nutrient Agar, Plate Count Agar or in specific enrichment conditions for salmonella, campylobacteria, listeria, yersinia or staphylococci, were isolated from 16 untreated paper mill pulps. After phenotypical screening the isolates were characterised by automated ribotyping and partial sequencing of the 16S rRNA gene. They could be divided into seven taxonomical classes representing 63 taxa (species): actinobacteria (11 species), bacilli (7), flavobacteria (3) alphaproteobacteria (10), betaproteobacteria (5), gammaproteobacteria (25) and sphingobacteria (2). Most of the gammaproteobacteria were enterobacteria, mainly species of the genera Enterobacter (7 species, 7 samples/3 mills) and Klebsiella (5 species, 6 samples/3 mills). Other commonly occurring bacteria were most closely related to Microbacterium barkeri (7 samples/3 mills), Cloacibacterium normanense (6 samples/2 mills), Pseudoxanthomonas taiwanensis (5 samples/2 mills) and Sphingobacterium composti (5 samples/1 mill). Sporadic isolates of Listeria innocua, L. monocytogenes, Enterococcus casseliflavus and Staphylococcus warneri were detected, from which only L. monocytogenes is considered to be a food pathogen. No isolates of the genera Campylobacter, Salmonella or Yersinia were detected. The detected bacteria may be harmful in process control, but the load of food pathogens with recycled fibres to paper machines is insignificant. Faecal contamination of the pulp samples was not indicated.

  13. Abundance of Common Aerobic Anoxygenic Phototrophic Bacteria in a Coastal Aquaculture Area.

    PubMed

    Sato-Takabe, Yuki; Nakao, Hironori; Kataoka, Takafumi; Yokokawa, Taichi; Hamasaki, Koji; Ohta, Kohei; Suzuki, Satoru

    2016-01-01

    Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10-53% of the total bacterial assemblage. By examining pufM gene sequence, a common phylogenetic AAnPB species was found in all sampling sites through the year. The common species and other season-specific species were phylogenetically close to unculturable clones recorded in the Sargasso Sea and Pacific Ocean. The present study suggests that the common species may be a cosmopolitan species with worldwide distribution that is abundant not only in the oligotrophic open ocean but also in eutrophic aquaculture areas.

  14. Culturing aerobic and anaerobic bacteria and mammalian cells with a microfluidic differential oxygenator.

    PubMed

    Lam, Raymond H W; Kim, Min-Cheol; Thorsen, Todd

    2009-07-15

    In this manuscript, we report on the culture of anaerobic and aerobic species within a disposable multilayer polydimethylsiloxane (PDMS) microfluidic device with an integrated differential oxygenator. A gas-filled microchannel network functioning as an oxygen-nitrogen mixer generates differential oxygen concentration. By controlling the relative flow rate of the oxygen and nitrogen input gases, the dissolved oxygen (DO) concentration in proximal microchannels filled with culture media are precisely regulated by molecular diffusion. Sensors consisting of an oxygen-sensitive dye embedded in the fluid channels permit dynamic fluorescence-based monitoring of the DO concentration using low-cost light-emitting diodes. To demonstrate the general utility of the platform for both aerobic and anaerobic culture, three bacteria with differential oxygen requirements (E. coli, A. viscosus, and F. nucleatum), as well as a model mammalian cell line (murine embryonic fibroblast cells (3T3)), were cultured. Growth characteristics of the selected species were analyzed as a function of eight discrete DO concentrations, ranging from 0 ppm (anaerobic) to 42 ppm (fully saturated).

  15. Analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms

    SciTech Connect

    Okabe, Satoshi; Itoh, Tsukasa; Satoh, Hisashi; Watanabe, Yoshimasa

    1999-11-01

    The vertical distribution of sulfate-reducing bacteria (SRB) in aerobic wastewater biofilms grown on rotating disk reactors was investigated by fluorescent in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes. To correlate the vertical distribution of SRB populations with their activity, the microprofiles of O{sub 2}, H{sub 2}S, NO{sub 2}{minus}, NH{sub 2}{sup +}, and pH were measured with microelectrodes. In addition, a cross-evaluation of the FISH and microelectrode analyses was performed by comparing them with culture-based approaches and biogeochemical measurements. In situ hybridization revealed that a relatively high abundance of the probe SRB385-stained cells were evenly distributed throughout the biofilm, even in the toxic surface. The probe SRB660-stained Desulfobulbus spp. were found to be numerically important members of SRB populations. The result of microelectrode measurements showed that a high sulfate-reducing activity was found in a narrow anaerobic zone located about 150 to 300 {micro}m below the biofilm surface and above which an intensive sulfide oxidation zone was found. The biogeochemical measurements showed that elemental sulfur (S{degree}) was an important intermediate of the sulfide reoxidation in such thin wastewater biofilms, which accounted for about 75% of the total S pool in the biofilm. The contribution of an internal Fe-sulfur cycle to the overall sulfur cycle in aerobic wastewater biofilms was insignificant (less than 1%) due to the relatively high sulfate reduction rate.

  16. Culturable aerobic and facultative bacteria from the gut of the polyphagic dung beetle Thorectes lusitanicus.

    PubMed

    Hernández, Noemi; Escudero, José A; San Millán, Álvaro; González-Zorn, Bruno; Lobo, Jorge M; Verdú, José R; Suárez, Mónica

    2015-04-01

    Unlike other dung beetles, the Iberian geotrupid, Thorectes lusitanicus, exhibits polyphagous behavior; for example, it is able to eat acorns, fungi, fruits, and carrion in addition to the dung of different mammals. This adaptation to digest a wider diet has physiological and developmental advantages and requires key changes in the composition and diversity of the beetle's gut microbiota. In this study, we isolated aerobic, facultative anaerobic, and aerotolerant microbiota amenable to grow in culture from the gut contents of T. lusitanicus and resolved isolate identity to the species level by sequencing 16S rRNA gene fragments. Using BLAST similarity searches and maximum likelihood phylogenetic analyses, we were able to reveal that the analyzed fraction (culturable, aerobic, facultative anaerobic, and aerotolerant) of beetle gut microbiota is dominated by the phyla Proteobacteria, Firmicutes, and Actinobacteria. Among Proteobacteria, members of the order Enterobacteriales (Gammaproteobacteria) were the most abundant. The main functions associated with the bacteria found in the gut of T. lusitanicus would likely include nitrogen fixation, denitrification, detoxification, and diverse defensive roles against pathogens.

  17. Analysis of methane monooxygenase genes in mono lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure.

    PubMed

    Lin, Ju-Ling; Joye, Samantha B; Scholten, Johannes C M; Schäfer, Hendrik; McDonald, Ian R; Murrell, J Colin

    2005-10-01

    Mono Lake is an alkaline hypersaline lake that supports high methane oxidation rates. Retrieved pmoA sequences showed a broad diversity of aerobic methane oxidizers including the type I methanotrophs Methylobacter (the dominant genus), Methylomicrobium, and Methylothermus, and the type II methanotroph Methylocystis. Stratification of Mono Lake resulted in variation of aerobic methane oxidation rates with depth. Methanotroph diversity as determined by analysis of pmoA using new denaturing gradient gel electrophoresis primers suggested that variations in methane oxidation activity may correlate with changes in methanotroph community composition.

  18. Comparison between rinse and crush-and-rub sampling for aerobic bacteria recovery from broiler hatching eggs after sanitization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study compared surface and deep eggshell aerobic bacteria recovered by rinse and crush-and-rub sampling methods for commercial hatching eggs after treatment with sanitizers. Eggs were arranged into 5 treatments consisting of No-treatment, Water, and three sanitizers. Sanitizers were Hydrogen ...

  19. Comparison between Rinse and Crush-and-Rub Sampling for Aerobic Bacteria Recovery from Hatching Eggs after Sanitization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study compared surface and deep eggshell aerobic bacteria recovered by rinse and crush-and-rub sampling methods for commercial hatching eggs after treatments with sanitizers. Eggs were arranged into 5 treatments consisting of three sanitizers, Water, and No-treatment. Sanitizers were Hydrogen...

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    -containing atmosphere at 37 °C. The isolates grow at a pH range of 3.5 to 8 and temperatures of 18-45 °C, and consume 160 nmol of CH4 h-1 mL-1 of culture. Soils from Favara Grande showed the largest diversity of methanotrophic bacteria detected until now in a geothermal soil. While methanotrophic Verrucomicrobia are reported as dominating 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.

  1. Acidophilic Methanotrophic Communities from Sphagnum Peat Bogs

    PubMed Central

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

    1998-01-01

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

  2. Growth of Aerobic Ripening Bacteria at the Cheese Surface Is Limited by the Availability of Iron

    PubMed Central

    Back, Alexandre; Irlinger, Françoise

    2012-01-01

    The microflora on the surface of smear-ripened cheeses is composed of various species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. The objective of the present study was to show that iron availability is a limiting factor in the growth of typical aerobic ripening bacteria in cheese. For that purpose, we investigated the effect of iron or siderophore addition in model cheeses that were coinoculated with a yeast and a ripening bacterium. Both iron and the siderophore desferrioxamine B stimulated the growth of ripening bacteria belonging to the genera Arthrobacter, Corynebacterium, and Brevibacterium. The extent of stimulation was strain dependent, and generally, the effect of desferrioxamine B was greater than that of iron. Measurements of the expression of genes related to the metabolism of iron by Arthrobacter arilaitensis Re117 by real-time reverse transcription-PCR showed that these genes were transcribed during growth in cheese. The addition of desferrioxamine B increased the expression of two genes encoding iron-siderophore ABC transport binding proteins. The addition of iron decreased the expression of siderophore biosynthesis genes and of part of the genes encoding iron-siderophore ABC transport components. It was concluded that iron availability is a limiting factor in the growth of typical cheese surface bacteria. The selection of strains with efficient iron acquisition systems may be useful for the development of defined-strain surface cultures. Furthermore, the importance of iron metabolism in the microbial ecology of cheeses should be investigated since it may result in positive or negative microbial interactions. PMID:22367081

  3. Growth of aerobic ripening bacteria at the cheese surface is limited by the availability of iron.

    PubMed

    Monnet, Christophe; Back, Alexandre; Irlinger, Françoise

    2012-05-01

    The microflora on the surface of smear-ripened cheeses is composed of various species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. The objective of the present study was to show that iron availability is a limiting factor in the growth of typical aerobic ripening bacteria in cheese. For that purpose, we investigated the effect of iron or siderophore addition in model cheeses that were coinoculated with a yeast and a ripening bacterium. Both iron and the siderophore desferrioxamine B stimulated the growth of ripening bacteria belonging to the genera Arthrobacter, Corynebacterium, and Brevibacterium. The extent of stimulation was strain dependent, and generally, the effect of desferrioxamine B was greater than that of iron. Measurements of the expression of genes related to the metabolism of iron by Arthrobacter arilaitensis Re117 by real-time reverse transcription-PCR showed that these genes were transcribed during growth in cheese. The addition of desferrioxamine B increased the expression of two genes encoding iron-siderophore ABC transport binding proteins. The addition of iron decreased the expression of siderophore biosynthesis genes and of part of the genes encoding iron-siderophore ABC transport components. It was concluded that iron availability is a limiting factor in the growth of typical cheese surface bacteria. The selection of strains with efficient iron acquisition systems may be useful for the development of defined-strain surface cultures. Furthermore, the importance of iron metabolism in the microbial ecology of cheeses should be investigated since it may result in positive or negative microbial interactions.

  4. Electroporation-Based Genetic Manipulation in Type I Methanotrophs

    PubMed Central

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

    2016-01-01

    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

  5. An initial investigation into the ecology of culturable aerobic postmortem bacteria.

    PubMed

    Chun, Lauren P; Miguel, Marcus J; Junkins, Emily N; Forbes, Shari L; Carter, David O

    2015-12-01

    Postmortem microorganisms are increasingly recognized for their potential to serve as physical evidence. Yet, we still understand little about the ecology of postmortem microbes, particularly those associated with the skin and larval masses. We conducted an experiment to characterize microbiological and chemical properties of decomposing swine (Sus scrofa domesticus) carcasses on the island of Oahu, Hawaii, USA, during June 2013. Bacteria were collected from the head, limb, and larval mass during the initial 145h of decomposition. We also measured the pH, temperature, and oxidation-reduction potential of larval masses in situ. Bacteria were cultured aerobically on Standard Nutrient Agar at 22°C and identified using protein or genetic signals. Carcass decomposition followed a typical sigmoidal pattern and associated bacterial communities differed by sampling location and time since death, although all communities were dominated by phyla Actinobacteria, Firmicutes, and Proteobacteria. Larval masses were reducing environments (~-200mV) of neutral pH (6.5-7.5) and high temperature (35°C-40°C). We recommend that culturable postmortem and larval mass microbiology and chemistry be investigated in more detail, as it has potential to complement culture-independent studies and serve as a rapid estimate of PMI.

  6. Reducing time to identification of aerobic bacteria and fastidious micro-organisms in positive blood cultures.

    PubMed

    Intra, J; Sala, M R; Falbo, R; Cappellini, F; Brambilla, P

    2016-12-01

    Rapid and early identification of micro-organisms in blood has a key role in the diagnosis of a febrile patient, in particular, in guiding the clinician to define the correct antibiotic therapy. This study presents a simple and very fast method with high performances for identifying bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after only 4 h of incubation. We used early bacterial growth on PolyViteX chocolate agar plates inoculated with five drops of blood-broth medium deposited in the same point and spread with a sterile loop, followed by a direct transfer procedure on MALDI-TOF MS target slides without additional modification. Ninety-nine percentage of aerobic bacteria were correctly identified from 600 monomicrobial-positive blood cultures. This procedure allowed obtaining the correct identification of fastidious pathogens, such as Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae that need complex nutritional and environmental requirements in order to grow. Compared to the traditional pathogen identification from blood cultures that takes over 24 h, the reliability of results, rapid performance and suitability of this protocol allowed a more rapid administration of optimal antimicrobial treatment in the patients.

  7. Acetic acid production from food wastes using yeast and acetic acid bacteria micro-aerobic fermentation.

    PubMed

    Li, Yang; He, Dongwei; Niu, Dongjie; Zhao, Youcai

    2015-05-01

    In this study, yeast and acetic acid bacteria strains were adopted to enhance the ethanol-type fermentation resulting to a volatile fatty acids yield of 30.22 g/L, and improve acetic acid production to 25.88 g/L, with food wastes as substrate. In contrast, only 12.81 g/L acetic acid can be obtained in the absence of strains. The parameters such as pH, oxidation reduction potential and volatile fatty acids were tested and the microbial diversity of different strains and activity of hydrolytic ferment were investigated to reveal the mechanism. The optimum pH and oxidation reduction potential for the acetic acid production were determined to be at 3.0-3.5 and -500 mV, respectively. Yeast can convert organic matters into ethanol, which is used by acetic acid bacteria to convert the organic wastes into acetic acid. The acetic acid thus obtained from food wastes micro-aerobic fermentation liquid could be extracted by distillation to get high-pure acetic acid.

  8. Space agriculture for habitation on Mars with hyper-thermophilic aerobic composting bacteria

    NASA Astrophysics Data System (ADS)

    Space Agriculture Task Force; Ishikawa, Y.; Tomita-Yokotani, K.; Hashimoto, H.; Kitaya, Y.; Yamashita, M.; Nagatomo, M.; Oshima, T.; Wada, H.

    Manned Mars exploration, especially for extended periods of time, will require recycle of materials to support human life. Here, a conceptual design is developed for a Martian agricultural system driven by biologically regenerative functions. One of the core biotechnologies function is the use of hyper-thermophilic aerobic composting bacterial ecology. These thermophilic bacteria can play an important role in increasing the effectiveness of the processing of human metabolic waste and inedible biomass and of converting them to fertilizer for the cultivation of plants. This microbial technology has been already well established for the purpose of processing sewage and waste materials for small local communities in Japan. One of the characteristics of the technology is that the metabolic heat release that occurs during bacterial fermentation raises the processing temperature sufficiently high at 80 100 °C to support hyper-thermophilic bacteria. Such a hyper-thermophilic system is found to have great capability of decomposing wastes including even their normally recalcitrant components, in a reasonably short period of time and of providing a better quality of fertilizer as an end-product. High quality compost has been shown to be a key element in creating a healthy regenerative food production system. In ground-based studies, the soil microbial ecology after the addition of high quality compost was shown to improve plant growth and promote a healthy symbiosis of arbuscular mycorrhizal fungi. Another advantage of such high processing temperature is the ability to sterilize the pathogenic organisms through the fermentation process and thus to secure the hygienic safety of the system. Plant cultivation is one of the other major systems. It should fully utilize solar energy received on the Martian surface for supplying energy for photosynthesis. Subsurface water and atmospheric carbon dioxide mined on Mars should be also used in the plant cultivation system. Oxygen and

  9. Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere

    PubMed Central

    Stiefel, Philipp; Zambelli, Tomaso

    2013-01-01

    In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria in situ, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources. PMID:23770907

  10. Safety assessment of dairy microorganisms: aerobic coryneform bacteria isolated from the surface of smear-ripened cheeses.

    PubMed

    Denis, Catherine; Irlinger, Françoise

    2008-09-01

    The group of "coryneform bacteria" belongs to the class of Actinobacteria including a diverse and heterogeneous collection of bacteria of various genera. Most of them are known as environmental residents and/or commensal flora of humans and they are isolated frequently in clinical studies. Actinobacteria include also several aerobic species, present at the surface of smear-ripened cheeses for decades and used as ripening culture in the dairy industry. Their clinical significance is controversial because an easy combination of phenotypic and molecular methods to characterize Actinobacteria at the species level is still lacking. A bibliographical survey was conducted to assess the safety status of Actinobacteria species used as starter culture in fermented dairy foods, according to their technological interest. Aerobic coryneform bacteria isolated from smear-ripened cheeses are most commonly recovered from soil, the environment or food. To date, no clinical infection or food toxi-infection related to smear cheese coryneform bacteria ingestion has been reported. From a taxonomic viewpoint, dairy species are distant from the reference species associated with known pathologies. From a physiological viewpoint, cheese smear coryneform bacteria appear to be related to particular ecological niches: they are all oxidative species, and most are psychrotrophic and unable to grow at 37 degrees C whereas medically relevant coryneform bacteria are facultative anaerobes and grow at 35-37 degrees C. Consequently, technological strains must be selected according to taxonomic criteria (nonpathogenic species) and ecological criteria.

  11. Organic osmolytes in aerobic bacteria from mono lake, an alkaline, moderately hypersaline environment.

    PubMed

    Ciulla, R A; Diaz, M R; Taylor, B F; Roberts, M F

    1997-01-01

    The identity and concentrations of intracellular organic solutes were determined by nuclear magnetic resonance spectroscopy for two strains of aerobic, gram-negative bacteria isolated from Mono Lake, Calif., an alkaline, moderately hypersaline lake. Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was the major endogenous solute in both organisms. Concentrations of ectoine varied with external NaCl levels in strain ML-D but not in strain ML-G, where the level was high but invariant from 1.5 to 3.0 M NaCl. Hydroxyectoine also occurred in strain ML-D, especially at elevated NaCl concentrations (2.5 and 3.0 M), but at levels lower than those of ectoine. Exogenous organic solutes that might occur in Mono Lake were examined for their effects on the de novo synthesis of ectoine. Dimethylsulfoniopropionate (DMSP) (0.1 or 1 mM) did not significantly lower ectoine levels in either isolate, and only strain ML-G showed any capacity for DMSP accumulation. With nitrogen limitation, however, DMSP (0.1 mM) substituted for ectoine in strain ML-G and became the main organic solute. Glycine betaine (GB) was more effective than DMSP in affecting ectoine levels, principally in strain ML-D. Strain ML-D accumulated GB to 50 or 67% of its organic solute pool at 2.5 M NaCl, at an external level of 0.1 or 1 mM GB, respectively. Strain ML-D also accumulated arsenobetaine. The methylated zwitterionic compounds, probably metabolic products of phytoplankton (DMSP and GB) or brine shrimps (arsenobetaine) in Mono Lake, may function as osmolytes for indigenous bacteria when present at high concentrations or under conditions of nitrogen limitation or salt stress.

  12. Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia.

    PubMed

    Bibiloni-Isaksson, Jaime; Seymour, Justin R; Ingleton, Tim; van de Kamp, Jodie; Bodrossy, Levente; Brown, Mark V

    2016-12-01

    Aerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 10(2) to 1.4 × 10(5) ml(-1) and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter-clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.

  13. Effects of exogenous aerobic bacteria on methane production and biodegradation of municipal solid waste in bioreactors.

    PubMed

    Ge, Sai; Liu, Lei; Xue, Qiang; Yuan, Zhiming

    2016-09-01

    Landfill is the most common and efficient ways of municipal solid waste (MSW) disposal and the landfill biogas, mostly methane, is currently utilized to generate electricity and heat. The aim of this work is to study the effects and the role of exogenous aerobic bacteria mixture (EABM) on methane production and biodegradation of MSW in bioreactors. The results showed that the addition of EABM could effectively enhance hydrolysis and acidogenesis processes of MSW degradation, resulting in 63.95% reduction of volatile solid (VS), the highest methane production rate (89.83Lkg(-1) organic matter) ever recorded and a threefold increase in accumulative methane production (362.9L) than the control (127.1L). In addition, it is demonstrated that white-rot fungi (WRF) might further promote the methane production through highly decomposing lignin, but the lower pH value in leachate and longer acidogenesis duration may cause methane production reduced. The data demonstrated that methane production and biodegradation of MSW in bioreactors could be significantly enhanced by EABM via enhanced hydrolysis and acidogenesis processes, and the results are of great economic importance for the future design and management of landfill.

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

    NASA Astrophysics Data System (ADS)

    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

  15. Characterization of aerobic spore-forming bacteria associated with industrial dairy processing environments and product spoilage.

    PubMed

    Lücking, Genia; Stoeckel, Marina; Atamer, Zeynep; Hinrichs, Jörg; Ehling-Schulz, Monika

    2013-09-02

    Due to changes in the design of industrial food processing and increasing international trade, highly thermoresistant spore-forming bacteria are an emerging problem in food production. Minimally processed foods and products with extended shelf life, such as milk products, are at special risk for contamination and subsequent product damages, but information about origin and food quality related properties of highly heat-resistant spore-formers is still limited. Therefore, the aim of this study was to determine the biodiversity, heat resistance, and food quality and safety affecting characteristics of aerobic spore-formers in the dairy sector. Thus, a comprehensive panel of strains (n=467), which originated from dairy processing environments, raw materials and processed foods, was compiled. The set included isolates associated with recent food spoilage cases and product damages as well as isolates not linked to product spoilage. Identification of the isolates by means of Fourier-transform infrared spectroscopy and molecular methods revealed a large biodiversity of spore-formers, especially among the spoilage associated isolates. These could be assigned to 43 species, representing 11 genera, with Bacillus cereus s.l. and Bacillus licheniformis being predominant. A screening for isolates forming thermoresistant spores (TRS, surviving 100°C, 20 min) showed that about one third of the tested spore-formers was heat-resistant, with Bacillus subtilis and Geobacillus stearothermophilus being the prevalent species. Strains producing highly thermoresistant spores (HTRS, surviving 125°C, 30 min) were found among mesophilic as well as among thermophilic species. B. subtilis and Bacillus amyloliquefaciens were dominating the group of mesophilic HTRS, while Bacillus smithii and Geobacillus pallidus were dominating the group of thermophilic HTRS. Analysis of spoilage-related enzymes of the TRS isolates showed that mesophilic strains, belonging to the B. subtilis and B. cereus

  16. [Biosynthesis of the bioprotectant ectoin by aerobic methylotrophic bacteria from methanol].

    PubMed

    Doronina, N V; Ezhov, V A; Beschastnyĭ, A P; Trotsenko, Iu A

    2010-01-01

    It is shown that neutrophilic methylobacteria Methylophaga thalassica and M. marina have higher rates of growth and ectoin accumulation compared to the haloalkaliphilic species M. alcalica and M. natronia and methanotrophs Methylomicrobium alcaliphilum and M. kenyense. The conditions of M. thalassica cultivation in methanol-containing medium were optimized. The yield of this process reached 60 g/l of absolutely dry biomass containing 15-19% (9-11 g/l) ectoine. The scheme of ectoin isolation from the biomass by extraction and subsequent purification, which allowed obtaining preparations of different degree of purity, was developed.

  17. Symbioses of methanotrophs and deep-sea mussels (Mytilidae: Bathymodiolinae).

    PubMed

    DeChaine, Eric G; Cavanaugh, Colleen M

    2006-01-01

    The symbioses between invertebrates and chemosynthetic bacteria allow both host and symbiont to colonize and thrive in otherwise inhospitable deep-sea habitats. Given the global distribution of the bathymodioline symbioses, this association is an excellent model for evaluating co-speciation and evolution of symbioses. Thus far, the methanotroph and chemoautotroph endosymbionts of mussels are tightly clustered within two independent clades of gamma Proteobacteria, respectively. Further physiological and genomic studies will elucidate the ecological and evolutionary roles that these bacterial clades play in the symbiosis and chemosynthetic community. Due to the overall abundance of the methanotrophic symbioses at hydrothermal vents and hydrocarbon seeps, they likely play a significant, but as of yet unquantified, role in the biogeochemical cycling of methane. With this in mind, the search for methanotrophic symbioses should not be restricted to these known deep-sea habitats, but rather should be expanded to include methane-rich coastal marine and freshwater environments inhabited by methanotrophs and bivalves. Our current understanding of the bathymodioline symbioses provides a strong foundation for future explorations into the origin, ecology, and evolution of methanotroph symbioses, which are now becoming possible through a combination of classical and advanced molecular techniques.

  18. Comparison between rinse and crush-and-rub sampling for aerobic bacteria recovery from broiler hatching eggs after sanitization.

    PubMed

    Spickler, J L; Buhr, R J; Cox, N A; Bourassa, D V; Rigsby, L L

    2011-07-01

    This study compared surface and deep eggshell aerobic bacteria recovered by the rinse and crush-and-rub sampling methods for commercial hatching eggs after treatment with sanitizers. Eggs were arranged into 5 treatments consisting of no treatment, water, and 3 sanitizers. The sanitizers were H(2)O(2), phenol, and Q(4)B (a compound chemical containing 4 quaternary ammoniums and 1 biguanide moiety). Eggs were sprayed according to treatment and allowed to dry for 1 h before sampling. To collect samples for the eggshell rinse, each egg was massaged in a plastic bag with 20 mL of saline. Eggshells were then aseptically opened and their contents were discarded before being individually crushed into 50-mL centrifuge tubes containing 20 mL of saline. Aerobic bacteria were enumerated on Petrifilm after 48 h of incubation at 37°C. Aerobic bacteria recovered (log(10) cfu/mL) from the eggshell rinse were highest and similar for the no-treatment (4.0) and water (3.7) groups, lower for the phenol (3.2) and H(2)O(2) (3.1) groups, and lowest for the Q(4)B (2.4) group. Aerobic bacteria levels with the crush-and-rub method were similar for the no-treatment (2.5) and water (2.3) groups, lower for the phenol (1.6) group, intermediate for the H(2)O(2) (1.2) group, and lowest for the Q(4)B (0.9) group. The overall correlation between the rinse and crush-and-rub sampling methods for individual egg aerobic bacteria counts was r = 0.71. The correlation within each treatment revealed the following r values: no treatment, 0.55; water, 0.72; H(2)O(2), 0.67; phenol, 0.73; and Q(4)B, 0.38. A second experiment was designed to further examine the lower aerobic bacterial levels recovered by the crush-and-rub method (for previously rinsed eggs) than the levels recovered in the initial eggshell rinse sample. Eggs were either rinsed and then crushed and rubbed, or they were only crushed and rubbed without a prior rinse. Results confirmed a significant decrease (1.5 log(10) cfu/mL) in bacteria levels

  19. Dynamics of phosphorus and phytate-utilizing bacteria during aerobic degradation of dairy cattle dung.

    PubMed

    Fuentes, Bárbara; Jorquera, Milko; Mora, María de la Luz

    2009-01-01

    During organic wastes degradation, P is transformed which may affect its availability. In this study, the dynamics of P and the occurrence of phytate-utilizing bacteria (PUB) were evaluated during aerobic degradation of dairy cattle dung in laboratory-scale reactors for 105 d. The results showed an increase of water-soluble inorganic P (Pi) (from 570 to 1890 mg kg(-1)) and biomass P (from 390 to 870 mg kg(-1)) during the initial 40 d. After this period, water-soluble Pi remained constant (around 1500 mg kg(-1)) and biomass P decreased (around 220 mg kg(-1)) probably due to the decrease of easily available C in dung. Under the acidic conditions in the first 20 d there was an increase in concentration of Al (25 mg kg(-1)) and Fe (27 mg kg(-1)) ions. These ions were no longer detectable in the alkaline conditions occurring after 40 d. In the same period, the Ca concentration increased (from 1170 to 2370 mg kg(-1)) and chemical speciation revealed permanent association of Ca ions with Pi. Sequential P fractionation showed a decrease of organic P in NaHCO(3), NaOH and HCl fractions and an increase of residual P (25-52% with respect to total P). Analysis by (31)P NMR also showed a decrease (from 14% to 1.6%) of phytic acid content during final experimental period (60 and 105 d). The bacteriological analysis revealed various PUB involved in degradation of the dung. Two morphotypes, genetically characterized as Enterobacter and Rahnella, which were dominant under higher content of residual P, showed strong utilization of phytate in vitro.

  20. Aerobic spore-forming bacteria for assessing quality of drinking water produced from surface water.

    PubMed

    Mazoua, Stephane; Chauveheid, Eric

    2005-12-01

    Cryptosporidium and Giardia represent a major microbiological issue for drinking water production from surface water. As their monitoring through a treatment process is rather tedious and as low-concentration goals should be reached for drinking water, aerobic spore-forming bacteria (ASFB) have been studied as an indicator microorganism for a drinking water treatment plant using surface water. The results reveal that monitoring naturally occurring ASFB better highlights daily achievable performances and identifies unusual process events for global disinfection, for both physical and chemical treatment steps in a multi-barrier drinking water treatment plant. Advantages of ASFB over usual process parameters are that these microorganisms are more sensitive to process fluctuations. The use of ASFB also showed that the efficiency of ozone disinfection is not as significantly influenced by the water temperature as reported, despite similar or higher CT values applied during warmer periods. Thus, the disinfection of resistant microorganisms with ozone can also be an efficient process at lower water temperature. ASFB have been shown to be a conservative indicator for Cryptosporidium and Giardia up to a 1st stage filtration and the ASFB Log removals can be used to estimate Log removals for Cryptosporidium and Giardia: compared to ASFB, the Log removals for Cryptosporidium or Giardia are at least equal or 50% higher, respectively. Thus, the monitoring of ASFB along a drinking water treatment process could be a useful tool for performing risk analysis for parasites such as Cryptosporidium and Giardia, and would further allow integration of daily variability into a risk analysis.

  1. Organic osmolytes in aerobic bacteria from Mono Lake, an alkaline, moderately hypersaline environment

    SciTech Connect

    Ciulla, R.A.; Roberts, M.F.; Diaz, M.R.; Taylor, B.F.

    1997-01-01

    The identity and concentrations of intracellular organic solutes were determined by nuclear magnetic resonance spectroscopy for two strains of aerobic, gram-negative bacteria isolated from Mono Lake, California, an alkaline, moderately hypersaline lake. Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was the major endogenous solute in both organisms. Concentrations of ectoine varied with external NaCl levels in strain ML-D but not in strain ML-G, where the level was high but invariant from 1.5 to 3.0 M NaCl. Hydroxyectoine also occurred in strain ML-D, especially at elevated NaCl concentrations (2.5 and 3.0 M), but at levels lower than those of ectoine. Exogenous organic solutes that might occur in Mono Lake were examined for their effects on the de novo synthesis of ectoine. Dimethylsulfoniopropionate (DMSP) (0.1 or 1 mM) did not significantly lower ectoine levels in either isolate, and only strain ML-G showed any capacity for DMSP accumulation. With nitrogen limitation, however, DMSP (0.1 mM) substituted for ectoine in strain ML-G showed any capacity for DMSP accumulation. With nitrogen limitation, however, DMSP (0.1 mM) substituted for ectoine in strain ML-G and became the main organic solute. Glycine betaine (GB) was more effective than DMSP in affecting ectoine levels, principally in strain ML-D. Strain ML-D accumulated GB to 50 or 67% of its organic solute pool at 2.5 M NaCl, at an external level of 0.1 or 1 mM GB, respectively. Strain ML-D also accumulated arsenobetaine. The methylated zwitterionic compounds, probably metabolic products of phytoplankton (DMSP and GB) or brine shrimps (arsenobetaine) in Mono Lake, may function as osmolytes for indigenous bacteria when present at high concentrations or under conditions of nitrogen limitation or salt stress. 33 refs., 5 figs., 2 tabs.

  2. Selective grazing of methanotrophs by protozoa in a rice field soil.

    PubMed

    Murase, Jun; Frenzel, Peter

    2008-09-01

    Biological methane oxidation is a key process in the methane cycle of wetland ecosystems. The methanotrophic biomass may be grazed by protozoa, thus linking the methane cycle to the soil microbial food web. In the present study, the edibility of different methanotrophs for soil protozoa was compared. The number of methanotroph-feeding protozoa in a rice field soil was estimated by determining the most-probable number (MPN) using methanotrophs as food bacteria; naked amoebae and flagellates were the dominant protozoa. Among ten methanotrophic strains examined as a food source, seven yielded a number of protozoa comparable with the yield with Escherichia coli [10(4) MPN (g soil dry weight)(-1)], and three out of four Methylocystis spp. yielded significantly fewer numbers [10(2)-10(3) MPN (g soil dry weight)(-1)]. The lower edibility of the Methylocystis spp. was not explained either by their growth phase or by harmful effects on protozoa. Incubation of the soil under methane resulted in a higher number of protozoa actively grazing on methanotrophs, especially on the less-edible group. Protozoa isolated from the soil demonstrated a grazing preference on the different methanotrophs consistent with the results of MPN counts. The results indicate that selective grazing by protozoa may be a biological factor affecting the methanotrophic community in a wetland soil.

  3. Preferential Use of Carbon Sources in Culturable Aerobic Mesophilic Bacteria of Coptotermes curvignathus's (Isoptera: Rhinotermitidae) Gut and Its Foraging Area.

    PubMed

    Wong, W Z; H'ng, P S; Chin, K L; Sajap, Ahmad Said; Tan, G H; Paridah, M T; Othman, Soni; Chai, E W; Go, W Z

    2015-10-01

    The lower termite, Coptotermes curvignathus, is one of the most prominent plantation pests that feed upon, digest, and receive nourishment from exclusive lignocellulose diets. The objective of this study was to examine the utilization of sole carbon sources by isolated culturable aerobic bacteria among communities from the gut and foraging pathway of C. curvignathus. We study the bacteria occurrence from the gut of C. curvignathus and its surrounding feeding area by comparing the obtained phenotypic fingerprint with Biolog's extensive species library. A total of 24 bacteria have been identified mainly from the family Enterobacteriaceae from the identification of Biolog Gen III. Overall, the bacteria species in the termite gut differ from those of foraging pathway within a location, except Acintobacter baumannii, which was the only bacteria species found in both habitats. Although termites from a different study area do not have the same species of bacteria in the gut, they do have a bacterial community with similar role in degrading certain carbon sources. Sugars were preferential in termite gut isolates, while nitrogen carbon sources were preferential in foraging pathway isolates. The preferential use of specific carbon sources by these two bacterial communities reflects the role of bacteria for regulation of carbon metabolism in the termite gut and foraging pathway.

  4. Effectiveness of Active Packaging on Control of Escherichia Coli O157:H7 and Total Aerobic Bacteria on Iceberg Lettuce.

    PubMed

    Lu, Haixia; Zhu, Junli; Li, Jianrong; Chen, Jinru

    2015-06-01

    Contaminated leafy green vegetables have been linked to several outbreaks of human gastrointestinal infections. Antimicrobial interventions that are adoptable by the fresh produce industry for control of pathogen contamination are in great demand. This study was undertaken to evaluate the efficacy of sustained active packaging on control of Escherichia coli O157:H7 and total aerobic bacteria on lettuce. Commercial Iceberg lettuce was inoculated with a 3-strain mixture of E. coli O157:H7 at 10(2) or 10(4) CFU/g. The contaminated lettuce and un-inoculated controls were placed respectively in 5 different active packaging structures. Traditional, nonactive packaging structure was included as controls. Packaged lettuce was stored at 4, 10, or 22 °C for 3 wk and sampled weekly for the population of E. coli O157:H7 and total aerobic bacteria. Results showed that packaging structures with ClO2 generator, CO2 generator, or one of the O2 scavengers effectively controlled the growth of E. coli O157:H7 and total aerobic bacteria under all storage conditions. Packaging structure with the ClO2 generator was most effective and no E. coli O157:H7 was detected in samples packaged in this structure except for those that were inoculated with 4 log CFU/g of E. coli O157:H7 and stored at 22 °C. Packaging structures with an oxygen scavenger and the allyl isothiocyanate generator were mostly ineffective in control of the growth of the bacteria on Iceberg lettuce. The research suggests that some of the packaging structures evaluated in the study can be used to control the presence of foodborne pathogens on leafy green vegetables.

  5. Determinative factors of competitive advantage between aerobic bacteria for niches at the air-liquid interface.

    PubMed

    Yamamoto, Kyosuke; Haruta, Shin; Kato, Souichiro; Ishii, Masaharu; Igarashi, Yasuo

    2010-01-01

    We focused on bacterial interspecies relationships at the air-liquid interface where the formation of pellicles by aerobes was observed. Although an obligate aerobe (Brevibacillus sp. M1-5) was initially dominant in the pellicle population, a facultative aerobe (Pseudoxanthomonas sp. M1-3) emerged and the viability of M1-5 rapidly decreased due to severe competition for oxygen. Supplementation of the medium with carbohydrates allowed the two species to coexist at the air-liquid interface. These results indicate that the population dynamics within pellicles are primarily governed by oxygen utilization which was affected by a combination of carbon sources.

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

    PubMed Central

    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 cloned component B gene as probe, methanotroph types I, II, and X and environmental and bioreactor samples were screened for the presence of the gene encoding soluble MMO. Fragments produced by digestion of DNA with rare cutting restriction endonucleases were separated by pulsed-field gel electrophoresis and transferred to Zeta-Probe membrane (Bio-Rad) for Southern blot analysis. Samples were also analyzed for the presence of soluble MMO by Western blot analysis and the ability to degrade TCE. The physiological groups of methanotrophs in each sample were determined by hybridizing cells with fluorescence-labelled signature probes. Among twelve pure or mixed cultures, DNA fragments of seven methanotrophs hybridized with the soluble MMO B gene probe. When grown in media with limited copper, all of these bacteria degraded TCE. All of them are type II methanotrophs. The soluble MMO component B gene of the type X methanotroph, Methylococcus capsulatus Bath, did not hybridize to the M. trichosporium OB3b soluble MMO component B gene probe, although M. capsulatus Bath also produces a soluble MMO. Images PMID:1349468

  7. Characterization of Two New Facultative Methanotrophs

    PubMed Central

    Lynch, Martha J.; Wopat, Ann E.; O'Connor, Mary L.

    1980-01-01

    Two new facultative methane-oxidizing bacteria have been isolated from lake water enrichments. The organisms have been characterized in terms of colony types, growth characteristics, the guanine plus cytosine content of their deoxyribonucleic acid, thin sections, oxidation rates, and carbon assimilation pathways. Methane-grown cells of both organisms contained intracytoplasmic membranes similar to those described as type II in other methanotrophic bacteria. Neither organism had such membranes when grown heterotrophically. Both organisms assimilated methane by way of the isocitrate lyase-negative serine pathway for formaldehyde incorporation. The enzymes of this pathway were high in specific activity in cells grown on methane and were at low levels in cells grown either on heterotrophic substrates or on heterotrophic substrates plus methane. It is proposed that both organisms be classified in the genus Methylobacterium as two new species, Methylobacterium ethanolicum and Methylobacterium hypolimneticum. Images PMID:16345617

  8. Effect of linear alkylbenzene sulfonates on the growth of aerobic heterotrophic cultivable bacteria isolated from an agricultural soil.

    PubMed

    Sánchez-Peinado, María del Mar; González-López, Jesús; Rodelas, Belén; Galera, Vanesa; Pozo, Clementina; Martínez-Toledo, María Victoria

    2008-08-01

    An enrichment culture technique was used to isolate soil bacteria capable of growing in the presence of two different concentrations of linear alkylbenzene sulfonates (LAS) (10 and 500 microg ml(-1)). Nine bacterial strains, representatives of the major colony types of aerobic heterotrophic cultivable bacteria in the enriched samples, were isolated and subsequently identified by PCR-amplification and partial sequencing of the 16S rRNA gene. Amongst the isolates, strains LAS05 (Pseudomonas syringae), LAS06 (Staphylococcus epidermidis), LAS07 (Delftia tsuruhatensis), LAS08 (Staphylococcus epidermidis) and LAS09 (Enterobacter aerogenes), were able to grow in pure culture in dialysed soil media amended with LAS (50 microg ml(-1)). The three Gram-negative strains grew to higher cell numbers in the presence of 50 microg ml(-1) of LAS, compared to LAS-unamended dialysed soil medium, and were selected for further testing of their ability to use LAS as carbon source. However, HPLC analysis of culture supernatants showed that the three strains can tolerate but not degrade LAS when grown in pure cultures. A higher concentration of soluble phosphates was recorded in dialysed soil media amended with LAS (50 microg ml(-1)) compared to unamended control media, suggesting an effect of the surfactant that enhanced the bioavailability of P from soil. The presence of LAS at a concentration of 50 microg ml(-1) had an important impact on growth of selected aerobic heterotrophic soil bacteria, a deleterious effect which may be relevant for the normal function and evolution of agricultural soil.

  9. Survival, injury and inactivation of Escherichia coli 0157:H7, salmonella and aerobic mesophilic bacteria in apple juice and cider amended with nisin-edta

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For health reasons, people are consuming fresh juices or minimally processed fruit and vegetable juices, thereby, exposing themselves to the risk of foodborne illness if such juices are contaminated with bacteria pathogens. Behavior of aerobic mesophilic bacteria, Escherichia coli O157:H7 and Salmon...

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

    PubMed

    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, and uses methane only for energy generation. As a result, techniques used to detect methanotrophs in the environment such as (13)CH(4)-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 labeling with (13)CO(2) and (13)CH(4), individually and in combination. Testing the protocol in "M. infernorum" strain V4 resulted in assimilation of (13)CO(2) but not (13)CH(4), verifying its autotrophic lifestyle. To specifically detect methanotrophs (as opposed to other autotrophs) via (13)CO(2)-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 (13)CH(4) + (12)CO(2) caused little shift in the density distribution of verrucomicrobial-pmoA genes relative to controls. However, labeling with (13)CO(2) in combination with (12)CH(4) or (13)CH(4) 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

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

    PubMed Central

    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, 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 labeling 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, labeling 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. PMID

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

    PubMed

    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.

  13. Application of Potential Phosphate-Solubilizing Bacteria and Organic Acids on Phosphate Solubilization from Phosphate Rock in Aerobic Rice

    PubMed Central

    Jusop, Shamshuddin; Naher, Umme Aminun; Othman, Radziah; Razi, Mohd Ismail

    2013-01-01

    A study was conducted at Universiti Putra Malaysia to determine the effect of phosphate-solubilizing bacteria (PSB) and organic acids (oxalic & malic) on phosphate (P) solubilization from phosphate rock (PR) and growth of aerobic rice. Four rates of each organic acid (0, 10, 20, and 30 mM), and PSB strain (Bacillus sp.) were applied to aerobic rice. Total bacterial populations, amount of P solubilization, P uptake, soil pH, and root morphology were determined. The results of the study showed significantly high P solubilization in PSB with organic acid treatments. Among the two organic acids, oxalic acid was found more effective compared to malic acid. Application of oxalic acid at 20 mM along with PSB16 significantly increased soluble soil P (28.39 mg kg−1), plant P uptake (0.78 P pot−1), and plant biomass (33.26 mg). Addition of organic acids with PSB and PR had no influence on soil pH during the planting period. A higher bacterial population was found in rhizosphere (8.78 log10 cfu g−1) compared to the nonrhizosphere and endosphere regions. The application of organic acids along with PSB enhanced soluble P in the soil solution, improved root growth, and increased plant biomass of aerobic rice seedlings without affecting soil pH. PMID:24288473

  14. A survey of culturable aerobic and anaerobic marine bacteria in de novo biofilm formation on natural substrates in St. Andrews Bay, Scotland.

    PubMed

    Finnegan, Lucy; Garcia-Melgares, Manuel; Gmerek, Tomasz; Huddleston, W Ryan; Palmer, Alexander; Robertson, Andrew; Shapiro, Sarah; Unkles, Shiela E

    2011-10-01

    This study reports a novel study of marine biofilm formation comprising aerobic and anaerobic bacteria. Samples of quartz and feldspar, minerals commonly found on the earth, were suspended 5 m deep in the North Sea off the east coast of St. Andrews, Scotland for 5 weeks. The assemblage of organisms attached to these stones was cultivated under aerobic and anaerobic conditions in the laboratory. Bacteria isolated on Marine Agar 2216 were all Gram-negative and identified to genus level by sequencing the gene encoding 16S rRNA. Colwellia, Maribacter, Pseudoaltermonas and Shewanella were observed in aerobically-grown cultures while Vibrio was found to be present in both aerobic and anaerobic cultures. The obligate anaerobic bacterium Psychrilyobacter atlanticus, a recently defined genus, was identified as a close relative of isolates grown anaerobically. The results provide valuable information as to the main players that attach and form de novo biofilms on common minerals in sea water.

  15. Validation of the Peel Plate™ AC for Detection of Total Aerobic Bacteria in Dairy and Nondairy Products.

    PubMed

    Salter, Robert S; Durbin, Gregory W; Bird, Patrick; Fisher, Kiel; Crowley, Erin; Hammack, Thomas; Chen, Yi; Clark, Dorn; Ziemer, Wayne

    2016-01-01

    Peel Plate™ AC (aerobic count) is a low-profile plastic 47 mm culture dish with adhesive top that contains a dried standard plate count medium with oxidation/reduction indicator triphenyl tetrazolium chloride (TTC) that turns red with dehydrogenase enzyme activity of growing aerobic bacteria. The method provides a conventional quantitative count with simple rehydration and incubation for 48 ± 3 h at 35 ± 1°C for most food matrixes and 32 ± 1°C for 48 ± 3 h for dairy products. Dairy matrixes claimed and supported with total aerobic count data are whole milk, skim milk, chocolate milk (2% fat), light cream (20% fat), pasteurized whole goat milk, ultra-high temperature pasteurized milk, nonfat dried milk, lactose-reduced milk, strawberry milk, raw cow milk, raw goat milk, raw sheep milk, condensed skim milk, and vanilla ice cream. Food matrixes claimed for aerobic count detection are raw ground beef, environmental sponge of stainless steel, raw ground turkey, dry dog food, liquid whole pasteurized eggs, milk chocolate, poultry carcass rinse, and large animal carcass sponge. The method has been independently evaluated for aerobic count in dairy products: whole milk, skim milk, chocolate milk, and light cream. The method was also independently evaluated for aerobic count in food matrixes: ground beef and sponge rinse from stainless steel surfaces. In the matrix study, each matrix was assessed separately at each contamination level in comparison to an appropriate reference method. Colony counts were determined for each level and then log10-transformed. The transformed data were evaluated for repeatability, mean comparison between methods with 95% confidence interval (CI), and r(2). A CI range of (-0.5, 0.5) on the mean difference was used as the acceptance criterion to establish significant statistical differences between methods. The evaluations demonstrate that the Peel Plate AC provides no statistical differences across most of the matrixes with r(2) > 0

  16. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Jeanthon, C.; Boeuf, D.; Dahan, O.; Le Gall, F.; Garczarek, L.; Bendif, E. M.; Lehours, A.-C.

    2011-07-01

    Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivable fraction. In total, 54 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94 %) was affiliated to the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies between culture-based and molecular methods, this study highlights the existing gaps in the understanding

  17. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Jeanthon, C.; Boeuf, D.; Dahan, O.; Le Gall, F.; Garczarek, L.; Bendif, E. M.; Lehours, A.-C.

    2011-05-01

    Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivable fraction. In total, 52 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94%) was affiliated with the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies between culture-based and molecular methods, this study highlights the existing gaps in the understanding

  18. Inhibition of Salmonella Typhimurium by Cultures of Cecal Bacteria during Aerobic Incubation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two trials were conducted to examine the ability of cecal bacterial cultures from broilers to inhibit growth of Salmonella Typhimurium during aerobic incubation. Cecal broth media was inoculated with 10 µl of cecal contents from 6 week old broilers taken from 2 separate flocks. Cultures were incubat...

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

    PubMed Central

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

    2011-01-01

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

  20. Anaerobic methanotrophic community of a 5346-m-deep vesicomyid clam colony in the Japan Trench.

    PubMed

    Felden, J; Ruff, S E; Ertefai, T; Inagaki, F; Hinrichs, K-U; Wenzhöfer, F

    2014-05-01

    Vesicomyidae clams harbor sulfide-oxidizing endosymbionts and are typical members of cold seep communities where active venting of fluids and gases takes place. We investigated the central biogeochemical processes that supported a vesicomyid clam colony as part of a locally restricted seep community in the Japan Trench at 5346 m water depth, one of the deepest seep settings studied to date. An integrated approach of biogeochemical and molecular ecological techniques was used combining in situ and ex situ measurements. In sediment of the clam colony, low sulfate reduction rates (maximum 128 nmol mL(-1) day(-1)) were coupled to the anaerobic oxidation of methane. They were observed over a depth range of 15 cm, caused by active transport of sulfate due to bioturbation of the vesicomyid clams. A distinct separation between the seep and the surrounding seafloor was shown by steep horizontal geochemical gradients and pronounced microbial community shifts. The sediment below the clam colony was dominated by anaerobic methanotrophic archaea (ANME-2c) and sulfate-reducing Desulfobulbaceae (SEEP-SRB-3, SEEP-SRB-4). Aerobic methanotrophic bacteria were not detected in the sediment, and the oxidation of sulfide seemed to be carried out chemolithoautotrophically by Sulfurovum species. Thus, major redox processes were mediated by distinct subgroups of seep-related microorganisms that might have been selected by this specific abyssal seep environment. Fluid flow and microbial activity were low but sufficient to support the clam community over decades and to build up high biomasses. Hence, the clams and their microbial communities adapted successfully to a low-energy regime and may represent widespread chemosynthetic communities in the Japan Trench. In this regard, they contributed to the restricted deep-sea trench biodiversity as well as to the organic carbon availability, also for non-seep organisms, in such oligotrophic benthic environment of the dark deep ocean.

  1. Anaerobic methanotrophic community of a 5346-m-deep vesicomyid clam colony in the Japan Trench

    PubMed Central

    Felden, J; Ruff, S E; Ertefai, T; Inagaki, F; Hinrichs, K-U; Wenzhöfer, F

    2014-01-01

    Vesicomyidae clams harbor sulfide-oxidizing endosymbionts and are typical members of cold seep communities where active venting of fluids and gases takes place. We investigated the central biogeochemical processes that supported a vesicomyid clam colony as part of a locally restricted seep community in the Japan Trench at 5346 m water depth, one of the deepest seep settings studied to date. An integrated approach of biogeochemical and molecular ecological techniques was used combining in situ and ex situ measurements. In sediment of the clam colony, low sulfate reduction rates (maximum 128 nmol mL−1 day−1) were coupled to the anaerobic oxidation of methane. They were observed over a depth range of 15 cm, caused by active transport of sulfate due to bioturbation of the vesicomyid clams. A distinct separation between the seep and the surrounding seafloor was shown by steep horizontal geochemical gradients and pronounced microbial community shifts. The sediment below the clam colony was dominated by anaerobic methanotrophic archaea (ANME-2c) and sulfate-reducing Desulfobulbaceae (SEEP-SRB-3, SEEP-SRB-4). Aerobic methanotrophic bacteria were not detected in the sediment, and the oxidation of sulfide seemed to be carried out chemolithoautotrophically by Sulfurovum species. Thus, major redox processes were mediated by distinct subgroups of seep-related microorganisms that might have been selected by this specific abyssal seep environment. Fluid flow and microbial activity were low but sufficient to support the clam community over decades and to build up high biomasses. Hence, the clams and their microbial communities adapted successfully to a low-energy regime and may represent widespread chemosynthetic communities in the Japan Trench. In this regard, they contributed to the restricted deep-sea trench biodiversity as well as to the organic carbon availability, also for non-seep organisms, in such oligotrophic benthic environment of the dark deep ocean. PMID

  2. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers.

    PubMed

    Stralis-Pavese, Nancy; Sessitsch, Angela; Weilharter, Alexandra; Reichenauer, Thomas; Riesing, Johann; Csontos, József; Murrell, J Colin; Bodrossy, Levente

    2004-04-01

    Landfill sites are responsible for 6-12% of global methane emission. Methanotrophs play a very important role in decreasing landfill site methane emissions. We investigated the methane oxidation capacity and methanotroph diversity in lysimeters simulating landfill sites with different plant vegetations. Methane oxidation rates were 35 g methane m-2 day-1 or higher for planted lysimeters and 18 g methane m-2 day-1 or less for bare soil controls. Best methane oxidation, as displayed by gas depth profiles, was found under a vegetation of grass and alfalfa. Methanotroph communities were analysed at high throughput and resolution using a microbial diagnostic microarray targeting the particulate methane monooxygenase (pmoA) gene of methanotrophs and functionally related bacteria. Members of the genera Methylocystis and Methylocaldum were found to be the dominant members in landfill site simulating lysimeters. Soil bacterial communities in biogas free control lysimeters, which were less abundant in methanotrophs, were dominated by Methylocaldum. Type Ia methanotrophs were found only in the top layers of bare soil lysimeters with relatively high oxygen and low methane concentrations. A competetive advantage of type II methanotrophs over type Ia methanotrophs was indicated under all plant covers investigated. Analysis of average and individual results from parallel samples was used to identify general trends and variations in methanotroph community structures in relation to depth, methane supply and plant cover. The applicability of the technology for the detection of environmental perturbations was proven by an erroneous result, where an unexpected community composition detected with the microarray indicated a potential gas leakage in the lysimeter being investigated.

  3. Remediation of polychlorinated biphenyl impacted sediment by concurrent bioaugmentation with anaerobic halorespiring and aerobic degrading bacteria

    PubMed Central

    Payne, Rayford B.; Fagervold, Sonja K.; May, Harold D.; Sowers, Kevin R.

    2013-01-01

    Bioremediation of sediments contaminated with commercial PCBs is potentially achievable by the sequential activity of anaerobic halorespiration to convert higher chlorinated congeners to less chlorinated congeners that are susceptible to aerobic respiratory degradation. The efficacy of bioaugmentation with anaerobic halorespiring “Dehalobium chlorocoercia” DF1 and aerobic Burkholderia xenovorans LB400 added concurrently with GAC as a delivery system was determined in 2-liter laboratory mesocosms containing weathered Aroclor-contaminated sediment from Baltimore Harbor, MD. The greatest effect was seen in the mesocosm bioaugmented with both DF1 and LB400 together, which resulted in an 80% decrease by mass of PCBs, from 8 mg/kg to less than 2 mg/kg after 120 days. There was no significant increase in lesser-chlorinated congeners, indicating that both anaerobic dechlorination by DF1 and aerobic degradation by LB400 occurred. In contrast, non-bioaugmented controls containing filtered culture supernatant showed only 25% decrease in total levels of PCBs after 365 days, which was likely due to biostimulation of the indigenous population by the medium. Direct colony counts and molecular analysis targeting a putative reductive dehalogenase gene of D. chlorocoercia, or the bphA gene of LB400 showed the presence of viable DF1 and LB400 in bioaugmented mesocosms after 365 days, indicating that both non-indigenous strains were sustainable within the indigenous microbial community. These results suggest that an in situ treatment employing the simultaneous application of anaerobic and aerobic microorganisms could be an effective, environmentally sustainable strategy to reduce PCBs levels in contaminated sediment. PMID:23463900

  4. Activity, distribution, and abundance of methane-oxidizing bacteria in the near surface soils of onshore oil and gas fields.

    PubMed

    Xu, Kewei; Tang, Yuping; Ren, Chun; Zhao, Kebin; Wang, Wanmeng; Sun, Yongge

    2013-09-01

    Methane-oxidizing bacteria (MOB) have long been used as an important biological indicator for oil and gas prospecting, but the ecological characteristics of MOB in hydrocarbon microseep systems are still poorly understood. In this study, the activity, distribution, and abundance of aerobic methanotrophic communities in the surface soils underlying an oil and gas field were investigated using biogeochemical and molecular ecological techniques. Measurements of potential methane oxidation rates and pmoA gene copy numbers showed that soils inside an oil and gas field are hot spots of methane oxidation and MOB abundance. Correspondingly, terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of pmoA genes also revealed considerable differences in the methanotrophic community composition between oil and gas fields and the surrounding soils. Principal component analysis ordination furthermore indicated a coincidence between elevated CH4 oxidation activity and the methanotrophic community structure with type I methanotrophic Methylococcus and Methylobacter, in particular, as indicator species of oil and gas fields. Collectively, our results show that trace methane migrated from oil and gas reservoirs can considerably influence not only the quantity but also the structure of the methanotrophic community.

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

    PubMed

    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.

  6. In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria.

    PubMed

    Teng, Jade L L; Yeung, Ming-Yiu; Yue, Geoffrey; Au-Yeung, Rex K H; Yeung, Eugene Y H; Fung, Ami M Y; Tse, Herman; Yuen, Kwok-Yung; Lau, Susanna K P; Woo, Patrick C Y

    2011-09-01

    This study provides guidelines on the usefulness of full and 527 bp 16S rRNA gene sequencing and Microseq databases for identifying medically important aerobic Gram-negative bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 26.1 % and 32.6 %, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15.2 % and 26.1 %, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level. Among the major groups of aerobic Gram-negative bacteria, the methods and databases are least useful for identification of Aeromonas, Bordetella and Bartonella species. None of the Aeromonas species can be confidently or doubtfully identified, whereas only 0 % and 0-33.3 % of Bordetella species and 0-10 % and 0-10 % of Bartonella species can be confidently and doubtfully identified, respectively. On the other hand, these methods and databases are most useful for identification of members of the families Pasteurellaceae and Legionellaceae and Campylobacter species: 29.6-59.3 % and 7.4-18.5 % of members of Pasteurellaceae, 36-52 % and 12-24 % of members of Legionellaceae, and 26.7-60 % and 0-13.3 % of Campylobacter species can be confidently and doubtfully identified, respectively. Thirty-nine medically important aerobic Gram-negative bacteria that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. Twenty-three medically important aerobic Gram-negative bacteria that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. Compared with results of our previous studies on anaerobic and Gram-positive bacteria, full and 527 bp 16S rRNA gene sequencing are able to confidently identify significantly more anaerobic Gram-positive and Gram-negative bacteria than aerobic Gram

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  8. Comparison of growth rates of aerobic anoxygenic phototrophic bacteria and other bacterioplankton groups in coastal Mediterranean waters.

    PubMed

    Ferrera, Isabel; Gasol, Josep M; Sebastián, Marta; Hojerová, Eva; Koblízek, Michal

    2011-11-01

    Growth is one of the basic attributes of any living organism. Surprisingly, the growth rates of marine bacterioplankton are only poorly known. Current data suggest that marine bacteria grow relatively slowly, having generation times of several days. However, some bacterial groups, such as the aerobic anoxygenic phototrophic (AAP) bacteria, have been shown to grow much faster. Two manipulation experiments, in which grazing, viruses, and resource competition were reduced, were conducted in the coastal Mediterranean Sea (Blanes Bay Microbial Observatory). The growth rates of AAP bacteria and of several important phylogenetic groups (the Bacteroidetes, the alphaproteobacterial groups Roseobacter and SAR11, and the Gammaproteobacteria group and its subgroups the Alteromonadaceae and the NOR5/OM60 clade) were calculated from changes in cell numbers in the manipulation treatments. In addition, we examined the role that top-down (mortality due to grazers and viruses) and bottom-up (resource availability) factors play in determining the growth rates of these groups. Manipulations resulted in an increase of the growth rates of all groups studied, but its extent differed largely among the individual treatments and among the different groups. Interestingly, higher growth rates were found for the AAP bacteria (up to 3.71 day⁻¹) and for the Alteromonadaceae (up to 5.44 day⁻¹), in spite of the fact that these bacterial groups represented only a very low percentage of the total prokaryotic community. In contrast, the SAR11 clade, which was the most abundant group, was the slower grower in all treatments. Our results show that, in general, the least abundant groups exhibited the highest rates, whereas the most abundant groups were those growing more slowly, indicating that some minor groups, such the AAP bacteria, very likely contribute much more to the recycling of organic matter in the ocean than what their abundances alone would predict.

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

    PubMed Central

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

    2016-01-01

    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 CH4 g dry weight soil−1 day−1. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the 13C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis (type II; Alphaproteobacteria), Methylomonas, and Methylovulum (both, type I; Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in 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 cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas. Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum (type I) can significantly contribute to aerobic methane oxidation in these ecosystems. PMID:26873322

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

    PubMed

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

    2016-04-01

    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 situ to 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 genera Methylocystis(type II;Alphaproteobacteria),Methylomonas, and Methylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in 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 cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.

  11. Radioassay for Hydrogenase Activity in Viable Cells and Documentation of Aerobic Hydrogen-Consuming Bacteria Living in Extreme Environments

    PubMed Central

    Schink, Bernhard; Lupton, F. S.; Zeikus, J. G.

    1983-01-01

    An isotopic tracer assay based on the hydrogenase-dependent formation of tritiated water from tritium gas was developed for in life analysis of microbial hydrogen transformation. This method allowed detection of bacterial hydrogen metabolism in pure cultures or in natural samples obtained from aquatic ecosystems. A differentiation between chemical-biological and aerobic-anaerobic hydrogen metabolism was established by variation of the experimental incubation temperature or by addition of selective inhibitors. Hydrogenase activity was shown to be proportional to the consumption or production of hydrogen by cultures of Desulfovibrio vulgaris, Clostridium pasteurianum, and Methanosarcina barkeri. This method was applied, in connection with measurements of free hydrogen and most-probable-number enumerations, in aerobic natural source waters to establish the activity and document the ecology of hydrogen-consuming bacteria in extreme acid, thermal, or saline environments. The utility of the assay is based in part on the ability to quantify bacterial hydrogen transformation at natural hydrogen partial pressures, without the use of artificial electron acceptors. PMID:16346288

  12. Space agriculture for habitation on Mars with hyper-thermophilic aerobic composting bacteria

    NASA Astrophysics Data System (ADS)

    Kanazawa, S.; Ishikawa, Y.; Tomita-Yokotani, K.; Hashimoto, H.; Kitaya, Y.; Yamashita, M.; Nagatomo, M.; Oshima, T.; Wada, H.; Space Agriculture Task Force, J.

    Manned Mars exploration requires recycle of materials to support human life A conceptual design is developed for space agriculture which is driven by the biologically regenerative function Hyper-thermophilic aerobic composting bacterial ecology is the core of materials recycling system to process human metabolic waste and inedible biomass and convert them to fertilizer for plants cultivation A photosynthetic reaction of plants will be driven by solar energy Water will be recycled by cultivation of plants and passing it through plant bodies Sub-surface water and atmospheric carbon dioxide are the natural resource available on Mars and these resources will be converted to oxygen and foods We envision that the agricultural system will be scaled up by importing materials from Martian environment Excess oxygen will be obtained from growing trees for structural and other components Minor elements including N P K and other traces will be introduced as fertilizers or nutrients into the agricultural materials circulation Nitrogen will be collected from Martian atmosphere We will assess biological fixation of nitrogen using micro-organisms responsible in Earth biosphere Hyper-thermophilic aerobic bacterial ecology is effective to convert waste materials into useful forms to plants This microbial technology has been well established on ground for processing sewage and waste materials For instance the hyper-thermophilic bacterial system is applied to a composting machine in a size of a trash box in home kitchen Since such a home electronics

  13. Recovery of methanotrophs from disturbance: population dynamics, evenness and functioning.

    PubMed

    Ho, Adrian; Lüke, Claudia; Frenzel, Peter

    2011-04-01

    Biodiversity is claimed to be essential for ecosystem functioning, but is threatened by anthropogenic disturbances. Prokaryotes have been assumed to be functionally redundant and virtually inextinguishable. However, recent work indicates that microbes may well be sensitive to environmental disturbance. Focusing on methane-oxidizing bacteria as model organisms, we simulated disturbance-induced mortality by mixing native with sterilized paddy soil in two ratios, 1:4 and 1:40, representing moderate and severe die-offs. Disturbed microcosms were compared with an untreated control. Recovery of activity and populations was followed over 4 months by methane uptake measurements, pmoA-qPCR, pmoA-based terminal restriction fragment length polymorphism and a pmoA-based diagnostic microarray. Diversity and evenness of methanotrophs decreased in disturbed microcosms, but functioning was not compromised. We consistently observed distinctive temporal shifts between type I and type II methanotrophs, and a rapid population growth leading to even higher cell numbers comparing disturbed microcosms with the control. Overcompensating mortality suggested that population size in the control was limited by competition with other bacteria. Overall, methanotrophs showed a remarkable ability to compensate for die-offs.

  14. Survival of Aerobic and Anaerobic Bacteria in Purulent Clinical Specimens Maintained in the Copan Venturi Transystem and Becton Dickinson Port-a-Cul Transport Systems

    PubMed Central

    Citron, Diane M.; Warren, Yumi A.; Hudspeth, Marie K.; Goldstein, Ellie J. C.

    2000-01-01

    Recovery of aerobic and anaerobic bacteria from clinical specimens maintained in the Copan Venturi Transystem and the Becton Dickinson Port-a-Cul transport was assessed. Of 54 anaerobes, 53 were recovered after 4 h, and 52 were recovered after 24 h, from both systems. After 48 h, 45 and 50 were recovered from the two systems, respectively. PMID:10655410

  15. Isolation of Aerobic Anoxygenic Photosynthetic Bacteria from Black Smoker Plume Waters of the Juan de Fuca Ridge in the Pacific Ocean

    PubMed Central

    Yurkov, Vladimir; Beatty, J. Thomas

    1998-01-01

    A strain of the aerobic anoxygenic photosynthetic bacteria was isolated from a deep-ocean hydrothermal vent plume environment. The in vivo absorption spectra of cells indicate the presence of bacteriochlorophyll a incorporated into light-harvesting complex I and a reaction center. The general morphological and physiological characteristics of this new isolate are described. PMID:16349490

  16. Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms.

    PubMed

    Coorevits, An; De Jonghe, Valerie; Vandroemme, Joachim; Reekmans, Rieka; Heyrman, Jeroen; Messens, Winy; De Vos, Paul; Heyndrickx, Marc

    2008-06-01

    Bacterial contamination of raw milk can originate from different sources: air, milking equipment, feed, soil, faeces and grass. It is hypothesized that differences in feeding and housing strategies of cows may influence the microbial quality of milk. This assumption was investigated through comparison of the aerobic spore-forming flora in milk from organic and conventional dairy farms. Laboratory pasteurized milk samples from five conventional and five organic dairy farms, sampled in late summer/autumn and in winter, were plated on a standard medium and two differential media, one screening for phospholipolytic and the other for proteolytic activity of bacteria. Almost 930 isolates were obtained of which 898 could be screened via fatty acid methyl ester analysis. Representative isolates were further analysed using 16S rRNA gene sequencing and (GTG)(5)-PCR. The majority of aerobic spore-formers in milk belonged to the genus Bacillus and showed at least 97% 16S rRNA gene sequence similarity with type strains of Bacillus licheniformis, Bacillus pumilus, Bacillus circulans, Bacillus subtilis and with type strains of species belonging to the Bacillus cereus group. About 7% of all isolates may belong to possibly new spore-forming taxa. Although the overall diversity of aerobic spore-forming bacteria in milk from organic vs. conventional dairy farms was highly similar, some differences between both were observed: (i) a relatively higher number of thermotolerant organisms in milk from conventional dairy farms compared to organic farms (41.2% vs. 25.9%), and (ii) a relatively higher number of B. cereus group organisms in milk from organic (81.3%) and Ureibacillus thermosphaericus in milk from conventional (85.7%) dairy farms. One of these differences, the higher occurrence of B. cereus group organisms in milk from organic dairy farms, may be linked to differences in housing strategy between the two types of dairy farming. However, no plausible clarification was found for

  17. Colonization by aerobic bacteria in karst: Laboratory and in situ experiments

    USGS Publications Warehouse

    Personne, J.-C.; Poty, F.; Mahler, B.J.; Drogue, C.

    2004-01-01

    Experiments were carried out to investigate the potential for bacterial colonization of different substrates in karst aquifers and the nature of the colonizing bacteria. Laboratory batch experiments were performed using limestone and PVC as substrates, a natural bacterial isolate and a known laboratory strain (Escherichia coli [E. coli]) as inocula, and karst ground water and a synthetic formula as growth media. In parallel, fragments of limestone and granite were submerged in boreholes penetrating two karst aquifers for more than one year; the boreholes are periodically contaminated by enteric bacteria from waste water. Once a month, rock samples were removed and the colonizing bacteria quantified and identified. The batch experiments demonstrated that the natural isolate and E. coli both readily colonized limestone surfaces using karst ground water as the growth medium. In contrast, bacterial colonization of both the limestone and granite substrates, when submerged in the karst, was less intense. More than 300 bacterial strains were isolated over the period sampled, but no temporal pattern in colonization was seen as far as strain, and colonization by E. coli was notably absent, although strains of Salmonella and Citrobacter were each observed once. Samples suspended in boreholes penetrating highly fractured zones were less densely colonized than those in the borehole penetrating a less fractured zone. The results suggest that contamination of karst aquifers by enteric bacteria is unlikely to be persistent. We hypothesize that this may be a result of the high flow velocities found in karst conduits, and of predation of colonizing bacteria by autochthonous zooplankton.

  18. Species distribution and antimicrobial susceptibility of gram-negative aerobic bacteria in hospitalized cancer patients

    PubMed Central

    Ashour, Hossam M; El-Sharif, Amany

    2009-01-01

    Background Nosocomial infections pose significant threats to hospitalized patients, especially the immunocompromised ones, such as cancer patients. Methods This study examined the microbial spectrum of gram-negative bacteria in various infection sites in patients with leukemia and solid tumors. The antimicrobial resistance patterns of the isolated bacteria were studied. Results The most frequently isolated gram-negative bacteria were Klebsiella pneumonia (31.2%) followed by Escherichia coli (22.2%). We report the isolation and identification of a number of less-frequent gram negative bacteria (Chromobacterium violacum, Burkholderia cepacia, Kluyvera ascorbata, Stenotrophomonas maltophilia, Yersinia pseudotuberculosis, and Salmonella arizona). Most of the gram-negative isolates from Respiratory Tract Infections (RTI), Gastro-intestinal Tract Infections (GITI), Urinary Tract Infections (UTI), and Bloodstream Infections (BSI) were obtained from leukemic patients. All gram-negative isolates from Skin Infections (SI) were obtained from solid-tumor patients. In both leukemic and solid-tumor patients, gram-negative bacteria causing UTI were mainly Escherichia coli and Klebsiella pneumoniae, while gram-negative bacteria causing RTI were mainly Klebsiella pneumoniae. Escherichia coli was the main gram-negative pathogen causing BSI in solid-tumor patients and GITI in leukemic patients. Isolates of Escherichia coli, Klebsiella, Enterobacter, Pseudomonas, and Acinetobacter species were resistant to most antibiotics tested. There was significant imipenem -resistance in Acinetobacter (40.9%), Pseudomonas (40%), and Enterobacter (22.2%) species, and noticeable imipinem-resistance in Klebsiella (13.9%) and Escherichia coli (8%). Conclusion This is the first study to report the evolution of imipenem-resistant gram-negative strains in Egypt. Mortality rates were higher in cancer patients with nosocomial Pseudomonas infections than any other bacterial infections. Policies restricting

  19. Diversity and activity of methanotrophs in landfill cover soils with and without landfill gas recovery systems.

    PubMed

    Su, Yao; Zhang, Xuan; Xia, Fang-Fang; Zhang, Qi-Qi; Kong, Jiao-Yan; Wang, Jing; He, Ruo

    2014-05-01

    Aerobic CH4 oxidation plays an important role in mitigating CH4 release from landfills to the atmosphere. Therefore, in this study, oxidation activity and community of methanotrophs were investigated in a subtropical landfill. Among the three sites investigated, the highest CH4 concentration was detected in the landfill cover soil of the site (A) without a landfill gas (LFG) recovery system, although the refuse in the site had been deposited for a longer time (∼14-15 years) compared to the other two sites (∼6-11 years) where a LFG recovery system was applied. In April and September, the higher CH4 flux was detected in site A with 72.4 and 51.7gm(-2)d(-1), respectively, compared to the other sites. The abundance of methanotrophs assessed by quantification of pmoA varied with location and season. A linear relationship was observed between the abundance of methanotrophs and CH4 concentrations in the landfill cover soils (R=0.827, P<0.001). The key factors influencing the methanotrophic diversity in the landfill cover soils were pH, the water content and the CH4 concentration in the soil, of which pH was the most important factor. Type I methanotrophs, including Methylococcus, Methylosarcina, Methylomicrobium and Methylobacter, and type II methanotrophs (Methylocystis) were all detected in the landfill cover soils, with Methylocystis and Methylosarcina being the dominant genera. Methylocystis was abundant in the slightly acidic landfill cover soil, especially in September, and represented more than 89% of the total terminal-restriction fragment abundance. These findings indicated that the LFG recovery system, as well as physical and chemical parameters, affected the diversity and activity of methanotrophs in landfill cover soils.

  20. The active methanotrophic community in a wetland from the High Arctic.

    PubMed

    Graef, Christiane; Hestnes, Anne Grethe; Svenning, Mette Marianne; Frenzel, Peter

    2011-08-01

    The dominant terminal process of carbon mineralization in most freshwater wetlands is methanogenesis. With methane being an important greenhouse gas, the predicted warming of the Arctic may provide a positive feedback. However, the amount of methane released to the atmosphere may be controlled by the activity of methane-oxidizing bacteria (methanotrophs) living in the oxic surface layer of wetlands. Previously, methanotrophs have been isolated and identified by genetic profiling in High Arctic wetlands showing the presence of only a few genotypes. Two isolates from Solvatnet (Ny-Ålesund, Spitsbergen; 79°N) are available: Methylobacter tundripaludum (type I) and Methylocystis rosea (type II), raising the question whether the low diversity is a cultivation effect. We have revisited Solvatnet applying stable isotope probing (SIP) with (13) C-labelled methane. 16S rRNA profiling revealed active type I methanotrophs including M. tundripaludum, while no active type II methanotrophs were identified. These results indicate that the extant M. tundripaludum is an active methane oxidizer at its locus typicus; furthermore, Methylobacter seems to be the dominant active genus. Diversity of methanotrophs was low as compared, e.g. to wetland rice fields in the Mediterranean. This low diversity suggests a high vulnerability of Arctic methanotroph communities, which deserves more attention.

  1. Aging well: methanotrophic potential and community structure along a paddy soil chronosequence of 2000 years.

    NASA Astrophysics Data System (ADS)

    Ho, Adrian; Frenzel, Peter

    2010-05-01

    Given that rice paddies are anthropogenic methane sources and the inevitable need to increase rice production to sustain human population growth, it is pertinent to identify the effects of long term agriculture on the selection of methanotrophs. Methanotrophs play a crucial role in mitigating methane emission from rice paddies. Therefore, we analyzed the methanotroph community along a chronosequence of paddy soils from China covering recently reclaimed sites to paddies under permanent agriculture since 2000 years (Cheng et al., 2009; doi:10.1016/j.geoderma.2009.03.016). Maximum potential methane oxidation rate (PMOR) increased monotonically with age. Our results also showed that long-term agriculture imposes a selection pressure on different groups of methanotrophs. In contrast to younger soils, type Ib methanotrophs were observed to multiply in correspondence with increasing PMOR in ancient soils, while other groups showed a relatively stable community composition as revealed by pmoA-based fingerprints (T-RFLP) and quantitative PCR. Cloning and sequencing the pmoA (a key gene in methane oxidation), the soils were found to harbour known and putative methanotrophs, ammonium-oxidizing bacteria, and interestingly, sequences affiliated to Crenothrix, a methane oxidizer with an unusual pmoA (Stoecker et al., 2006; doi:10.1073/pnas.0506361103). In summary, long-term agriculture shapes the community and allows for an elevated level of potential methane oxidation.

  2. Effect of applying lactic acid bacteria and propionic acid on fermentation quality and aerobic stability of oats-common vetch mixed silage on the Tibetan plateau.

    PubMed

    Zhang, Jie; Guo, Gang; Chen, Lei; Li, Junfeng; Yuan, Xianjun; Yu, Chengqun; Shimojo, Masataka; Shao, Tao

    2015-06-01

    The objective of this study was to evaluate effects of lactic acid bacteria and propionic acid on the fermentation quality and aerobic stability of oats-common vetch mixed silage by using a small-scale fermentation system on the Tibetan plateau. (i) An inoculant (Lactobacillus plantarum) (L) or (ii) propionic acid (P) or (iii) inoculant + propionic acid (PL) were used as additives. After fermenting for 60 days, silos were opened and the aerobic stability was tested for the following 15 days. The results showed that all silages were well preserved with low pH and NH3 -N, and high lactic acid content and V-scores. L and PL silages showed higher (P < 0.05) lactic acid and crude protein content than the control silage. P silage inhibited lactic acid production. Under aerobic conditions, L silage had similar yeast counts as the control silage (> 10(5) cfu/g fresh matter (FM)); however, it numerically reduced aerobic stability for 6 h. P and PL silages showed fewer yeasts (< 10(5) cfu/g FM) (P < 0.05) and markedly improved the aerobic stability (> 360 h). The result suggested that PL is the best additive as it could not only improved fermentation quality, but also aerobic stability of oats-common vetch mixed silage on the Tibetan plateau.

  3. Anaerobic and aerobic bacteriology of the saliva and gingiva from 16 captive Komodo dragons (Varanus komodoensis): new implications for the "bacteria as venom" model.

    PubMed

    Goldstein, Ellie J C; Tyrrell, Kerin L; Citron, Diane M; Cox, Cathleen R; Recchio, Ian M; Okimoto, Ben; Bryja, Judith; Fry, Bryan G

    2013-06-01

    It has been speculated that the oral flora of the Komodo dragon (Varanus komodoensis) exerts a lethal effect on its prey; yet, scant information about their specific oral flora bacteriology, especially anaerobes, exists. Consequently, the aerobic and anaerobic oral bacteriology of 16 captive Komodo dragons (10 adults and six neonates), aged 2-17 yr for adults and 7-10 days for neonates, from three U.S. zoos were studied. Saliva and gingival samples were collected by zoo personnel, inoculated into anaerobic transport media, and delivered by courier to a reference laboratory. Samples were cultured for aerobes and anaerobes. Strains were identified by standard methods and 16S rRNA gene sequencing when required. The oral flora consisted of 39 aerobic and 21 anaerobic species, with some variation by zoo. Adult dragons grew 128 isolates, including 37 aerobic gram-negative rods (one to eight per specimen), especially Enterobacteriaceae; 50 aerobic gram-positive bacteria (two to nine per specimen), especially Staphylococcus sciuri and Enterococcusfaecalis, present in eight of 10 and nine of 10 dragons, respectively; and 41 anaerobes (one to six per specimen), especially clostridia. All hatchlings grew aerobes but none grew anaerobes. No virulent species were isolated. As with other carnivores, captive Komodo oral flora is simply reflective of the gut and skin flora of their recent meals and environment and is unlikely to cause rapid fatal infection.

  4. (An)aerobic bacteria found in secondary-cataract material. A SEM/TEM study.

    PubMed

    Kalicharan, D; Jongebloed, W L; Los, L I; Worst, J G

    1992-01-01

    Twenty four patients, who had marked reduction of vision due to secondary-cataract developed after an ECCE, were treated by surgical cleaning of the posterior lens capsule. During this procedure globular secondary-cataract material was removed and collected for morphological examination by SEM and TEM. Fragments of various sizes and shapes, including some with a 'golf ball' structure, were seen; these closely resembled particles frequently found in cataractous lenses. In addition, in 18 patients micro-organisms were found: rod-shaped bacteria, cocci, and in 2 cases yeasts. These findings were the more remarkable because these were clinically quiet eyes with no signs of intra-ocular inflammation and cultures have been persistently negative. We imagine that these bacteria must have entered the eye during the cataract extraction and have settled there without causing an infection.

  5. Aerobic methanotrophy within the pelagic redox-zone of the Gotland Deep (central Baltic Sea)

    NASA Astrophysics Data System (ADS)

    Schmale, O.; Blumenberg, M.; Kießlich, K.; Jakobs, G.; Berndmeyer, C.; Labrenz, M.; Thiel, V.; Rehder, G.

    2012-12-01

    Water column samples taken in summer 2008 from the stratified Gotland Deep (central Baltic Sea) showed a strong gradient in dissolved methane concentrations from high values in the saline deep water (max. 504 nM) to low concentrations in the less dense, brackish surface water (about 4 nM). The steep methane-gradient (between 115 and 135 m water depth) within the redox-zone, which separates the anoxic deep part from the oxygenated surface water (oxygen concentration 0-0.8 mL L-1), implies a methane consumption rate of 0.28 nM d-1. The process of microbial methane oxidation within this zone was evident by a shift of the stable carbon isotope ratio of methane between the bottom water (δ13C CH4 = -82.4‰ and the redox-zone (δ13C CH4 = -38.7‰. Water column samples between 80 and 119 m were studied to identify the microorganisms responsible for the methane turnover in that depth interval. Notably, methane monooxygenase gene expression analyses for water depths covering the whole redox-zone demonstrated that accordant methanotrophic activity was probably due to only one phylotype of the aerobic type I methanotrophic bacteria. An imprint of these organisms on the particular organic matter was revealed by distinctive lipid biomarkers showing bacteriohopanepolyols and lipid fatty acids characteristic for aerobic type I methanotrophs (e.g., 35-aminobacteriohopane-30,31,32,33,34-pentol), corroborating their role in aerobic methane oxidation in the redox-zone of the central Baltic Sea.

  6. Aerobic degradation of a mixture of azo dyes in a packed bed reactor having bacteria-coated laterite pebbles.

    PubMed

    Senan, Resmi C; Shaffiqu, T S; Roy, J Jegan; Abraham, T Emilia

    2003-01-01

    A microbial consortium capable of aerobic degradation of a mixture of azo dyes consisting of two isolated strains (RRL,TVM) and one known strain of Pseudomonas putida (MTCC 1194) was immobilized on laterite stones. The amount of bacterial biomass attached to the laterite stones was 8.64 g per 100 g of the stone on a dry weight basis. The packed bed reactor was filled with these stones and had a total capacity of 850 mL and a void volume of 210 mL. The feed consisted of an equal mixture of seven azo dyes both in water as well as in a simulated textile effluent, at a pH of 9.0 and a salinity of 900 mg/L. The dye concentrations of influent were 25, 50, and 100 microg/mL. The residence time was varied between 0.78 and 6.23 h. It was found that at the lowest residence time 23.55, 45.73, and 79.95 microg of dye was degraded per hour at an initial dye concentration of 25, 50, and 100 microg, respectively. The pH was reduced from 9.0 to 7.0. Simulated textile effluent containing 50 microg/mL dye was degraded by 61.7%. Analysis of degradation products by TLC and HPLC showed that the dye mixture was degraded to nontoxic smaller molecules. The bacteria-coated pebbles were stable, there was no washout even after 2 months, and the reactor was found to be suitable for the aerobic degradation of azo dyes.

  7. [Sensitivity and resistance of aerobic bacteria isolated from patients with periodontitis towards antibiotics and bacteriophages (comparative analysis)].

    PubMed

    Nemsadze, T D; Mshvenieradze, D D; Apridonidze, K G

    2006-03-01

    In order to examine sensitivity and resistance of isolated aerobic bacteria from periodontitis materials towards antibiotics and bacteriophages, there has been studied exudations taken from 737 patients' periodontic pockets or the tissue taken from curettage. According to the rate of identified microorganisms, they have been arranged as follows: S. epidermidis 39,34+/-1,56%; S. pyogenes 18,84+/-1,25%; M. catarrhalis 17,09+/-1,2%; S. aureus 10,71+/-0,99%; E.coli-5,66+/-0,74%; Diphtheroids in 1,13+/-0,33%; S. Mucilaginosus 1,02+/-0,32%, proteus vulgaris - 0,72+/-0,27%; H. parainfluenzae - 0,72+/-0,27%; S. intermedium 0,61+/-0,24%; P. aeruginosa - 0,61+/-0,24%; H. influenzae - 0,51+/-0,22%, S. saprophiticus - 0,51+/-0,22%; S. viridans - 0,51+/-0,22%; S. pneumoniae - 0,41+/-0,2%; K. pneumoniae - 0,41+/-0,22%; S. haemoliticus - 0,41+/-0,2%; B. adolescentics - 0,3+/-0,17%; L. acidophilus -0,3+/-0,17%; S. salivarius-0,1+/-0,1%. It has been stated that percentage of polyresistant strains is growing. While having aerobic infections of periodontitis, kefzol, cephazolin, cephamezin, zinaceph, klaphoran, cephdazidim (cephalosporins I, II, II generation); tetracycline, doxycycline, (tetracyclines); 5-noks, cyprophloxacyne (chinolons I, II generation); ryphamphcyne (rymphamicynes); but standby medicines may be also considered: penicillin G, procaine penicillin (penicillines); streptomycin, kanamicin, gentamicin (aminoglycosides); lincomycin, clindamycin, (lincosamides); eritromycin, macropen (macrolides); chloramphenicol. Since the resistance of microbial strains was not developed towards bacteriophages during the treatment it is considerable to apply simultaneously the bacteriophages and standby antibiotics.

  8. Effect of a preparation containing lactic fermentation bacteria on the hygienic status and aerobic stability of silages.

    PubMed

    Selwet, M

    2008-01-01

    The objective of this study was to determine the influence of biological silage additive (Bonsilage) on the hygiene quality and nutritive value of maize and grass-legume silages. The experiments were conducted on FAO 240 maize (Zea mays L.) and a mixture of italian ryegrass (Lolium multiflorum L.), 50% with alfalfa (Medicago media Pers.), 50%. Group 1 was a control and comprised silage without any additives, group 2 was ensiled with the addition of 4 cm3 kg(-1) biological silage additive. After 60 days of silage process individual silages were subjected to microbiological composition, and chemical analyses of silages were also determined. Similar analyses were repeated at day 7 following exposure to oxygen. The applied biological silage additive was found to reduce (P<0.05) numbers of Clostridium, Enterobacteriaceae, yeasts and mold fungi cells, and increase (P<0.05) the number of LAB (lactic acid bacteria) in comparison with the control in both silages. Chemical analysis of the maize silage showed that the biological additive caused an increase (P<0.05) in DM (dry matter), CP (crude protein), WSC (water soluble carbohydrates), LA (lactic acid), AA (acetic acid), ethanol, and a decrease (P<0.05) in the concentration of BA (butyric acid), N-NH3 and pH value in comparison with the control. Chemical analysis of silage samples from the grass-legume mixture showed that the additive caused an increase (P<0.05) in the content of DM, CP, WSC, LA and AA in comparison with the control. Samples of silage with the addition of an inoculant were characterized by a lower (P<0.05) content of BA, N-NH3, ethanol and pH value. The biological additive impoved the aerobic stability of silages in the aerobic phase.

  9. Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient.

    PubMed

    Ferrera, Isabel; Sarmento, Hugo; Priscu, John C; Chiuchiolo, Amy; González, José M; Grossart, Hans-Peter

    2017-01-01

    Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient).

  10. Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient

    PubMed Central

    Ferrera, Isabel; Sarmento, Hugo; Priscu, John C.; Chiuchiolo, Amy; González, José M.; Grossart, Hans-Peter

    2017-01-01

    Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient). PMID:28275369

  11. Feasibility of atmospheric methane removal using methanotrophic biotrickling filters.

    PubMed

    Yoon, Sukhwan; Carey, Jeffrey N; Semrau, Jeremy D

    2009-07-01

    Methane is a potent greenhouse gas with a global warming potential ~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(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(2) credits is increased, can also be economically attractive.

  12. Reductive dechlorination of trichloroethylene and tetrachloroethylene under aerobic conditions in a sediment column

    SciTech Connect

    Enzien, M.V.; Picardal, F.; Hazen, T.

    1994-06-01

    This study investigated the bioremediation of chlorinated solvents in a sediment column. Biodegradation potentials of trichloroethylene and tetrachloroethylene during aerobic methanotrophic biostimulation were studied at the Savannah River Site. 30 refs., 3 figs., 3 tabs.

  13. Aerobic respiration metabolism in lactic acid bacteria and uses in biotechnology.

    PubMed

    Pedersen, Martin B; Gaudu, Philippe; Lechardeur, Delphine; Petit, Marie-Agnès; Gruss, Alexandra

    2012-01-01

    The lactic acid bacteria (LAB) are essential for food fermentations and their impact on gut physiology and health is under active exploration. In addition to their well-studied fermentation metabolism, many species belonging to this heterogeneous group are genetically equipped for respiration metabolism. In LAB, respiration is activated by exogenous heme, and for some species, heme and menaquinone. Respiration metabolism increases growth yield and improves fitness. In this review, we aim to present the basics of respiration metabolism in LAB, its genetic requirements, and the dramatic physiological changes it engenders. We address the question of how LAB acquired the genetic equipment for respiration. We present at length how respiration can be used advantageously in an industrial setting, both in the context of food-related technologies and in novel potential applications.

  14. Formation of polyhydroxyalkanoate in aerobic anoxygenic phototrophic bacteria and its relationship to carbon source and light availability.

    PubMed

    Xiao, Na; Jiao, Nianzhi

    2011-11-01

    Aerobic anoxygenic phototrophic bacteria (AAPB) are unique players in carbon cycling in the ocean. Cellular carbon storage is an important mechanism regulating the nutrition status of AAPB but is not yet well understood. In this paper, six AAPB species (Dinoroseobacter sp. JL1447, Roseobacter denitrificans OCh 114, Roseobacter litoralis OCh 149, Dinoroseobacter shibae DFL 12(T), Labrenzia alexandrii DFL 11(T), and Erythrobacter longus DSMZ 6997) were examined, and all of them demonstrated the ability to form the carbon polymer polyhydroxyalkanoate (PHA) in the cell. The PHA in Dinoroseobacter sp. JL1447 was identified as poly-beta-hydroxybutyrate (PHB) according to evidence from Fourier transform infrared spectroscopy, differential scanning calorimetry, and (1)H nuclear magnetic resonance spectroscopy examinations. Carbon sources turned out to be critical for PHA production in AAPB. Among the eight media tested with Dinoroseobacter sp. JL1447, sodium acetate, giving a PHA production rate of 72%, was the most productive carbon source, followed by glucose, with a 68% PHA production rate. Such PHA production rates are among the highest recorded for all bacteria. The C/N ratio of substrates was verified by the experiments as another key factor in PHA production. In the case of R. denitrificans OCh 114, PHA was not detected when the organism was cultured at C/N ratios of <2 but became apparent at C/N ratios of >3. Light is also important for the formation of PHA in AAPB. In the case of Dinoroseobacter sp. JL1447, up to a one-quarter increase in PHB production was observed when the culture underwent growth in a light-dark cycle compared to growth completely in the dark.

  15. Real-time PCR assays compared to culture-based approaches for identification of aerobic bacteria in chronic wounds.

    PubMed

    Melendez, J H; Frankel, Y M; An, A T; Williams, L; Price, L B; Wang, N-Y; Lazarus, G S; Zenilman, J M

    2010-12-01

    Chronic wounds cause substantial morbidity and disability. Infection in chronic wounds is clinically defined by routine culture methods that can take several days to obtain a final result, and may not fully describe the community of organisms or biome within these wounds. Molecular diagnostic approaches offer promise for a more rapid and complete assessment. We report the development of a suite of real-time PCR assays for rapid identification of bacteria directly from tissue samples. The panel of assays targets 14 common, clinically relevant, aerobic pathogens and demonstrates a high degree of sensitivity and specificity using a panel of organisms commonly associated with chronic wound infection. Thirty-nine tissue samples from 29 chronic wounds were evaluated and the results compared with those obtained by culture. As revealed by culture and PCR, the most common organisms were methicillin-resistant Staphylococcus aureus (MRSA) followed by Streptococcus agalactiae (Group B streptococcus) and Pseudomonas aeruginosa. The sensitivities of the PCR assays were 100% and 90% when quantitative and qualitative culture results were used as the reference standard, respectively. The assays allowed the identification of bacterial DNA from ten additional organisms that were not revealed by quantitative or qualitative cultures. Under optimal conditions, the turnaround time for PCR results is as short as 4-6 h. Real-time PCR is a rapid and inexpensive approach that can be easily introduced into clinical practice for detection of organisms directly from tissue samples. Characterization of the anaerobic microflora by real-time PCR of chronic wounds is warranted.

  16. Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica.

    PubMed

    Pinheiro, Guilherme L; Correa, Raquel F; Cunha, Raquel S; Cardoso, Alexander M; Chaia, Catia; Clementino, Maysa M; Garcia, Eloi S; de Souza, Wanderley; Frasés, Susana

    2015-01-01

    The enzymatic hydrolysis of cellulose by cellulases is one of the major limiting steps in the conversion of lignocellulosic biomass to yield bioethanol. To overcome this hindrance, significant efforts are underway to identify novel cellulases. The snail Achatina fulica is a gastropod with high cellulolytic activity, mainly due to the abundance of glycoside hydrolases produced by both the animal and its resident microbiota. In this study, we partially assessed the cellulolytic aerobic bacterial diversity inside the gastrointestinal tract of A. fulica by culture-dependent methods and evaluated the hydrolytic repertoire of the isolates. Forty bacterial isolates were recovered from distinct segments of the snail gut and identified to the genus level by 16S rRNA gene sequence analysis. Additional phenotypic characterization was performed using biochemical tests provided by the Vitek2 identification system. The overall enzymatic repertoire of the isolated strains was investigated by enzymatic plate assays, containing the following substrates: powdered sugarcane bagasse, carboxymethylcellulose (CMC), p-nitrophenyl-β-D-glucopyranoside (pNPG), p-nitrophenyl-β-D-cellobioside (pNPC), 4-methylumbelliferyl-β-D-glucopyranoside (MUG), 4-methylumbelliferyl-β-D-cellobioside (MUC), and 4-methylumbelliferyl-β-D-xylopyranoside (MUX). Our results indicate that the snail A. fulica is an attractive source of cultivable bacteria that showed to be valuable resources for the production of different types of biomass-degrading enzymes.

  17. Production of autoinducer-2 by aerobic endospore-forming bacteria isolated from the West African fermented foods.

    PubMed

    Qian, Yang; Kando, Christine Kere; Thorsen, Line; Larsen, Nadja; Jespersen, Lene

    2015-11-01

    Autoinducer-2 (AI-2) is a quorum-sensing (QS) molecule which mediates interspecies signaling and affects various bacterial behaviors in food fermentation. Biosynthesis of AI-2 is controlled by S-ribosylhomocysteine lyase encoded by the luxS gene. The objective of this study was to investigate production of AI-2 by aerobic endospore-forming bacteria (AEB) isolated from the West African alkaline fermented seed products Mantchoua and Maari. The study included 13 AEB strains of Bacillus subtilis, B. cereus, B. altitudinis, B. amyloliquefaciens, B. licheniformis, B. aryabhattai, B. safensis, Lysinibacillus macroides and Paenibacillus polymyxa. All the tested strains harbored the luxS gene and all strains except for P. polymyxa B314 were able to produce AI-2 during incubation in laboratory medium. Production of AI-2 by AEB was growth phase dependent, showing maximum activity at the late exponential phase. AI-2 was depleted from the culture medium at the beginning of the stationary growth phase, indicating that the tested AEB possess a functional AI-2 receptor that internalizes AI-2. This study provides the evidences of QS system in Bacillus spp. and L. macroides and new knowledge of AI-2 production by AEB. This knowledge contributes to the development of QS-based strategies for better control of alkaline fermentation.

  18. Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica

    PubMed Central

    Pinheiro, Guilherme L.; Correa, Raquel F.; Cunha, Raquel S.; Cardoso, Alexander M.; Chaia, Catia; Clementino, Maysa M.; Garcia, Eloi S.; de Souza, Wanderley; Frasés, Susana

    2015-01-01

    The enzymatic hydrolysis of cellulose by cellulases is one of the major limiting steps in the conversion of lignocellulosic biomass to yield bioethanol. To overcome this hindrance, significant efforts are underway to identify novel cellulases. The snail Achatina fulica is a gastropod with high cellulolytic activity, mainly due to the abundance of glycoside hydrolases produced by both the animal and its resident microbiota. In this study, we partially assessed the cellulolytic aerobic bacterial diversity inside the gastrointestinal tract of A. fulica by culture-dependent methods and evaluated the hydrolytic repertoire of the isolates. Forty bacterial isolates were recovered from distinct segments of the snail gut and identified to the genus level by 16S rRNA gene sequence analysis. Additional phenotypic characterization was performed using biochemical tests provided by the Vitek2 identification system. The overall enzymatic repertoire of the isolated strains was investigated by enzymatic plate assays, containing the following substrates: powdered sugarcane bagasse, carboxymethylcellulose (CMC), p-nitrophenyl-β-D-glucopyranoside (pNPG), p-nitrophenyl-β-D-cellobioside (pNPC), 4-methylumbelliferyl-β-D-glucopyranoside (MUG), 4-methylumbelliferyl-β-D-cellobioside (MUC), and 4-methylumbelliferyl-β-D-xylopyranoside (MUX). Our results indicate that the snail A. fulica is an attractive source of cultivable bacteria that showed to be valuable resources for the production of different types of biomass-degrading enzymes. PMID:26347735

  19. Biodegradation of 17β-estradiol by bacteria isolated from deep sea sediments in aerobic and anaerobic media.

    PubMed

    Fernández, Lucía; Louvado, António; Esteves, Valdemar I; Gomes, Newton C M; Almeida, Adelaide; Cunha, Ângela

    2017-02-05

    Endocrine disrupting compounds (EDCs) are considered as high research priority being a source of potential adverse ecological health effects in environmental waters. 17β-Estradiol (E2), a recalcitrant natural estrogen, is typically encountered in wastewater treatment plants (WWTPs) at levels ranging 10-30ngL(-1) in the influent flow and 1-3ngL(-1) in the effluent flow. The exposure to even extremely low concentrations of E2 may interfere with the normal function of the endocrine system of organisms. In this study, five bacteria isolated from enrichment cultures of sediments of mud volcanoes of the Gulf of Cadiz (Moroccan-Iberian margin) were identified as aerobic E2 biodegraders, which produce low amounts of biotransformed estrone (E1). Analysis of 16S rDNA gene sequences identified three of them as Virgibacillus halotolerans, Bacillus flexus and Bacillus licheniformis. Among the set of strains, Bacillus licheniformis showed also ability to biodegrade E2 under anaerobic conditions.

  20. Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.

    PubMed

    Hink, Linda; Nicol, Graeme W; Prosser, James I

    2016-03-11

    Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N2 O production under conditions of high inorganic ammonia (NH3 ) input, but result mainly from the activity of AOA when NH3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N2 O production. In unamended soils, ammonia oxidation and N2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N2 O emissions from fertilised agricultural soils.

  1. Hexavalent chromium reduction by aerobic heterotrophic bacteria indigenous to chromite mine overburden

    PubMed Central

    Dey, Satarupa; Paul, A.K.

    2013-01-01

    Microbiological analysis of overburden samples collected from chromite mining areas of Orissa, India revealed that they are rich in microbial density as well as diversity and dominated by Gram-negative (58%) bacteria. The phenotypically distinguishable bacterial isolates (130) showed wide degree of tolerance to chromium (2–8 mM) when tested in peptone yeast extract glucose agar medium. Isolates (92) tolerating 2 mM chromium exhibited different degrees of Cr+6 reducing activity in chemically defined Vogel Bonner (VB) broth and complex KSC medium. Three potent isolates, two belonging to Arthrobacter spp. and one to Pseudomonas sp. were able to reduce more than 50 and 80% of 2 mM chromium in defined and complex media respectively. Along with Cr+6 (MIC 8.6–17.8 mM), the isolates showed tolerance to Ni+2, Fe+3, Cu+2 and Co+2 but were extremely sensitive to Hg+2 followed by Cd+2, Mn+2 and Zn+2. In addition, they were resistant to antibiotics like penicillin, methicillin, ampicillin, neomycin and polymyxin B. During growth under shake-flask conditions, Arthrobacter SUK 1201 and SUK 1205 showed 100% reduction of 2 mM Cr+6 in KSC medium with simultaneous formation of insoluble precipitates of chromium salts. Both the isolates were also equally capable of completely reducing the Cr+6 present in mine seepage when grown in mine seepage supplemented with VB concentrate. PMID:24159321

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

    PubMed

    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.

  3. Methanotrophs Contribute to Peatland Nitrogen

    NASA Astrophysics Data System (ADS)

    Larmola, Tuula; Leppänen, Sanna M.; Tuittila, Eeva-Stiina; Aarva, Maija; Merilä, Päivi; Fritze, Hannu; Tiirola, Marja

    2016-04-01

    Atmospheric nitrogen (N2) fixation is potentially an important N input mechanism to peatland ecosystems, but the extent of this process may have been underestimated because of the methods traditionally used inhibit the activity of methanothrophs. We examined the linkage of methane (CH4) oxidation and N2 fixation using 15N2 technique. Dominant flark and hummock Sphagnum species were collected from twelve pristine peatlands in Siikajoki, Finland, which varied in age from 200 to 2,500 y due to the postglacial rebound. The mosses were incubated in a two-day field 15N2 and 13CH4 pulse labelling experiment and the incorporation of 15N2 and 13CH4 in biomass was measured with Isotope Ratio Mass Spectrometer. The rates of Sphagnum-associated N2 fixation (0.1-2.9 g N m-2 y-1) were up to 10 times the current N deposition rates. Methane-induced N2 fixation contributed to over 1/3 of moss-associated N2 fixation in younger stages, but was switched off in old successional stages, despite active CH4 oxidation in these stages. Both the N2 fixation rates and the methanotrophic contribution to N2 fixation during peatland succession were primarily constrained by phosphorus availability. Previously overlooked methanotrophic N contribution may explain rapid peat and N accumulation during fen stages of peatland development. Reference. Larmola T., Leppänen S.M., Tuittila E.-S, Aarva M., Merilä P., Fritze H., Tiirola M. (2014) Methanotrophy induces nitrogen fixation during peatland development. Proceedings of the National Academy of Sciences USA 111 (2): 734-739.

  4. The determination of the real nano-scale sizes of bacteria in chernozem during microbial succession by means of hatching of a soil in aerobic and anaerobic conditions

    NASA Astrophysics Data System (ADS)

    Gorbacheva, M.

    2012-04-01

    M.A. Gorbacheva,L.M. Polyanskaya The Faculty of Soil Science, Moscow State University, Leninskie Gory, GSP-1, Moscow,119991,Russia In recent years there's been particular attention paid to the smallest life's forms- bacteria which size can be measured in nanometer. These are the forms of bacteria with diameter of 5-200 nm. Theoretical calculations based on the content of the minimum number of DNA, enzyme, lipids in and ribosome in cells indicates impossibility of existence of a living cells within diameter less than 300 nm. It is theoretically possible for a living cell to exist within possible diameter of approximately 140 nm. Using a fluorescence microscope there's been indicated in a number of samples from lakes, rivers, soil, snow and rain water that 200 nm is the smallest diameter of a living cell. Supposingly, such a small size of bacteria in soil is determined by natural conditions which limit their development by nutritious substances and stress-factors. Rejuvenescence of nanobacteria under unfavourable natural conditions and stress-factors is studied in laboratory environment. The object of the current study has become the samples of typical arable chernozem of the Central Chernozem State Biosphere Reserve in Kursk. The detailed morphological description of the soil profile and its basic analytical characteristics are widely represented in scientific publications. The soil is characterized by a high carbon content which makes up 3,96% ,3,8% , and 2,9% for the upper layers of the A horizon, and 0,79% for the layer of the B horizon. A microbial succession was studied under aerobic and anaerobic conditions by means of experiments with microcosms in upper A horizons and B horizon of a chernozem. The final aim is to identify the cells size of bacteria in aerobic and anaerobic soil conditions in chernozem during the microbial succession, by dampening and application of chitin by means of «cascade filtration» method. The study of the microcosms is important for

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

    PubMed Central

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

    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 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. PMID:27682101

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Aerobic and anaerobic methane oxidation in terrestrial mud volcanoes in the Northern Apennines

    NASA Astrophysics Data System (ADS)

    Wrede, C.; Brady, S.; Rockstroh, S.; Dreier, A.; Kokoschka, S.; Heinzelmann, S. M.; Heller, C.; Reitner, J.; Taviani, M.; Daniel, R.; Hoppert, M.

    2012-07-01

    Methane oxidizing prokaryotes are ubiquitous in oxic and anoxic habitats wherever C1-compounds are present. Thus, methane saturated mud volcano fluids should be a preferred habitat of methane consuming prokaryotes, using the readily available electron donors. In order to understand the relevance of methane as a carbon and energy source in mud volcano communities, we investigate the diversity of prokaryotic organisms involved in oxidation of methane in fluid samples from the Salse di Nirano mud volcano field situated in the Northern Apennines. Cell counts were at approximately 0.7 × 106 microbial cells/ml. A fraction of the microbial biomass was identified as ANME (anaerobic methanotroph) archaea by fluorescence in situ hybridization (FISH) analysis. They are associated in densely colonized flakes, of some tens of μm in diameter, embedded in a hyaline matrix. Diversity analysis based on the 16S rDNA genes, retrieved from amplified and cloned environmental DNA, revealed a high proportion of archaea, involved in anaerobic oxidation of methane (AOM). Aerobic methane-oxidizing proteobacteria could be highly enriched from mud volcano fluids, indicating the presence of aerobic methanotrophic bacteria, which may contribute to methane oxidation, whenever oxygen is readily available. The results imply that biofilms, dominated by ANME archaea, colonize parts of the mud volcano venting system.

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

    SciTech Connect

    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.

  9. Growth parameters of Escherichia coli O157:H7, Salmonella spp., Listeria monocytogenes, and aerobic mesophilic bacteria of apple cider amended with nisin-EDTA.

    PubMed

    Ukuku, Dike O; Zhang, Howard; Huang, Lihan

    2009-05-01

    The effect of nisin (0 or 300 IU/mL), ethylenediamine tetraacetic acid (EDTA, 20 mM), and nisin (300 IU)-EDTA (20 mM) on growth parameters, including lag period (LP) and generation time, of Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella spp. in the presence or absence of aerobic mesophilic bacteria of apple cider during storage at 5 degrees C for up to 16 days or 23 degrees C for 16 h was investigated. The growth data were analyzed and fitted to the modified Gompertz model. The LP values for aerobic mesophilic bacteria of apple cider (control) and those amended with EDTA and nisin during storage at 5 degrees C were 1.61, 1.76, and 5.45 days, respectively. In apple cider stored at 23 degrees C for 16 h, the LP values for the same bacteria and treatment were 3.24, 3.56, and 5.85 h, respectively. The LP values for E. coli O157:H7 determined in the presence of aerobic mesophilic bacteria of apple cider stored at 23 degrees C for 16 h was 1.48 h, while populations for L. monocytogenes and Salmonella in the same cider declined. In sterile apple cider left at 23 degrees C for 16 h, the LP values for E. coli O157:H7, Salmonella, and L. monocytogenes averaged 2.74, 2.37, and 3.16 h, respectively. The generation time for these pathogens were 0.402, 0.260, and 0.187 log (CFU/mL)/h, respectively. Addition of nisin and EDTA combination caused a decline in lag phase duration and the populations for all pathogens tested, suggesting possible addition of this additive to freshly prepared apple cider to enhance its microbial safety and prevent costly recalls.

  10. ["In vitro" susceptibility of some aerobic and anaerobic bacteria to three 5-nitro-imidazole derivatives: metronidazole, ornidazole and tinidazole (author's transl)].

    PubMed

    Dublanchet, A; Durieux, R

    1980-01-01

    As shown earlier, the three drugs are effective against most anaerobic bacteria. However, with Bacteroides fragilis the geometric mean MIC of metronidazole (0.43 microgram/ml), ornidazole (0.37 microgram/ml) and tinidazole (0.20 microgram/ml) are statistically different. Moreover, and contrary to generally accepted opinion, some aerobic bacteria such as Moraxella and Bacillus can be susceptible to nitro-imidazoles. The results suggest another mechanism for the action of nitro-imidazoles, different from that previously described. This underscores the major role of the reduction of the nitrogroup by a low-redox-potential. Two strains of strictly anaerobic bacteria show a relative resistance in the microaerophilic zone.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed Central

    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. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning. PMID:24708438

  13. Genes and enzymes of ectoine biosynthesis in halotolerant methanotrophs.

    PubMed

    Reshetnikov, Alexander S; Khmelenina, Valentina N; Mustakhimov, Ildar I; Trotsenko, Yuri A

    2011-01-01

    Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) is a widely distributed compatible solute accumulated by halophilic and halotolerant microorganisms to prevent osmotic stress in highly saline environments. Ectoine as a highly water keeping compound stabilizing biomolecules and whole cells can be used in scientific work, cosmetics, and medicine. Detailed understanding of the organization/regulation of the ectoine biosynthetic pathway in various producers is an active area of research. Here we review current knowledge on some genetic and enzymatic aspects of ectoine biosynthesis in halophilic and halotolerant methanotrophs. By using PCR methodology, the genes coding for the specific enzymes of ectoine biosynthesis, diaminobutyric acid (DABA) aminotransferase (EctB), DABA acetyltransferase (EctA), and ectoine synthase (EctC), were identified in several methanotrophic species. Organization of these genes in either ectABC or ectABC-ask operons, the latter additionally encoding aspartate kinase isozyme (Ask), correlated well with methanotroph halotolerance and intracellular ectoine level. A new gene, ectR1 encoding the MarR-like transcriptional regulatory protein EctR1, negatively controlling transcription of ectoine biosynthetic genes was found upstream of ectABC-ask operon in Methylomicrobium alcaliphilum 20Z. The ectR-like genes were also found in halotolerant methanol utilizers Methylophaga alcalica and Methylophaga thalassica as well as in several genomes of nonmethylotrophic species. The His(6)-tagged DABA acetyltransferases from Mm. alcaliphilum, M. alcalica, and M. thalassica were purified and the enzyme properties were found to correlate with the ecophysiologies of these bacteria. All these discoveries should be very helpful for better understanding the biosynthetic mechanism of this important natural compound, and for the targeted metabolic engineering of its producers.

  14. Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of West Siberian rivers.

    PubMed

    Oshkin, Igor Y; Wegner, Carl-Eric; Lüke, Claudia; Glagolev, Mikhail V; Filippov, Illiya V; Pimenov, Nikolay V; Liesack, Werner; Dedysh, Svetlana N

    2014-10-01

    A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h(-1), while some seeps emitted up to 5.54 g CH4 h(-1). The δ(13)C value of methane released from these seeps varied between -71.1 and -71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml(-1) day(-1)) were measured in mud samples. Fluorescence in situ hybridization detected 10(7) methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies.

  15. Lactic Acid Bacteria in Total Mixed Ration Silage Containing Soybean Curd Residue: Their Isolation, Identification and Ability to Inhibit Aerobic Deterioration

    PubMed Central

    Li, Y.; Wang, F.; Nishino, N.

    2016-01-01

    We investigated the effects of the predominant lactic acid bacteria (LAB) on the fermentation characteristics and aerobic stability of total mixed ration (TMR) silage containing soybean curd residue (SC-TMR silage). The SC-TMR materials were ensiled in laboratory silos for 14 or 56 days. LAB predominant in SC-TMR silage were identified (Exp. 1). Lactobacillus fermentum (L. fermentum) and Streptococcus bovis (S. bovis) were found in the untreated materials, Leuconostoc pseudomesenteroides (L. pseudomesenteroides) in 14-day silage and Lactobacillus plantarum (L. plantarum) in all silages. Pediococcus acidilactici (P. acidilactici), Lactobacillus paracasei (L. paracasei), and Lactobacillus brevis (L. brevis) formed more than 90% of the isolates in 56-day silage. Italian ryegrass and whole crop maize were inoculated with P. acidilactici and L. brevis isolates and the fermentation and aerobic stability determined (Exp. 2). Inoculation with P. acidilactici and L. brevis alone or combined improved the fermentation products in ryegrass silage and markedly enhanced its aerobic stability. In maize silage, P. acidilactici and L. brevis inoculation caused no changes and suppressed deterioration when combined with increases in acetic acid content. The results indicate that P. acidilactici and L. brevis may produce a synergistic effect to inhibit SC-TMR silage deterioration. Further studies are needed to identify the inhibitory substances, which may be useful for developing potential antifungal agents. PMID:26949952

  16. Effects of carbon dioxide on the fate of Listeria monocytogenes, of aerobic bacteria and on the development of spoilage in minimally processed fresh endive.

    PubMed

    Carlin, F; Nguyen-the, C; Abreu Da Silva, A; Cochet, C

    1996-09-01

    Minimally processed fresh broad-leaved endive (Cichorium endivia L.) were stored at 3 and 10 degrees C in modified atmospheres containing air, 10% CO2/10% O2, 30% CO2/10% O2, and 50% CO2/10% O2. The effects of these modified atmospheres on the fate of both aerobic bacteria and three strains of Listeria monocytogenes, was investigated. Increases in CO2 concentrations significantly reduced the growth of the aerobic microflora. The best preservation of the visual quality occurred on endive leaves stored in 10% CO2/10% O2, whereas leaves stored in 30% CO2/10% O2 and 50% CO2/10% O2, and to a lesser extent in air, showed extensive spoilage after storage. Listeria monocytogenes was slightly affected at 3 degrees C by the modified atmospheres, as compared to air. At 10 degrees C, results varied between replicate experiments, but L. monocytogenes generally grew better as the CO2 concentration was increased. The three test strains behaved in a similar way. In conclusion, among the modified atmospheres tested, a modified atmosphere containing 10% CO2/10% O2 resulted in improved visual quality of minimally processed fresh endive, without a marked effect on the growth of the aerobic microflora or of L. monocytogenes.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Presence and resistance of Streptococcus agalactiae in vaginal specimens of pregnant and adult non-pregnant women and association with other aerobic bacteria.

    PubMed

    Numanović, Fatima; Smajlović, Jasmina; Gegić, Merima; Delibegović, Zineta; Bektaš, Sabaheta; Halilović, Emir; Nurkić, Jasmina

    2017-02-01

    Aim To determine the prevalence rate and resistance profile of Streptococcus agalactiae (S. agalactiae) in vaginal swabs of pregnant and adult non-pregnant women in the Tuzla region, Bosnia and Herzegovina (B&H), as well as its association with other aerobic bacteria. Methods This prospective study included 200 women, 100 pregnant and 100 adult non-pregnant. The research was conducted at the Institute of Microbiology, University Clinical Center Tuzla from October to December 2015. Standard aerobic microbiological techniques were used for isolation and identification of S. agalactiae and other aerobic bacteria. Antimicrobial susceptibility was determined by the disk diffusion and microdilution method(VITEK 2/AES instrument). Results Among 200 vaginal swabs, 17 (8.50%) were positive for S. agalactiae, e. g., 7% (7/100) of pregnant and 10% (10/100) of adult non-pregnant women. In the pregnant group, 71.4% (5/7) of S. agalactiae isolates were susceptible to clindamycin and 85.7%(6/7) to erythromycin. In the adult non-pregnant group, only resistance to clindamycin was observed in one patient (1/10; 10%). S. agalactiae as single pathogen was isolated in 57.14% (4/7) of pregnant and 60% (6/10) of adult non-pregnant S. agalactiae positive women. In mixed microbial cultures S. agalactiae was most frequently associated with Enterococcus faecalis and Escherichia coli. Conclusion The rate of S. agalactiae positive women in the population of pregnant and adult non-pregnant women of Tuzla Canton, B&H is comparable with other European countries. Large studies are needed to develop a common national strategy for the prevention of S. agalactiae infection in B&H, especially during pregnancy.

  19. Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

    PubMed Central

    Thornton, Christopher N.; Hyer, Alex; Twing, Katrina I.; Longino, August A.; Lang, Susan Q.; Lilley, Marvin D.; Früh-Green, Gretchen L.; Schrenk, Matthew O.

    2017-01-01

    The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif. PMID:28149702

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

    PubMed

    Kampman, Christel; Piai, Laura; Hendrickx, Tim L G; Temmink, Hardy; Zeeman, Grietje; Buisman, Cees J N

    2014-01-01

    The activity of denitrifying methanotrophic bacteria at 11-30 °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 °C had an optimum temperature of 20-25 °C and that activity dropped as temperature was increased to 30 °C. Biomass enriched at 30 °C had an optimum temperature of 25-30 °C. These results indicated that biomass from low-temperature inocula adjusted to the enrichment temperature and that low-temperature enrichment is suitable for applications in low-temperature wastewater treatment. Biomass growth at ≤20 °C still needs to be studied.

  1. Selection of Type I and Type II Methanotrophic Proteobacteria in a Fluidized Bed Reactor under Non-Sterile Conditions

    DTIC Science & Technology

    2011-08-01

    2009). Polyhydroxyalkanoates (PHAs), which can be used as bioplastics (Reddy et al., 2003), are intracellular granules that accumulate in some bacteria...of methanotrophs in lake sediments. Appl. Environ. Microb. 65, 5066–5074. DiGregorio, B., 2009. Biobased performance bioplastic : mirel. Chem. Biol

  2. Methanotrophic gastropods from a bathyal hydrocarbon seep, Gulf of Mexico

    SciTech Connect

    Anderson, L.C.; Aharon, P.; Gupta, S. )

    1992-01-01

    Two gastropods, Neritina sp. and Truncatella sp., collected live from a Gulf of Mexico active gas seep with the submersible Johnson Sea Link in September 1991, apparently incorporate methane-derived carbon in their soft tissues. Flesh of an individual Neritina sp. had a delta C-13 of [minus]50.92 per mil PDB, and that of two coexisting individuals of Truncatella sp. had values of [minus]45.11 and [minus]49.27 per mil. These isotope values are comparable to those reported for the methanotrophic mytilid bivalve Bathymodiolus sp. from other hydrocarbon seeps on the Gulf of Mexico, and are lighter than published isotopic values of chemosynthetic organisms with sulfur-oxidizing symbionts. The anomalously light carbon-isotopic values of Neritina sp. and Truncatella sp. may steam from one of three causes: (1) these gastropods host symbiotic methanotrophic bacteria, (2) their chief food is methane-oxidizing bacteria present at the seep, or (3) they incorporate some carbon from the periostracum of mussels on which they may graze. The presence of abundant juveniles of Bathymodiolus, reported to settle preferentially in areas of active seepage and high methane release, indicates that methane was abundant and supported a community with multiple trophic levels. Generally, studies of hydrocarbon-seep communities have focused on larger community members, especially bivalves and tube worms. The presence of living Neritina and Truncatella at the authors sampling site, however, draws attention to the fact that these gastropods are integral and significant parts of hydrocarbon-seep communities. Both gastropod species are members of genera that characteristically inhabit shallow marine, intertidal, and semiterrestrial environments. The presence of these genera in bathyal hydrocarbon seeps indicates that they have very broad environmental ranges, thus limiting their utility in paleoecologic reconstructions.

  3. Starvation and recovery in the deep-sea methanotroph Methyloprofundus sedimenti.

    PubMed

    Tavormina, Patricia L; Kellermann, Matthias Y; Antony, Chakkiath Paul; Tocheva, Elitza I; Dalleska, Nathan F; Jensen, Ashley J; Valentine, David L; Hinrichs, Kai-Uwe; Jensen, Grant J; Dubilier, Nicole; Orphan, Victoria J

    2017-01-01

    In the deep ocean, the conversion of methane into derived carbon and energy drives the establishment of diverse faunal communities. Yet specific biological mechanisms underlying the introduction of methane-derived carbon into the food web remain poorly described, due to a lack of cultured representative deep-sea methanotrophic prokaryotes. Here, the response of the deep-sea aerobic methanotroph Methyloprofundus sedimenti to methane starvation and recovery was characterized. By combining lipid analysis, RNA analysis, and electron cryotomography, it was shown that M. sedimenti undergoes discrete cellular shifts in response to methane starvation, including changes in headgroup-specific fatty acid saturation levels, and reductions in cytoplasmic storage granules. Methane starvation is associated with a significant increase in the abundance of gene transcripts pertinent to methane oxidation. Methane reintroduction to starved cells stimulates a rapid, transient extracellular accumulation of methanol, revealing a way in which methane-derived carbon may be routed to community members. This study provides new understanding of methanotrophic responses to methane starvation and recovery, and lays the initial groundwork to develop Methyloprofundus as a model chemosynthesizing bacterium from the deep sea.

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

    USGS Publications Warehouse

    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.

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

    PubMed

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

    2013-06-01

    Seepage of coal-bed methane (CBM) through soils is a potential source of atmospheric CH4 and also a likely source of ancient (i.e. (14) C-dead) carbon to soil microbial communities. Natural abundance (13) C and (14) C 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 δ(13) C 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 δ(13) C values that were intermediate indicating assimilation of both plant- and CBM-derived carbon. Δ(14) C 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.

  6. Impact of freshwater diversion projects on diversity and activity of methanotrophic communities in freshwater wetlands

    NASA Astrophysics Data System (ADS)

    Isaac, J.; Schulz, C. J.; Childers, G. W.

    2009-12-01

    Methanotrophic bacteria are key players in the carbon cycle capable of using methane as a sole carbon and energy source. Methanotrophs are ubiquitous in soil environments and play a key role in decreasing methane flux from anaerobic environments to the atmosphere, reducing the concentration of this greenhouse gas. Wetlands are a particularly important source of methane to the atmosphere, even though methanotrophs can consume the majority of the methane produced. Decreases in methanotrophic activity in wetland environments due to disturbance can have negative impacts with regard to greenhouse gas emissions, especially if the impact is widespread. Currently, several freshwater diversion projects are active and/or scheduled to come online in south Louisiana, delivering freshwater, sediments, and nutrients to coastal wetlands en masse to help combat subsidence and coastal erosion. Along with freshwater, these diversions also deliver other components of the Mississippi River including substantial bicarbonate alkalinity, reactive nitrogen, and sulfate. Analogous to the large scale diversion projects are smaller restoration projects that deliver treated wastewater effluent to wetlands. In particular, the Joyce Wildlife Management Area (JWMA) in southeast Louisiana has been the recipient of ~5 million gallons of treated domestic effluent per day since 2006. Both the composition of the marsh receiving the effluent and the effluent itself have similarities to Mississippi River diversions. We collected pre and post JWMA sediment microbial community DNA and created cloned libraries of genes encoding particulate methane monooxygenase (pmoA) as a proxy for methanotrophic community composition. Water chemistry data was also collected. Shifts in methanotrophic community composition were apparent as well as shifts in water chemistry. The most notable shift in water chemistry was pH, which changed from mildly acidic to slightly alkaline conditions, due to the increased alkalinity of

  7. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph

    SciTech Connect

    Dunfield, P.F. |; Liesack, W.; Henckel, T.; Conrad, R.; Knowles, R.

    1999-03-01

    Methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (CH{sub 4}). After 4 years of growth and periodic dilution, a mixed culture was obtained which displayed an apparent half-saturation constant [K{sub m(app)}] for CH{sub 4} of 56 to 186 nM (40 to 132 ppmv). This value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure cultures of methane oxidizers. However, the K{sub m(app)} increased when the culture was transferred to higher mixing ratios of CH{sub 4}. Denaturing gradient gel electrophoresis of the enrichment grown on <275 ppmv of CH{sub 4} revealed a single gene product of pmoA, which codes for a subunit of particulate methane monooxygenase. This suggested that only one methanotroph species was present. This organism was isolated from a sample of the enrichment culture grown on 1% CH{sub 4} and phylogenetically positioned based on its 16S rRNA, pmoA, and mxaF gene sequences as a type II strain of the Methlocystis/Methylosinus group. A coculture of this strain with a Variovorax sp., when grown on <275 ppmv of CH{sub 4}, had a K{sub m(app)} similar to that of the initial enrichment culture. The data suggest that the affinity of methanotrophic bacteria for CH{sub 4} varies with growth conditions and that the oxidation of atmospheric CH{sub 4} observed in this soil is carried out by type II methanotrophic bacteria which are similar to characterized species.

  8. Isolation of aerobic, gliding, xylanolytic and laminarinolytic bacteria from acidic Sphagnum peatlands and emended description of Chitinophaga arvensicola Kampfer et al. 2006.

    PubMed

    Pankratov, Timofei A; Kulichevskaya, Irina S; Liesack, Werner; Dedysh, Svetlana N

    2006-12-01

    Four aerobic, heterotrophic, yellow-pigmented and flexirubin-producing bacterial strains with gliding motility were isolated from acidic Sphagnum-dominated wetlands of Northern Russia. These bacteria are capable of degrading xylan, laminarin and some other polysaccharides, but not cellulose, pectin or chitin. The four strains possess almost identical 16S rRNA gene sequences and are most closely related (98.9-99.5 % sequence similarity) to the recently reclassified species of the phylum Bacteroidetes, Chitinophaga arvensicola Kämpfer et al. 2006, formerly known as [Cytophaga] arvensicola Oyaizu et al. 1983. However, the novel isolates from Sphagnum peat differed from C. arvensicola DSM 3695(T) in their ability to degrade xylan and starch, by greater tolerance of acidic pH and by their inability to reduce nitrate. An emended description of this species is proposed.

  9. Multicenter Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Gram-Positive Aerobic Bacteria

    PubMed Central

    Burnham, Carey-Ann D.; Bythrow, Maureen; Garner, Omai B.; Ginocchio, Christine C.; Jennemann, Rebecca; Lewinski, Michael A.; Manji, Ryhana; Mochon, A. Brian; Procop, Gary W.; Richter, Sandra S.; Sercia, Linda; Westblade, Lars F.; Ferraro, Mary Jane; Branda, John A.

    2013-01-01

    Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting. PMID:23658261

  10. Iodide Accumulation by Aerobic Bacteria Isolated from Subsurface Sediments of a 129I-Contaminated Aquifer at the Savannah River Site, South Carolina ▿

    PubMed Central

    Li, Hsiu-Ping; Brinkmeyer, Robin; Jones, Whitney L.; Zhang, Saijin; Xu, Chen; Schwehr, Kathy A.; Santschi, Peter H.; Kaplan, Daniel I.; Yeager, Chris M.

    2011-01-01

    129I is of major concern because of its mobility in the environment, excessive inventory, toxicity (it accumulates in the thyroid), and long half-life (∼16 million years). The aim of this study was to determine if bacteria from a 129I-contaminated oxic aquifer at the F area of the U.S. Department of Energy's Savannah River Site, SC, could accumulate iodide at environmentally relevant concentrations (0.1 μM I−). Iodide accumulation capability was found in 3 out of 136 aerobic bacterial strains isolated from the F area that were closely related to Streptomyces/Kitasatospora spp., Bacillus mycoides, and Ralstonia/Cupriavidus spp. Two previously described iodide-accumulating marine strains, a Flexibacter aggregans strain and an Arenibacter troitsensis strain, accumulated 2 to 50% total iodide (0.1 μM), whereas the F-area strains accumulated just 0.2 to 2.0%. Iodide accumulation by FA-30 was stimulated by the addition of H2O2, was not inhibited by chloride ions (27 mM), did not exhibit substrate saturation kinetics with regard to I− concentration (up to 10 μM I−), and increased at pH values of <6. Overall, the data indicate that I− accumulation likely results from electrophilic substitution of cellular organic molecules. This study demonstrates that readily culturable, aerobic bacteria of the F-area aquifer do not accumulate significant amounts of iodide; however, this mechanism may contribute to the long-term fate and transport of 129I and to the biogeochemical cycling of iodine over geologic time. PMID:21278282

  11. Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria.

    PubMed

    Rychert, Jenna; Burnham, Carey-Ann D; Bythrow, Maureen; Garner, Omai B; Ginocchio, Christine C; Jennemann, Rebecca; Lewinski, Michael A; Manji, Ryhana; Mochon, A Brian; Procop, Gary W; Richter, Sandra S; Sercia, Linda; Westblade, Lars F; Ferraro, Mary Jane; Branda, John A

    2013-07-01

    Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting.

  12. Methanotrophic symbionts provide carbon for photosynthesis in peat bogs.

    PubMed

    Raghoebarsing, Ashna A; Smolders, Alfons J P; Schmid, Markus C; Rijpstra, W Irene C; Wolters-Arts, Mieke; Derksen, Jan; Jetten, Mike S M; Schouten, Stefan; Sinninghe Damsté, Jaap S; Lamers, Leon P M; Roelofs, Jan G M; Op den Camp, Huub J M; Strous, Marc

    2005-08-25

    Wetlands are the largest natural source of atmospheric methane, the second most important greenhouse gas. Methane flux to the atmosphere depends strongly on the climate; however, by far the largest part of the methane formed in wetland ecosystems is recycled and does not reach the atmosphere. The biogeochemical controls on the efficient oxidation of methane are still poorly understood. Here we show that submerged Sphagnum mosses, the dominant plants in some of these habitats, consume methane through symbiosis with partly endophytic methanotrophic bacteria, leading to highly effective in situ methane recycling. Molecular probes revealed the presence of the bacteria in the hyaline cells of the plant and on stem leaves. Incubation with (13)C-methane showed rapid in situ oxidation by these bacteria to carbon dioxide, which was subsequently fixed by Sphagnum, as shown by incorporation of (13)C-methane into plant sterols. In this way, methane acts as a significant (10-15%) carbon source for Sphagnum. The symbiosis explains both the efficient recycling of methane and the high organic carbon burial in these wetland ecosystems.

  13. Methane oxidation in a crude oil contaminated aquifer: Delineation of aerobic reactions at the plume fringes

    USGS Publications Warehouse

    Amos, R.T.; Bekins, B.A.; Delin, G.N.; Cozzarelli, I.M.; Blowes, D.W.; Kirshtein, J.D.

    2011-01-01

    High resolution direct-push profiling over short vertical distances was used to investigate CH4 attenuation in a petroleum contaminated aquifer near Bemidji, Minnesota. The contaminant plume was delineated using dissolved gases, redox sensitive components, major ions, carbon isotope ratios in CH4 and CO2, and the presence of methanotrophic bacteria. Sharp redox gradients were observed near the water table. Shifts in ??13CCH4 from an average of - 57.6??? (?? 1.7???) in the methanogenic zone to - 39.6??? (?? 8.7???) at 105 m downgradient, strongly suggest CH4 attenuation through microbially mediated degradation. In the downgradient zone the aerobic/anaerobic transition is up to 0.5 m below the water table suggesting that transport of O2 across the water table is leading to aerobic degradation of CH4 at this interface. Dissolved N2 concentrations that exceeded those expected for water in equilibrium with the atmosphere indicated bubble entrapment followed by preferential stripping of O2 through aerobic degradation of CH4 or other hydrocarbons. Multivariate and cluster analysis were used to distinguish between areas of significant bubble entrapment and areas where other processes such as the infiltration of O 2 rich recharge water were important O2 transport mechanisms. ?? 2011 Elsevier B.V. All rights reserved.

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

    PubMed

    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.

  15. Novel pod for chlorine dioxide generation and delivery to control aerobic bacteria on the inner surface of floor drains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Floor drains in poultry processing and further processing plants are a harborage site for bacteria both free swimming and in biofilms. This population can include Listeria monocytogenes which has been shown to have potential for airborne spreading from mishandled open drains. Chlorine dioxide (ClO...

  16. Comparison of two transport systems available in Japan (TERUMO kenkiporter II and BBL Port-A-Cul) for maintenance of aerobic and anaerobic bacteria.

    PubMed

    Fujimoto, Daichi; Takegawa, Hiroshi; Doi, Asako; Sakizono, Kenji; Kotani, Yoko; Miki, Kanji; Naito, Takuya; Niki, Marie; Miyamoto, Junko; Tamai, Koji; Nagata, Kazuma; Nakagawa, Atsushi; Tachikawa, Ryo; Otsuka, Kojiro; Katakami, Nobuyuki; Tomii, Keisuke

    2014-01-01

    The kenkiporter II (KP II) transport system is commonly used in many hospitals in Japan for transporting bacterial specimens to microbiology laboratories. Recently, the BBL Port-A-Cul (PAC) fluid vial became available. However, no reports thus far have compared the effectiveness of these two transport systems. We chose 4 aerobic and facultative anaerobic bacteria as well as 8 anaerobic organisms, and prepared three strains of each bacterium in culture media for placement into PAC and KP II containers. We compared the effectiveness of each transport system for preserving each organism at 6, 24, and 48 h after inoculation at room temperature. Thirty-six strains out of 12 bacteria were used in this study. The PAC system yielded better recovery in quantity of organisms than the KP II system at 6, 24 and 48 h. More strains were significantly recovered with the PAC system than with the KP II at 24 h (36/36 vs. 23/36, P < 0.001) and 48 h (30/36 vs. 12/36, P < 0.001). The PAC system was better in the recovery of viable organisms counted at 24 and 48 h after inoculation compared with the KP II system. The PAC system may be recommended for the transfer of bacterial specimens in clinical settings.

  17. Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus.

    PubMed Central

    Millward-Sadler, S J; Davidson, K; Hazlewood, G P; Black, G W; Gilbert, H J; Clarke, J H

    1995-01-01

    To test the hypothesis that selective pressure has led to the retention of cellulose-binding domains (CBDs) by hemicellulase enzymes from aerobic bacteria, four new xylanase (xyn) genes from two cellulolytic soil bacteria, Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus, have been isolated and sequenced. Pseudomonas genes xynE and xynF encoded modular xylanases (XYLE and XYLF) with predicted M(r) values of 68,600 and 65000 respectively. XYLE contained a glycosyl hydrolase family 11 catalytic domain at its N-terminus, followed by three other domains; the second of these exhibited sequence identity with NodB from rhizobia. The C-terminal domain (40 residues) exhibited significant sequence identity with a non-catalytic domain of previously unknown function, conserved in all the cellulases and one of the hemicellulases previously characterized from the pseudomonad, and was shown to function as a CBD when fused to the reporter protein glutathione-S-transferase. XYLF contained a C-terminal glycosyl hydrolase family 10 catalytic domain and a novel CBD at its N-terminus. C. mixtus genes xynA and xynB exhibited substantial sequence identity with xynE and xynF respectively, and encoded modular xylanases with the same molecular architecture and, by inference, the same functional properties. In the absence of extensive cross-hybridization between other multiple cel (cellulase) and xyn genes from P. fluorescens subsp. cellulosa and genomic DNA from C. mixtus, similarity between the two pairs of xylanases may indicate a recent transfer of genes between the two bacteria. Images Figure 1 Figure 4 PMID:7492333

  18. Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo—Brazil)

    PubMed Central

    Cuadrat, Rafael R. C.; Ferrera, Isabel; Grossart, Hans-Peter; Dávila, Alberto M. R.

    2016-01-01

    Abstract Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean. PMID:26871866

  19. Central Role of Dynamic Tidal Biofilms Dominated by Aerobic Hydrocarbonoclastic Bacteria and Diatoms in the Biodegradation of Hydrocarbons in Coastal Mudflats

    PubMed Central

    Coulon, Frédéric; Chronopoulou, Panagiota-Myrsini; Fahy, Anne; Païssé, Sandrine; Goñi-Urriza, Marisol; Peperzak, Louis; Acuña Alvarez, Laura; McKew, Boyd A.; Brussaard, Corina P. D.; Underwood, Graham J. C.; Timmis, Kenneth N.; Duran, Robert

    2012-01-01

    Mudflats and salt marshes are habitats at the interface of aquatic and terrestrial systems that provide valuable services to ecosystems. Therefore, it is important to determine how catastrophic incidents, such as oil spills, influence the microbial communities in sediment that are pivotal to the function of the ecosystem and to identify the oil-degrading microbes that mitigate damage to the ecosystem. In this study, an oil spill was simulated by use of a tidal chamber containing intact diatom-dominated sediment cores from a temperate mudflat. Changes in the composition of bacteria and diatoms from both the sediment and tidal biofilms that had detached from the sediment surface were monitored as a function of hydrocarbon removal. The hydrocarbon concentration in the upper 1.5 cm of sediments decreased by 78% over 21 days, with at least 60% being attributed to biodegradation. Most phylotypes were minimally perturbed by the addition of oil, but at day 21, there was a 10-fold increase in the amount of cyanobacteria in the oiled sediment. Throughout the experiment, phylotypes associated with the aerobic degradation of hydrocarbons, including polycyclic aromatic hydrocarbons (PAHs) (Cycloclasticus) and alkanes (Alcanivorax, Oleibacter, and Oceanospirillales strain ME113), substantively increased in oiled mesocosms, collectively representing 2% of the pyrosequences in the oiled sediments at day 21. Tidal biofilms from oiled cores at day 22, however, consisted mostly of phylotypes related to Alcanivorax borkumensis (49% of clones), Oceanospirillales strain ME113 (11% of clones), and diatoms (14% of clones). Thus, aerobic hydrocarbon biodegradation is most likely to be the main mechanism of attenuation of crude oil in the early weeks of an oil spill, with tidal biofilms representing zones of high hydrocarbon-degrading activity. PMID:22407688

  20. Constraints in the colonization of natural and engineered subterranean igneous rock aquifers by aerobic methane-oxidizing bacteria inferred by culture analysis.

    PubMed

    Chi Fru, E

    2008-08-01

    The aerobic methane-oxidizing bacteria (MOB) are suggested to be important for the removal of oxygen from subterranean aquifers that become oxygenated by natural and engineering processes. This is primarily because MOB are ubiquitous in the environment and in addition reduce oxygen efficiently. The biogeochemical factors that will control the success of the aerobic MOB in these kinds of underground aquifers remain unknown. In this study, viable and cultivable MOB occurring at natural and engineered deep granitic aquifers targeted for the disposal of spent nuclear fuel (SNF) in the Fennoscandian Shield (approximately 3-1000 m) were enumerated. The numbers were correlated with in situ salinity, methane concentrations, conductivity, pH, and depth. A mixed population habiting freshwater aquifers (approximately 3-20 m), a potential source for the inoculation of MOB into the deeper aquifers was tested for tolerance to NaCl, temperature, pH, and an ability to produce cysts and exospores. Extrapolations show that due to changing in situ parameters (salinity, conductivity, and pH), the numbers of MOB in the aquifers dropped quickly with depth. A positive correlation between the most probable numbers of MOB and methane concentrations was observed. Furthermore, the tolerance-based tests of cultured strains indicated that the MOB in the shallow aquifers thrived best in mesophilic and neutrophilic conditions as opposed to the hyperthermophilic and alkaliphilic conditions expected to develop in an engineered subterranean SNF repository. Overall, the survival of the MOB both quantitatively and physiologically in the granitic aquifers was under the strong influence of biogeochemical factors that are strongly depth-dependent.

  1. Evaluation of the Removal of Indicator Bacteria from Domestic Sludge Processed by Autothermal Thermophilic Aerobic Digestion (ATAD)

    PubMed Central

    Piterina, Anna V.; Bartlett, John; Pembroke, Tony J.

    2010-01-01

    The degradation of sludge solids in an insulated reactor during Autothermal Thermophilic Aerobic Digestion (ATAD) processing results in auto-heating, thermal treatment and total solids reduction, however, the ability to eliminate pathogenic organisms has not been analysed under large scale process conditions. We evaluated the ATAD process over a period of one year in a two stage, full scale Irish ATAD plant established in Killarney and treating mixed primary and secondary sludge, by examining the sludge microbiologically at various stages during and following ATAD processing to determine its ability to eliminate indicator organisms. Salmonella spp. (pathogen) and fecal-coliform (indicator) densities were well below the limits used to validate class A biosolids in the final product. Enteric pathogens present at inlet were deactivated during the ATAD process and were not detected in the final product using both traditional microbial culture and molecular phylogenetic techniques. A high DNase activity was detected in the bulk sludge during the thermophilic digestion stage which may be responsible for the rapid turn over of DNA from lysed cells and the removal of mobile DNA. These results offer assurance for the safe use of ATAD sludge as a soil supplement following processing. PMID:20948933

  2. Availability of O2 as a substrate in the cytoplasm of bacteria under aerobic and microaerobic conditions.

    PubMed

    Arras, T; Schirawski, J; Unden, G

    1998-04-01

    The growth rates of Pseudomonas putida KT2442 and mt-2 on benzoate, 4-hydroxybenzoate, or 4-methylbenzoate showed an exponential decrease with decreasing oxygen tensions (partial O2 tension [pO2] values). The oxygen tensions resulting in half-maximal growth rates were in the range of 7 to 8 mbar of O2 (corresponding to 7 to 8 microM O2) (1 bar = 10(5) Pa) for aromatic compounds, compared to 1 to 2 mbar for nonaromatic compounds like glucose or succinate. The decrease in the growth rates coincided with excretion of catechol or protocatechuate, suggesting that the activity of the corresponding oxygenases became limiting. The experiments directly establish that under aerobic and microaerobic conditions (about 10 mbar of O2), the diffusion of O2 into the cytoplasm occurs at high rates sufficient for catabolic processes. This is in agreement with calculated O2 diffusion rates. Below 10 mbar of O2, oxygen became limiting for the oxygenases, probably due to their high Km values, but the diffusion of O2 into the cytoplasm presumably should be sufficiently rapid to maintain ambient oxygen concentrations at oxygen tensions as low as 1 mbar of O2. The consequences of this finding for the availability of O2 as a substrate or as a regulatory signal in the cytoplasm of bacterial cells are discussed.

  3. Availability of O2 as a Substrate in the Cytoplasm of Bacteria under Aerobic and Microaerobic Conditions

    PubMed Central

    Arras, Tanja; Schirawski, Jan; Unden, Gottfried

    1998-01-01

    The growth rates of Pseudomonas putida KT2442 and mt-2 on benzoate, 4-hydroxybenzoate, or 4-methylbenzoate showed an exponential decrease with decreasing oxygen tensions (partial O2 tension [pO2] values). The oxygen tensions resulting in half-maximal growth rates were in the range of 7 to 8 mbar of O2 (corresponding to 7 to 8 μM O2) (1 bar = 105 Pa) for aromatic compounds, compared to 1 to 2 mbar for nonaromatic compounds like glucose or succinate. The decrease in the growth rates coincided with excretion of catechol or protocatechuate, suggesting that the activity of the corresponding oxygenases became limiting. The experiments directly establish that under aerobic and microaerobic conditions (about 10 mbar of O2), the diffusion of O2 into the cytoplasm occurs at high rates sufficient for catabolic processes. This is in agreement with calculated O2 diffusion rates. Below 10 mbar of O2, oxygen became limiting for the oxygenases, probably due to their high Km values, but the diffusion of O2 into the cytoplasm presumably should be sufficiently rapid to maintain ambient oxygen concentrations at oxygen tensions as low as 1 mbar of O2. The consequences of this finding for the availability of O2 as a substrate or as a regulatory signal in the cytoplasm of bacterial cells are discussed. PMID:9555896

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

    NASA Astrophysics Data System (ADS)

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

    PubMed Central

    Cai, Yuanfeng; Zheng, Yan; Bodelier, Paul L. E.; Conrad, Ralf; 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 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. PMID:27248847

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Physiology, biochemistry, and specific inhibitors of CH4, NH4+, and CO oxidation by methanotrophs and nitrifiers.

    PubMed Central

    Bédard, C; Knowles, R

    1989-01-01

    their inhibitor profiles are similar. Inhibitors thought to be specific to ammonia oxidizers have been used in environmental studies of nitrification. However, almost all of the numerous compounds found to inhibit ammonia oxidizers also inhibit methanotrophs, and most of the inhibitors act upon the monooxygenases. Many probably exert their effect by chelating copper, which is essential to the proper functioning of some monooxygenases. The lack of inhibitors specific for one or the other of the two groups of bacteria hampers the determination of their relative roles in nature. PMID:2496288

  8. A novel thermophilic methane-oxidizing bacteria from thermal springs of Uzon volcano caldera, Kamchatka

    NASA Astrophysics Data System (ADS)

    Dvorianchikova, E.; Kizilova, A.; Kravchenko, I.; Galchenko, V.

    2012-04-01

    Methane is a radiatively active trace gas, contributing significantly to the greenhouse effect. It is 26 times more efficient in absorbing and re-emitting infrared radiation than carbon dioxide. Methanotrophs play an essential role in the global carbon cycle by oxidizing 50-75% of the biologically produced methane in situ, before it reaches the atmosphere. Methane-oxidizing bacteria are isolated from the various ecosystems and described at present. Their biology, processes of methane oxidation in fresh-water, marsh, soil and marine habitats are investigated quite well. Processes of methane oxidation in places with extreme physical and chemical conditions (high or low , salinity and temperature values) are studied in much smaller degree. Such ecosystems occupy a considerable part of the Earth's surface. The existence of aerobic methanotrophs inhabiting extreme environments has been verified so far by cultivation experiments and direct detection of methane monooxygenase genes specific to almost all aerobic methanotrophs. Thermophilic and thermotolerant methanotrophs have been isolated from such extreme environments and consist of the gammaproteobacterial (type I) genera Methylothermus, Methylocaldum, Methylococcus and the verrucomicrobial genus Methylacidiphilum. Uzon volcano caldera is a unique area, where volcanic processes still happen today. Hydrothermal springs of the area are extreme ecosystems which microbial communities represent considerable scientific interest of fundamental and applied character. A thermophilic aerobic methane-oxidising bacterium was isolated from a sediment sample from a hot spring (56.1; 5.3) of Uzon caldera. Strain S21 was isolated using mineral low salt medium. The headspace gas was composed of CH4, Ar, CO2, and O2 (40:40:15:5). The temperature of cultivation was 50, pH 5.5. Cells of strain S21 in exponential and early-stationary phase were coccoid bacilli, about 1 μm in diameter, and motile with a single polar flagellum. PCR and

  9. Dissimilatory perchlorate reduction linked to aerobic methane oxidation via chlorite dismutase

    NASA Astrophysics Data System (ADS)

    Oremland, R. S.; Baesman, S. M.; Miller, L. G.

    2013-12-01

    The presence of methane (CH4) in the atmosphere of Mars is controversial yet the evidence has aroused scientific interest, as CH4 could be a harbinger of extant or extinct microbial life. There are various oxidized compounds present on the surface of Mars that could serve as electron acceptors for the anaerobic oxidation of CH4, including perchlorate (ClO4-). We examined the role of perchlorate, chlorate (ClO3-) and chlorite (ClO2-) as oxidants linked to CH4 oxidation. Dissimilatory perchlorate reduction begins with reduction of ClO4- to ClO2- and ends with dismutation of chlorite to yield chloride (Cl-) and molecular oxygen (O2). We explored the potential for aerobic CH4 oxidizing bacteria to couple with oxygen derived from chlorite dismutation during dissimilatory perchlorate reduction. Methane (0.2 kPa) was completely removed within several days from the N2-flushed headspace above cell suspensions of methanotrophs (Methylobacter albus strain BG8) and perchlorate reducing bacteria (Dechloromonas agitata strain CKB) in the presence of 5 mM ClO2-. Similar rates of CH4 consumption were observed for these mixed cultures whether they were co-mingled or segregated under a common headspace, indicating that direct contact of cells was not required for methane consumption to occur. We also observed complete removal of 0.2 kPa CH4 in bottles containing dried soil (enriched in methanotrophs by CH4 additions over several weeks) and D. agitata CKB and in the presence of 10 mM ClO2-. This soil (seasonally exposed sediment) collected from the shoreline of a freshwater lake (Searsville Lake, CA) demonstrated endogenous CH4 uptake as well as perchlorate, chlorate and chlorite reduction/dismutation. However, these experiments required physical separation of soil from the aqueous bacterial culture to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although dissimilatory reduction of ClO4- and ClO3- could be inferred from the

  10. Effect of nitrogen fertilization on the activity and diversity of methane oxidising bacteria in the littoral zone of a boreal lake

    NASA Astrophysics Data System (ADS)

    Saari, A.; Siljanen, H. M. P.; Hämäläinen, S.; Bodrossy, L.; Martikainen, P. J.

    2009-04-01

    Freshwater lakes are generally net sources of CH4 and in boreal lakes a major part of the CH4 emissions originates from the littoral zone during the ice-free season. Aerobic CH4 oxidising bacteria, methanotrophs, significantly limit the flux of CH4 to the atmosphere from sediments. Increased N load causes eutrophication and subsequent anoxia, which probably enhances CH4 production. In addition, inorganic nitrogen (ammonium and nitrate) can inhibit CH4 oxidation. Our study belongs to the research consortium METHECO (Eurodiversity programme of European Science Foundation), where the activity and diversity of methane oxidising bacteria are studied in various European ecosystems. We studied with in situ manipulation the effects of eutrophication (added nitrogen) on the activity and diversity of methanotrophs in a littoral wetland of a small and shallow hyper-eutrophic lake in east-central Finland. We established in the area growing sedges (7-10 m from the shore line) three sampling plots (1.2 m x 1.2 m), which were irrigated four times (from 4th July to 9th August) with ammonium nitrate solution giving 10 g N m-2for the total additional nitrogen load during the growing season. Three control plots were irrigated with equivalent amount of distilled water. The amount of added ammonium nitrate solution or water did not exceed 10% of the long-term (30 years) average rainfall in the area during the growing season. Sediment samples were taken from the depths of 0-2 cm, 2-10cm, 10-20 cm and 20-30 cm before, during and after the N treatment. Methane oxidation potential was studied in 550-ml flasks with sediment slurries and initial headspace CH4 concentration of 0.1%. The diversity of methanotrophs was studied with pmoA-microarray. Methane oxidation was most active in the organic surface sediment layer of 0-10 cm and the activity decreased with depth. Nitrogen addition in situ did not affect significantly the potential CH4 oxidation rates, although nitrate inhibited CH4

  11. Fate of mesophilic aerobic bacteria and Salmonella enterica on the surface of eggs as affected by chicken feces, storage temperature, and relative humidity.

    PubMed

    Park, Sunhyung; Choi, Seonyeong; Kim, Hoikyung; Kim, Yoonsook; Kim, Byeong-sam; Beuchat, Larry R; Ryu, Jee-Hoon

    2015-06-01

    We compared the microbiological quality of chicken eggshells obtained from a traditional wholesale market and a modern supermarket. We also determined the survival and growth characteristics of naturally occurring mesophilic aerobic bacteria (MAB) and artificially inoculated Salmonella enterica on eggshells under various environmental conditions (presence of chicken feces, temperature [4, 12, or 25 °C], and relative humidity [RH; 43 or 85%]). The populations of MAB, coliforms, and molds and yeasts on eggshells purchased from a traditional wholesale market were significantly (P ≤ 0.05) higher than those from a modern supermarket. In the second study, when we stored uninoculated eggs under various storage conditions, the population of MAB on eggshells (4.7-4.9 log CFU/egg) remained constant for 21 days, regardless of storage conditions. However, when eggshells were inoculated with S. enterica and stored under the same conditions, populations of the pathogen decreased significantly (P ≤ 0.05) under all tested conditions. Survival of S. enterica increased significantly (P ≤ 0.05) in the presence of feces, at low temperatures, and at low RH. These observations will be of value when predicting the behavior of microorganisms on eggshells and selecting storage conditions that reduce the populations of S. enterica on eggshells during distribution.

  12. Microbiological Quality of Ready-to-Eat Vegetables Collected in Mexico City: Occurrence of Aerobic-Mesophilic Bacteria, Fecal Coliforms, and Potentially Pathogenic Nontuberculous Mycobacteria

    PubMed Central

    Cerna-Cortes, Jorge Francisco; Leon-Montes, Nancy; Cortes-Cueto, Ana Laura; Salas-Rangel, Laura P.; Helguera-Repetto, Addy Cecilia; Lopez-Hernandez, Daniel; Rivera-Gutierrez, Sandra; Fernandez-Rendon, Elizabeth; Gonzalez-y-Merchand, Jorge Alberto

    2015-01-01

    The aims of this study were to evaluate the microbiological quality and the occurrence of nontuberculous mycobacteria (NTM) in a variety of salads and sprouts from supermarkets and street vendors in Mexico City. Aerobic-mesophilic bacteria (AMB) were present in 100% of RTE-salads samples; 59% of samples were outside guidelines range (>5.17 log10 CFU per g). Although fecal coliforms (FC) were present in 32% of samples, only 8% of them exceeded the permissible limit (100 MPN/g). Regarding the 100 RTE-sprouts, all samples were also positive for AMB and total coliforms (TC) and 69% for FC. Seven NTM species were recovered from 7 salad samples; they included three M. fortuitum, two M. chelonae, one M. mucogenicum, and one M. sp. Twelve RTE-sprouts samples harbored NTM, which were identified as M. porcinum (five), M. abscessus (two), M. gordonae (two), M. mucogenicum (two), and M. avium complex (one). Most RTE-salads and RTE-sprouts had unsatisfactory microbiological quality and some harbored NTM associated with illness. No correlation between the presence of coliforms and NTM was found. Overall, these results suggest that RTE-salads and RTE-sprouts might function as vehicles for NTM transmission in humans; hence, proper handling and treatment before consumption of such products might be recommendable. PMID:25918721

  13. Aerobic bacteria from mucous membranes, ear canals, and skin wounds of feral cats in Grenada, and the antimicrobial drug susceptibility of major isolates.

    PubMed

    Hariharan, Harry; Matthew, Vanessa; Fountain, Jacqueline; Snell, Alicia; Doherty, Devin; King, Brittany; Shemer, Eran; Oliveira, Simone; Sharma, Ravindra N

    2011-03-01

    In a 2-year period 54 feral cats were captured in Grenada, West Indies, and a total of 383 samples consisting of swabs from rectum, vagina, ears, eyes, mouth, nose and wounds/abscesses, were cultured for aerobic bacteria and campylobacters. A total of 251 bacterial isolates were obtained, of which 205 were identified to species level and 46 to genus level. A commercial bacterial identification system (API/Biomerieux), was used for this purpose. The most common species was Escherichia coli (N=60), followed by Staphylococcus felis/simulans (40), S. hominis (16), S. haemolyticus (12), Streptococcus canis (9), Proteus mirabilis (8), Pasteurella multocida (7), Streptococcus mitis (7), Staphylococcus xylosus (7), S. capitis (6), S. chromogenes (4), S. sciuri (3), S. auricularis (2), S. lentus (2), S. hyicus (2), Streptococcus suis (2) and Pseudomonas argentinensis (2). Sixteen other isolates were identified to species level. A molecular method using 16S rRNA sequencing was used to confirm/identify 22 isolates. Salmonella or campylobacters were not isolated from rectal swabs. E. coli and S. felis/simulans together constituted 50% of isolates from vagina. S. felis/simulans was the most common species from culture positive ear and eye samples. P. multocida was isolated from 15% of mouth samples. Coagulase-negative staphylococci were the most common isolates from nose and wound swabs. Staphylococcus aureus, or S. intemedius/S. pseudintermedius were not isolated from any sample. Antimicrobial drug resistance was minimal, most isolates being susceptible to all drugs tested against, including tetracycline.

  14. Adequacy of Petrifilm™ Aerobic Count plates supplemented with de Man, Rogosa & Sharpe broth and chlorophenol red for enumeration of lactic acid bacteria in salami.

    PubMed

    de Castilho, Natália Parma Augusto; Okamura, Vivian Tiemi; Camargo, Anderson Carlos; Pieri, Fábio Alessandro; Nero, Luís Augusto

    2015-12-01

    The present study aimed to assess the performance of alternative protocols to enumerate lactic acid bacteria (LAB) in salami. Fourteen cultures and two mixed starter cultures were plated using six protocols: 1) Petrifilm™ Aerobic Count (AC) with MRS broth and chlorophenol red (CR), incubated under aerobiosis or 2) under anaerobiosis, 3) MRS agar with CR, 4) MRS agar with bromocresol purple, 5) MRS agar at pH5.7, and 6) All Purpose Tween agar. Samples of salami were obtained and the LAB microbiota was enumerated by plating according protocols 1, 2, 3 and 5. Regression analysis showed a significant correlation between the tested protocols, based on culture counts (p<0.05). Similar results were observed for salami, and no significant differences of mean LAB counts between selected protocols (ANOVA, p>0.05). Colonies were confirmed as LAB, indicating proper selectivity of the protocols. The results showed the adequacy of Petrifilm™ AC supplemented with CR for the enumeration of LAB in salami.

  15. Microbiological Quality of Ready-to-Eat Vegetables Collected in Mexico City: Occurrence of Aerobic-Mesophilic Bacteria, Fecal Coliforms, and Potentially Pathogenic Nontuberculous Mycobacteria.

    PubMed

    Cerna-Cortes, Jorge Francisco; Leon-Montes, Nancy; Cortes-Cueto, Ana Laura; Salas-Rangel, Laura P; Helguera-Repetto, Addy Cecilia; Lopez-Hernandez, Daniel; Rivera-Gutierrez, Sandra; Fernandez-Rendon, Elizabeth; Gonzalez-y-Merchand, Jorge Alberto

    2015-01-01

    The aims of this study were to evaluate the microbiological quality and the occurrence of nontuberculous mycobacteria (NTM) in a variety of salads and sprouts from supermarkets and street vendors in Mexico City. Aerobic-mesophilic bacteria (AMB) were present in 100% of RTE-salads samples; 59% of samples were outside guidelines range (>5.17 log10 CFU per g). Although fecal coliforms (FC) were present in 32% of samples, only 8% of them exceeded the permissible limit (100 MPN/g). Regarding the 100 RTE-sprouts, all samples were also positive for AMB and total coliforms (TC) and 69% for FC. Seven NTM species were recovered from 7 salad samples; they included three M. fortuitum, two M. chelonae, one M. mucogenicum, and one M. sp. Twelve RTE-sprouts samples harbored NTM, which were identified as M. porcinum (five), M. abscessus (two), M. gordonae (two), M. mucogenicum (two), and M. avium complex (one). Most RTE-salads and RTE-sprouts had unsatisfactory microbiological quality and some harbored NTM associated with illness. No correlation between the presence of coliforms and NTM was found. Overall, these results suggest that RTE-salads and RTE-sprouts might function as vehicles for NTM transmission in humans; hence, proper handling and treatment before consumption of such products might be recommendable.

  16. Inhibition of the growth of Paenibacillus larvae, the causal agent of American foulbrood of honeybees, by selected strains of aerobic spore-forming bacteria isolated from apiarian sources.

    PubMed

    Alippi, Adriana M; Reynaldi, Francisco J

    2006-03-01

    The bacterium Paenibacillus larvae, the causative agent of American foulbrood disease of honeybee larvae, occurs throughout the world and is found in many beekeeping areas of Argentina. The potential as biocontrol agents of antagonic aerobic spore-forming bacteria isolated from honey samples and other apiarian sources were evaluated. Each isolate was screened against one strain of Paenibacillus larvae (ATCC 9545) by using a perpendicular streak technique. Ten randomly selected bacterial strains from the group that showed the best antagonistic effect to P. larvae ATCC 9545 were selected for further study. These were identified as Bacillus subtilis (m351), B. pumilus (m350), B. licheniformis (m347), B. cereus (mv33), B. cereus (m387), B. cereus (m6c), B. megaterium (m404), Brevibacillus laterosporus (BLAT169), B. laterosporus (BLAT170), and B. laterosporus (BLAT171). The antagonistic strains were tested against 17 P. larvae strains from different geographical origins by means of a spot test in wells. The analysis of variance and posterior comparison of means by Tukey method (P < 0.01) showed that the best antagonists were B. megaterium (m404), B. licheniformis (m347), B. cereus (m6c), B. cereus (mv33), and B. cereus (m387).

  17. A distinct pathway for tetrahymanol synthesis in bacteria

    PubMed Central

    Banta, Amy B.; Wei, Jeremy H.; Welander, Paula V.

    2015-01-01

    Tetrahymanol is a polycyclic triterpenoid lipid first discovered in the ciliate Tetrahymena pyriformis whose potential diagenetic product, gammacerane, is often used as a biomarker for water column stratification in ancient ecosystems. Bacteria are also a potential source of tetrahymanol, but neither the distribution of this lipid in extant bacteria nor the significance of bacterial tetrahymanol synthesis for interpreting gammacerane biosignatures is known. Here we couple comparative genomics with genetic and lipid analyses to link a protein of unknown function to tetrahymanol synthesis in bacteria. This tetrahymanol synthase (Ths) is found in a variety of bacterial genomes, including aerobic methanotrophs, nitrite-oxidizers, and sulfate-reducers, and in a subset of aquatic and terrestrial metagenomes. Thus, the potential to produce tetrahymanol is more widespread in the bacterial domain than previously thought. However, Ths is not encoded in any eukaryotic genomes, nor is it homologous to eukaryotic squalene-tetrahymanol cyclase, which catalyzes the cyclization of squalene directly to tetrahymanol. Rather, heterologous expression studies suggest that bacteria couple the cyclization of squalene to a hopene molecule by squalene-hopene cyclase with a subsequent Ths-dependent ring expansion to form tetrahymanol. Thus, bacteria and eukaryotes have evolved distinct biochemical mechanisms for producing tetrahymanol. PMID:26483502

  18. A distinct pathway for tetrahymanol synthesis in bacteria

    NASA Astrophysics Data System (ADS)

    Banta, Amy B.; Wei, Jeremy H.; Welander, Paula V.

    2015-11-01

    Tetrahymanol is a polycyclic triterpenoid lipid first discovered in the ciliate Tetrahymena pyriformis whose potential diagenetic product, gammacerane, is often used as a biomarker for water column stratification in ancient ecosystems. Bacteria are also a potential source of tetrahymanol, but neither the distribution of this lipid in extant bacteria nor the significance of bacterial tetrahymanol synthesis for interpreting gammacerane biosignatures is known. Here we couple comparative genomics with genetic and lipid analyses to link a protein of unknown function to tetrahymanol synthesis in bacteria. This tetrahymanol synthase (Ths) is found in a variety of bacterial genomes, including aerobic methanotrophs, nitrite-oxidizers, and sulfate-reducers, and in a subset of aquatic and terrestrial metagenomes. Thus, the potential to produce tetrahymanol is more widespread in the bacterial domain than previously thought. However, Ths is not encoded in any eukaryotic genomes, nor is it homologous to eukaryotic squalene-tetrahymanol cyclase, which catalyzes the cyclization of squalene directly to tetrahymanol. Rather, heterologous expression studies suggest that bacteria couple the cyclization of squalene to a hopene molecule by squalene-hopene cyclase with a subsequent Ths-dependent ring expansion to form tetrahymanol. Thus, bacteria and eukaryotes have evolved distinct biochemical mechanisms for producing tetrahymanol.

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

    PubMed

    Crombie, Andrew T; Murrell, J Colin

    2014-06-05

    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. Meta-analysis of effects of inoculation with homofermentative and facultative heterofermentative lactic acid bacteria on silage fermentation, aerobic stability, and the performance of dairy cows.

    PubMed

    Oliveira, André S; Weinberg, Zwi G; Ogunade, Ibukun M; Cervantes, Andres A P; Arriola, Kathy G; Jiang, Yun; Kim, Donghyeon; Li, Xujiao; Gonçalves, Mariana C M; Vyas, Diwakar; Adesogan, Adegbola T

    2017-03-22

    Forages are usually inoculated with homofermentative and facultative heterofermentative lactic acid bacteria (LAB) to enhance lactic acid fermentation of forages, but effects of such inoculants on silage quality and the performance of dairy cows are unclear. Therefore, we conducted a meta-analysis to examine the effects of LAB inoculation on silage quality and preservation and the performance of dairy cows. A second objective was to examine the factors affecting the response to silage inoculation with LAB. The studies that met the selection criteria included 130 articles that examined the effects of LAB inoculation on silage quality and 31 articles that investigated dairy cow performance responses. The magnitude of the effect (effect size) was evaluated using raw mean differences (RMD) between inoculated and uninoculated treatments. Heterogeneity was explored by meta-regression and subgroup analysis using forage type, LAB species, LAB application rate, and silo scale (laboratory or farm-scale) as covariates for the silage quality response and forage type, LAB species, diet type [total mixed ration (TMR) or non-TMR], and the level of milk yield of the control cows as covariates for the performance responses. Inoculation with LAB (≥10(5) cfu/g as fed) markedly increased silage fermentation and dry matter recovery in temperate and tropical grasses, alfalfa, and other legumes. However, inoculation did not improve the fermentation of corn, sorghum, or sugarcane silages. Inoculation with LAB reduced clostridia and mold growth, butyric acid production, and ammonia-nitrogen in all silages, but it had no effect on aerobic stability. Silage inoculation (≥10(5) cfu/g as fed) increased milk yield and the response had low heterogeneity. However, inoculation had no effect on diet digestibility and feed efficiency. Inoculation with LAB improved the fermentation of grass and legume silages and the performance of dairy cows but did not affect the fermentation of corn, sorghum

  1. Short-term variations of methane concentrations and methanotrophic activity in a coastal inlet (Eckernförde Bay, Germany)

    NASA Astrophysics Data System (ADS)

    Richner, Dominik; Niemann, Helge; Steinle, Lea; Schneider von Deimling, Jens; Urban, Peter; Hoffmann, Jasper; Schmidt, Mark; Treude, Tina; Lehmann, Moritz

    2016-04-01

    Large quantities of methane are produced in anoxic sediments of continental margins and may be liberated into the overlying water column and, potentially, into the atmosphere. However, a sequence of microbially mediated methane oxidation pathways in sediments and the water column mitigate the contribution of oceans to the atmospheric methane budget. Of particular importance are methanotrophic bacteria in the water column that mediate the aerobic oxidation of methane (MOx), and represent the final sink for methane before its release to the atmosphere where it acts as a potent greenhouse gas. However methane cycling in (aerobic) marine waters is not well constrained. Particularly little is known about spatiotemporal aspects of MOx activity and the underlying key physical, chemical and biological factors. Here we show results from our investigations on methane dynamics on very short time scales of hours to days in the Eckernförde Bay (E-Bay), a costal inlet of the Baltic Sea in northern Germany featuring seasonal bottom water hypoxia/anoxia. In autumn 2014, we observed highly spatiotemporal variations in water column methane contents and MOx activity: Anoxic bottom waters in a trough in the northern part of the bay contained extremely high methane concentrations of up to 800 nM, which sharply declined at the midwater redox interface (methane remained supersaturated with respect to the atmospheric equilibrium throughout the water column at all times). The methane decrease at the redox interface was related to highly active MOx communities consuming methane under microoxic conditions at rates of up 40 nM/d. About 12 hours later, the methane content and the extend of bottom water anoxia was much lower and MOx activity was highly reduced in the northern part but strongly elevated in the southern part of the bay. A few days later, bottom water anoxia, methane loading and MOx activity was partially re-established. In this contribution, we will discuss potential forcing

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

    PubMed Central

    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, indicating that local sources of nitrogen are assimilated and that novel mechanisms of nitrogen metabolism may be involved. Although these symbioses have access to rich sources of ammonium (NH4+ and NH3) and/or nitrate, several investigators have proposed that N2 fixation may account for some of these isotope values. Here we report that [15N]ammonium and, to a lesser degree, [15N]nitrate are assimilated into organic compounds by Solemya reidi, a gutless clam containing S-oxidizing bacteria, and seep mussel Ia, an undescribed mytilid containing methanotrophic bacteria. In contrast, Riftia pachyptila, the giant hydrothermal vent tube worm symbiotic with S-oxidizing bacteria, assimilated nitrate but not exogenous ammonium. The rates of assimilation of these sources are sufficient to at least partially support C1 compound metabolism. N2 assimilation was not exhibited by the symbionts tested. PMID:16349279

  3. Dry matter and nutritional losses during aerobic deterioration of corn and sorghum silages as influenced by different lactic acid bacteria inocula.

    PubMed

    Tabacco, E; Righi, F; Quarantelli, A; Borreani, G

    2011-03-01

    The economic damage that results from aerobic deterioration of silage is a significant problem for farm profitability and feed quality. This paper quantifies the dry matter (DM) and nutritional losses that occur during the exposure of corn and sorghum silages to air over 14 d and assesses the possibility of enhancing the aerobic stability of silages through inoculation with lactic acid bacteria (LAB). The trial was carried out in Northern Italy on corn (50% milk line) and grain sorghum (early dough stage) silages. The crops were ensiled in 30-L jars, without a LAB inoculant (C), with a Lactobacillus plantarum inoculum (LP), and with a Lactobacillus buchneri inoculum (LB; theoretical rate of 1 × 10(6) cfu/g of fresh forage). The pre-ensiled material, the silage at silo opening, and the aerobically exposed silage were analyzed for DM content, fermentative profiles, yeast and mold count, starch, crude protein, ash, fiber components, 24-h and 48-h DM digestibility and neutral detergent fiber (NDF) degradability. The yield and nutrient analysis data of the corn and sorghum silages were used as input for Milk2006 to estimate the total digestible nutrients, net energy of lactation, and milk production per Mg of DM. The DM fermentation and respiration losses were also calculated. The inocula influenced the in vitro NDF digestibility at 24h, the net energy for lactation (NE(L)), and the predicted milk yield per megagram of DM, whereas the length of time of air exposure influenced DM digestibility at 24 and 48 h, the NE(L), and the predicted milk yield per megagram of DM in the corn silages. The inocula only influenced the milk yield per megagram of DM and the air exposure affected the DM digestibility at 24h, the NE(L), and the milk yield per megagram of DM in the sorghum silages. The milk yield, after 14 d of air exposure, decreased to 1,442, 1,418, and 1,277 kg/Mg of DM for C, LB, and LP corn silages, respectively, compared with an average value of 1,568 kg of silage at

  4. Poly-3-hydroxybutyrate metabolism in the type II methanotroph Methylocystis parvus OBBP.

    PubMed

    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.

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

    EPA Science Inventory

    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...

  6. Ulcerative enteritis in Homarus americanus: case report and molecular characterization of intestinal aerobic bacteria of apparently healthy lobsters in live storage.

    PubMed

    Battison, Andrea L; Després, Béatrice M; Greenwood, Spencer J

    2008-10-01

    An intermoult male American lobster, Homarus americanus, with severe intestinal lesions was encountered while collecting samples of aerobic intestinal bacteria from lobsters held in an artificial sea-water recirculation aquarium system. Grossly, the intestine was firm, thickened, and white. Histologic examination revealed a severe, diffuse, ulcerative enteritis which spared the chitin-lined colon, somewhat similar to hemocytic enteritis of shrimp. The bacterial isolates from this lobster were compared to 11 other lobsters lacking gross intestinal lesions. Two organisms, one identified as Vibrio sp. and another most similar to an uncultured proteobacterium (98.9%), clustering with Rhanella and Serratia species using 16S rDNA PCR, were isolated from the intestines of the 11, grossly normal, lobsters and the affected lobster. An additional two intestinal isolates were cultured only from the lobster with ulcerative enteritis. One, a Flavobacterium, similar to Lutibacter litoralis (99.3%), possibly represented a previously described commensal of the distal intestine. The second, a Vibrio sp., was unique to the affected animal. While the etiology of the ulcerative enteritis remains undetermined, this report represents the first description of gross and histologic findings in H. americanus of a condition which has morphologic similarities to hemocytic enteritis of shrimp. An additional observation was a decrease in the number of intestinal isolates recovered from the 11 apparently healthy lobsters compared to that previously reported for recently harvested lobster. More comprehensive studies of the relationship between the health of lobsters, gut microbial flora and the husbandry and environment maintained within holding units are warranted.

  7. Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants.

    PubMed

    Bao, Zhihua; Okubo, Takashi; Kubota, Kengo; Kasahara, Yasuhiro; Tsurumaru, Hirohito; Anda, Mizue; Ikeda, Seishi; Minamisawa, Kiwamu

    2014-08-01

    In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH4 oxidation and N2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4 oxidation and N2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots.

  8. Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions

    PubMed Central

    Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

    2014-01-01

    Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. PMID:24245852

  9. Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation

    PubMed Central

    Skennerton, Connor T.; Ward, Lewis M.; Michel, Alice; Metcalfe, Kyle; Valiente, Chanel; Mullin, Sean; Chan, Ken Y.; Gradinaru, Viviana; Orphan, Victoria J.

    2015-01-01

    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. PMID:26779119

  10. Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation.

    PubMed

    Skennerton, Connor T; Ward, Lewis M; Michel, Alice; Metcalfe, Kyle; Valiente, Chanel; Mullin, Sean; Chan, Ken Y; Gradinaru, Viviana; Orphan, Victoria J

    2015-01-01

    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.

  11. Reverse Methanogenesis and Respiration in Methanotrophic Archaea

    PubMed Central

    Koehorst, Jasper J.; Jetten, Mike S. M.; Stams, Alfons J. M.

    2017-01-01

    Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types. PMID:28154498

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

    NASA Technical Reports Server (NTRS)

    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.

  13. Transcriptomic evidence for net methane oxidation and net methane production in putative ANaerobic MEthanotrophic (ANME) archaea

    NASA Astrophysics Data System (ADS)

    Lloyd, K. G.; Alperin, M. J.; Teske, A.

    2010-12-01

    Anaerobic methane oxidation regulates methane emissions in marine sediments and is thought to be mediated by uncultured methanogen-like archaea collectively labeled ANME (for ANaerobic MEthanotrophs). ANME archaea are often assumed to be obligate methanotrophs that are incapable of net methanogenesis, and are therefore used as proxies for anaerobic methane oxidation in many environments in spite of uncertainty regarding their metabolic capabilities. We tested this assumption by detecting and quantifying methanogenic gene transcription of ANME archaea across clearly differentiated zones of methane oxidation vs. methane production in sediments from the White Oak River estuary, NC. ANME-1 archaea (a group of putative obligate methanotrophs) consistently transcribe 16S rRNA and mRNA of methyl coenzyme M reductase (mcrA) the key gene for methanogenesis, up to 45 cm into methanogenic sediments. CARD-FISH shows that ANME-1 archaea exist as single rod-shaped cells or pairs of cells, and in very low numbers. Integrating normalized depth-distributions of 16S rDNA and rRNA (measured with qPCR and RT-qPCR, respectively) shows that 26-77 % of the rDNA proxy for ANME-1 cell numbers, and 18-74 % of the rRNA proxy for ANME-1 activity occurs within methane-producing sediments. mRNA transcripts of dissimilatory sulfite reductase (dsrAB) from sulfate reducing bacteria, the putative syntrophic partners of sulfate-dependent methane oxidation, were amplified consistently from methane-oxidizing sediments, and inconsistently from methane-producing sediments. These results change the perspective from ANME-1 archaea as obligate methane oxidizers to methanogens that are also capable of methane oxidation.

  14. Phosphoketolase overexpression increases biomass and lipid yield from methane in an obligate methanotrophic biocatalyst.

    PubMed

    Henard, Calvin A; Smith, Holly K; Guarnieri, Michael T

    2017-04-01

    Microbial conversion of methane to high-value bio-based chemicals and materials offers a path to mitigate GHG emissions and valorize this abundant-yet -underutilized carbon source. In addition to fermentation optimization strategies, rational methanotrophic bacterial strain engineering offers a means to reach industrially relevant titers, carbon yields, and productivities of target products. The phosphoketolase pathway functions in heterofermentative bacteria where carbon flux through two sugar catabolic pathways to mixed acids (lactic acid and acetic acid) increases cellular ATP production. Importantly, this pathway also serves as an alternative route to produce acetyl-CoA that bypasses the CO2 lost through pyruvate decarboxylation in the Embden-Meyerhof-Parnas pathway. Thus, the phosphoketolase pathway can be leveraged for carbon efficient biocatalysis to acetyl-CoA-derived intermediates and products. Here, we show that the industrially promising methane biocatalyst, Methylomicrobium buryatense, encodes two phosphoketolase isoforms that are expressed in methanol- and methane-grown cells. Overexpression of the PktB isoform led to a 2-fold increase in intracellular acetyl-CoA concentration, and a 2.6-fold yield enhancement from methane to microbial biomass and lipids compared to wild-type, increasing the potential for methanotroph lipid-based fuel production. Off-gas analysis and metabolite profiling indicated that global metabolic rearrangements, including significant increases in post-translational protein acetylation and gene expression of the tetrahydromethanopterin-linked pathway, along with decreases in several excreted products, coincided with the superior biomass and lipid yield observed in the engineered strain. Further, these data suggest that phosphoketolase may play a key regulatory role in methanotrophic bacterial metabolism. Given that acetyl-CoA is a key intermediate in several biosynthetic pathways, phosphoketolase overexpression offers a viable

  15. Bioreactor Performance Parameters for an Industrially-Promising Methanotroph Methylomicrobium buryatense 5GB1

    DOE PAGES

    Gilman, Alexey; Laurens, Lieve M.; Puri, Aaron W.; ...

    2015-11-16

    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. But, to take advantage of the potential of this methanotroph, it is important to generate comprehensive bioreactor-based datasets for different growth conditions to compare bioprocess parameters. The datasets of growth parameters, gas utilization rates, and products (total biomass, extracted fatty acids, glycogen, excreted acids) were obtained formore » cultures of M. buryatense 5GB1 grown in continuous culture under methane limitation and O2 limitation conditions. Additionally, experiments were performed involving unrestricted batch growth conditions with both methane and methanol as substrate. All four growth conditions show significant differences. The most notable changes are the high glycogen content and high formate excretion for cells grown on methanol (batch), and high O2:CH4 utilization ratio for cells grown under methane limitation. The results presented here represent the most comprehensive published bioreactor datasets for a gamma-proteobacterial methanotroph. This information shows that metabolism by M. buryatense 5GB1 differs significantly for each of the four conditions tested. O2 limitation resulted in the lowest relative O2 demand and fed-batch growth on methane the highest. Future studies are needed to understand the metabolic basis of these differences. However, these results suggest that both batch and continuous culture conditions have specific advantages, depending on the product of interest.« less

  16. Bioreactor Performance Parameters for an Industrially-Promising Methanotroph Methylomicrobium buryatense 5GB1

    SciTech Connect

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

    2015-11-16

    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. But, to take advantage of the potential of this methanotroph, it is important to generate comprehensive bioreactor-based datasets for different growth conditions to compare bioprocess parameters. The datasets of growth parameters, gas utilization rates, and products (total biomass, extracted fatty acids, glycogen, excreted acids) were obtained for cultures of M. buryatense 5GB1 grown in continuous culture under methane limitation and O2 limitation conditions. Additionally, experiments were performed involving unrestricted batch growth conditions with both methane and methanol as substrate. All four growth conditions show significant differences. The most notable changes are the high glycogen content and high formate excretion for cells grown on methanol (batch), and high O2:CH4 utilization ratio for cells grown under methane limitation. The results presented here represent the most comprehensive published bioreactor datasets for a gamma-proteobacterial methanotroph. This information shows that metabolism by M. buryatense 5GB1 differs significantly for each of the four conditions tested. O2 limitation resulted in the lowest relative O2 demand and fed-batch growth on methane the highest. Future studies are needed to understand the metabolic basis of these differences. However, these results suggest that both batch and continuous culture conditions have specific advantages, depending on the product of interest.

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

    PubMed Central

    Fradet, Danielle T.; 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

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

    NASA Astrophysics Data System (ADS)

    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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    Methane is a major contributor to the greenhouse effect, its atmospheric concentration being more than doubled since the XIX century. Every year 22 Tg of methane are released to the atmosphere from several natural and anthropogenic sources. Natural sources include geothermal/volcanic areas but the estimation of the total methane emission from these areas is currently not well defined since the balance between emission through degassing and microbial oxidation within the soils is not well known. Microbial oxidation in soils contributes globally for about 3-9% to the removal of methane from the atmosphere and recent studies evidenced methanotrophic activity also in soils of volcanic/geothermal areas despite their harsh environmental conditions (high temperatures, low pH and high concentrations of H2S and NH3). Methanotrophs are a diverse group of bacteria that are able to metabolize methane as their only source of carbon and energy and are found within the Alpha and Gamma classes of Proteobacteria and within the phylum Verrucomicrobia. Our purpose was to study the interaction between methanotrophic communities and the methane emitted from the geothermally most active site of Pantelleria island (Italy), Favara Grande, whose total methane emission has been previously estimated in about 2.5 t/a. Laboratory incubation experiments with soil samples from Favara Grande showed methane consumption values of up to 9500 ng g-1 dry soil per hour while soils collected outside the geothermal area consume less than 6 ng g-1 h-1. The maximum consumption was measured in the shallowest part of the soil profile (1-3 cm) and high values (>100 ng g-1 h-1) were maintained up to a depht of 15 cm. Furthermore, the highest consumption was measured at 37°C, and a still recognizable consumption (>20 ng g-1 h-1) at 80°C, with positive correlation with the methane concentration in the incubation atmosphere. These results can be considered a clear evidence of the presence of methanotrophs that

  20. Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments.

    PubMed

    Nercessian, Olivier; Bienvenu, Nadège; Moreira, David; Prieur, Daniel; Jeanthon, Christian

    2005-01-01

    To contribute to the identification of methanogens, methanotrophs and sulfate-reducing bacteria (SRB) in microbial communities from the 13 degrees N (East Pacific Rise) and Rainbow (Mid-Atlantic Ridge) hydrothermal vent fields, we investigated the diversity of mcrA, pmoA and dsrAB genes sequences. Clone libraries were obtained using DNA isolated from fragments of diffuse vents, sediment and in situ samplers. The clones were categorized by restriction fragment length polymorphism, and representatives of each group were sequenced. Sequences were related to that of hyperthermophilic (order Methanopyrales and family Methanocaldococcaceae), thermophilic and mesophilic (family Methanococcaceae) methanogens, thermophilic (proposed genus 'Methylothermus') and mesophilic type I methanotrophs, and hyperthermophilic (order Archaeoglobales), thermophilic (order Thermodesulfobacteriales) and mesophilic (family Desulfobulbaceae) SRB. Several of the obtained sequences were distantly related to the genes of cultivated organisms, providing evidence of the existence of novel lineages in the three functional groups. This study provides for the first time an insight into the diversity of several functional genes of deep-sea hydrothermal system microorganisms.

  1. Methylomonas scandinavica sp. nov., a new methanotrophic psychrotrophic bacterium isolated from deep igneous rock ground water of Sweden.

    PubMed

    Kalyuzhnaya, M G; Khmelenina, V N; Kotelnikova, S; Holmquist, L; Pedersen, K; Trotsenko, Y A

    1999-12-01

    Methane-utilizing bacteria were enriched from deep igneous rock environments and affiliated by amplification of functional and phylogenetic gene probes. Type I methanotrophs belonging to the genera Methylomonas and Methylobacter dominated in enrichment cultures from depths below 400 m. A pure culture of an obligate methanotroph (strain SR5) was isolated and characterized. Pink-pigmented motile rods of the new isolate contained intracytoplasmic membranes as stacks of vesicles, assimilated methane via the ribulose monophosphate pathway and had an incomplete tricarboxylic acid cycle. Phosphatidyl glycerol, methylene ubiquinone and cytochrome c552 were prevailing. The DNA G+C content is 53.3 mol %. Strain SR5 grew at temperatures between 5 and 30 degrees C with optimum at 15 degrees C, close to its in situ temperature. Analyses of 16S rRNA gene, whole cell protein, enzymatic and physiological analyses of strain SR-5 revealed significant differences compared to the other representatives of Type I methanotrophs. Based on pheno- and genotypic characteristics we propose to refer the strain SR5 as to a new species, Methylomonas scandinavica.

  2. Growth parameters of escherichia coli O157:H7, salmonella and listeria monocytogenes and aerobic mesophilic bacteria of apple cider amended with nisin-EDTA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effect of nisin (0 or 300 IU), Ethylenediamine Tetraacetic Acid (EDTA, 20 mM) and (nisin 300 IU+ EDTA 20 mM) on growth parameters; including lag period (LP) and growth rate (GR) of Escherichia coli O157:H7, L. monocytogenes and Salmonella spp. in the presence or absence of aerobic mesophilic bac...

  3. (Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor

    PubMed Central

    Carlström, Charlotte I.; Loutey, Dana; Bauer, Stefan; Clark, Iain C.; Rohde, Robert A.; Iavarone, Anthony T.; Lucas, Lauren

    2015-01-01

    ABSTRACT The pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2−), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms. PMID:25805732

  4. Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on methanotroph abundance and methane uptake in a grazed pasture soil.

    PubMed

    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.

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

    PubMed

    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).

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

    NASA Technical Reports Server (NTRS)

    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).

  7. Effect of applying molasses or inoculants containing homofermentative or heterofermentative bacteria at two rates on the fermentation and aerobic stability of corn silage.

    PubMed

    Huisden, C M; Adesogan, A T; Kim, S C; Ososanya, T

    2009-02-01

    This study determined how the fermentation and aerobic stability of corn silage are affected by treatment with molasses or 2 dual-purpose inoculants applied at or above the recommended rate. Corn forage (DeKalb 69-70) was harvested at 39% dry matter (DM) and ensiled after treatment with no additives (control, CON), molasses (MOL), Buchneri 500 inoculant, or Pioneer 11C33 inoculant. Molasses was applied at 3% of forage DM. Buchneri 500 was applied at the recommended rate of 8 mg/kg fresh forage to supply 1 x 10(5) cfu/g of Pediococcus pentosaceus 12455 and 4 x 10(5) cfu/g of Lactobacillus buchneri 40788 (BB) or at twice the recommended rate (DBB). Pioneer 11C33 inoculant was applied at the recommended rate of 1.1 mg/kg fresh forage to supply 1 x 10(5) cfu/g of a mixture of Lactobacillus plantarum, L. buchneri, and Enteroccocus faecium (PN) or at twice the recommended rate (DPN). Each treatment was applied in quadruplicate and the treated forages were ensiled within 20-L mini silos for 135 d at 18 to 35 degrees C. Molasses-treated silages had greater ash and starch concentrations than CON silages and greater lactate and ethanol concentrations than other silages. Like CON silages, MOL silages had high yeast counts (>10(5) cfu/g); consequently, they deteriorated within 30 h as shown by temperature increase. Inoculant-treated silages had lower lactate to acetate ratios than CON or MOL silages largely because they had greater acetate concentrations. Consequently, all inoculant-treated silages had fewer yeasts (<10(5) cfu/g) and were more stable (>30 h) than CON and MOL silages. When applied at recommended rates, PN and BB had similar effects on silage chemical composition, fermentation, fungal counts, and aerobic stability, except for a lower lactate concentration in PN silages. Concentrations of VFA, and NH(3)-N, pH, and extent of aerobic stability were similar for PN, DPN, BB, and DBB silages. However, lactate concentration was greater in DPN than in PN. In conclusion

  8. Aquatic plant surface as a niche for methanotrophs.

    PubMed

    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 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 10(5)-10(7) 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.

  9. Aquatic plant surface as a niche for methanotrophs

    PubMed Central

    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 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 105–107 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. PMID:24550901

  10. Aerobic microbial enhanced oil recovery

    SciTech Connect

    Torsvik, T.; Gilje, E.; Sunde, E.

    1995-12-31

    In aerobic MEOR, the ability of oil-degrading bacteria to mobilize oil is used to increase oil recovery. In this process, oxygen and mineral nutrients are injected into the oil reservoir in order to stimulate growth of aerobic oil-degrading bacteria in the reservoir. Experiments carried out in a model sandstone with stock tank oil and bacteria isolated from offshore wells showed that residual oil saturation was lowered from 27% to 3%. The process was time dependent, not pore volume dependent. During MEOR flooding, the relative permeability of water was lowered. Oxygen and active bacteria were needed for the process to take place. Maximum efficiency was reached at low oxygen concentrations, approximately 1 mg O{sub 2}/liter.

  11. Microbial Removal of Atmospheric Carbon Tetrachloride in Bulk Aerobic Soils▿

    PubMed Central

    Mendoza, Y.; Goodwin, K. D.; Happell, J. D.

    2011-01-01

    Atmospheric concentrations of carbon tetrachloride (CCl4) were removed by bulk aerobic soils from tropical, subtropical, and boreal environments. Removal was observed in all tested soil types, indicating that the process was widespread. The flux measured in field chamber experiments was 0.24 ± 0.10 nmol CCl4 (m2 day)−1 (average ± standard deviation [SD]; n = 282). Removal of CCl4 and removal of methane (CH4) were compared to explore whether the two processes were linked. Removal of both gases was halted in laboratory samples that were autoclaved, dry heated, or incubated in the presence of mercuric chloride (HgCl2). In marl soils, treatment with antibiotics such as tetracycline and streptomycin caused partial inhibition of CCl4 (50%) and CH4 (76%) removal, but removal was not affected in soils treated with nystatin or myxothiazol. These data indicated that bacteria contributed to the soil removal of CCl4 and that microeukaryotes may not have played a significant role. Amendments of methanol, acetate, and succinate to soil samples enhanced CCl4 removal by 59%, 293%, and 72%, respectively. Additions of a variety of inhibitors and substrates indicated that nitrification, methanogenesis, or biological reduction of nitrate, nitrous oxide, or sulfate (e.g., occurring in possible anoxic microzones) did not play a significant role in the removal of CCl4. Methyl fluoride inhibited removal of CH4 but not CCl4, indicating that CH4 and CCl4 removals were not directly linked. Furthermore, CCl4 removal was not affected in soils amended with copper sulfate or methane, supporting the results with MeF and suggesting that the observed CCl4 removal was not significantly mediated by methanotrophs. PMID:21724884

  12. Aerobic Tennis.

    ERIC Educational Resources Information Center

    Stewart, Michael J.; Ahlschwede, Robert

    1989-01-01

    Increasing the aerobic nature of tennis drills in the physical education class may be necessary if tennis is to remain a part of the public school curriculum. This article gives two examples of drills that can be modified by teachers to increase activity level. (IAH)

  13. Evidence of intense archaeal and bacterial methanotrophic activity in the Black Sea water column.

    PubMed

    Durisch-Kaiser, Edith; Klauser, Lucia; Wehrli, Bernhard; Schubert, Carsten

    2005-12-01

    In the northwestern Black Sea, methane oxidation rates reveal that above shallow and deep gas seeps methane is removed from the water column as efficiently as it is at sites located off seeps. Hence, seeps should not have a significant impact on the estimated annual flux of approximately 4.1 x 10(9) mol methane to the atmosphere [W. S. Reeburgh, B. B. Ward, S. C. Wahlen, K. A. Sandbeck, K. A. Kilatrick, and L. J. Kerkhof, Deep-Sea Res. 38(Suppl. 2):S1189-S1210, 1991]. Both the stable carbon isotopic composition of dissolved methane and the microbial community structure analyzed by fluorescent in situ hybridization provide strong evidence that microbially mediated methane oxidation occurs. At the shelf, strong isotope fractionation was observed above high-intensity seeps. This effect was attributed to bacterial type I and II methanotrophs, which on average accounted for 2.5% of the DAPI (4',6'-diamidino-2-phenylindole)-stained cells in the whole oxic water column. At deep sites, in the oxic-anoxic transition zone, strong isotopic fractionation of methane overlapped with an increased abundance of Archaea and Bacteria, indicating that these organisms are involved in the oxidation of methane. In underlying anoxic water, we successfully identified the archaeal methanotrophs ANME-1 and ANME-2, eachof which accounted for 3 to 4% of the total cell counts. ANME-1 and ANME-2 appear as single cells in anoxicwater, compared to the sediment, where they may form cell aggregates with sulfate-reducing bacteria (A. Boetius, K. Ravenschlag, C. J. Schubert, D. Rickert, F. Widdel, A. Giesecke, R. Amann, B. B. Jørgensen, U. Witte, and O. Pfannkuche, Nature 407:623-626, 2000; V. J. Orphan, C. H. House, K.-U. Hinrichs, K. D. McKeegan, and E. F. DeLong, Proc. Natl. Acad. Sci. USA 99:7663-7668, 2002).

  14. Methane Emission From the Congo Deep Sea Fan and Subsequent Aerobic Oxidation in the Quaternary Tropical Atlantic

    NASA Astrophysics Data System (ADS)

    Handley, L.; Cooke, M. P.; Talbot, H. M.; Wagner, T.

    2008-12-01

    The Congo Fan is a well-documented region of important methane (CH4) storage and gas seepage: gas hydrates abound at and just below the sediment surface as do large deeply-buried reservoirs of thermogenic methane linked with hydrocarbon source rocks. In the Congo Fan, both sources of methane are intimately connected through a complex network of faults, structuring this massive sediment wedge in a unique way. Methane release from both reservoirs has the potential to drive or respond to changes in local and global climate, thus causing changes in ocean chemical properties and biotic responses. Understanding these poorly-constrained mechanisms of methane emission and reconstructing the history of past emissions in the ocean is the main focus of our study. The ultimate fate of CH4 is, typically, its oxidation to CO2; this process can occur aerobically and anaerobically. Compared to anaerobic processes, aerobic methane oxidation, and its underlying mechanisms and possible feedbacks for the ocean-climate system, has received little attention. Here we present molecular evidence from Congo Fan sediments for aerobic methane oxidation and highlight how the process may play a previously unrecognised role in carbon cycling and oxygen availability in the water column. Bacteriohopanepolyols (BHPs) are lipid membrane constituents and occur with a wide range of structural and functional variability in many bacteria. Amino-BHPs are produced in large abundances by methane-oxidising bacteria and the 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) is a highly specific biomarker for aerobic methane oxidation. The Congo Fan record (ODP Leg 175, Site 1075; 2996 m depth) spans the last 1 Myr and reveals remarkable organic biomarker preservation, with a suite of 13 different BHPs identified in most sediment horizons, including aminopentol. Aminopentol abundance varies widely throughout the section and appears to do so cyclically, with markedly greater concentrations between ca

  15. Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

    PubMed Central

    Bao, Zhihua; Okubo, Takashi; Kubota, Kengo; Kasahara, Yasuhiro; Tsurumaru, Hirohito; Anda, Mizue; Ikeda, Seishi

    2014-01-01

    In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH4 oxidation and N2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4 oxidation and N2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots. PMID:24928870

  16. Genetics in methylotrophic bacteria: Appendix. Final report

    SciTech Connect

    Lidstrom, M.E.

    1998-09-01

    This research has focused primarily on promoters in Methylobacterium extorquens AM1 and in methanotrophic bacteria. In Methylobacterium extorquens work continued on the moxF promoter. The author constructed chromosomal lacZ fusions of this promoter to avoid the regulation problems of plasmid-borne fragments and has shown that this is regulated normally in the chromosome. She has constructed lacZ fusions to some of the mox genes involved in the synthesis of the cofactor, PQQ, in order to carry out similar analysis of transcription of PQQ genes. The author has continued to isolate mox genes in methanotrophs for the purpose of studying their promoters and transcriptional regulation.

  17. Geographic and seasonal variation of dissolved methane and aerobic methane oxidation in Alaskan lakes

    NASA Astrophysics Data System (ADS)

    Martinez-Cruz, K.; Sepulveda-Jauregui, A.; Anthony, K. Walter; Thalasso, F.

    2015-08-01

    Methanotrophic bacteria play an important role oxidizing a significant fraction of methane (CH4) produced in lakes. Aerobic CH4 oxidation depends mainly on lake CH4 and oxygen (O2) concentrations, in such a manner that higher MO rates are usually found at the oxic/anoxic interface, where both molecules are present. MO also depends on temperature, and via methanogenesis, on organic carbon input to lakes, including from thawing permafrost in thermokarst (thaw)-affected lakes. Given the large variability in these environmental factors, CH4 oxidation is expected to be subject to large seasonal and geographic variations, which have been scarcely reported in the literature. In the present study, we measured CH4 oxidation rates in 30 Alaskan lakes along a north-south latitudinal transect during winter and summer with a new field laser spectroscopy method. Additionally, we measured dissolved CH4 and O2 concentrations. We found that in the winter, aerobic CH4 oxidation was mainly controlled by the dissolved O2 concentration, while in the summer it was controlled primarily by the CH4 concentration, which was scarce compared to dissolved O2. The permafrost environment of the lakes was identified as another key factor. Thermokarst (thaw) lakes formed in yedoma-type permafrost had significantly higher CH4 oxidation rates compared to other thermokarst and non-thermokarst lakes formed in non-yedoma permafrost environments. As thermokarst lakes formed in yedoma-type permafrost have been identified to receive large quantities of terrestrial organic carbon from thaw and subsidence of the surrounding landscape into the lake, confirming the strong coupling between terrestrial and aquatic habitats and its influence on CH4 cycling.

  18. Environmental control on aerobic methane oxidation in coastal waters

    NASA Astrophysics Data System (ADS)

    Steinle, Lea; Maltby, Johanna; Engbersen, Nadine; Zopfi, Jakob; Bange, Hermann; Elvert, Marcus; Hinrichs, Kai-Uwe; Kock, Annette; Lehmann, Moritz; Treude, Tina; Niemann, Helge

    2016-04-01

    Large quantities of methane are produced in anoxic sediments of continental margins and may be liberated to the overlying water column, where some of it is consumed by aerobic methane oxidizing bacteria (MOB). Aerobic methane oxidation (MOx) in the water column is consequently the final sink for methane before its release to the atmosphere, where it acts as a potent greenhouse gas. In the context of the ocean's contribution to atmospheric methane, coastal seas are particularly important accounting >75% of global methane emission from marine systems. Coastal oceans are highly dynamic, in particular with regard to the variability of methane and oxygen concentrations as well as temperature and salinity, all of which are potential key environmental factors controlling MOx. To determine important environmental controls on the activity of MOBs in coastal seas, we conducted a two-year time-series study with measurements of physicochemical water column parameters, MOx activity and the composition of the MOB community in a coastal inlet in the Baltic Sea (Boknis Eck Time Series Station, Eckernförde Bay - E-Bay). In addition, we investigated the influence of temperature and oxygen on MOx during controlled laboratory experiments. In E-Bay, hypoxia developed in bottom waters towards the end of the stratification period. Constant methane liberation from sediments resulted in bottom water methane accumulations and supersaturation (with respect to the atmospheric equilibrium) in surface waters. Here, we will discuss the factors impacting MOx the most, which were (i) perturbations of the water column (ii) temperature and (iii) oxygen concentration. (i) Perturbations of the water column caused by storm events or seasonal mixing led to a decrease in MOx, probably caused by replacement of stagnant water with a high standing stock of MOB by 'new' waters with a lower abundance of methanotrophs. b) An increase in temperature generally led to higher MOx rates. c) Even though methane was

  19. Consumption of Tropospheric Levels of Methyl Bromide by C1 Compound-Utilizing Bacteria and Comparison to Saturation Kinetics

    USGS Publications Warehouse

    Goodwin, K.D.; Varner, R.K.; Crill, P.M.; Oremland, R.S.

    2001-01-01

    Pure cultures of methylotrophs and methanotrophs are known to oxidize methyl bromide (MeBr); however, their ability to oxidize tropospheric concentrations (parts per trillion by volume [pptv]) has not been tested. Methylotrophs and methanotrophs were able to consume MeBr provided at levels that mimicked the tropospheric mixing ratio of MeBr (12 pptv) at equilibrium with surface waters (???2 pM). Kinetic investigations using picomolar concentrations of MeBr in a continuously stirred tank reactor (CSTR) were performed using strain IMB-1 and Leisingeria methylohalidivorans strain MB2T - terrestrial and marine methylotrophs capable of halorespiration. First-order uptake of MeBr with no indication of threshold was observed for both strains. Strain MB2T displayed saturation kinetics in batch experiments using micromolar MeBr concentrations, with an apparent Ks of 2.4 ??M MeBr and a Vmax of 1.6 nmol h-1 (106 cells)-1. Apparent first-order degradation rate constants measured with the CSTR were consistent with kinetic parameters determined in batch experiments, which used 35- to 1 ?? 107-fold-higher MeBr concentrations. Ruegeria algicola (a phylogenetic relative of strain MB2T), the common heterotrophs Escherichia coli and Bacillus pumilus, and a toluene oxidizer, Pseudomonas mendocina KR1, were also tested. These bacteria showed no significant consumption of 12 pptv MeBr; thus, the ability to consume ambient mixing ratios of MeBr was limited to C1 compound-oxidizing bacteria in this study. Aerobic C1 bacteria may provide model organisms for the biological oxidation of tropospheric MeBr in soils and waters.

  20. Consumption of tropospheric levels of methyl bromide by C(1) compound-utilizing bacteria and comparison to saturation kinetics.

    PubMed

    Goodwin, K D; Varner, R K; Crill, P M; Oremland, R S

    2001-12-01

    Pure cultures of methylotrophs and methanotrophs are known to oxidize methyl bromide (MeBr); however, their ability to oxidize tropospheric concentrations (parts per trillion by volume [pptv]) has not been tested. Methylotrophs and methanotrophs were able to consume MeBr provided at levels that mimicked the tropospheric mixing ratio of MeBr (12 pptv) at equilibrium with surface waters ( approximately 2 pM). Kinetic investigations using picomolar concentrations of MeBr in a continuously stirred tank reactor (CSTR) were performed using strain IMB-1 and Leisingeria methylohalidivorans strain MB2(T) - terrestrial and marine methylotrophs capable of halorespiration. First-order uptake of MeBr with no indication of threshold was observed for both strains. Strain MB2(T) displayed saturation kinetics in batch experiments using micromolar MeBr concentrations, with an apparent K(s) of 2.4 microM MeBr and a V(max) of 1.6 nmol h(-1) (10(6) cells)(-1). Apparent first-order degradation rate constants measured with the CSTR were consistent with kinetic parameters determined in batch experiments, which used 35- to 1 x 10(7)-fold-higher MeBr concentrations. Ruegeria algicola (a phylogenetic relative of strain MB2(T)), the common heterotrophs Escherichia coli and Bacillus pumilus, and a toluene oxidizer, Pseudomonas mendocina KR1, were also tested. These bacteria showed no significant consumption of 12 pptv MeBr; thus, the ability to consume ambient mixing ratios of MeBr was limited to C(1) compound-oxidizing bacteria in this study. Aerobic C(1) bacteria may provide model organisms for the biological oxidation of tropospheric MeBr in soils and waters.

  1. Identification of aerobic gut bacteria from the kala azar vector, Phlebotomus argentipes: a platform for potential paratransgenic manipulation of sand flies.

    PubMed

    Hillesland, Heidi; Read, Amber; Subhadra, Bobban; Hurwitz, Ivy; McKelvey, Robin; Ghosh, Kashinath; Das, Pradeep; Durvasula, Ravi

    2008-12-01

    Visceral leishmaniasis is an understudied parasitic disease responsible for significant global morbidity and mortality. We are presently investigating a method of disease prevention termed paratransgenesis. In this approach, symbiotic or commensal bacteria are transformed to produce anti-Leishmania molecules. The transformed bacteria are delivered back to sand flies to inactivate the parasite within the vector itself. In this study, we identified 28 distinct gut microorganisms from Phlebotomus argentipes trapped from four visceral leishmaniasis-endemic sites in India. A significant percent of Staphylococcus spp., environmental bacteria, and Enterobacteriaceae were identified. Two non-pathogenic organisms, Bacillus megaterium and Brevibacterium linens, were also isolated. Both organisms are also used extensively in industry. Our results indicate that B. megaterium and B. linens are possible candidates for use in a model of paratransgenesis to prevent transmission of Leishmania.

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

    PubMed

    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.

  3. Light-Dependent Aerobic Methane Oxidation Reduces Methane Emissions from Seasonally Stratified Lakes

    PubMed Central

    Oswald, Kirsten; Milucka, Jana; Brand, Andreas; Littmann, Sten; Wehrli, Bernhard; Kuypers, Marcel M. M.; Schubert, Carsten J.

    2015-01-01

    Lakes are a natural source of methane to the atmosphere and contribute significantly to total emissions compared to the oceans. Controls on methane emissions from lake surfaces, particularly biotic processes within anoxic hypolimnia, are only partially understood. Here we investigated biological methane oxidation in the water column of the seasonally stratified Lake Rotsee. A zone of methane oxidation extending from the oxic/anoxic interface into anoxic waters was identified by chemical profiling of oxygen, methane and δ13C of methane. Incubation experiments with 13C-methane yielded highest oxidation rates within the oxycline, and comparable rates were measured in anoxic waters. Despite predominantly anoxic conditions within the zone of methane oxidation, known groups of anaerobic methanotrophic archaea were conspicuously absent. Instead, aerobic gammaproteobacterial methanotrophs were identified as the active methane oxidizers. In addition, continuous oxidation and maximum rates always occurred under light conditions. These findings, along with the detection of chlorophyll a, suggest that aerobic methane oxidation is tightly coupled to light-dependent photosynthetic oxygen production both at the oxycline and in the anoxic bottom layer. It is likely that this interaction between oxygenic phototrophs and aerobic methanotrophs represents a widespread mechanism by which methane is oxidized in lake water, thus diminishing its release into the atmosphere. PMID:26193458

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

    PubMed Central

    Ma, Ke; Conrad, Ralf

    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 monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced

  5. Dry/Wet cycles change the activity and population dynamics of methanotrophs in rice field soil.

    PubMed

    Ma, Ke; Conrad, Ralf; Lu, Yahai

    2013-08-01

    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 monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced

  6. Enumeration of Free-Living Aerobic N2-Fixing H2-Oxidizing Bacteria by Using a Heterotrophic Semisolid Medium and Most-Probable-Number Technique

    PubMed Central

    Barraquio, Wilfredo L.; Dumont, Ann; Knowles, Roger

    1988-01-01

    A heterotrophic semisolid medium was used with two sensitive assay methods, C2H2 reduction and O2-dependent tritium uptake, to determine nitrogenase and hydrogenase activities, respectively. Organisms known to be positive for both activities showed hydrogenase activity in both the presence and absence of 1% C2H2, and thus, it was possible to test a single culture for both activities. Hydrogen uptake activity was detected for the first time in N2-fixing strains of Pseudomonas stutzeri. The method was then applied to the most-probable-number method of counting N2-fixing and H2-oxidizing bacteria in some natural systems. The numbers of H2-oxidizing diazotrophs were considerably higher in soil surrounding nodules of white beans than they were in the other systems tested. This observation is consistent with reports that the rhizosphere may be an important ecological niche for H2 transformation. PMID:16347643

  7. Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers.

    PubMed

    Lee, Sung-Woo; Im, Jeongdae; Dispirito, Alan A; Bodrossy, Levente; Barcelona, Michael J; Semrau, Jeremy D

    2009-11-01

    Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5% moisture content) along with 15 mg NH (4) (+) (kg soil)(-1) and 0.1 mg phenylacetylene(kg soil)(-1) provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

  8. Widespread methanotrophic primary production in lowland chalk rivers.

    PubMed

    Shelley, Felicity; Grey, Jonathan; Trimmer, Mark

    2014-05-22

    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 rivers. In 15 of these, the potential for methane oxidation (methanotrophy) was also compared with photosynthesis. In addition, we performed detailed concurrent measurements of photosynthesis and methanotrophy in one large chalk river over a complete annual cycle, where we found methanotrophy to be active to at least 15 cm into the riverbed and to be strongly substrate limited. The seasonal trend in methanotrophic activity reflected that of the riverine methane concentrations, and thus the highest rates were measured in mid-summer. At the sediment surface, photosynthesis was limited by light for most of the year with heavy shading induced by dense beds of aquatic macrophytes. Across 15 rivers, in late summer, we conservatively calculated that net methanotrophy was equivalent to between 1% and 46% of benthic net photosynthetic production within the gravel riverbed, with a median value of 4%. Hence, riverbed chemosynthesis, coupled to the oxidation of methane, is widespread and significant in English chalk rivers.

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

    SciTech Connect

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

    2016-02-23

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

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

    DOE PAGES

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

    2016-02-23

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

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

    PubMed

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

    2016-02-23

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

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

    PubMed Central

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

    2016-01-01

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

  13. Stability of Trifluoromethane in Forest Soils and Methanotrophic Cultures

    NASA Technical Reports Server (NTRS)

    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.

  14. Microbial utilization of the industrial wastewater pollutants 2-ethylhexylthioglycolic acid and iso-octylthioglycolic acid by aerobic gram-negative bacteria.

    PubMed

    Toups, Mario; Wübbeler, Jan Hendrik; Steinbüchel, Alexander

    2010-04-01

    Industrial wastewater from the production of sulfur containing esters and the resulting products of this synthesis, 2-ethylhexylthioglycolic acid (EHTG) and iso-octylthioglycolic acid (IOTG), were deployed in this study to enrich novel bacterial strains, since no wastewater and EHTG or IOTG degrading microorganisms were hitherto described or available. In addition, nothing is known about the biodegradation of these thiochemicals. The effect of this specific wastewater on the growth behaviour of microorganisms was investigated using three well-known Gram-negative bacteria (Escherichia coli, Pseudomonas putida, and Ralstonia eutropha). Concentrations of 5% (v/v) wastewater in complex media completely inhibited growth of these three bacterial strains. Six bacterial strains were successfully isolated, characterized and identified by sequencing their 16S rRNA genes. Two isolates referred to as Achromobacter sp. strain MT-E3 and Pseudomonas sp. strain MT-I1 used EHTG or IOTG, respectively, as well as the wastewater as sole source of carbon and energy for weak growth. More notably, both isolates removed these sulfur containing esters in remarkable amounts from the cultures supernatant. One further isolate was referred to as Klebsiella sp. strain 58 and exhibited an unusual high tolerance against the wastewater's toxicity without utilizing the contaminative compounds. If cultivated with gluconic acid as additional carbon source, the strain grew even in presence of more than 40% (v/v) wastewater. Three other isolates belonging to the genera Bordetella and Pseudomonas tolerated these organic sulfur compounds but showed no degradation abilities.

  15. Optimum detection times for bacteria and yeast species with the BACTEC 9120 aerobic blood culture system: evaluation for a 5-year period in a Turkish university hospital.

    PubMed

    Durmaz, Gül; Us, Tercan; Aydinli, Aydin; Kiremitci, Abdurrahman; Kiraz, Nuri; Akgün, Yurdanur

    2003-02-01

    We tracked and documented the time of positivity of blood cultures by using the BACTEC 9120 (Becton Dickinson Diagnostic Instrument Systems) blood culture system over a 5-year study period. A 7-day protocol of the incubation period was selected, and a total of 11156 blood cultures were evaluated. The clinically significant microorganisms (32.95%) were isolated in 3676 specimens. Gram-positive and -negative bacterial isolation rates were found to be 41.07 and 44.88%, respectively. Yeasts were found in 14.03% of all pathogens. Both the false-positivity and -negativity rates were very low (0.1 and 0.3%, respectively). The mean detection times for all of the pathogens were determined to be 19.45 h. Yeasts, nonfermentative gram-negative bacteria, and Brucella melitensis strains were isolated within 5 days. By taking these data into account, we decided to establish a 5-day-incubation protocol in our laboratory instead of the 7 days that are commonly used.

  16. Optimum Detection Times for Bacteria and Yeast Species with the BACTEC 9120 Aerobic Blood Culture System: Evaluation for a 5-Year Period in a Turkish University Hospital

    PubMed Central

    Durmaz, Gül; Us, Tercan; Aydinli, Aydin; Kiremitci, Abdurrahman; Kiraz, Nuri; Akgün, Yurdanur

    2003-01-01

    We tracked and documented the time of positivity of blood cultures by using the BACTEC 9120 (Becton Dickinson Diagnostic Instrument Systems) blood culture system over a 5-year study period. A 7-day protocol of the incubation period was selected, and a total of 11,156 blood cultures were evaluated. The clinically significant microorganisms (32.95%) were isolated in 3,676 specimens. Gram-positive and -negative bacterial isolation rates were found to be 41.07 and 44.88%, respectively. Yeasts were found in 14.03% of all pathogens. Both the false-positivity and -negativity rates were very low (0.1 and 0.3%, respectively). The mean detection times for all of the pathogens were determined to be 19.45 h. Yeasts, nonfermentative gram-negative bacteria, and Brucella melitensis strains were isolated within 5 days. By taking these data into account, we decided to establish a 5-day-incubation protocol in our laboratory instead of the 7 days that are commonly used. PMID:12574291

  17. Enrichment and characteristics of mixed methane-oxidizing bacteria from a Chinese coal mine.

    PubMed

    Jiang, Hao; Duan, Changhong; Luo, Mingfang; Xing, Xin-Hui

    2016-12-01

    In methane-rich environments, methane-oxidizing bacteria usually occur predominantly among consortia including other types of microorganisms. In this study, artificial coal bed gas and methane gas were used to enrich mixed methanotrophic cultures from the soil of a coal mine in China, respectively. The changes in microbial community structure and function during the enrichment were examined. The microbial diversity was reduced as the enrichment proceeded, while the capacity for methane oxidation was significantly enhanced by the increased abundance of methanotrophs. The proportion of type II methanotrophs increased greatly from 7.84 % in the sampled soil to about 50 % in the enrichment cultures, due to the increase of methane concentration. After the microbial community of the cultures got stable, Methylomonas and Methylocystis became the dominant type I and type II methanotrophs, while Methylophilus was the prevailing methylotroph. The sequences affiliated with pigment-producing strains, Methylomonas rubra, Hydrogenophaga sp. AH-24, and Flavobacterium cucumis, could explain the orange appearance of the cultures. Comparing the two cultures, the multi-carbon sources in the artificial coal bed gas caused more variety of non-methanotrophic bacteria, but did not help to maintain the diversity or to increase the quantity and activity of methanotrophs. The results could help to understand the succession and interaction of microbial community in a methane-driven ecosystem.

  18. Community structure, abundance, and activity of methanotrophs in the Zoige wetland of the Tibetan Plateau.

    PubMed

    Yun, Juanli; Zhuang, Guoqiang; Ma, Anzhou; Guo, Hongguang; Wang, Yanfen; Zhang, Hongxun

    2012-05-01

    The Zoige wetland of the Tibetan Plateau is a high-altitude tundra wetland and one of the biggest methane emission centers in China. In this study, methanotrophs with respect to community structure, abundance, and activity were investigated in peat soils collected in the vicinity of different marshland plants that dominate different regions of the wetland, including Polygonum amphibium, Carex muliensis, and Eleocharis valleculosa (EV). 16S rRNA gene and particulate methane monooxygenase gene (pmoA) clone library sequence data indicated the presence of methanotrophs with two genera, Methylobacter and Methylocystis. Methylococcus, like pmoA gene sequences, were also retrieved and showed low similarity to those from Methylococcus spp. and thus indicates the existence of novel methanotrophs in the Zoige wetland. Quantitative polymerase chain reaction (qPCR) assays were used to measure the abundance of methantrophs and detected 10(7) to 10(8) of total pmoA gene copies per gram dry weight of soil in the three marshes. Group-specific qPCR and reverse transcriptase qPCR results found that the Methylobacter genus dominates the wetland, and Methylocystis methanotrophs were less abundant, although this group of methanotrophs was estimated to be more active according to mRNA/DNA ratio. Furthermore, EV marsh demonstrated the highest methanotrophs abundance and activity among the three marshes investigated. Our study suggests that both type I and type II methanotrophs contribute to the methane oxidation in the Zoige wetland.

  19. Natural hot spots for gain of multiple resistances: arsenic and antibiotic resistances in heterotrophic, aerobic bacteria from marine hydrothermal vent fields.

    PubMed

    Farias, Pedro; Espírito Santo, Christophe; Branco, Rita; Francisco, Romeu; Santos, Susana; Hansen, Lars; Sorensen, Soren; Morais, Paula V

    2015-04-01

    Microorganisms are responsible for multiple antibiotic resistances that have been associated with resistance/tolerance to heavy metals, with consequences to public health. Many genes conferring these resistances are located on mobile genetic elements, easily exchanged among phylogenetically distant bacteria. The objective of the present work was to isolate arsenic-, antimonite-, and antibiotic-resistant strains and to determine the existence of plasmids harboring antibiotic/arsenic/antimonite resistance traits in phenotypically resistant strains, in a nonanthropogenically impacted environment. The hydrothermal Lucky Strike field in the Azores archipelago (North Atlantic, between 11°N and 38°N), at the Mid-Atlantic Ridge, protected under the OSPAR Convention, was sampled as a metal-rich pristine environment. A total of 35 strains from 8 different species were isolated in the presence of arsenate, arsenite, and antimonite. ACR3 and arsB genes were amplified from the sediment's total DNA, and 4 isolates also carried ACR3 genes. Phenotypic multiple resistances were found in all strains, and 7 strains had recoverable plasmids. Purified plasmids were sequenced by Illumina and assembled by EDENA V3, and contig annotation was performed using the "Rapid Annotation using the Subsystems Technology" server. Determinants of resistance to copper, zinc, cadmium, cobalt, and chromium as well as to the antibiotics β-lactams and fluoroquinolones were found in the 3 sequenced plasmids. Genes coding for heavy metal resistance and antibiotic resistance in the same mobile element were found, suggesting the possibility of horizontal gene transfer and distribution of theses resistances in the bacterial population.

  20. Natural Hot Spots for Gain of Multiple Resistances: Arsenic and Antibiotic Resistances in Heterotrophic, Aerobic Bacteria from Marine Hydrothermal Vent Fields

    PubMed Central

    Farias, Pedro; Espírito Santo, Christophe; Branco, Rita; Francisco, Romeu; Santos, Susana; Hansen, Lars; Sorensen, Soren

    2015-01-01

    Microorganisms are responsible for multiple antibiotic resistances that have been associated with resistance/tolerance to heavy metals, with consequences to public health. Many genes conferring these resistances are located on mobile genetic elements, easily exchanged among phylogenetically distant bacteria. The objective of the present work was to isolate arsenic-, antimonite-, and antibiotic-resistant strains and to determine the existence of plasmids harboring antibiotic/arsenic/antimonite resistance traits in phenotypically resistant strains, in a nonanthropogenically impacted environment. The hydrothermal Lucky Strike field in the Azores archipelago (North Atlantic, between 11°N and 38°N), at the Mid-Atlantic Ridge, protected under the OSPAR Convention, was sampled as a metal-rich pristine environment. A total of 35 strains from 8 different species were isolated in the presence of arsenate, arsenite, and antimonite. ACR3 and arsB genes were amplified from the sediment's total DNA, and 4 isolates also carried ACR3 genes. Phenotypic multiple resistances were found in all strains, and 7 strains had recoverable plasmids. Purified plasmids were sequenced by Illumina and assembled by EDENA V3, and contig annotation was performed using the “Rapid Annotation using the Subsystems Technology” server. Determinants of resistance to copper, zinc, cadmium, cobalt, and chromium as well as to the antibiotics β-lactams and fluoroquinolones were found in the 3 sequenced plasmids. Genes coding for heavy metal resistance and antibiotic resistance in the same mobile element were found, suggesting the possibility of horizontal gene transfer and distribution of theses resistances in the bacterial population. PMID:25636836

  1. Characterization of the ectoine biosynthesis genes of haloalkalotolerant obligate methanotroph "Methylomicrobium alcaliphilum 20Z".

    PubMed

    Reshetnikov, Alexander S; Khmelenina, Valentina N; Trotsenko, Yuri A

    2006-01-01

    The genes involved in biosynthesis of the major compatible solute ectoine (1,4,5,6-tetrahydro-2-methylpyrimidine carboxylic acid) in halotolerant obligate methanotroph "Methylomicrobium alcaliphilum 20Z" were studied. The complete nucleotide sequences of the structural genes encoding L: -aspartokinase (Ask), L-2,4-diaminobutyric acid transaminase (EctB), L-2,4-diaminobutyric acid acetyltransferase (EctA), and L-ectoine synthase (EctC) were defined and shown to be transcribed as a single operon ectABCask. Phylogenetic analysis revealed high sequence identities (34-63%) of the Ect proteins to those from halophilic heterotrophs with the highest amino acid identities being to Vibrio cholerae enzymes. The chromosomal DNA fragment from "M. alcaliphilum 20Z" containing ectABC genes and putative promoter region was expressed in Escherichia coli. Recombinant cells could grow in the presence of 4% NaCl and synthesize ectoine. The data obtained suggested that despite the ectoine biosynthesis pathway being evolutionary well conserved with respect to the genes and enzymes involved, some differences in their organization and regulation could occur in various halophilic bacteria.

  2. Summary report on the aerobic degradation of diesel fuel and the degradation of toluene under aerobic, denitrifying and sulfate reducing conditions

    SciTech Connect

    Coyne, P.; Smith, G.

    1995-08-15

    This report contains a number of studies that were performed to better understand the technology of the biodegradation of petroleum hydrocarbons. Topics of investigation include the following: diesel fuel degradation by Rhodococcus erythropolis; BTEX degradation by soil isolates; aerobic degradation of diesel fuel-respirometry; aerobic degradation of diesel fuel-shake culture; aerobic toluene degradation by A3; effect of HEPES, B1, and myo-inositol addition on the growth of A3; aerobic and anaerobic toluene degradation by contaminated soils; denitrifying bacteria MPNs; sulfate-reducing bacteria MPNs; and aerobic, DNB and SRB enrichments.

  3. Anaerobic Oxidation of Methane Coupled to Nitrite Reduction by Halophilic Marine NC10 Bacteria

    PubMed Central

    He, Zhanfei; Geng, Sha; Cai, Chaoyang; Liu, Shuai; Liu, Yan; Pan, Yawei; Lou, Liping; Zheng, Ping; Xu, Xinhua

    2015-01-01

    Anaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA and pmoA gene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescence in situ hybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite. PMID:26048927

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

    PubMed

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

    2011-12-01

    Landfills represent a major source of methane in the atmosphere. In a previous study, we demonstrated that earthworm activity in landfill cover soil can increase soil methane oxidation capacity. In this study, a simulated landfill cover soil mesocosm (1 m × 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. mRNA-based pmoA microarray analysis revealed that earthworm activity in landfill cover soil stimulated activity of type I methanotrophs (Methylobacter, Methylomonas, Methylosarcina spp.) compared to type II methanotrophs (particularly Methylocystis spp.). These results, along with previous studies of methanotrophs in landfill cover soil, can now be used to plan in situ field studies to integrate earthworm-induced methanotrophy with other landfill management practises in order to maximize soil methane oxidation and reduce methane emissions from landfills.

  5. Teaching Aerobic Fitness Concepts.

    ERIC Educational Resources Information Center

    Sander, Allan N.; Ratliffe, Tom

    2002-01-01

    Discusses how to teach aerobic fitness concepts to elementary students. Some of the K-2 activities include location, size, and purpose of the heart and lungs; the exercise pulse; respiration rate; and activities to measure aerobic endurance. Some of the 3-6 activities include: definition of aerobic endurance; heart disease risk factors;…

  6. Effect of long term anaerobic and intermittent anaerobic/aerobic starvation on aerobic granules.

    PubMed

    Pijuan, Maite; Werner, Ursula; Yuan, Zhiguo

    2009-08-01

    The effect of long term anaerobic and intermittent anaerobic/aerobic starvation on the structure and activity of aerobic granules was studied. Aerobic granular sludge treating abattoir wastewater and achieving high levels of nutrient removal was subjected to 4-5 week starvation under anaerobic and intermittent anaerobic/aerobic conditions. Microscopic pictures of granules at the beginning of the starvation period presented a round and compact surface morphology with a much defined external perimeter. Under both starvation conditions, the morphology changed at the end of starvation with the external border of the granules surrounded by floppy materials. The loss of granular compactness was faster and more pronounced under anaerobic/aerobic starvation conditions. The release of Ca(2+) at the onset of anaerobic/aerobic starvation suggests a degradation of extracellular polymeric substances. The activity of ammonia oxidizing bacteria was reduced by 20 and 36% during anaerobic and intermittent anaerobic/aerobic starvation, respectively. When fresh wastewater was reintroduced, the granules recovered their initial morphology within 1 week of normal operation and the nutrient removal activity recovered fully in 3 weeks. The results show that both anaerobic and intermittent anaerobic/aerobic conditions are suitable for maintaining granule structure and activity during starvation.

  7. Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows.

    PubMed

    Krause, Sascha; Niklaus, Pascal A; Badwan Morcillo, Sara; Meima Franke, Marion; Lüke, Claudia; Reim, Andreas; Bodelier, Paul L E

    2015-11-01

    The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.

  8. Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes.

    PubMed

    Samad, Md Sainur; Bertilsson, Stefan

    2017-01-01

    Lakes are significant sources of methane (CH4) to the atmosphere. Within these systems, methanotrophs consume CH4 and act as a potential biofilter mitigating the emission of this potent greenhouse gas. However, it is still not well understood how spatial and temporal variation in environmental parameters influence the abundance, diversity, and community structure of methanotrophs in lakes. To address this gap in knowledge, we collected water samples from three depths (surface, middle, and bottom) representing oxic to suboxic or anoxic zones of five different Swedish lakes in winter (ice-covered) and summer. Methanotroph abundance was determined by quantitative real time polymerase chain reaction and a comparison to environmental variables showed that temperature, season as well as depth, phosphate concentration, dissolved oxygen, and CH4 explained the observed variation in methanotroph abundance. Due to minimal differences in methane concentrations (0.19 and 0.29 μM for summer and winter, respectively), only a weak and even negative correlation was observed between CH4 and methanotrophs, which was possibly due to usage of CH4. Methanotrophs were present at concentrations ranging from 10(5) to 10(6) copies/l throughout the oxic (surface) and suboxic/anoxic (bottom) water mass of the lakes, but always contributed less than 1.3% to the total microbial community. Relative methanotroph abundance was significantly higher in winter than in summer and consistently increased with depth in the lakes. Phylogenetic analysis of pmoA genes in two clone libraries from two of the ice-covered lakes (Ekoln and Ramsen) separated the methanotrophs into five distinct clusters of Methylobacter sp. (Type I). Terminal restriction fragment length polymorphism analysis of the pmoA gene further revealed significant differences in methanotrophic communities between lakes as well as between winter and summer while there were no significant differences between water layers. The study provides

  9. Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes

    PubMed Central

    Samad, Md Sainur; Bertilsson, Stefan

    2017-01-01

    Lakes are significant sources of methane (CH4) to the atmosphere. Within these systems, methanotrophs consume CH4 and act as a potential biofilter mitigating the emission of this potent greenhouse gas. However, it is still not well understood how spatial and temporal variation in environmental parameters influence the abundance, diversity, and community structure of methanotrophs in lakes. To address this gap in knowledge, we collected water samples from three depths (surface, middle, and bottom) representing oxic to suboxic or anoxic zones of five different Swedish lakes in winter (ice-covered) and summer. Methanotroph abundance was determined by quantitative real time polymerase chain reaction and a comparison to environmental variables showed that temperature, season as well as depth, phosphate concentration, dissolved oxygen, and CH4 explained the observed variation in methanotroph abundance. Due to minimal differences in methane concentrations (0.19 and 0.29 μM for summer and winter, respectively), only a weak and even negative correlation was observed between CH4 and methanotrophs, which was possibly due to usage of CH4. Methanotrophs were present at concentrations ranging from 105 to 106 copies/l throughout the oxic (surface) and suboxic/anoxic (bottom) water mass of the lakes, but always contributed less than 1.3% to the total microbial community. Relative methanotroph abundance was significantly higher in winter than in summer and consistently increased with depth in the lakes. Phylogenetic analysis of pmoA genes in two clone libraries from two of the ice-covered lakes (Ekoln and Ramsen) separated the methanotrophs into five distinct clusters of Methylobacter sp. (Type I). Terminal restriction fragment length polymorphism analysis of the pmoA gene further revealed significant differences in methanotrophic communities between lakes as well as between winter and summer while there were no significant differences between water layers. The study provides new

  10. Diversity and distribution of methanotrophic archaea at cold seeps.

    PubMed

    Knittel, Katrin; Lösekann, Tina; Boetius, Antje; Kort, Renate; Amann, Rudolf

    2005-01-01

    In this study we investigated by using 16S rRNA-based methods the distribution and biomass of archaea in samples from (i) sediments above outcropping methane hydrate at Hydrate Ridge (Cascadia margin off Oregon) and (ii) massive microbial mats enclosing carbonate reefs (Crimea area, Black Sea). The archaeal diversity was low in both locations; there were only four (Hydrate Ridge) and five (Black Sea) different phylogenetic clusters of sequences, most of which belonged to the methanotrophic archaea (ANME). ANME group 2 (ANME-2) sequences were the most abundant and diverse sequences at Hydrate Ridge, whereas ANME-1 sequences dominated the Black Sea mats. Other seep-specific sequences belonged to the newly defined group ANME-3 (related to Methanococcoides spp.) and to the Crenarchaeota of marine benthic group B. Quantitative analysis of the samples by fluorescence in situ hybridization (FISH) showed that ANME-1 and ANME-2 co-occurred at the cold seep sites investigated. At Hydrate Ridge the surface sediments were dominated by aggregates consisting of ANME-2 and members of the Desulfosarcina-Desulfococcus branch (DSS) (ANME-2/DSS aggregates), which accounted for >90% of the total cell biomass. The numbers of ANME-1 cells increased strongly with depth; these cells accounted 1% of all single cells at the surface and more than 30% of all single cells (5% of the total cells) in 7- to 10-cm sediment horizons that were directly above layers of gas hydrate. In the Black Sea microbial mats ANME-1 accounted for about 50% of all cells. ANME-2/DSS aggregates occurred in microenvironments within the mat but accounted for only 1% of the total cells. FISH probes for the ANME-2a and ANME-2c subclusters were designed based on a comparative 16S rRNA analysis. In Hydrate Ridge sediments ANME-2a/DSS and ANME-2c/DSS aggregates differed significantly in morphology and abundance. The relative abundance values for these subgroups were remarkably different at Beggiatoa sites (80% ANME-2a, 20

  11. Phylogenetic analysis and development of probes for differentiating methylotrophic bacteria.

    PubMed Central

    Brusseau, G A; Bulygina, E S; Hanson, R S

    1994-01-01

    Fifteen small-subunit rRNAs from methylotrophic bacteria have been sequenced. Comparisons of these sequences with 22 previously published sequences further defined the phylogenetic relationships among these bacteria and illustrated the agreement between phylogeny and physiological characteristics of the bacteria. Phylogenetic trees were constructed with 16S rRNA sequences from methylotrophic bacteria and representative organisms from subdivisions within the class Proteobacteria on the basis of sequence similarities by using a weighted least-mean-square difference method. The methylotrophs have been separated into coherent clusters in which bacteria shared physiological characteristics. The clusters distinguished bacteria which used either the ribulose monophosphate or serine pathway for carbon assimilation. In addition, methanotrophs and methylotrophs which do not utilize methane were found to form distinct clusters within these groups. Five new deoxyoligonucleotide probes were designed, synthesized, labelled with digoxigenin-11-ddUTP, and tested for the ability to hybridize to RNA extracted from the bacteria represented in the unique clusters and for the ability to detect RNAs purified from soils enriched for methanotrophs by exposure to a methane-air atmosphere for one month. The 16S rRNA purified from soil hybridized to the probe which was complementary to sequences present in 16S rRNA from serine pathway methanotrophs and hybridized to a lesser extent with a probe complementary to sequences in 16S rRNAs of ribulose monophosphate pathway methanotrophs. The nonradioactive detection system used performed reliably at amounts of RNA from pure cultures as small as 10 ng. Images PMID:7510941

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

    PubMed Central

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

    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°C, and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH4 oxidation activity was measured in microcosm incubations containing sediments at all temperatures, with the highest CH4 oxidation potential of 37.5 μmol g−1 day−1 in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and of the 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in 13C-labeled DNA obtained by SIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisition from 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 (R = 0.82) with the relative abundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophic communities in arctic lake sediments respond to temperature variations. PMID:22522690

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

    PubMed

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

    2012-07-01

    Methane (CH(4)) flux to the atmosphere is mitigated via microbial CH(4) 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 CH(4) 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°C, and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH(4) oxidation activity was measured in microcosm incubations containing sediments at all temperatures, with the highest CH(4) oxidation potential of 37.5 μmol g(-1) day(-1) in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and of the 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in (13)C-labeled DNA obtained by SIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisition from CH(4) 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 CH(4), especially in the deeper sediments (depth, 15 to 20 cm) at low temperatures (4°C and 10°C), and showed a good linear relationship (R = 0.82) with the relative abundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophic communities in arctic lake sediments respond to temperature variations.

  14. Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria

    PubMed Central

    Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi

    2015-01-01

    Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO2, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs. PMID:27682083

  15. Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems.

    PubMed

    Crevecoeur, Sophie; Vincent, Warwick F; Comte, Jérôme; Lovejoy, Connie

    2015-01-01

    Permafrost thawing leads to the formation of thermokarst ponds that potentially emit CO2 and CH4 to the atmosphere. In the Nunavik subarctic region (northern Québec, 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.

  16. Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems

    PubMed Central

    Crevecoeur, Sophie; Vincent, Warwick F.; Comte, Jérôme; Lovejoy, Connie

    2015-01-01

    Permafrost thawing leads to the formation of thermokarst ponds that potentially emit CO2 and CH4 to the atmosphere. In the Nunavik subarctic region (northern Québec, 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. PMID:25926816

  17. Succession of methanotrophs in oxygen-methane counter-gradients of flooded rice paddies.

    PubMed

    Krause, Sascha; Lüke, Claudia; Frenzel, Peter

    2010-12-01

    Little is known about population dynamics and contribution of specific taxa to methane oxidation in flooded rice paddies. In this article we investigate the succession of methanotrophs in oxygen-methane counter-gradients. We used a gradient microcosm system that simulates oxic-anoxic interfaces of a water-saturated paddy soils, and measured pmoA-based (gene encoding particulate methane monooxygenase) terminal restriction fragment length polymorphism (T-RFLP) profiles at both the transcription (mRNA) and the population (DNA) levels. The DNA T-RFLP profiles indicated that the methanotrophic community present clearly differed from the active methanotrophic community. We observed a succession of the methanotrophic community over time without any direct effect of pore water chemistry on the community structure. Both the total population and the active subpopulation changed with time, whereas methane oxidation rates remained nearly constant. Hence, we suggest that a diverse microbial seed bank of methanotrophs is important in maintaining the function in a dynamic ecosystem.

  18. Methane source strength and energy flow shape methanotrophic communities in oxygen-methane counter-gradients.

    PubMed

    Krause, Sascha; Lüke, Claudia; Frenzel, Peter

    2012-04-01

    The role of microbial diversity for ecosystem functioning has become an important subject in microbial ecology. Recent work indicates that microbial communities and microbial processes can be very sensitive to anthropogenic disturbances. However, to what extent microbial communities may change upon, resist to, or overcome disturbances might differ depending on substrate availability. We used soil from an Italian rice field in gradient microcosms, and analysed the response of methanotrophic communities to an NH4 (+) pulse as a potential disturbance under two different CH4 source strengths. We found a significant influence of source strength, i.e. the energy flow through the methanotrophic community, while NH4 (+) had no effect. Our data suggest that historical contingencies, i.e. nitrogen fertilization, led to an ammonium-tolerant MOB community. Methanotrophs were able to oxidize virtually all CH4 diffusing into the oxic-anoxic boundary layer regardless of NH4 (+) addition. Total and active methanotrophic communities were assessed by a pmoA-specific microarray. From the reservoir of dormant methanotrophs, different species became active with Methylobacter and an environmental cluster affiliated with paddy soils being indicative for high CH4 source strength. Thus, a microbial seed bank is an important prerequisite to maintain functioning in a fluctuating environment.

  19. [Advances in degradation of chlorinated hydrocarbons by obligate and facultative methanotrophs].

    PubMed

    Xing, Zhilin; Zhang, Lijie; Zhao, Tiantao

    2014-04-01

    Bioremediation is one of the most effective ways to treat and dispose of chlorinated hydrocarbons, and methanotrophs are potentially useful to do so. Recent studies found that facultative methanotrophs can use compounds containing C-C bond as sources of carbon and energy, thus overcoming the limitation that obligate methanotrophsone uses only C1 compounds for this process. This is a unique metabolic approach that is becoming increasingly attractive in the field of contaminant biodegradation. Here, we summarized the bioremediation of chlorinated hydrocarbons by obligate and facultative methanotrophs. This process involves the degradation of various chlorinated hydrocarbons by diverse strains, including pure cultures and mixed cultures. We also compare the activity expression and catalytic properties of different types of methane monooxygenases in various substrates. We furthermore summarize the kinetic characteristics of the degradation of chlorinated hydrocarbons using the model strain Methylosinus trichosporium OB3b, and outline the degradation and potential of chlorinated hydrocarbons by facultative methanotrophs. Lastly, we discuss current problems and future research directions for degradation of chlorinated hydrocarbons by methanotrophs.

  20. Peatland succession induces a shift in the community composition of Sphagnum-associated active methanotrophs.

    PubMed

    Putkinen, Anuliina; Larmola, Tuula; Tuomivirta, Tero; Siljanen, Henri M P; Bodrossy, Levente; Tuittila, Eeva-Stiina; Fritze, Hannu

    2014-06-01

    Sphagnum-associated methanotrophs (SAM) are an important sink for the methane (CH4) formed in boreal peatlands. We aimed to reveal how peatland succession, which entails a directional change in several environmental variables, affects SAM and their activity. Based on the pmoA microarray results, SAM community structure changes when a peatland develops from a minerotrophic fen to an ombrotrophic bog. Methanotroph subtypes Ia, Ib, and II showed slightly contrasting patterns during succession, suggesting differences in their ecological niche adaptation. Although the direct DNA-based analysis revealed a high diversity of type Ib and II methanotrophs throughout the studied peatland chronosequence, stable isotope probing (SIP) of the pmoA gene indicated they were active mainly during the later stages of succession. In contrast, type Ia methanotrophs showed active CH4 consumption in all analyzed samples. SIP-derived (13)C-labeled 16S rRNA gene clone libraries revealed a high diversity of SAM in every succession stage including some putative Methylocella/Methyloferula methanotrophs that are not detectable with the pmoA-based approach. In addition, a high diversity of 16S rRNA gene sequences likely representing cross-labeled nonmethanotrophs was discovered, including a significant proportion of Verrucomicrobia-related sequences. These results help to predict the effects of changing environmental conditions on SAM communities and activity.

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

    PubMed

    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.

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

    PubMed Central

    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 active epibiotic methanotrophs on S. crosnieri setae consisted of gammaproteobacterial type Ia and Ib methanotrophs. The effect of different RNA stabilization procedures on the abundance of pmoA and 16S rRNA transcripts in the epibiotic community was estimated by quantitative RT-PCR. Our novel RNA fixation method performed immediately after sampling effectively preserved cellular RNA assemblages, particularly labile mRNA populations, including pmoA mRNA. Methane consumption in live S. crosnieri was also estimated by continuous-flow incubation under atmospheric and in situ hydrostatic pressures, and provided a clear evidence of methane oxidation activity of the epibiotic microbial community, which was not significantly affected by hydrostatic pressure. Our study revealed the significant ecological function and nutritional contribution of epibiotic methanotrophs to the predominant S. crosnieri populations in the Okinawa Trough deep-sea hydrothermal systems. In conclusion, our study gave clear facts about diversity and methane oxidation of active methanotrophs in the epibiotic community associated with invertebrates. PMID:24401859

  3. The Leeuwenhoek Lecture 2000 The natural and unnatural history of methane-oxidizing bacteria

    PubMed Central

    Dalton, Howard

    2005-01-01

    Methane gas is produced from many natural and anthropogenic sources. As such, methane gas plays a significant role in the Earth's climate, being 25 times more effective as a greenhouse gas than carbon dioxide. As with nearly all other naturally produced organic molecules on Earth, there are also micro-organisms capable of using methane as their sole source of carbon and energy. The microbes responsible (methanotrophs) are ubiquitous and, for the most part, aerobic. Although anaerobic methanotrophs are believed to exist, so far, none have been isolated in pure culture. Methanotrophs have been known to exist for over 100 years; however, it is only in the last 30 years that we have begun to understand their physiology and biochemistry. Their unique ability to use methane for growth is attributed to the presence of a multicomponent enzyme system—methane monooxygenase (MMO)—which has two distinct forms: soluble (sMMO) and membrane-associated (pMMO); however, both convert methane into the readily assimilable product, methanol. Our understanding of how bacteria are capable of effecting one of the most difficult reactions in chemistry—namely, the controlled oxidation of methane to methanol—has been made possible by the isolation, in pure form, of the enzyme components. The mechanism by which methane is activated by sMMO involves abstraction of a hydrogen atom from methane by a high-valence iron species (FeIV or possibly FeV) in the hydroxylase component of the MMO complex to form a methyl radical. The radical combines with a captive oxygen atom from dioxygen to form the reaction product, methanol, which is further metabolized by the cell to produce multicarbon intermediates. Regulation of the sMMO system relies on the remarkable properties of an effector protein, protein B. This protein is capable of facilitating component interactions in the presence of substrate, modifying the redox potential of the diiron species at the active site. These interactions permit

  4. The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria.

    PubMed

    Dalton, Howard

    2005-06-29

    Methane gas is produced from many natural and anthropogenic sources. As such, methane gas plays a significant role in the Earth's climate, being 25 times more effective as a greenhouse gas than carbon dioxide. As with nearly all other naturally produced organic molecules on Earth, there are also micro-organisms capable of using methane as their sole source of carbon and energy. The microbes responsible (methanotrophs) are ubiquitous and, for the most part, aerobic. Although anaerobic methanotrophs are believed to exist, so far, none have been isolated in pure culture. Methanotrophs have been known to exist for over 100 years; however, it is only in the last 30 years that we have begun to understand their physiology and biochemistry. Their unique ability to use methane for growth is attributed to the presence of a multicomponent enzyme system-methane monooxygenase (MMO)-which has two distinct forms: soluble (sMMO) and membrane-associated (pMMO); however, both convert methane into the readily assimilable product, methanol. Our understanding of how bacteria are capable of effecting one of the most difficult reactions in chemistry-namely, the controlled oxidation of methane to methanol-has been made possible by the isolation, in pure form, of the enzyme components.The mechanism by which methane is activated by sMMO involves abstraction of a hydrogen atom from methane by a high-valence iron species (FeIV or possibly FeV) in the hydroxylase component of the MMO complex to form a methyl radical. The radical combines with a captive oxygen atom from dioxygen to form the reaction product, methanol, which is further metabolized by the cell to produce multicarbon intermediates. Regulation of the sMMO system relies on the remarkable properties of an effector protein, protein B. This protein is capable of facilitating component interactions in the presence of substrate, modifying the redox potential of the diiron species at the active site. These interactions permit access of

  5. Fly ash application in nutrient poor agriculture soils: impact on methanotrophs population dynamics and paddy yields.

    PubMed

    Singh, Jay Shankar; Pandey, Vimal Chandra

    2013-03-01

    There are reports that the application of fly ash, compost and press mud or a combination thereof, improves plant growth, soil microbial communities etc. Also, fly ash in combination with farmyard manure or other organic amendments improves soil physico-chemical characteristics, rice yield and microbial processes in paddy fields. However, the knowledge about the impact of fly ash inputs alone or in combination with other organic amendments on soil methanotrophs number in paddy soils is almost lacking. We hypothesized that fly ash application at lower doses in paddy agriculture soil could be a potential amendment to elevate the paddy yields and methanotrophs number. Here we demonstrate the impact of fly ash and press mud inputs on number of methanotrophs, antioxidants, antioxidative enzymatic activities and paddy yields at agriculture farm. The impact of amendments was significant for methanotrophs number, heavy metal concentration, antioxidant contents, antioxidant enzymatic activities and paddy yields. A negative correlation was existed between higher doses of fly ash-treatments and methanotrophs number (R(2)=0.833). The content of antioxidants and enzymatic activities in leaves of higher doses fly ash-treated rice plants increased in response to stresses due to heavy metal toxicity, which was negatively correlated with rice grain yield (R(2)=0.944) and paddy straw yield (R(2)=0.934). A positive correlation was noted between heavy metals concentrations and different antioxidant and enzymatic activities across different fly ash treated plots.The data of this study indicate that heavy metal toxicity of fly ash may cause oxidative stress in the paddy crop and the antioxidants and related enzymes could play a defensive role against phytotoxic damages. We concluded that fly ash at lower doses with press mud seems to offer the potential amendments to improving soil methanotrophs population and paddy crop yields for the nutrient poor agriculture soils.

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

    USGS Publications Warehouse

    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.

  7. Field measures show methanotroph sensitivity to soil moisture follows precipitation regime of the grassland sites across the US Great Plains

    NASA Astrophysics Data System (ADS)

    Koyama, A.; Webb, C. T.; Johnson, N. G.; Brewer, P. E.; von Fischer, J. C.

    2015-12-01

    Methane uptake rates are known to have temporal variation in response to changing soil moisture levels. However, the relative importance of soil diffusivity vs. methanotroph physiology has not been disentangled to date. Testing methanotroph physiology in the laboratory can lead to misleading results due to changes in the fine-scale habitat where methanotrophs reside. To assay the soil moisture sensitivity of methanotrophs under field conditions, we studied 22 field plots scattered across eight Great Plains grassland sites that differed in precipitation regime and soil moisture, making ca. bi-weekly measures during the growing seasons over three years. Quantification of methanotroph activity was achieved from chamber-based measures of methane uptake coincident with SF6-derived soil diffusivity, and interpretation in a reaction-diffusion model. At each plot, we also measured soil water content (SWC), soil temperature and inorganic nitrogen (N) contents. We also assessed methanotroph community composition via 454 sequencing of the pmoA gene. Statistical analyses showed that methanotroph activity had a parabolic response with SWC (concave down), and significant differences in the shape of this response among sites. Moreover, we found that the SWC at peak methanotroph activity was strongly correlated with mean annual precipitation (MAP) of the site. The sequence data revealed distinct composition patterns, with structure that was associated with variation in MAP and soil texture. These results suggest that local precipitation regime shapes methanotroph community composition, which in turn lead to unique sensitivity of methane uptake rates with soil moisture. Our findings suggest that methanotroph activity may be more accurately modeled when the biological and environmental responses are explicitly described.

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

    PubMed

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

    2011-01-01

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

  9. [Isolation and identification of electrochemically active microorganism from micro-aerobic environment].

    PubMed

    Wu, Song; Xiao, Yong; Zheng, Zhi-Yong; Zheng, Yue; Yang, Zhao-Hui; Zhao, Feng

    2014-10-01

    Extracellular electron transfer of electrochemically active microorganism plays vital role in biogeochemical cycling of metals and carbon and in biosynthesis of bioenergy. Compared to anaerobic anode, micro-aerobic anode captures more energy from microbial fuel cell. However, most of previous researches focused on functioning bacteria in anaerobic anode, functioning bacteria in micro-aerobic anode was rarely studied. Herein, we used the traditional aerobic screening technology to isolate functioning bacteria from a micro-aerobic anode. Three pure cultures Aeromonas sp. WS-XY2, Citrobacter sp. WS-XY3 and Bacterium strain WS-XY4 were obtained. WS-XY2 and WS-XY3 were belonged to Proteobacteria, whereas WS-XY4 was possibly a new species. Cyclic voltammetry and chronoamperometry analysis demonstrated all of them showed the electrochemical activity by direct extracellular electron transfer, and micro-aerobic anode could select bacteria that have similar electrochemical activity to proliferate on the anode. We further conclude that functioning bacteria in micro-aerobic anode are more efficient than that of anaerobic anode may be the reason that micro-aerobic anode has better performance than anaerobic anode. Therefore, a thorough study of functioning bacteria in micro-aerobic anode will significantly promote the energy recovery from microbial fuel cell.

  10. Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993.

    PubMed

    Belova, Svetlana E; Kulichevskaya, Irina S; Bodelier, Paul L E; Dedysh, Svetlana N

    2013-03-01

    A novel species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2s(T) and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat-bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2s(T) and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aerotolerant nitrogenase. Strains H2s(T) and S284 grow between pH 4.2 and 7.6 (optimum pH 6.0-6.5) and at 8-37 °C (optimum 25-30 °C). The major fatty acids are C18 : 1ω8c, C18 : 1ω7c and C16 : 1ω7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2s(T) and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3 % similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2s(T) and S284 are classified as members of a novel species, for which the name Methylocystis bryophila sp. nov. is proposed; strain H2s(T) ( = DSM 21852(T)  = VKM B-2545(T)) is the type strain.

  11. Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation

    SciTech Connect

    Shigematsu, Toru; Hanada, Satoshi; Eguchi, Masahiro; Kamagata, Yoichi; Kanagawa, Takahiro; Kurane; Ryuichiro

    1999-12-01

    The soluble MMO (sMMO) gene clusters from group 1 methanotrophs were characterized. An 9.1-kb KpmI 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 gene clusters of the group 2 and group 10 methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporium OB3b and Methylocystis sp. strain M in the group 2 methanotrophs. Based on the sequence data of sMMO genes of the strains and other methanotrophs, the authors designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring the mmoX gene. The primer set was successfully used for detecting methanotrophs in the ground-water of trichloroethylene-contaminated sites during in situ-biostimulation treatments.

  12. [Effect of operational modes on community structure of type I methanotroph in the cover soil of municipal solid waste landfill].

    PubMed

    Yu, Ting; He, Pin-Jing; Lü, Fan; Shao, Li-Ming

    2008-10-01

    Type I methanotroph is crucial for methane oxidization and it responses fast to the changes in environment. In this study, 16S rDNA-based denaturing gradient gel electrophoresis (DGGE) gene fingerprint technology was applied to investigate the effect of operational modes, i. e. high-density polyethylene liner (HDPE) isolation or subsurface irrigation of landfill leachate and vegetation, on community structure and diversity of type I methanotroph in soils covering municipal solid waste landfill. 16S rDNA based phylogenetic analysis reveals type I methanotroph in all tested soils belongs to Methylobacter. According to Shannon-Wiener diversity index and principal component analysis, landfill leachate subsurface irrigation and vegetation have more impact on type I methanotroph community structure and diversity than HDPE liner isolation does, and they reduce type I methanotroph diversity. Leachate irrigation is supposed to inhibit the growth of Methylobacter population. Community structure of type I methanotroph in landfill cover soil isolated by HDPE, i.e. invaded by landfill gas, shifts during long-term gas interference. When cover age is 1.5 years old, Shannon-Wiener diversity index of type I methanotroph reaches its maximum.

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

    PubMed Central

    Poehlein, Anja; Deutzmann, Jörg S.; 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. PMID:24356841

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

    PubMed

    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.

  15. Ageing well: methane oxidation and methane oxidizing bacteria along a chronosequence of 2000 years.

    PubMed

    Ho, Adrian; Lüke, Claudia; Cao, Zhihong; Frenzel, Peter

    2011-12-01

    Rice is the staple food for more than half of the world's growing population. While the area planted to wetland rice is expected to increase further, virtually nothing is known about the long-term development of the respective microbial communities, and how these might influence biogeochemistry. Focusing on methane oxidizing bacteria, we studied a chronosequence of paddy fields in China aged 50-2000 years. Potential methanotrophic activity increased substantially with age of soil. Community composition was relatively similar in all fields. However, growth and activity of one particular subgroup of methanotrophs correlated to soil age suggesting an intricate abiotic control on methanotrophs evolving with time. Our results demonstrate that continuous rice agriculture does not only shape the microbial community, but also modifies the micro-environment in a way enabling faster growth and higher activity of selected populations.

  16. What Is Aerobic Dancing?

    MedlinePlus

    ... aerobics can reach up to six times the force of gravity, which is transmitted to each of the 26 bones in the foot. Because of the many side-to-side motions, shoes need an arch design that will compensate ...

  17. Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway)--denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures.

    PubMed

    Wartiainen, Ingvild; Hestnes, Anne Grethe; Svenning, Mette M

    2003-10-01

    The methanotrophic community in arctic soil from the islands of Svalbard, Norway (78 degrees N) was analysed by combining group-specific PCR with PCR of the highly variable V3 region of the 16S rRNA gene and then by denaturing gradient gel electrophoresis (DGGE). Selected bands were sequenced for identification. The analyses were performed with DNA extracted directly from soil and from enrichment cultures at 10 and 20 degrees C. The two genera Methylobacter and Methylosinus were found in all localities studied. The DGGE band patterns were simple, and DNA fragments with single base differences were separated. The arctic tundra is a potential source of extensive methane emission due to climatic warming because of its large reservoirs of stored organic carbon. Higher temperatures due to climatic warming can cause increased methane production, and the abundance and activity of methane-oxidizing bacteria in the arctic soil may be important regulators for methane emission to the atmosphere.

  18. One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil.

    PubMed

    Reim, Andreas; Lüke, Claudia; Krause, Sascha; Pratscher, Jennifer; Frenzel, Peter

    2012-11-01

    Aerobic methane-oxidizing bacteria (MOB) use a restricted substrate range, yet >30 species-equivalent operational taxonomical units (OTUs) are found in one paddy soil. How these OTUs physically share their microhabitat is unknown. Here we highly resolved the vertical distribution of MOB and their activity. Using microcosms and cryosectioning, we sub-sampled the top 3-mm of a water-saturated soil at near in situ conditions in 100-μm steps. We assessed the community structure and activity using the particulate methane monooxygenase gene pmoA as a functional and phylogenetic marker by terminal restriction fragment length polymorphism (t-RFLP), a pmoA-specific diagnostic microarray, and cloning and sequencing. pmoA genes and transcripts were quantified using competitive reverse transcriptase PCR combined with t-RFLP. Only a subset of the methanotroph community was active. Oxygen microprofiles showed that 89% of total respiration was confined to a 0.67-mm-thick zone immediately above the oxic-anoxic interface, most probably driven by methane oxidation. In this zone, a Methylobacter-affiliated OTU was highly active with up to 18 pmoA transcripts per cell and seemed to be adapted to oxygen and methane concentrations in the micromolar range. Analysis of transcripts with a pmoA-specific microarray found a Methylosarcina-affiliated OTU associated with the surface zone. High oxygen but only nanomolar methane concentrations at the surface suggested an adaptation of this OTU to oligotrophic conditions. No transcripts of type II methanotrophs (Methylosinus, Methylocystis) were found, which indicated that this group was represented by resting stages only. Hence, different OTUs within a single guild shared the same microenvironment and exploited different niches.

  19. Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96

    SciTech Connect

    Svenning, Mette M; Hestnes, Anne Grethe; Wartiainen, Ingvild; Stein, Lisa Y.; Klotz, Martin G; Kalyuzhnaya, Marina G.; Spang, Anja; Bringel, Francoise O.; Vuilleumier, Stephane; Lajus, Aurelie; Cheng, Jan-Fang; Goodwin, Lynne A.; Ivanova, N; Han, James; Han, Cliff; Hauser, Loren John; Held, Brittany; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Nolan, Matt; Pitluck, Sam; Woyke, Tanja

    2011-01-01

    Methylobacter tundripaludum SV96(T) (ATCC BAA-1195) is a psychrotolerant aerobic methane-oxidizing gammaproteobacterium (Methylococcales, Methylococcaceae) living in High Arctic wetland soil. The strain was isolated from soil harvested in July 1996 close to the settlement Ny-Alesund, Svalbard, Norway (78 degrees 56'N, 11 degrees 53'E), and described as a novel species in 2006. The genome includes pmo and pxm operons encoding copper membrane monooxygenases (Cu-MMOs), genes required for nitrogen fixation, and the nirS gene implicated in dissimilatory nitrite reduction to NO but no identifiable inventory for further processing of nitrogen oxides. These genome data provide the basis to investigate M. tundripaludum SV96, identified as a major player in the biogeochemistry of Arctic environments.

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

    PubMed

    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.

  1. Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils.

    PubMed

    Seghers, Dave; Top, Eva M; Reheul, Dirk; Bulcke, Robert; Boeckx, Pascal; Verstraete, Willy; Siciliano, Steven D

    2003-10-01

    Agricultural practices, such as mineral nitrogen fertilization, have an impact on the soil's ability to oxidize methane, but little is known about the shifts in the methanotrophic community composition associated with these practices. Therefore, the long-term effect of both mineral (NH4NO3) and organic (manure and GFT-compost) fertilizer applications on the soil methanotrophic community activity and structure were investigated. Both high and low affinity methane oxidation rates were lower in the soil treated with mineral fertilizer compared to the other soils. An enhanced nitrate concentration was observed in the mineral fertilized soil but nitrate did not show a direct affect on the high affinity methane oxidation. In contrast, the low affinity methane oxidation was slowed down by increased nitrate concentrations, which suggests a direct effect of nitrate on low affinity methane oxidation. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments specific for methanotrophs revealed a distinct community between the mineral and organic fertilized soils as extra Type I methanotrophic bands (phylotypes) became visible in the organic fertilized soils. These phylotypes were not visible in the patterns of the added organic fertilizers suggesting an indirect effect of the organic fertilizers on the methanotrophic community. Additionally, a molecular analysis was performed after the low affinity methane oxidation test. The enhanced methane concentrations used in the test enriched certain low affinity methanotrophs in the organic fertilized soils but not in the mineral fertilized soil. Supporting the molecular and functional observations, fatty acids characteristic for methanotrophs were less abundant in the soil treated with mineral fertilizer compared to the soil treated with compost. In conclusion, the function and molecular and chemical composition of the methanotrophic community are all altered in soil fertilized with mineral fertilizer.

  2. Dance--Aerobic and Anaerobic.

    ERIC Educational Resources Information Center

    Cohen, Arlette

    1984-01-01

    This article defines and explains aerobic exercise and its effects on the cardiovascular system. Various studies on dancers are cited indicating that dance is an anaerobic activity with some small degree of aerobic benefit. (DF)

  3. [Continuous biosynthesis of epoxypropane in a methanotrophic attached-films reactor].

    PubMed

    Xin, Jia-Ying; Cui, Jun-Ru; Chen, Jian-Bo; Li, Shu-Ben; Xia, Chun-Gu

    2002-01-01

    Using a fluidized bed as immobilization system, mixed culture methanotrophic attached-films were developed on diatomite particles. The Methane Monooxygenase (MMO) activity was found to increase obviously as soon as the lag phase ended. Greater than 90% of the MMO activity in the bed was attached. Biofilm concentration of 3.3-3.7 mg dry weight cell/g DS was observed. Batch experiments were performed to explore the possibility of producing epoxypropane by a cooxidation process. The effect of methane on the oxidation of propene to epoxypropane and the effect of propene on the growth of methanotroph were also studied. In continuous experiments, optimum mixed gaseous substrates (methane: 35%; propene: 20%; oxygen: 45%) were continuously circulated through the fluidized bed reactor to remove product. Initial epoxypropane productivity was 110-150 mumol/d. The bioreactor operated continuously for 25 d without obvious loss of epoxypropane productivity.

  4. Cyclic, alternating methane and nitrogen limitation increases PHB production in a methanotrophic community.

    PubMed

    Pieja, Allison J; Sundstrom, Eric R; Criddle, Craig S

    2012-03-01

    To identify feast-famine strategies that favor PHB accumulation in Type II methanotrophic proteobacteria, three sequencing batch reactors seeded with a defined inoculum of Type II methanotrophs were subjected to 24-h cycles consisting of (1) repeated nitrogen limitation, (2) repeated nitrogen and oxygen limitation, and (3) repeated nitrogen and methane limitation. PHB levels within each reactor and capacity to produce PHB in offline batch incubations were monitored over 11 cycles. PHB content increased only in the reactor limited by both nitrogen and methane. This reactor became dominated by Methylocystis parvus OBBP with no detectable minority populations. It was concluded that repeated nitrogen and methane limitations favored PHB accumulation in strain OBBP and provided it with a competitive advantage under the conditions imposed.

  5. Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies.

    PubMed

    Lüke, Claudia; Frenzel, Peter

    2011-09-01

    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.

  6. Electrolytic methanogenic-methanotrophic coupling for tetrachloroethylene bioremediation: proof of concept.

    PubMed

    Guiot, Serge R; Cimpoia, Ruxandra; Kuhn, Ramona; Alaplantive, Aude

    2008-04-15

    Coupling of methanogenic and methanotrophic catabolisms was performed in a single-stage technology equipped with a water electrolysis cell placed in the effluent recirculation loop. The electrolysis-generated hydrogen served as an electron donor for both bicarbonate reduction into CH4 and reductive dechlorination, while the O2 and CH4, supported the cometabolic oxidation of chlorinated intermediates left over by the tetrachloroethylene (PCE) transformation. The electrolytical methanogenic/methanotrophic coupled (eMaMoC) process was tested in a laboratory-scale setup at PCE loads ranging from 5 to 50 micromol/L(rx) x d (inlet concentrations from 4 to 11 mg/L), and at various hydraulic residence times (HRT). Degradation followed essentially a reductive dechlorination pathway from PCE to cis-1,2-dichloroethene (DCE), and an oxidative pathway from DCE to CO2. PCE reductive dechlorination to DCE was consistently over 98% while a maximum oxidative DCE mineralization of 89% was obtained at a load of 4.3 micromol PCE/ L(rx) x d and an HRT of 6 days. Controlling dissolved oxygen concentrations within a relatively low range (2-3 mg/L) seemed instrumental to sustain the overall degradation capacity. Degradation kinetics were further evaluated: the apparent half-saturation constant (K(s)) had to be set relatively high (29 microM) for the simulated data to best fit the experimental ones. In spite of such kinetic limitations, the eMaMoC system, while fueled by water electrolysis, was effective in building and sustaining a functional methanogenic/methanotrophic consortium capable of significant PCE mineralization in a single-stage process. Hence, degradation standards are within reach so long as the methanotrophic DCE-oxidizing potential, including substrate affinity, are optimized and HRT accordingly adjusted.

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

    PubMed

    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.

  8. Characterization of the methanotrophic bacterial community present in a trichloroethylene-contaminated subsurface groundwater site.

    PubMed Central

    Bowman, J P; Jiménez, L; Rosario, I; Hazen, T C; Sayler, G S

    1993-01-01

    Groundwater, contaminated with trichloroethylene (TCE) and tetrachloroethylene (PCE), was collected from 13 monitoring wells at Area M on the U.S. Department of Energy Savannah River Site near Aiken, S.C. Filtered groundwater samples were enriched with methane, leading to the isolation of 25 methanotrophic isolates. The phospholipid fatty acid profiles of all the isolates were dominated by 18:1 omega 8c (60 to 80%), a signature lipid for group II methanotrophs. Subsequent phenotypic testing showed that most of the strains were members of the genus Methylosinus and one isolate was a member of the genus Methylocystis. Most of the methanotroph isolates exhibited soluble methane monooxygenase (sMMO) activity. This was presumptively indicated by the naphthalene oxidation assay and confirmed by hybridization with a gene probe encoding the mmoB gene and by cell extract assays. TCE was degraded at various rates by most of the sMMO-producing isolates, whereas PCE was not degraded. Savannah River Area M and other groundwaters, pristine and polluted, were found to support sMMO activity when supplemented with nutrients and then inoculated with Methylosinus trichosporium OB3b. The maximal sMMO-specific activity obtained in the various groundwaters ranged from 41 to 67% compared with maximal rates obtained in copper-free nitrate mineral salts media. This study partially supports the hypothesis that stimulation of indigenous methanotrophic communities can be efficacious for removal of chlorinated aliphatic hydrocarbons from subsurface sites and that the removal can be mediated by sMMO. PMID:8368829

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

    PubMed Central

    Cheema, Simrita; 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 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

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

    PubMed

    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.

  11. Application of fluorescent antibody and enzyme-linked immunosorbent assays for TCE and PAH degrading bacteria

    SciTech Connect

    Brigmon, R.L.; Franck, M.; Brey, J.; Scott, D.; Lanclos, K.; Fliermans, C.

    1996-07-01

    Historically, methods used to identify methanotrophic and polyaromatic hydrocarbon-degrading (PAH) bacteria in environmental samples have been inadequate because isolation and identification procedures are time-consuming and often fail to separate specific bacteria from other environmental microorganisms. Methanotrophic bacteria have been isolated and characterized from TCE-contaminated soils (Bowman et al. 1993; Fliermans et al., 1988). Fliermans et al., (1988) and others demonstrated that cultures enriched with methane and propane could cometabolically degrade a wide variety of chlorinated aliphatic hydrocarbons including ethylene; 1,2-cisdichloroethylene (c-DCE); 1,2-trans-dichloroethylene (t-DCE); vinyl chloride (VC); toluene; phenol and cresol. Characterization of select microorganisms in the natural setting is important for the evaluation of bioremediation potential and its effectiveness. This realization has necessitated techniques that are selective, sensitive and easily applicable to soils, sediments, and groundwater (Fliermans, et al., 1994). Additionally these techniques can identify and quantify microbial types in situ in real time

  12. Implementation of Aerobic Programs.

    ERIC Educational Resources Information Center

    American Alliance for Health, Physical Education, Recreation and Dance (AAHPERD).

    This information is intended for health professionals interested in implementing aerobic exercise programs in public schools, institutions of higher learning, and business and industry workplaces. The papers are divided into three general sections. The introductory section presents a basis for adhering to a health fitness lifestyle, using…

  13. Aerobic Dance in Public Schools.

    ERIC Educational Resources Information Center

    Chiles, Barbara Ann; Moore, Suzanne

    1981-01-01

    Aerobic dance offers a challenging workout in a social atmosphere. Though some physical education instructors tend to exclude dance units from the curriculum, most could teach aerobic dance if they had a basic knowledge of aerobic routines. The outline for a unit to be used in the class is presented. (JN)

  14. Analyses of Methanobactin, a Novel Copper-Binding Compound, or Chalkophore, from Methanotrophs

    NASA Astrophysics Data System (ADS)

    Semrau, J. D.; Yoon, S.; Dispirito, A.; Kraemer, S.

    2009-12-01

    Methanotrophs, cells that utilize methane as their sole carbon and energy source are known to have high requirements for copper. Many of these cells are known to synthesize a copper-chelating agent, or chalkophore, termed methanobactin that appears integral to copper uptake. Structural analyses indicate that methanobactin is a small chromopeptide that binds copper utilizing two alkylidene oxazolone rings. Using a suite of spectrophotemetric and calorimetry analyses, it was discovered that methanobactin preferentially binds copper, but also binds other metals, including gold, forming gold nanoparticles. To screen methanobactin production by methanotrophs, as well as to determine if other cells make chalkophores, a plate assay developed from the Chromo Azurol S (CAS) assay for siderophore production, was modified. In the standard CAS assay, a color change in CAS plate is observed as iron (III) ion weakly bound to CAS is taken up by siderophores. In our modified assay, iron (III) chloride of the initial CAS solution was substituted with copper(II) chloride. Assay results indicated that of the four tested methanotrophs (Methylomicrobium album BG8, Methylosinus trichosporium OB3b, Methylococcus capsulatus Bath, and Methylocystis parvus OBBP), only M. album BG8, M. trichosporium OB3b, and M. capsulatus produced methanobactin, while M. parvus OBBP did not. The assay can be easily adopted for detection of chalkophores in other microorganisms and detection as well as for screening of putative mutants of chalkophore synthesis.

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

    PubMed Central

    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

  16. Aerobic and anaerobic cecal bacterial flora of commercially processed broilers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Differences in the bacterial flora of aerobic and anaerobic cultures of broiler ceca collected from a commercial poultry processing facility were determined. Bacterial isolates from cecal cultures were selected based on the ability of the bacteria to grow in media supplemented with lactate and succ...

  17. Growth of Campylobacter Incubated Aerobically in Media Supplemented with Peptones

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Growth of Campylobacter cultures incubated aerobically in media supplemented with peptones was studied, and additional experiments were conducted to compare growth of the bacteria in media supplemented with peptones to growth in media supplemented with fumarate-pyruvate-minerals-vitamins (FPMV). A b...

  18. Direct immunofluorescence and enzyme-linked immunosorbent assays for evaluating chlorinated hydrocarbon degrading bacteria

    SciTech Connect

    Brigmon, R.L.; Franck, M.M.; Brey, J.; Fliermans, C.B.; Scott, D.; Lanclos, K.

    1997-06-01

    Immunological procedures were developed to enumerate chlorinated hydrocarbon degrading bacteria. Polyclonal antibodies (Pabs) were produced by immunizing New Zealand white rabbits against 18 contaminant-degrading bacteria. These included methanotrophic and chlorobenzene (CB) degrading species. An enzyme-linked immunosorbent assay (ELISA) was used to test for specificity and sensitivity of the Pabs. Direct fluorescent antibodies (DFAs) were developed with these Pabs against select methanotrophic bacteria isolated from a trichloroethylene (TCE) contaminated landfill at the Savannah River Site (SRS) and cultures from the American Type Culture Collection (ATCC). Analysis of cross reactivity testing data showed some of the Pabs to be group specific while others were species specific. The threshold of sensitivity for the ELISA is 105 bacteria cells/ml. The DFA can detect as few as one bacterium per ml after concentration. Results from the DFA and ELISA techniques for enumeration of methanotrophic bacteria in groundwater were higher but not significantly different (P < 0.05) compared to indirect microbiological techniques such as MPN. These methods provide useful information on in situ community structure and function for bioremediation applications within 1--4 hours of sampling.

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

    PubMed

    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.

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

    PubMed

    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.

  1. Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses.

    PubMed

    Chen, Yin; Dumont, Marc G; McNamara, Niall P; Chamberlain, Paul M; Bodrossy, Levente; Stralis-Pavese, Nancy; Murrell, J Colin

    2008-02-01

    The active methanotroph community was investigated for the first time in heather (Calluna)-covered moorlands and Sphagnum/Eriophorum-covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH(4) oxidation in situ, because only pmoA transcripts (encoding a subunit of particulate methane monooxygenase) were readily detectable. Differences in methanotroph community structures were observed between the Calluna-covered moorland and Sphagnum/Eriophorum-covered gully habitats. As with many other Sphagnum-covered peatlands, the Sphagnum/Eriophorum-covered gullies were dominated by Methylocystis. Methylocella and Methylocapsa-related species were also present. Methylobacter-related species were found as demonstrated by the use of a pmoA-based diagnostic microarray. In Calluna-covered moorlands, in addition to Methylocella and Methylocystis, a unique group of peat-associated type I methanotrophs (Gammaproteobacteria) and a group of uncultivated type II methanotrophs (Alphaproteobacteria) were also found. The pmoA sequences of the latter were only distantly related to Methylocapsa and also to the RA-14 group of methanotrophs, which are believed to be involved in oxidation of atmospheric concentrations of CH(4). Soil samples were also labelled with (13)CH(4), and subsequent analysis of the (13)C-labelled phospholipid fatty acids (PLFAs) showed that 16:1 omega 7, 18:1 omega 7 and 18:1 omega 9 were the major labelled PLFAs. The presence of (13)C-labelled 18:1 omega 9, which was not a major PLFA of any extant methanotrophs, indicated the presence of novel methanotrophs in this peatland.

  2. Effect of nitrogen fertilization on methane oxidation, abundance, community structure, and gene expression of methanotrophs in the rice rhizosphere.

    PubMed

    Shrestha, Minita; Shrestha, Pravin Malla; Frenzel, Peter; Conrad, Ralf

    2010-12-01

    Nitrogen, one of the limiting factors for the yield of rice, can also have an important function in methane oxidation, thus affecting its global budget. Rice microcosms, planted in the greenhouse, were treated with the N-fertilizers urea (UPK) and ammonium sulfate (APK) or were only treated with phosphorous and potassium (PK). Methane oxidation rates in PK and UPK treatments were similar during most of the rice-growing season, revealing no effect of urea. However, ammonium sulfate strongly suppressed methanogenesis providing an unfavorable environment for methanotrophs in APK treatment. Roots and rhizospheric soil samples, collected from six different growth stages of the rice plant, were analyzed by terminal restriction fragment length polymorphism (T-RFLP) of the pmoA gene. Assignment of abundant T-RFs to cloned pmoA sequences indicated that the populations on roots were dominated by type-I methanotrophs, whereas the populations in rhizospheric soil were dominated by type-II methanotrophs irrespectively of growth stages and fertilizer treatments. Non-metric multidimensional scaling ordination analysis of T-RFLP profiles revealed that the methanotrophic community was significantly (P<0.001) affected by the different fertilizer treatments; however, the effect was stronger on the roots than in the rhizospheric soil. Contrary to pmoA gene-based analysis, pmoA transcript-based T-RFLP/cloning/sequencing analysis in rhizospheric soil showed type I as the predominant methanotrophs in both PK and UPK treatments. Collectively, our study showed that type-I methanotrophs were dominant and probably active in rhizospheric soil throughout the season irrespective of nitrogen fertilizer used, whereas type-II methanotrophs were relatively more dominant under unfavorable conditions, such as in APK treatment.

  3. On the relationship between methane production and oxidation by anaerobic methanotrophic communities from cold seeps of the Gulf of Mexico.

    PubMed

    Orcutt, Beth; Samarkin, Vladimir; Boetius, Antje; Joye, Samantha

    2008-05-01

    The anaerobic oxidation of methane (AOM) in the marine subsurface is a significant sink for methane in the environment, yet our understanding of its regulation and dynamics is still incomplete. Relatively few groups of microorganisms consume methane in subsurface environments--namely the anaerobic methanotrophic archaea (ANME clades 1, 2 and 3), which are phylogenetically related to methanogenic archaea. Anaerobic oxidation of methane presumably proceeds via a 'reversed' methanogenic pathway. The ANME are generally associated with sulfate-reducing bacteria (SRB) and sulfate is the only documented final electron acceptor for AOM in marine sediments. Our comparative study explored the coupling of AOM with sulfate reduction (SR) and methane generation (MOG) in microbial communities from Gulf of Mexico cold seep sediments that were naturally enriched with methane and other hydrocarbons. These sediments harbour a variety of ANME clades and SRB. Following enrichment under an atmosphere of methane, AOM fuelled 50-100% of SR, even in sediment slurries containing petroleum-associated hydrocarbons and organic matter. In the presence of methane and sulfate, the investigated microbial communities produce methane at a small fraction ( approximately 10%) of the AOM rate. Anaerobic oxidation of methane, MOG and SR rates decreased significantly with decreasing concentration of methane, and in the presence of the SR inhibitor molybdate, but reacted differently to the MOG inhibitor 2-bromoethanesulfonate (BES). The addition of acetate, a possible breakdown product of petroleum in situ and a potential intermediate in AOM/SR syntrophy, did not suppress AOM activity; rather acetate stimulated microbial activity in oily sediment slurries.

  4. Ecology of aerobic anoxygenic phototrophs in aquatic environments.

    PubMed

    Koblížek, Michal

    2015-11-01

    Recognition of the environmental role of photoheterotrophic bacteria has been one of the main themes of aquatic microbiology over the last 15 years. Aside from cyanobacteria and proteorhodopsin-containing bacteria, aerobic anoxygenic phototrophic (AAP) bacteria are the third most numerous group of phototrophic prokaryotes in the ocean. This functional group represents a diverse assembly of species which taxonomically belong to various subgroups of Alpha-, Beta- and Gammaproteobacteria. AAP bacteria are facultative photoheterotrophs which use bacteriochlorophyll-containing reaction centers to harvest light energy. The light-derived energy increases their bacterial growth efficiency, which provides a competitive advantage over heterotrophic species. Thanks to their enzymatic machinery AAP bacteria are active, rapidly growing organisms which contribute significantly to the recycling of organic matter. This chapter summarizes the current knowledge of the ecology of AAP bacteria in aquatic environments, implying their specific role in the microbial loop.

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

    PubMed

    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.

  6. [Evaluation of normal aerobic skin flora (author's transl)].

    PubMed

    Crémieux, A; Cazac, J L

    1980-01-01

    This work attempts the quantitative and qualitative evaluation of the bacterial population from two different areas: elbow and groin. Bacteria are recovered using the method of Williamson and Kligman modified by Fleurette and Transy. Aerobic flora is determined from bacterial counts on various media. Results show a density of 475 to 630 bacteria/cm2 for elbow, and 1.9 to 2.4 X 10(5) bacteria/cm2 for groin (geometric and arithmetic mean, respectively). Percentages of different species and types are calculated, and skin population is represented by a circular diagram.

  7. Aerobic Microbial Degradation of Glucoisosaccharinic Acid

    PubMed Central

    Strand, S. E.; Dykes, J.; Chiang, V.

    1984-01-01

    α-Glucoisosaccharinic acid (GISA), a major by-product of kraft paper manufacture, was synthesized from lactose and used as the carbon source for microbial media. Ten strains of aerobic bacteria capable of growth on GISA were isolated from kraft pulp mill environments. The highest growth yields were obtained with Ancylobacter spp. at pH 7.2 to 9.5. GISA was completely degraded by cultures of an Ancylobacter isolate. Ancylobacter cell suspensions consumed oxygen and produced carbon dioxide in response to GISA addition. A total of 22 laboratory strains of bacteria were tested, and none was capable of growth on GISA. GISA-degrading isolates were not found in forest soils. Images PMID:16346467

  8. Antimicrobial susceptibility and extended-spectrum beta-lactamase rates in aerobic gram-negative bacteria causing intra-abdominal infections in Vietnam: report from the Study for Monitoring Antimicrobial Resistance Trends (SMART 2009-2011).

    PubMed

    Biedenbach, Douglas J; Bouchillon, Samuel K; Hoban, Daryl J; Hackel, Meredith; Phuong, Doan Mai; Nga, Tran Thi Thanh; Phuong, Nguyen Tran My; Phuong, Tran Thi Lan; Badal, Robert E

    2014-08-01

    Treatment options for multidrug-resistant pathogens remain problematic in many regions and individual countries, warranting ongoing surveillance and analysis. Limited antimicrobial susceptibility information is available for pathogens from Vietnam. This study determined the bacterial susceptibility of aerobic gram-negative pathogens of intra-abdominal infections among patients in Vietnam during 2009-2011. A total of 905 isolates were collected from 4 medical centers in this investigation as part of the Study for Monitoring Antimicrobial Resistance Trends. Antimicrobial susceptibility and extended-spectrum beta-lactamase (ESBL) rates among the appropriate species were determined by a central laboratory using Clinical and Laboratory Standards Institute methods. Among the species collected, Escherichia coli (48.1% ESBL-positive) and Klebsiella pneumoniae (39.5% ESBL-positive) represented the majority (46.4%) of the isolates submitted for this study. Ertapenem MIC90 values were lowest for these 2 species at 0.12 and 0.25μg/mL and remained unchanged for ESBL-positive isolates. Imipenem MIC90 values were also the same for all isolates and ESBL-positive strains at 0.25 and 0.5μg/mL, respectively. Ertapenem MIC90 values for additional species with sufficient numbers for analysis, including Enterobacter cloacae, Proteus mirabilis, Acinetobacter baumannii, and Pseudomonas aeruginosa, were 1, 0.06, >4, and >4μg/mL, respectively. Analysis of beta-lactamases in a subset of 132 phenotypically ESBL-positive Enterobacteriaceae demonstrated that CTX-M variants, particularly CTX-M-27 and CTX-M-15, were the predominant enzymes. High resistance rates in Vietnam hospitals dictate continuous monitoring as antimicrobial inactivating enzymes continue to spread throughout Asia and globally.

  9. Biotechnology of Anoxygenic Phototrophic Bacteria.

    PubMed

    Frigaard, Niels-Ulrik

    Anoxygenic phototrophic bacteria are a diverse collection of organisms that are defined by their ability to grow using energy from light without evolving oxygen. The dominant groups are purple sulfur bacteria, purple nonsulfur bacteria, green sulfur bacteria, and green and red filamentous anoxygenic phototrophic bacteria. They represent several bacterial phyla but they all have bacteriochlorophylls and carotenoids and photochemical reaction centers which generate ATP and cellular reductants used for CO2 fixation. They typically have an anaerobic lifestyle in the light, although some grow aerobically in the dark. Some of them oxidize inorganic sulfur compounds for light-dependent CO2 fixation; this ability can be exploited for photobiological removal of hydrogen sulfide from wastewater and biogas. The anoxygenic phototrophic bacteria also perform bioremediation of recalcitrant dyes, pesticides, and heavy metals under anaerobic conditions. Finally, these organisms may be useful for overexpression of membrane proteins and photobiological production of H2 and other valuable compounds.

  10. Anaerobic bacteria

    MedlinePlus

    Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these bacteria ... Goldstein EJ. Diseases caused by non-spore forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman's Cecil ...

  11. Aerobic landfill bioreactor

    SciTech Connect

    Hudgins, Mark P; Bessette, Bernard J; March, John; McComb, Scott T.

    2000-01-01

    The present invention includes a method of decomposing municipal solid waste (MSW) within a landfill by converting the landfill to aerobic degradation in the following manner: (1) injecting air via the landfill leachate collection system (2) injecting air via vertical air injection wells installed within the waste mass; (3) applying leachate to the waste mass using a pressurized drip irrigation system; (4) allowing landfill gases to vent; and (5) adjusting air injection and recirculated leachate to achieve a 40% to 60% moisture level and a temperature between 120.degree. F. and 140.degree. F. in steady state.

  12. Aerobic landfill bioreactor

    SciTech Connect

    Hudgins, Mark P; Bessette, Bernard J; March, John C; McComb, Scott T.

    2002-01-01

    The present invention includes a system of decomposing municipal solid waste (MSW) within a landfill by converting the landfill to aerobic degradation in the following manner: (1) injecting air via the landfill leachate collection system (2) injecting air via vertical air injection wells installed within the waste mass; (3) applying leachate to the waste mass using a pressurized drip irrigation system; (4) allowing landfill gases to vent; and (5) adjusting air injection and recirculated leachate to achieve a 40% to 60% moisture level and a temperature between 120.degree. F. and 140.degree. F. in steady state.

  13. Aerobic landfill bioreactor

    SciTech Connect

    Hudgins, M.P.; Bessette, B.J.; March, J.; McComb, S.T.

    2000-02-15

    The present invention includes a method of decomposing municipal solid waste (MSW) within a landfill by converting the landfill to aerobic degradation in the following manner: (1) injecting air via the landfill leachate collection system (2) injecting air via vertical air injection wells installed within the waste mass; (3) applying leachate to the waste mass using a pressurized drip irrigation system; (4) allowing landfill gases to vent; and (5) adjusting air injection and recirculated leachate to achieve a 40% to 60% moisture level and a temperature between 120 F and 140 F in steady state.

  14. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

    PubMed

    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

  15. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

    PubMed Central

    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

  16. Variants of the obligate methanotroph isolate 761M capable of growth on glucose in the absence of methane

    SciTech Connect

    Zhao, S.J.; Hanson, R.S.

    1984-10-01

    Isolate 761M is an unusual type I methanotroph that possess a complete tricarboxylic acid cycle. Variants of this methanotroph that were capable of growth with methanol (isolate 761AR) or glucose (isolate 761H) have been isolated. Cultures of isolate 761H grown with glucose and casein hydrolysate as the sole carbon and energy sources retained the ability to grow on methane, contained methane monooxygenase and 3-hexulose phosphate synthase, and possessed intracytoplasmic membranes similar to those found in thin sections of isolate 761M grown on methane. Methane monooxygenase was also present in cultures of isolate 761AR grown on methanol and casein hydrolysate. 18 references, 4 figures, 2 tables.

  17. Exercise, Animal Aerobics, and Interpretation?

    ERIC Educational Resources Information Center

    Oliver, Valerie

    1996-01-01

    Describes an aerobic activity set to music for children that mimics animal movements. Example exercises include walking like a penguin or jumping like a cricket. Stresses basic aerobic principles and designing the program at the level of children's motor skills. Benefits include reaching people who normally don't visit nature centers, and bridging…

  18. Effects of nutrient dosing on subsurface methanotrophic populations and trichloroethylene degradation.

    PubMed

    Pfiffner, S M; Palumbo, A V; Phelps, T J; Hazen, T C

    1997-01-01

    In in situ bioremediation demonstration at the Savannah River Site in Aiken, South Carolina, trichloroethyle degrading microorganisms were stimulated by delivering nutrients to the TCE-contaminated subsurface via horizontal injection wells. Microbial and chemical monitoring of groundwater from 12 vertical wells was used to examine the effects of methane and nutrient (nitrogen and phosphorus) dosing on the methanotrophic populations and on the potential of the subsurface microbial communities to degrade TCE. Densities of methanotrophs increased 3-5 orders of magnitude during the methane- and nutrient-injection phases; this increase coinclded with the higher methane levels observed in the monitoring wells. TCE degradation capacity, although not directly tied to methane concentration, responded to the methane injection, and responded more dramatically to the multiple-nutrient injection. tion. These results support the crucial role of methane, nitrogen, and phosphorus as amended nutrients in TCE bioremediation. The enhancing effects of nutrient dosing on microbial abundance and degradative potentials, coupled with increased chloride concentrations, provided multiple lines of evidence substantiating the effectiveness of this integrated in situ bioremediation process.

  19. Characterization and phylogeny of a novel methanotroph, Methyloglobulus morosus gen. nov., spec. nov.

    PubMed

    Deutzmann, J S; Hoppert, M; Schink, B

    2014-05-01

    A novel methanotrophic gammaproteobacterium, strain KoM1, was isolated from the profundal sediment of Lake Constance after initial enrichment in opposing gradients of methane and oxygen. Strain KoM1 grows on methane or methanol as its sole source of carbon and energy. It is a Gram-negative methanotroph, often expressing red pigmentation. Cells are short rods and occur sometimes in pairs or short chains. Strain KoM1 grows preferably at reduced oxygen concentrations (pO2=0.05-0.1bar). It can fix nitrogen, and grows at neutral pH and at temperatures between 4 and 30°C. Phylogenetically, the closest relatives are Methylovulum miyakonense and Methylosoma difficile showing 91% 16S rRNA gene sequence identity. The only respiratory quinone is ubiquinone Q8; the main polar lipids are phosphatidyl ethanolamine and phosphatidyl glycerol. The major cellular fatty acids are summed feature 3 (presumably C16:1ω7c) and C16:1ω5c, and the G+C content of the DNA is 47.7mol%. Strain KoM1 is described as the type strain of a novel species within a new genus, Methyloglobulus morosus gen. nov., sp. nov.

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

    SciTech Connect

    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 addition resulted in increased initial specific TCE transformation rates (2.1 mg/mg of cells per day) and elevated transformation capacity (0.073 mg of TCE per mg of cells). Significant declines in methane conversion rates following exposure to TCE were observed for both resting and formate-fed cells, suggesting toxic effects caused by TCE or its transformation products. TCE transformation and methane consumption rates of resting cells decreased with time much more rapidly when cells were shaken and aerated than when they remained dormant, suggesting that the transformation ability of methanotrophs is best preserved by storage under anoxic conditions.

  1. Rare earth metals are essential for methanotrophic life in volcanic mudpots.

    PubMed

    Pol, Arjan; Barends, Thomas R M; Dietl, Andreas; Khadem, Ahmad F; Eygensteyn, Jelle; Jetten, Mike S M; Op den Camp, Huub J M

    2014-01-01

    Growth of Methylacidiphilum fumariolicum SolV, an extremely acidophilic methanotrophic microbe isolated from an Italian volcanic mudpot, is shown to be strictly dependent on the presence of lanthanides, a group of rare earth elements (REEs) such as lanthanum (Ln), cerium (Ce), praseodymium (Pr) and neodymium (Nd). After fractionation of the bacterial cells and crystallization of the methanol dehydrogenase (MDH), it was shown that lanthanides were essential as cofactor in a homodimeric MDH comparable with one of the MDHs of Methylobacterium extorquens AM1. We hypothesize that the lanthanides provide superior catalytic properties to pyrroloquinoline quinone (PQQ)-dependent MDH, which is a key enzyme for both methanotrophs and methylotrophs. Thus far, all isolated MxaF-type MDHs contain calcium as a catalytic cofactor. The gene encoding the MDH of strain SolV was identified to be a xoxF-ortholog, phylogenetically closely related to mxaF. Analysis of the protein structure and alignment of amino acids showed potential REE-binding motifs in XoxF enzymes of many methylotrophs, suggesting that these may also be lanthanide-dependent MDHs. Our findings will have major environmental implications as metagenome studies showed (lanthanide-containing) XoxF-type MDH is much more prominent in nature than MxaF-type enzymes.

  2. Earthworm cast as a promising filter bed material and its methanotrophic contribution to methane removal.

    PubMed

    Moon, Kyung-Eun; Lee, Soo-Yeon; Lee, Sang Hyon; Ryu, Hee Wook; Cho, Kyung-Suk

    2010-04-15

    The use of biocovers is a promising strategy toward mitigating CH(4) emission from smaller and/or older landfills. In this study, a filter bed material consisting of a mixture of earthworm cast and rice paddy soil in a biocover was evaluated. Although the CH(4) oxidation rate of the enriched paddy soil was 4.9 microg g-dry soil(-1) h(-1), it was enhanced to 25.1 microg g-dry soil(-1) h(-1) by adding an earthworm cast with a 3:7 ratio of earthworm cast:soil (wet weight). CO(2) was found as the final oxidation product of CH(4), and the mole ratio of CO(2) production to CH(4) consumption was 0.27. At a moisture content range of 15-40% and a temperature range of 20-40 degrees C, the CH(4) oxidation rates of the enriched mixture were more than 57% of the maximum rate obtained at 25% moisture content and 25 degrees C. By denaturing gradient gel electrophoresis analysis employing primers for the universal bacterial 16S rRNA gene, and terminal-restriction fragment length polymorphism analysis using primers for the pmoA gene, the bacterial and methanotrophic communities in the enriched mixture were mainly originate from paddy soil and earthworm cast, respectively. Both type I (mainly Methylocaldum) and type II methanotrophs (mainly Methylocystis) played important roles in CH(4) oxidation in the enriched mixture.

  3. Structure and function of methanotrophic communities in a landfill-cover soil.

    PubMed

    Henneberger, Ruth; Lüke, Claudia; Mosberger, Lona; Schroth, Martin H

    2012-07-01

    In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH(4) oxidation at this landfill.

  4. Molecular characterization of a deep-sea methanotrophic mussel symbiont that carries a RuBisCO gene.

    PubMed

    Elsaied, Hosam Easa; Kaneko, Ryo; Naganuma, Takeshi

    2006-01-01

    In our previous investigation on the genes of 1,5-ribulose 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 examined the symbiont source of the RuBisCO cbbL gene along with the genes of 16S ribosomal RNA (16S rDNA) and particulate methane monooxygenase (EC 1.14.13.25; pmoA) and probed for the presence of the ATP sulfurylase gene (EC 2.7.7.4; sopT). The 16S rDNA sequence analysis indicated that the mussel harbors a monospecific methanotrophic Gammaproteobacterium. This was confirmed by amplification and sequencing of the methanotrophic pmoA, while thiotrophic sopT was not amplified from the same symbiotic genome DNA. Fluorescence in situ hybridization demonstrated simultaneous occurrence of the symbiont-specific 16S rDNA, cbbL and pmoA, but not sopT, in the mussel gill. This is the first molecular and visual evidence for a methanotrophic bacterial endosymbiont that bears the RuBisCO cbbL gene relevant to autotrophic CO(2) fixation.

  5. EMERGING TECHNOLOGY SUMMARY: PILOT-SCALE DEMONSTRATION OF A TWO-STAGE METHANOTROPHIC BIOREACTOR FOR BIODEGRADATION OF TRICHLOROETHENE IN GROUNDWATER

    EPA Science Inventory

    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...

  6. A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria.

    PubMed

    Abbasian, Firouz; Lockington, Robin; Mallavarapu, Megharaj; Naidu, Ravi

    2015-06-01

    Hydrocarbons are relatively recalcitrant compounds and are classified as high-priority pollutants. However, these compounds are slowly degraded by a large variety of microorganisms. Bacteria are able to degrade aliphatic saturated and unsaturated hydrocarbons via both aerobic and anaerobic pathways. Branched hydrocarbons and cyclic hydrocarbons are also degraded by bacteria. The aerobic bacteria use different types of oxygenases, including monooxygenase, cytochrome-dependent oxygenase and dioxygenase, to insert one or two atoms of oxygen into their targets. Anaerobic bacteria, on the other hand, employ a variety of simple organic and inorganic molecules, including sulphate, nitrate, carbonate and metals, for hydrocarbon oxidation.

  7. Warmer and drier conditions and nitrogen fertilizer application altered methanotroph abundance and methane emissions in a vegetable soil.

    PubMed

    Ran, Yu; Xie, Jianli; Xu, Xiaoya; Li, Yong; Liu, Yapeng; Zhang, Qichun; Li, Zheng; Xu, Jianming; Di, Hongjie

    2017-01-01

    Methane (CH4) is a potent greenhouse gas, and soil can both be a source and sink for atmospheric CH4. It is not clear how future climate change may affect soil CH4 emissions and related microbial communities. The aim of this study was to determine the interactive effects of a simulated warmer and drier climate scenarios and the application of different nitrogen (N) sources (urea and manure) on CH4 emissions and related microbial community abundance in a vegetable soil. Greenhouses were used to control simulated climate conditions which gave 2.99 °C warmer and 6.2% lower water content conditions. The field experiment was divided into two phases. At the beginning of phase II, half of the greenhouses were removed to study possible legacy effects of the simulated warmer and drier conditions. The responses in methanogen and methanotroph abundance to a simulated climate change scenario were determined using real-time PCR. The results showed that the simulated warmer and drier conditions in the greenhouses significantly decreased CH4 emissions largely due to the lower soil moisture content. For the same reason, CH4 emissions of treatments in phase I were much lower than the same treatments in phase II. The abundance of methanotrophs showed a more significant response than methanogens to the simulated climate change scenario, increasing under simulated drier conditions. Methanogenic community abundance remained low, except where manure was applied which provided a source of organic C that stimulated methanogen growth. Soil moisture content was a major driver for methanotroph abundance and strongly affected CH4 emissions. The application of N source decreased CH4 emissions probably because of increased methanotrophic activity. CH4 emissions were positively correlated to methanogenic abundance and negatively correlated to methanotrophic abundance. These results demonstrate that projected future climate change conditions can have a feedback impact on CH4 emissions from the

  8. Genetics of bacteria that utilize one-carbon compounds

    SciTech Connect

    Hanson, R.S.

    1989-11-01

    Methylotrophic bacteria that grow on the one-carbon compounds; methane, methanol, methylamines and dichloromethane are a morphologically and physiologically diverse group of eubacteria. The 16S rRNA molecules of several gram-negative methylotrophs have been sequenced. Two phylogenetically related groups containing type I and type II methylotrophs have been identified. Each group contains two subgroups of bacteria. DNA probes homologous to 16S rRNA's of each group of methanotrophs have been synthesized and have been shown to hybridize only to the 16S rRNA's from target bacteria. We have mapped the positions of 15 genes controlling the synthesis of methanol dehydrogenase, cytochrome C{sub L} and other functions required for the oxidation of methanol to formaldehyde in three species of type II methanotrophs. We have isolated a DNA-binding protein that binds to a cloned 172 bp sequence that is located upstream from the MDH structural gene. The function of this protein in the regulation of MDH synthesis will be investigated. The gene encoding the methane monooxygenase B component of {ital Methylosinus trichosporium} OB3b has been cloned and expressed in {ital Escherichia coli}. We intend to clone and map all five genes required for the expression of soluble MMO activity in {ital M. trichosporium} OB3b and to study the regulation of their synthesis. 5 refs.

  9. Unexpected DNA-fingerprinting pattern in a deep peat bog: evidence for methanotrophs at the bottom?

    NASA Astrophysics Data System (ADS)

    Steinmann, P.; Rossi, P.; Huon, S.; Eilrich, B.; Casati, S.

    2003-04-01

    With the goal of a better understanding of the fate of methane in the deep layers of peat bogs, we analysed the microbial 16S rDNA gene pool and measured the stable carbon isotope composition of bulk peat of a deep (6 m) peat bog profile (Etang de la Gruyère, Switzerland). Both Bacterial and Archaean communities were assessed using respectively TTGE (Temporal Temperature Gradient Electrophoresis) and SSCP (Single Strand Conformation Polymorphism), with fragments of the V1-V3 region of the 16S rDNA gene. The "relative diversity" shown in the TTGE AND SSCP gel patterns is presented using indices and band numbers per sample (Simpson evenness). PCA was calculated on the basis of the intensities of all bands found in the TTGE and SSCP fingerprinting profiles. These DNA fingerprinting patterns reveal the presence of a structured microbial community throughout the whole depth profile. Clear differences can be observed between the communities found in the near surface layers and those found at depth. Surprisingly, for both Archaean and Bacterial communities, the deepest samples display a high similarity level with those found in the first 20 centimeters. The δ13C values of the peat are relatively constant from the surface of the bog down to a depth of 5 m (values between 25.5 ppm and 26.5 ppm). Below 5 m the values decrease considerably with depth ( 28.5 ppm). As a working hypothesis to explain the two observations, we consider the possibility of the presence of methanotrophs in the deepest parts of the bogs. The electron acceptors needed for methane oxidation could be derived from lateral advection of less reducing groundwater. However, available pore water analyses suggest that neither molecular oxygen, nor sulfate or nitrate are present. One possible oxidising agent would be trivalent iron (solid or colloidal). Indeed are the iron concentrations in the deeper pore waters are elevated. Such deep methanotrophic microbial community could be similar to those found near

  10. Bugs digest chlorinated organics

    SciTech Connect

    Not Available

    1993-02-01

    This article describes a new bioreactor that uses a consortium of aerobic bacteria to biodegrade chlorinated aromatic hydrocarbons. Methanotrophic bacteria are cultivated for their MMO enzyme. After the MMO enzyme breaks down the chlorinated organics by oxidation, non-methanotrophic bacteria consume the byproducts. Pilot-scale testing has demonstrated successful treatment of groundwater containing coal-tar constituents, toluene, trichloroethylene, vinyl chlorides, chlorobenzene, and methyl methacrylate from three Superfund sites.

  11. Denitrification of groundwater with methane as sole hydrogen donor.

    PubMed

    Eisentraeger, A; Klag, P; Vansbotter, B; Heymann, E; Dott, W

    2001-06-01

    It was examined, whether methane can be used as hydrogen donor for an in situ denitrification of groundwater. It is demonstrated, that groundwater can serve as liquid medium and that the denitrification can occur at 10 degrees C. Efforts to enrich methanotrophic bacteria under anoxic conditions have not been successful. No methane oxidation occurred in the absence of oxygen. For this reason, the denitrification with methane must be performed in a two-stage process with aerobic methanotrophic bacteria producing metabolites, that are used as hydrogen donor by non-methanotrophic bacteria in anoxic areas. This kind of indirect denitrification was proved by quantifying nitrogen and nitrous oxide in enrichment cultures that were not stirred or shaken. Large numbers of non-methanotrophic bacteria being able to denitrify with methanol, acetate or proteins as sole hydrogen donor were enriched besides the methanotrophic bacteria under these conditions.

  12. Aerobic condition increases carotenoid production associated with oxidative stress tolerance in Enterococcus gilvus.

    PubMed

    Hagi, Tatsuro; Kobayashi, Miho; Nomura, Masaru

    2014-01-01

    Although it is known that a part of lactic acid bacteria can produce carotenoid, little is known about the regulation of carotenoid production. The objective of this study was to determine whether aerobic growth condition influences carotenoid production in carotenoid-producing Enterococcus gilvus. Enterococcus gilvus was grown under aerobic and anaerobic conditions. Its growth was slower under aerobic than under anaerobic conditions. The decrease in pH levels and production of lactic acid were also lower under aerobic than under anaerobic conditions. In contrast, the amount of carotenoid pigments produced by E. gilvus was significantly higher under aerobic than under anaerobic conditions. Further, real-time quantitative reverse transcription PCR revealed that the expression level of carotenoid biosynthesis genes crtN and crtM when E. gilvus was grown under aerobic conditions was 2.55-5.86-fold higher than when it was grown under anaerobic conditions. Moreover, after exposure to 16- and 32-mM H2O2, the survival rate of E. gilvus grown under aerobic conditions was 61.5- and 72.5-fold higher, respectively, than when it was grown under anaerobic conditions. Aerobic growth conditions significantly induced carotenoid production and the expression of carotenoid biosynthesis genes in E. gilvus, resulting in increased oxidative stress tolerance.

  13. Degradation of TCE using sequential anaerobic biofilm and aerobic immobilized bed reactor

    NASA Technical Reports Server (NTRS)

    Chapatwala, Kirit D.; Babu, G. R. V.; Baresi, Larry; Trunzo, Richard M.

    1995-01-01

    Bacteria capable of degrading trichloroethylene (TCE) were isolated from contaminated wastewaters and soil sites. The aerobic cultures were identified as Pseudomonas aeruginosa (four species) and Pseudomonas fluorescens. The optimal conditions for the growth of aerobic cultures were determined. The minimal inhibitory concentration values of TCE for Pseudomonas sps. were also determined. The aerobic cells were immobilized in calcium alginate in the form of beads. Degradation of TCE by the anaerobic and dichloroethylene (DCE) by aerobic cultures was studied using dual reactors - anaerobic biofilm and aerobic immobilized bed reactor. The minimal mineral salt (MMS) medium saturated with TCE was pumped at the rate of 1 ml per hour into the anaerobic reactor. The MMS medium saturated with DCE and supplemented with xylenes and toluene (3 ppm each) was pumped at the rate of 1 ml per hour into the fluidized air-uplift-type reactor containing the immobilized aerobic cells. The concentrations of TCE and DCE and the metabolites formed during their degradation by the anaerobic and aerobic cultures were monitored by GC. The preliminary study suggests that the anaerobic and aerobic cultures of our isolates can degrade TCE and DCE.

  14. Clinical microbiology of coryneform bacteria.

    PubMed Central

    Funke, G; von Graevenitz, A; Clarridge, J E; Bernard, K A

    1997-01-01

    Coryneform bacteria are aerobically growing, asporogenous, non-partially-acid-fast, gram-positive rods of irregular morphology. Within the last few years, there has been a massive increase in the number of publications related to all aspects of their clinical microbiology. Clinical microbiologists are often confronted with making identifications within this heterogeneous group as well as with considerations of the clinical significance of such isolates. This review provides comprehensive information on the identification of coryneform bacteria and outlines recent changes in taxonomy. The following genera are covered: Corynebacterium, Turicella, Arthrobacter, Brevibacterium, Dermabacter. Propionibacterium, Rothia, Exiguobacterium, Oerskovia, Cellulomonas, Sanguibacter, Microbacterium, Aureobacterium, "Corynebacterium aquaticum," Arcanobacterium, and Actinomyces. Case reports claiming disease associations of coryneform bacteria are critically reviewed. Minimal microbiological requirements for publications on disease associations of coryneform bacteria are proposed. PMID:8993861

  15. Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China.

    PubMed

    Liu, Huifeng; Wu, Xing; Li, Zongshan; Wang, Qing; Liu, Dan; Liu, Guohua

    2017-03-01

    Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH4 fluxes, whereas fertilization did not distinctly affect soil CH4 fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH4 fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH4 fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH4 fluxes

  16. C4-Dicarboxylate Utilization in Aerobic and Anaerobic Growth.

    PubMed

    Unden, Gottfried; Strecker, Alexander; Kleefeld, Alexandra; Kim, Ok Bin

    2016-06-01

    C4-dicarboxylates and the C4-dicarboxylic amino acid l-aspartate support aerobic and anaerobic growth of Escherichia coli and related bacteria. In aerobic growth, succinate, fumarate, D- and L-malate, L-aspartate, and L-tartrate are metabolized by the citric acid cycle and associated reactions. Because of the interruption of the citric acid cycle under anaerobic conditions, anaerobic metabolism of C4-dicarboxylates depends on fumarate reduction to succinate (fumarate respiration). In some related bacteria (e.g., Klebsiella), utilization of C4-dicarboxylates, such as tartrate, is independent of fumarate respiration and uses a Na+-dependent membrane-bound oxaloacetate decarboxylase. Uptake of the C4-dicarboxylates into the bacteria (and anaerobic export of succinate) is achieved under aerobic and anaerobic conditions by different sets of secondary transporters. Expression of the genes for C4-dicarboxylate metabolism is induced in the presence of external C4-dicarboxylates by the membrane-bound DcuS-DcuR two-component system. Noncommon C4-dicarboxylates like l-tartrate or D-malate are perceived by cytoplasmic one-component sensors/transcriptional regulators. This article describes the pathways of aerobic and anaerobic C4-dicarboxylate metabolism and their regulation. The citric acid cycle, fumarate respiration, and fumarate reductase are covered in other articles and discussed here only in the context of C4-dicarboxylate metabolism. Recent aspects of C4-dicarboxylate metabolism like transport, sensing, and regulation will be treated in more detail. This article is an updated version of an article published in 2004 in EcoSal Plus. The update includes new literature, but, in particular, the sections on the metabolism of noncommon C4-dicarboxylates and their regulation, on the DcuS-DcuR regulatory system, and on succinate production by engineered E. coli are largely revised or new.

  17. Importance of methane-oxidizing bacteria in the methane budget as revealed by the use of a specific inhibitor

    USGS Publications Warehouse

    Oremland, R.S.; Culbertson, C.W.

    1992-01-01

    METHANE is a greenhouse gas whose concentration in the atmosphere is increasing1-3 Much of this methane is derived from the metabolism of methane-generating (methanogenic) bacteria4,5, and over the past two decades much has been learned about the ecology of methanogens; specific inhibitors of methanogenesis, such as 2-bromoethanesulphonic acid, have proved useful in this regard6. In contrast, although much is known about the biochemistry of methane-oxidizing (methanotrophic) bacteria7, ecological investigations have been hampered by the lack of an analogous specific inhibitor6. Methanotrophs limit the flux of methane to the atmosphere from sediments8,9 and consume atmospheric methane10, but the quantitative importance of methanotrophy in the global methane budget is not well known5. Methylfluoride (CH3F) is known to inhibit oxygen consumption by Methylococcus capsulatus11, and to inhibit the oxidation of 14CH4 to 14CO2 by endosymbionts in mussel gill tissues12. Here we report that methylfluoride (MF) inhibits the oxidation of methane by methane monooxygenase, and by using methylfluoride in field investigations, we find that methanotrophic bacteria can consume more than 90% of the methane potentially available.

  18. Petrifilm plates for enumeration of bacteria counts in goat milk

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PetrifilmTM Aerobic Count (AC) and Coliform Count (CC) plates were validated against standard methods for enumeration of coliforms, total bacteria, and psychrotrophic bacteria in raw (n = 39) and pasteurized goat milk (n = 17) samples. All microbiological data were transformed into log form and sta...

  19. Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field.

    PubMed

    Liu, Yuan; Liu, Xiaoyu; Cheng, Kun; Li, Lianqing; Zhang, Xuhui; Zheng, Jufeng; Zheng, Jinwei; Pan, Genxing

    2016-01-01

    Although climate change is predicted to affect methane (CH4) emissions in paddy soil, the dynamics of methanogens and methanotrophs in paddy fields under climate change have not yet been fully investigated. To address this issue, a multifactor climate change experiment was conducted in a Chinese paddy field using the following experimental treatments: (1) enrichment of atmospheric CO2 concentrations (500 ppm, CE), (2) canopy air warming (2°C above the ambient, WA), (3) combined CO2 enrichment and warming (CW), and (4) ambient conditions (CK). We analyzed the abundance of methanogens and methanotrophs, community structures, CH4 production and oxidation potentials, in situ CH4 emissions using real-time PCR, T-RFLP, and clone library techniques, as well as biochemical assays. Compared to the control under CE and CW treatments, CH4 production potential, methanogenic gene abundance and soil microbial biomass carbon significantly increased; the methanogenic community, however, remained stable. The canopy air warming treatment only had an effect on CH4 oxidation potential at the ripening stage. Phylogenic analysis indicated that methanogens in the rhizosphere were dominated by Methanosarcina, Methanocellales, Methanobacteriales, and Methanomicrobiales, while methanotrophic sequences were classified as Methylococcus, Methylocaldum, Methylomonas, Methylosarcina (Type I) and Methylocystis (Type II). However, the relative abundance of Methylococcus (Type I) decreased under CE and CW treatments and the relative abundance of Methylocystis (Type II) increased. The in situ CH4 fluxes indicated similar seasonal patterns between treatments; both CE and CW increased CH4 emissions. In conclusion results suggest that methanogens and methanotrophs respond differently to elevated atmospheric CO2 concentrations and warming, thus adding insights into the effects of simulated global climate change on CH4 emissions in paddy fields.

  20. Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field

    PubMed Central

    Liu, Yuan; Liu, Xiaoyu; Cheng, Kun; Li, Lianqing; Zhang, Xuhui; Zheng, Jufeng; Zheng, Jinwei; Pan, Genxing

    2016-01-01

    Although climate change is predicted to affect methane (CH4) emissions in paddy soil, the dynamics of methanogens and methanotrophs in paddy fields under climate change have not yet been fully investigated. To address this issue, a multifactor climate change experiment was conducted in a Chinese paddy field using the following experimental treatments: (1) enrichment of atmospheric CO2 concentrations (500 ppm, CE), (2) canopy air warming (2°C above the ambient, WA), (3) combined CO2 enrichment and warming (CW), and (4) ambient conditions (CK). We analyzed the abundance of methanogens and methanotrophs, community structures, CH4 production and oxidation potentials, in situ CH4 emissions using real-time PCR, T-RFLP, and clone library techniques, as well as biochemical assays. Compared to the control under CE and CW treatments, CH4 production potential, methanogenic gene abundance and soil microbial biomass carbon significantly increased; the methanogenic community, however, remained stable. The canopy air warming treatment only had an effect on CH4 oxidation potential at the ripening stage. Phylogenic analysis indicated that methanogens in the rhizosphere were dominated by Methanosarcina, Methanocellales, Methanobacteriales, and Methanomicrobiales, while methanotrophic sequences were classified as Methylococcus, Methylocaldum, Methylomonas, Methylosarcina (Type I) and Methylocystis (Type II). However, the relative abundance of Methylococcus (Type I) decreased under CE and CW treatments and the relative abundance of Methylocystis (Type II) increased. The in situ CH4 fluxes indicated similar seasonal patterns between treatments; both CE and CW increased CH4 emissions. In conclusion results suggest that methanogens and methanotrophs respond differently to elevated atmospheric CO2 concentrations and warming, thus adding insights into the effects of simulated global climate change on CH4 emissions in paddy fields. PMID:27933055

  1. Dynamics Associated with Prolonged Ensiling and Aerobic Deterioration of Total Mixed Ration Silage Containing Whole Crop Corn

    PubMed Central

    Wang, Huili; Ning, Tingting; Hao, Wei; Zheng, Mingli; Xu, Chuncheng

    2016-01-01

    This study investigated the dynamics associated with prolonged ensiling and aerobic deterioration of whole crop corn (WCC) silages and total mixed ration (TMR) silages containing WCC (C-TMR silages) to clarify the differences that account for the enhanced aerobic stability of TMR silages. Laboratory-scale barrel silos were randomly opened after 7, 14, 28, and 56 d of ensiling and were subjected to analyses of fermentation quality, microbial and temperature dynamics during aerobic exposure. WCC and C-TMR silages were both well preserved and microorganisms were inhibited with prolonged ensiling, including lactic acid bacteria. Yeast were inhibited to below the detection limit of 500 cfu/g fresh matter within 28 d of ensiling. Aerobic stability of both silages was enhanced with prolonged ensiling, whereas C-TMR silages were more aerobically stable than WCC silages for the same ensiling period. Besides the high moisture content, the weak aerobic stability of WCC silage is likely attributable to the higher lactic acid content and yeast count, which result from the high water-soluble carbohydrates content in WCC. After silo opening, yeast were the first to propagate and the increase in yeast levels is greater than that of other microorganisms in silages before deterioration. Besides, increased levels of aerobic bacteria were also detected before heating of WCC silages. The temperature dynamics also indicated that yeast are closely associated with the onset of the aerobic deterioration of C-TMR silage, whereas for WCC silages, besides yeast, aerobic bacteria also function in the aerobic deterioration. Therefore, the inclusion of WCC might contribute to the survival of yeast during ensiling but not influence the role of yeast in deterioration of C-TMR silages. PMID:26732329

  2. Methane dynamics in an alpine fen: a field-based study on methanogenic and methanotrophic microbial communities.

    PubMed

    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.

  3. Methanotrophs, Methylosinus trichosporium OB3b, sMMO, and their application to bioremediation.

    PubMed

    Sullivan, J P; Dickinson, D; Chase, H A

    1998-01-01

    One of the most problematic groups of the USEPA and EU priority pollutants are the halogenated organic compounds. These substances have a wide range of industrial applications, such as solvents and cleaners. Inadequate disposal techniques and accidental spillages have led to their detection in soil, groundwater, and river sediments. Persistence of these compounds in the environment has resulted from low levels of biodegradation due to chemical structural features that preclude or retard biological attack. Research has indicated the idea that treatment systems based on methanotrophic co-metabolic transformation may be a cost-effective and efficient alternative to physical methods because of the potential for high transformation rates, the possibility of complete compound degradation without the formation of toxic metabolites, applicability to a broad spectrum of compounds, and the use of a widely available and inexpensive growth substrate. A substantial amount of work concerning methanotrophic cometabolic transformations has been carried out using the soluble form of methane monooxygenase (sMMO) from the obligate methanotroph Methylosinus trichosporium OB3b. This NADH-dependent monooxygenase is derepressed when cells are grown under copper stress. sMMO has a wider specificity than the particulate form. sMMO has been shown to degrade trichloroethylene (TCE) at a rate of at least one order of magnitude faster than obtained with other mixed and pure cultures, suggesting it has a wider application to bioremediation. Furthermore, sMMO catalyzes an unusually wide range of oxidation reactions, including the hydroxylation of alkanes, epoxidation of alkenes, ethers, halogenated methanes, cyclic and aromatic compounds including compounds, that are resistant to degradation in the environment. However, the practical application of methantrophs and Methylosinus trichosporium OB3b to the treatment of chlorinated organics has met with mixed success. Although oxidation rates are

  4. Genetics of bacteria that utilize one carbon compounds: Annual report, March 1, 1988--December 24, 1988

    SciTech Connect

    Hanson, R.S.

    1988-12-01

    Bacteria that grow on methane, methanol and methylamine are a morphologically and physiologically diverse group of bacteria. Several of these bacteria have been shown to be clustered in two phylogenetically related groups by analysis of 16S RNA sequences. This information is useful for the synthesis of probes to detect methanotrophs in samples from bioreactors and in a variety of environments. We have observed considerable sequence homology in the methanol dehydrogenase genes of all gram negative methylotrophs. However, the upstream regulatory sequences of the two methylotrophic bacteria from which MDH genes have been completely sequenced have little similarity. The genetic maps of 12 genes required for MDH synthesis show several differences in two closely related methylotrophs. The MDH messenger RNA has a chemical half life of approximately one-minute although the protein represents 20% of the cellular protein. We now intend to map and sequence cloned genes encoding five proteins of Methylosinus trichosporium OB3B required for methane monooxygenase activity. We will continue to characterize the fourteen genes (and their gene products) required for MDH synthesis and will continue 16S rRNA sequencing in order to complete the molecular phylogeny of methanotrophic bacteria. 3 refs.

  5. Die aerobe Glykolyse der Tumorzelle

    NASA Astrophysics Data System (ADS)

    Schneider, Friedhelm

    1981-01-01

    A high aerobic glycolysis (aerobic lactate production) is the most significant feature of the energy metabolism of rapidly growing tumor cells. Several mechanisms, which may be different in different cell lines, seem to be involved in this characteristic of energy metabolism of the tumor cell. Changes in the cell membrane leading to increased uptake and utilization of glucose, a high level of fetal types of isoenzymes, a decreased number of mitochondria and a reduced capacity to metabolize pyruvate are some factors which must be taken into consideration. It is not possible to favour one of them at the present time.

  6. Improving aerobic stability and biogas production of maize silage using silage additives.

    PubMed

    Herrmann, Christiane; Idler, Christine; Heiermann, Monika

    2015-12-01

    The effects of air stress during storage, exposure to air at feed-out, and treatment with silage additives to enhance aerobic stability on methane production from maize silage were investigated at laboratory scale. Up to 17% of the methane potential of maize without additive was lost during seven days exposure to air on feed-out. Air stress during storage reduced aerobic stability and further increased methane losses. A chemical additive containing salts of benzoate and propionate, and inoculants containing heterofermentative lactic acid bacteria were effective to increase aerobic stability and resulted in up to 29% higher methane yields after exposure to air. Exclusion of air to the best possible extent and high aerobic stabilities should be primary objectives when ensiling biogas feedstocks.

  7. The Transition from Aerobic to Anaerobic Metabolism.

    ERIC Educational Resources Information Center

    Skinner, James S.; McLellan, Thomas H.

    1980-01-01

    The transition from aerobic to anaerobic metabolism is discussed. More research is needed on different kinds of athletes and athletic activities and how they may affect aerobic and anaerobic metabolisms. (CJ)

  8. Transcriptional activities of methanogens and methanotrophs vary with methane emission flux in rice soils under chronic nutrient constraints of phosphorus and potassium

    NASA Astrophysics Data System (ADS)

    Sheng, Rong; Chen, Anlei; Zhang, Miaomiao; Whiteley, Andrew S.; Kumaresan, Deepak; Wei, Wenxue

    2016-12-01

    Nutrient status in soil is crucial for the growth and development of plants which indirectly or directly affect the ecophysiological functions of resident soil microorganisms. Soil methanogens and methanotrophs can be affected by soil nutrient availabilities and plant growth, which in turn modulate methane (CH4) emissions. Here, we assessed whether deficits in soil-available phosphorus (P) and potassium (K) modulated the activities of methanogens and methanotrophs in a long-term (20 year) experimental system involving limitation in either one or both nutrients. Results showed that a large amount of CH4 was emitted from paddy soil at rice tillering stage (flooding) while CH4 flux was minimum at ripening stage (drying). Compared to soils amended with NPK fertiliser treatment, the soils without P input significantly reduced methane flux rates, whereas those without K input did not. Under P limitation, methanotroph transcript copy number significantly increased in tandem with a decrease in methanogen transcript abundance, suggesting that P-deficiency-induced changes in soil physio-chemical properties, in tandem with rice plant growth, might constrain the activity of methanogens, whereas the methanotrophs might be adaptive to this soil environment. In contrast, lower transcript abundance of both methanogen and methanotrophs were observed in K-deficient soils. Assessments of community structures based upon transcripts indicated that soils deficient in P induced greater shifts in the active methanotrophic community than K-deficient soils, while similar community structures of active methanogens were observed in both treatments. These results suggested that the population dynamics of methanogens and methanotrophs could vary along with the changes in plant growth states and soil properties induced by nutrient deficiency.

  9. Comparative investigation on microbial community and electricity generation in aerobic and anaerobic enriched MFCs.

    PubMed

    Quan, Xiang-chun; Quan, Yan-ping; Tao, Kun; Jiang, Xiao-man

    2013-01-01

    This study compared the difference in microbial community and power generation capacity of air-cathode MFCs enriched under anode aerobic and anaerobic conditions. Results showed that MFCs successfully started with continuous air inputting to anode chamber. The aerobic enriched MFC produced comparable and even more electricity with the fuels of acetate, glucose and ethanol compared to the anaerobic MFC when returning to anaerobic condition. The two MFCs showed a slightly different microbial community for anode biofilms (a similarity of 77%), but a highly similar microbial community (a similarity of 97%) for anolyte microbes. The anode biofilm of aerobic enriched MFC showed the presence of some specific bacteria closely related to Clostridium sticklandii, Leucobacter komagatae and Microbacterium laevaniformans. The anaerobic enriched MFC found the presence of a large number of yeast Trichosporon sp. This research demonstrates that it is possible to enrich oxygen-tolerant anode respiring bacteria through purposely aeration in anode chamber.

  10. Integrated Anaerobic-Aerobic Biodegradation of Multiple Contaminants Including Chlorinated Ethylenes, Benzene, Toluene, and Dichloromethane.

    PubMed

    Yoshikawa, Miho; Zhang, Ming; Toyota, Koki

    2017-01-01

    Complete bioremediation of soils containing multiple volatile organic compounds (VOCs) remains a challenge. To explore the possibility of complete bioremediation through integrated anaerobic-aerobic biodegradation, laboratory feasibility tests followed by alternate anaerobic-aerobic and aerobic-anaerobic biodegradation tests were performed. Chlorinated ethylenes, including tetrachloroethylene (PCE), trichloroethylene (TCE), cis-dichloroethylene (cis-DCE), and vinyl chloride (VC), and dichloromethane (DCM) were used for anaerobic biodegradation, whereas benzene, toluene, and DCM were used for aerobic biodegradation tests. Microbial communities involved in the biodegradation tests were analyzed to characterize the major bacteria that may contribute to biodegradation. The results demonstrated that integrated anaerobic-aerobic biodegradation was capable of completely degrading the seven VOCs with initial concentration of each VOC less than 30 mg/L. Benzene and toluene were degraded within 8 days, and DCM was degraded within 20 to 27 days under aerobic conditions when initial oxygen concentrations in the headspaces of test bottles were set to 5.3% and 21.0%. Dehalococcoides sp., generally considered sensitive to oxygen, survived aerobic conditions for 28 days and was activated during the subsequent anaerobic biodegradation. However, degradation of cis-DCE was suppressed after oxygen exposure for more than 201 days, suggesting the loss of viability of Dehalococcoides sp., as they are the only known anaerobic bacteria that can completely biodegrade chlorinated ethylenes to ethylene. Anaerobic degradation of DCM following previous aerobic degradation was complete, and yet-unknown microbes may be involved in the process. The findings may provide a scientific and practical basis for the complete bioremediation of multiple contaminants in situ and a subject for further exploration.

  11. Aerobic granulation of aggregating consortium X9 isolated from aerobic granules and role of cyclic di-GMP.

    PubMed

    Wan, Chunli; Yang, Xue; Lee, Duu-Jong; Wang, Xin-Yue; Yang, Qiaoli; Pan, Xiangliang

    2014-01-01

    This study monitored the granulation process of an aggregating functional consortium X9 that was consisted of Pseudomonas putida X-1, Acinetobacter sp. X-2, Alcaligenes sp. X-3 and Comamonas testosteroni X-4 in shaken reactors. The growth curve of X9 was fit using logistic model as follows y=1.49/(1+21.3*exp(-0.33x)), the maximum specific cell growth rate for X9 was 0.33 h(-1). Initially X9 consumed polysaccharides (PS) and secreted proteins (PN) to trigger granulation. Then X9 grew in biomass and formed numerous micro-granules, driven by increasing hydrophobicity of cell membranes and of accumulated extracellular polymeric substances (EPS). In later stage the intracellular cyclic diguanylate (c-di-GMP) was at high levels for inhibiting bacteria swarming motility, thereby promotion formation of large aerobic granules. The findings reported herein advise the way to accelerate granule formation and to stabilize operation in aerobic granular reactors.

  12. Arthritis and Aerobic Exercise: A Review.

    ERIC Educational Resources Information Center

    Ike, Robert W.; And Others

    1989-01-01

    Arthritic patients who regularly do aerobic exercise make significant gains in aerobic and functional status, and in subjective areas like pain tolerance and mood. Still, they are often advised to curtail physical activity. Guidelines are presented for physicians prescribing aerobic exercise. An exercise tolerance test is recommended. (SM)

  13. Two-liquid phase partitioning biotrickling filters for methane abatement: exploring the potential of hydrophobic methanotrophs.

    PubMed

    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.

  14. Field-Scale Stable-Isotope Probing of Active Methanotrophs in a Landfill-Cover Soil

    NASA Astrophysics Data System (ADS)

    Schroth, M. H.; Henneberger, R.; Chiri, E.

    2012-12-01

    The greenhouse gas methane (CH4) is an important contributor to global climate change. While its atmospheric concentration is increasing, a large portion of produced CH4 never reaches the atmosphere, but is consumed by aerobic methane-oxidizing bacteria (MOB). The latter are ubiquitous in soils and utilize CH4 as sole source of energy and carbon. Among other methods, MOB may be differentiated based on characteristic phospholipid fatty acids (PLFA). Stable-isotope probing (SIP) on PLFA has been widely applied to identify active members of MOB communities in laboratory incubation studies, but results are often difficult to extrapolate to the field. Thus, novel field-scale approaches are needed to link activity and identity of MOB in their natural environment. We present results of field experiments in which we combined PLFA-SIP with gas push-pull tests (GPPTs) to label active MOB at the field-scale while simultaneously quantifying CH4 oxidation activity. During a SIP-GPPT, a mixture of reactive (here 13CH4, O2) and non-reactive tracer gases (e.g., Ar, Ne, He) is injected into the soil at a location of interest. Thereafter, gas flow is reversed and the gas mixture diluted with soil air is extracted from the same location and sampled periodically. Rate constants for CH4 oxidation can be calculated by analyzing breakthrough curves of 13CH4 and a suitable non-reactive tracer gas. SIP-GPPTs were performed in a landfill-cover soil, and feasibility of this novel approach was tested at several locations along a gradient of MOB activity and soil temperature. Soil samples were collected before and after SIP-GPPTs, total PLFA were extracted, and incorporation of 13C in the polar lipid fraction was analyzed. Potential CH4 oxidation rates derived from SIP-GPPTs were similar to those derived from regular GPPTs (using unlabeled CH4) performed at the same locations prior to SIP-GPPTs, indicating that application of 13CH4 did not adversely affect bacterial CH4 oxidation rates. Rates

  15. A Field-Suitable, Semisolid Aerobic Enrichment Medium for Isolation of Campylobacter jejuni in Small Numbers

    PubMed Central

    Jeffrey, J. S.; Hunter, A.; Atwill, E. R.

    2000-01-01

    The objective of this study was to produce an economical, easy to prepare, field-suitable enrichment medium for detection of Campylobacter jejuni in small numbers. A semisolid aerobic enrichment medium was developed. Rates of recovery from inoculated medium, sterile swabs, and mixed cultures of C. jejuni and coliform bacteria were tested. PMID:10747165

  16. Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

    PubMed Central

    Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.; Kellermann, Matthias Y.; Redmond, Molly C.; Andersen, Gary L.; Valentine, David L.

    2017-01-01

    The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane and CO2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems. PMID:28289403

  17. Developmental intestinal aerobic microflora in the kori bustard (Ardeotis kori).

    PubMed

    Naldo, J L; Silvanose, C D; Samour, J H; Bailey, T A

    1998-01-01

    A study was carried out to investigate the normal aerobic bacterial flora of developing kori bustard (Ardeotis kori) chicks, captive bred at the National Avian Research Center, Abu Dhabi, United Arab Emirates. Faecal samples were collected from 14 birds at different ages from the first day of hatching until 99 days old and were cultured for aerobic bacteria. Several bacterial species were isolated from the cultures, they included Escherichia coli, Streptococcus viridians, Enterococcus faecalis, Klebsiella oxytoca, Proteus spp., Enterobacter, spp. and Serratia marcescens. Gram-negative bacilli were isolated from all but one of the faecal samples collected. They were also the predominant bacteria, accounting for between 55.6 and 73.4% of the mean colony count of faecal cultures from all age groups. E. coli was the most frequently isolated bacteria, the frequency and mean colony count increased as the birds grew older. Gram-positive cocci were isolated from between 50 and 100% of the faecal samples from all age groups, and they accounted for between 26.6 and 44.4% of the mean colony count. Results from this study indicated that Gram-negative bacilli and Gram-positive cocci can be isolated frequently from the faeces of developing, clinically normal, captive bred kori bustard chicks.

  18. Sulphur bacteria mediated formation of Palaeoproterozoic phosphorites

    NASA Astrophysics Data System (ADS)

    Joosu, Lauri; Lepland, Aivo; Kirsimäe, Kalle

    2014-05-01

    Modern phosphorite formation is typically associated with high productivity in upwelling areas where apatite (Ca-phosphate) precipitation is mediated by sulphur oxidising bacteria [1]. They inhabit the oxic/anoxic interface within the upper few centimetres of sediment column, accumulating phosphate in their cells under oxic conditions and releasing it rapidly when conditions become anoxic. Sulphur bacteria are known to live in close association with a consortium of anaerobic methane oxidising archaea and syntrophic sulphate-reducing bacteria. Paleoproterozoic, c. 2.0 Ga Zaonega Formation in Karelia, Russia contains several P-rich intervals in the upper part of 1500 m thick succession of organic-rich sedimentary rocks interlayered with mafic tuffs and lavas. Apatite in these P-rich intervals forms impure laminae, lenses and round-oval nodules which diameters typically range from 300 to 1000 μm. Individual apatite particles in P-rich laminae and nodules commonly occur as cylinders that are 1-8 μm long and have diameters of 0.5-4 μm. Cross-sections of best preserved cylindrical apatite particles reveal a thin outer rim whereas the internal parts consist of small anhedral elongated crystallites, intergrown with carbonaceous material. During recrystallization the outer rim thickens towards interior and cylinders may attain hexagonal crystal habit, but their size and shape remains largely unchanged [2]. The sizes of Zaonega nodules are similar to giant sulphide-oxidising bacteria known from modern and ancient settings [3, 4]. Individual apatite cylinders and aggregates have shapes and sizes similar to the methanotrophic archaea that inhabit microbial mats in modern seep/vent areas where they operate in close associations with sulphur-oxidising microbial communities [5]. Seep/vent influence during the Zaonega phosphogenesis is indicated by variable, though positive Eu anomaly, expected in magmatically active sedimentary environment experiencing several lava flows

  19. Fractionation of the methane isotopologues 13CH4, 12CH3D, and 13CH3D during aerobic oxidation of methane by Methylococcus capsulatus (Bath)

    NASA Astrophysics Data System (ADS)

    Wang, David T.; Welander, Paula V.; Ono, Shuhei

    2016-11-01

    Aerobic oxidation of methane plays a major role in reducing the amount of methane emitted to the atmosphere from freshwater and marine settings. We cultured an aerobic methanotroph, Methylococcus capsulatus (Bath) at 30 and 37 °C, and determined the relative abundance of 12CH4, 13CH4, 12CH3D, and 13CH3D (a doubly-substituted, or ;clumped; isotopologue of methane) to characterize the clumped isotopologue effect associated with aerobic methane oxidation. In batch culture, the residual methane became enriched in 13C and D relative to starting methane, with D/H fractionation a factor of 9.14 (Dε/13ε) larger than that of 13C/12C. As oxidation progressed, the Δ13CH3D value (a measure of the excess in abundance of 13CH3D relative to a random distribution of isotopes among isotopologues) of residual methane decreased. The isotopologue fractionation factor for 13CH3D/12CH4 was found to closely approximate the product of the measured fractionation factors for 13CH4/12CH4 and 12CH3D/12CH4 (i.e., 13C/12C and D/H). The results give insight into enzymatic reversibility in the aerobic methane oxidation pathway. Based on the experimental data, a mathematical model was developed to predict isotopologue signatures expected for methane in the environment that has been partially-oxidized by aerobic methanotrophy. Measurement of methane clumped isotopologue abundances can be used to distinguish between aerobic methane oxidation and alternative methane-cycling processes.

  20. Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008.

    PubMed

    Dedysh, Svetlana N; Kulichevskaya, Irina S; Serkebaeva, Yulia M; Mityaeva, Maria A; Sorokin, Vladimir V; Suzina, Natalia E; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe

    2012-03-01

    An aerobic, pink-pigmented, chemo-organotrophic bacterium, designated strain SN10(T), was isolated from a methanotrophic enrichment culture obtained from an acidic Sphagnum peat. This isolate was represented by Gram-negative, non-motile rods that multiply by normal cell division and form rosettes. Strain SN10(T) is an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.2-6.6 (with an optimum at pH 4.7-5.2) and at 6-32 °C (with an optimum at 20-24 °C). The preferred growth substrates are sugars and several heteropolysaccharides of plant and microbial origin, such as pectin, lichenan, fucoidan and gellan gum. While not being capable of growth on C(1) compounds, strain SN10(T) can develop in co-culture with exopolysaccharide-producing methanotrophs by utilization of their capsular material. The major fatty acids determined in strain SN10(T) using the conventional lipid extraction procedure are iso-C(15:0) and C(16:1)ω7c. Upon hydrolysis of total cell material, substantial amounts of the uncommon membrane-spanning lipid 13,16-dimethyl octacosanedioic acid (isodiabolic acid) were also detected. The polar lipids are two phosphohexoses, phosphatidylethanolamine, phosphatidylglycerol and several phospholipids of unknown structure. The major quinone is MK-8. Pigments are carotenoids. The G+C content of the DNA is 60.7 mol%. Strain SN10(T) forms a separate lineage within subdivision 1 of the phylum Acidobacteria and displays 94.0-95.4% 16S rRNA gene sequence similarity to members of the genera Edaphobacter and Granulicella, 93.0-93.7% similarity to members of the genus Terriglobus and 92.2-92.3 % similarity to the type strains of Telmatobacter bradus and Acidobacterium capsulatum. Therefore, strain SN10(T) is classified within a novel genus and species, for which the name Bryocella elongata gen. nov., sp. nov. is proposed. Strain SN10(T) (=LMG 25276(T) =DSM 22489(T)) is the type strain of Bryocella elongata. An emended description of Edaphobacter

  1. Calcium precipitate induced aerobic granulation.

    PubMed

    Wan, Chunli; Lee, Duu-Jong; Yang, Xue; Wang, Yayi; Wang, Xingzu; Liu, Xiang

    2015-01-01

    Aerobic granulation is a novel biotechnology for wastewater treatment. This study refined existing aerobic granulation mechanisms as a sequencing process including formation of calcium precipitate under alkaline pH to form inorganic cores, followed by bacterial attachment and growth on these cores to form the exopolysaccharide matrix. Mature granules comprised an inner core and a matrix layer and a rim layer with enriched microbial strains. The inorganic core was a mix of different crystals of calcium and phosphates. Functional strains including Sphingomonas sp., Paracoccus sp. Sinorhizobium americanum strain and Flavobacterium sp. attached onto the cores. These functional strains promote c-di-GMP production and the expression by Psl and Alg genes for exopolysaccharide production to enhance formation of mature granules.

  2. WWOX loss activates aerobic glycolysis.

    PubMed

    Abu-Remaileh, Muhannad; Seewaldt, Victoria L; Aqeilan, Rami I

    2015-01-01

    Cancer cells undergo reprogramming of glucose metabolism to limit energy production to glycolysis-a state known as "aerobic glycolysis." Hypoxia-inducible factor 1 (HIF1α) is a transcription factor that regulates many genes responsible for this switch. As disc