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Sample records for aerobic methane-oxidizing bacteria

  1. 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. PMID:9464387

  2. Toxic effects of butyl elastomers on aerobic methane oxidation

    NASA Astrophysics Data System (ADS)

    Niemann, Helge; Steinle, Lea I.; Blees, Jan H.; Krause, Stefan; Bussmann, Ingeborg; Lehmann, Moritz F.; Treude, Tina

    2013-04-01

    Large quantities of the potent greenhouse gas methane are liberated into the water column of marine and lacustrine environments where it may be consumed by aerobic methane oxidising bacteria before reaching the atmosphere.The reliable quantification of aerobic methane oxidation (MOx) rates is consequently of paramount importance for estimating methane budgets and to understand the controls on water column methane cycling. A widely used set of methods for measuring MOx rates is based on the incubation of water samples during which the consumption of methane is monitored, for instance with radio-tracer assays. Typically, incubation vessels are sealed with butyl rubber stoppers because these elastomers are essentially impermeable for gases at the relevant time scales. We tested the effect of different stopper materials (unmodified- and halogenated butyl rubber) on MOx activity in environmental samples and in cultures of methane oxidising bacteria. MOx rates in samples sealed with unmodified butyl rubber were > 75% lower compared to parallel incubations with halogenated butyl rubber seals, suggesting inhibiting/toxic effects associated with the use of unmodified butyl elastomers. To further explore the cause of these effects, we analysed aqueous extracts of the different stoppers. Halogenated butyl rubber stoppers appeared to bleed off comparably little amounts of organics. In stark contrast, extracts of unmodified butyl rubber were contaminated with various organic compounds including potential bactericides such as benzyltoluenes, phenylalkanes and benzuothiazoles. We also found tetramethylthiourea, a scavenger of active oxygen species, which may inhibit the MOx pathway.

  3. 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

  4. Aerobic Methane Oxidation in Alaskan Lakes Along a Latitudinal Transect

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Karla Martinez-Cruz* **, Armando Sepulveda-Jauregui*, Katey M. Walter Anthony*, Peter Anthony*, and Frederic Thalasso**. * Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, Alaska. ** Biotechnology and Bioengineering Department, Cinvestav, Mexico city, D. F., Mexico. Methane (CH4) is the third most important greenhouse gas in the atmosphere, after carbon dioxide and water vapor. Boreal lakes play an important role in the current global warming by contributing as much as 6% of global atmospheric CH4 sources annually. On the other hand, aerobic methane oxidation (methanotrophy) in lake water is a fundamental process in global methane cycling that reduces the amount of CH4 emissions to the atmosphere. Several environmental factors affect aerobic methane oxidation in the water column both directly and indirectly, including concentration of CH4 and O2, temperature and carbon budgets of lakes. We analyzed the potential of aerobic methane oxidation (PMO) rates in incubations of water collected from 30 Alaskan lakes along a north-south transect during winter and summer 2011. Our findings showed an effect of CH4 and O2 concentrations, temperature and yedoma thawing permafrost on PMO activity in the lake water. The highest PMO rates were observed in summer by lakes situated on thawing yedoma permafrost, most of them located in the interior of Alaska. We also estimated that 60-80% of all CH4 produced in Alaskan lakes could be taken up by methanotrophs in the lake water column, showing the significant influence of aerobic methane oxidation of boreal lakes to the global CH4 budget.

  5. 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.

  6. 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

  7. 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

  8. High resolution and comprehensive techniques to analyze aerobic methane oxidation in mesocosm experiments

    NASA Astrophysics Data System (ADS)

    Chan, E. W.; Kessler, J. D.; Redmond, M. C.; Shiller, A. M.; Arrington, E. C.; Valentine, D. L.; Colombo, F.

    2015-12-01

    Many studies of microbially mediated aerobic methane oxidation in oceanic environments have examined the many different factors that control the rates of oxidation. However, there is debate on how quickly methane is oxidized once a microbial population is established and what factor(s) are limiting in these types of environments. These factors include the availability of CH4, O2, trace metals, nutrients, and the density of cell population. Limits to these factors can also control the temporal aspects of a methane oxidation event. In order to look at this process in its entirety and with higher temporal resolution, a mesocosm incubation system was developed with a Dissolved Gas Analyzer System (DGAS) coupled with a set of analytical tools to monitor aerobic methane oxidation in real time. With the addition of newer laser spectroscopy techniques (cavity ringdown spectroscopy), stable isotope fractionation caused by microbial processes can also be examined on a real time and automated basis. Cell counting, trace metal, nutrient, and DNA community analyses have also been carried out in conjunction with these mesocosm samples to provide a clear understanding of the biology in methane oxidation dynamics. This poster will detail the techniques involved to provide insights into the chemical and isotopic kinetics controlling aerobic methane oxidation. Proof of concept applications will be presented from seep sites in the Hudson Canyon and the Sleeping Dragon seep field, Mississippi Canyon 118 (MC 118). This system was used to conduct mesocosm experiments to examine methane consumption, O2 consumption, nutrient consumption, and biomass production.

  9. Methane formation and methane oxidation by methanogenic bacteria.

    PubMed Central

    Zehnder, A J; Brock, T D

    1979-01-01

    Methanogenic bacteria were found to form and oxidize methane at the same time. As compared to the quantity of methane formed, the amount of methane simultaneously oxidized varied between 0.3 and 0.001%, depending on the strain used. All the nine tested strains of methane producers (Methanobacterium ruminantium, Methanobacterium strain M.o.H., M. formicicum, M. thermoautotrophicum, M. arbophilicum, Methanobacterium strain AZ, Methanosarcina barkeri, Methanospirillum hungatii, and the "acetate organism") reoxidized methane to carbon dioxide. In addition, they assimilated a small part of the methane supplied into cell material. Methanol and acetate also occurred as oxidation products in M. barkeri cultures. Acetate was also formed by the "acetate organism," a methane bacterium unable to use methanogenic substrates other than acetate. Methane was the precursor of the methyl group of the acetate synthesized in the course of methane oxidation. Methane formation and its oxidation were inhibited equally by 2-bromoethanesulfonic acid. Short-term labeling experiments with M. thermoautotrophicum and M. hungatii clearly suggest that the pathway of methane oxidation is not identical with a simple back reaction of the methane formation process. Images PMID:762019

  10. Evaluation of methyl fluoride and dimethyl ether as inhibitors of aerobic methane oxidation

    USGS Publications Warehouse

    Oremland, R.S.; Culbertson, C.W.

    1992-01-01

    Methyl fluoride (MF) and dimethyl ether (DME) were effective inhibitors of aerobic methanotrophy in a variety of soils. MF and DME blocked consumption of CH4 as well as the oxidation of 14CH4 to 14CO2, but neither MF nor DME affected the oxidation of [14C]methanol or [14C]formate to 14CO2. Cooxidation of ethane and propane by methane-oxidizing soils was also inhibited by MF. Nitrification (ammonia oxidation) in soils was inhibited by both MF and DME. Production of N2O via nitrification was inhibited by MF; however, MF did not affect N2O production associated with denitrification. Methanogenesis was partially inhibited by MF but not by DME. Methane oxidation was ~100-fold more sensitive to MF than was methanogenesis, indicating that an optimum concentration could be employed to selectively block methanotrophy. MF inhibited methane oxidation by cell suspensions of Methylococcus capsulatus; however, DME was a much less effective inhibitor.

  11. Environmental Controls on Aerobic Methane Oxidation in Coastal Waters

    NASA Astrophysics Data System (ADS)

    Steinle, L.; Maltby, J.; Engbersen, N.; Zopfi, J.; Bange, H. W.; Elvert, M.; Hinrichs, K. U.; Kock, A.; Lehmann, M. F.; Treude, T.; Niemann, H.

    2015-12-01

    Large quantities of the greenhouse gas CH4 are produced in anoxic sediments of continental margins and may be liberated to the overlying water column, and later into the atmosphere. Indeed, coastal seas account for more than 75% of global oceanic CH4 emissions. Yet, aerobic CH4 oxidizing bacteria (MOB) consume an important part of CH4 in the water column, thus mitigating CH4 release to the atmosphere. Coastal oceans are highly dynamic systems, in particular with regard to the variability of temperature, salinity and oxygen concentrations, all of which are potential key environmental factors controlling MOx. To determine the most important controlling factors, we conducted a two-year time-series study with measurements of CH4, MOx, the composition of the MOB community, and physicochemical water column parameters in a coastal inlet in the Baltic Sea (Eckernförde(E-) Bay, Boknis Eck Time Series Station). In addition, we investigated the influence of temperature and oxygen on MOx during controlled laboratory experiments. In E-Bay, seasonal stratification leads to hypoxia in bottom waters towards the end of the stratification period. Methane is produced year-round in the sediments, resulting in accumulation of methane in bottom waters, and supersaturation (with respect to the atmospheric equilibrium) in surface waters. Here, we will discuss the factors impacting MOx the most, which were a) perturbations of the water column caused by storm events, currents or seasonal mixing, b) temperature and c) oxygen concentration. a) Perturbations of the water column led to a sharp decrease in MOx within hours, probably caused by replacement of 'old' water with a high standing stock of MOB by 'new' waters with a lower abundance of MOB. b) An increase in temperature generally led to higher MOx rates. c) Even though CH4 was abundant at all depths, MOx was highest in bottom waters (1-5 nM/d), which usually contain the lowest O2 concentrations. Lab-based experiments with adjusted O2

  12. 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

  13. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea.

    PubMed

    Lösekann, Tina; Knittel, Katrin; Nadalig, Thierry; Fuchs, Bernhard; Niemann, Helge; Boetius, Antje; Amann, Rudolf

    2007-05-01

    Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56%+/-8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94%+/-2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and

  14. 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. PMID:23090054

  15. 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

    accumulation of chloride ions either in spent media or in slurries prepared from Searsville Lake soil, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soils enriched in methanotrophs. This result leads us to surmise that the release of O2 during enzymatic perchlorate reduction was low, and that the oxygen produced was unavailable to the aerobic methanotrophs. This was borne out by patterns of O2 and CO2 production during experiments with lake soil, growth media, and pure cultures of dissimilatory perchlorate reducing bacteria. We observed that O2 release during incubation of D. agitata CKB with 10 mM ClO4- or ClO3- was decoupled from metabolism. More O2 was released during incubations without added acetate than with 10 mM acetate and an even greater amount of O2 was released during incubation with heat-killed cells. This suggests a chemical mechanism of O2 production during reaction with ClO4- and ClO3-. Hence, perchlorate reducing bacteria need not be present to facilitate O2 release from the surface of Mars, in support of recent interpretations of Viking LR and GEx experiments.

  16. Isolation of methanobactin from the spent media of methane-oxidizing bacteria.

    PubMed

    Bandow, Nathan L; Gallagher, Warren H; Behling, Lee; Choi, Dong W; Semrau, Jeremy D; Hartsel, Scott C; Gilles, Valerie S; Dispirito, Alan A

    2011-01-01

    Chalkophores are low molecular mass modified peptides involved in copper acquisition in methane-oxidizing bacteria (MOB). A screening method for the detection of this copper-binding molecule is presented in Chapter 16. Here we describe methods to (1) maximize expression and secretion of chalkophores, (2) concentrate chalkophores from the spent media of MOB, and (3) purify chalkophores. PMID:21419927

  17. Effect of nitrogen source on growth and trichloroethylene degradation by methane-oxidizing bacteria

    SciTech Connect

    Chu, K.H.; Alvarez-Cohen, L.

    1998-09-01

    The effect of nitrogen source on methane-oxidizing bacteria with respect to cellular growth and trichloroethylene (TCE) degradation ability were examined. One mixed chemostat culture and two pure type II methane-oxidizing strains, Methylosinus trichosporium OB3b and strain CAC-2, which was isolated from the chemostat culture, were used in this study. All cultures were able to grow with each of three different nitrogen sources: ammonia, nitrate, and molecular nitrogen. Both M. trichosporium OB3b and strain CAC-2 showed slightly lower net cellular growth rates and cell yields but exhibited higher methane uptake rates, levels of poly-{beta}-hydroxybutyrate (PHB) production, and naphthalene oxidation rates when grown under nitrogen-fixing conditions. The TCE-degrading ability of each culture was measured in terms of initial TCE oxidation rates and TCE transformation capacities, measured both with and without external energy sources. Higher initial TCE oxidation rates and TCE transformation capacities were observed in nitrogen-fixing mixed, M. trichosporium OB3b, and CAC-2 cultures than in nitrate- or ammonia-supplied cells. TCE transformation capacities were found to correlate with cellular PHB content in all three cultures. The results of this study suggest that the nitrogen-fixing capabilities of methane-oxidizing bacteria can be used to select for high-activity TCE degraders for the enhancement of bioremediation in fixed-nitrogen-limited environments.

  18. 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

  19. Fractionation of carbon and hydrogen isotopes by methane-oxidizing bacteria

    USGS Publications Warehouse

    Coleman, D.D.; Risatti, J.B.; Schoell, M.

    1981-01-01

    Carbon isotopic analysis of methane has become a popular technique in the exploration for oil and gas because it can be used to differentiate between thermogenic and microbial gas and can sometimes be used for gas-source rock correlations. Methane-oxidizing bacteria, however, can significantly change the carbon isotopic composition of methane; the origin of gas that has been partially oxidized by these bacteria could therefore be misinterpreted. We cultured methane-oxidizing bacteria at two different temperatures and monitored the carbon and hydrogen isotopic compositions of the residual methane. The residual methane was enriched in both 13C and D. For both isotopic species, the enrichment at equivalent levels of conversion was greater at 26??C than at 11.5??C. The change in ??D relative to the change in ??13C was independent of temperature within the range studied. One culture exhibited a change in the fractionation pattern for carbon (but not for hydrogen) midway through the experiment, suggesting that bacterial oxidation of methane may occur via more than one pathway. The change in the ??D value for the residual methane was from 8 to 14 times greater than the change in the ??13C value, indicating that combined carbon and hydrogen isotopic analysis may be an effective way of identifying methane which has been subjected to partial oxidation by bacteria. ?? 1981.

  20. Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria

    SciTech Connect

    Pancost, R.D.; Damste, J.S.S.; Lint, S. De; Maarel, M.J.E.C. van der; Gottschal, J.C.

    2000-03-01

    Although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. In order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the Mediterranean consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the Mediterranean Ridge were collected via the submersible Nautile. Geochemical data strongly indicate that methane is oxidized under aerobic conditions, and compound-specific carbon isotope analyses indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate that this reaction is facilitated by a consortium of archaea and bacteria. Specifically, these methane-rich sediments contain high abundances of methanogen-specific biomarkers that are significantly depleted in {sup 13}C ({delta}{sup 13}C values are as low as {minus}95%). Biomarkers inferred to derive from sulfate-reducing bacteria and other heterotrophic bacteria are similarly depleted. Consistent with previous work, such depletion can be explained by consumption of {sup 13}C-depleted methane by methanogens operating in reverse and as part a consortium of organisms in which sulfate serves as the terminal electron acceptor. Moreover, their results indicate that this process is widespread in Mediterranean mud volcanoes and in some localized settings in the predominant microbiological process.

  1. 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

  2. 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.

  3. 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.

  4. Effect of process design and operating parameters on aerobic methane oxidation in municipal WWTPs.

    PubMed

    Daelman, Matthijs R J; Van Eynde, Tamara; van Loosdrecht, Mark C M; Volcke, Eveline I P

    2014-12-01

    Methane is a potent greenhouse gas and its emission from municipal wastewater treatment plants (WWTPs) should be prevented. One way to do this is to promote the biological conversion of dissolved methane over stripping in aeration tanks. In this study, the well-established Activated Sludge Model n°1 (ASM1) and Benchmark Simulation Model n°1 (BSM1) were extended to study the influence of process design and operating parameters on biological methane oxidation. The aeration function used in BSM 1 was upgraded to more accurately describe gas-liquid transfer of oxygen and methane in aeration tanks equipped with subsurface aeration. Dissolved methane could be effectively removed in an aeration tank at an aeration rate that is in agreement with optimal effluent quality. Subsurface bubble aeration proved to be better than surface aeration, while a CSTR configuration was superior to plug flow conditions in avoiding methane emissions. The conversion of methane in the activated sludge tank benefits from higher methane concentrations in the WWTP's influent. Finally, if an activated sludge tank is aerated with methane containing off-gas, a limited amount of methane is absorbed and converted in the mixed liquor. This knowledge helps to stimulate the methane oxidizing capacity of activated sludge in order to abate methane emissions from wastewater treatment to the atmosphere. PMID:25225767

  5. Regulation of Methane Oxidation in a Freshwater Wetland by Water Table Changes and Anoxia

    NASA Technical Reports Server (NTRS)

    Roslev, Peter; King, Gary M.

    1996-01-01

    The effects of water table fluctuations and anoxia on methane emission and methane oxidation were studied in a freshwater marsh. Seasonal aerobic methane oxidation rates varied between 15% and 76% of the potential diffusive methane flux (diffusive flux in the absence of aerobic oxidation). On an annual basis, approximately 43% of the methane diffusing into the oxic zone was oxidized before reaching the atmosphere. The highest methane oxidation was observed when the water table was below the peat surface. This was confirmed in laboratory experiments where short-term decreases in water table levels increased methane oxidation but also net methane emission. Although methane emission was generally not observed during the winter, stems of soft rush (Juncus effusus) emitted methane when the marsh was ice covered. Indigenous methanotrophic bacteria from the wetiand studied were relatively anoxia tolerant. Surface peat incubated under anoxic conditions maintained 30% of the initial methane oxidation capacity after 32 days of anoxia. Methanotrophs from anoxic peat initiated aerobic methane oxidation relatively quickly after oxygen addition (1-7 hours). These results were supported by culture experiments with the methanotroph Methylosinus trichosporium OB3b. This organism maintained a greater capacity for aerobic methane oxidation when starved under anoxic compared to oxic conditions. Anoxic incubation of M. trichosporium OB3b in the presence of sulfide (2 mM) and a low redox potential (-110 mV) did not decrease the capacity for methane oxidation relative to anoxic cultures incubated without sulfide. The results suggest that aerobic methane oxidation was a major regulator of seasonal methane emission front the investigated wetland. The observed water table fluctuations affected net methane oxidation presumably due to associated changes in oxygen gradients. However, changes from oxic to anoxic conditions in situ had relatively little effect on survival of the methanotrophic

  6. Cultivation of nitrite-dependent anaerobic methane-oxidizing bacteria: impact of reactor configuration.

    PubMed

    Hu, Baolan; He, Zhanfei; Geng, Sha; Cai, Chen; Lou, Liping; Zheng, Ping; Xu, Xinhua

    2014-09-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) is mediated by bacteria that anaerobically oxidize methane coupled with nitrite reduction and is a potential bioprocess for wastewater treatment. In this work, the effect of reactor configuration on n-damo bacterial cultivation was investigated. A magnetically stirred gas lift reactor (MSGLR), a sequencing batch reactor (SBR), and a continuously stirred tank reactor (CSTR) were selected to cultivate the bacteria. Microbial community was monitored by using quantitative PCR, 16S rRNA gene sequencing, pmoA gene sequencing, and fluorescence in situ hybridization (FISH). The effects of substrate inhibition, methane mass transfer, and biomass washout in the three reactors were focused on. The results indicated that the MSGLR had the best performance among the three reactor systems, with the highest total and specific n-damo activities. Its maximum volumetric nitrogen removal rate was up to 76.9 mg N L(-1) day(-1), which was higher than previously reported values (5.1-37.8 mg N L(-1) d(-1)). PMID:24880628

  7. Atmospheric methane removal by methane-oxidizing bacteria immobilized on porous building materials.

    PubMed

    Ganendra, Giovanni; De Muynck, Willem; Ho, Adrian; Hoefman, Sven; De Vos, Paul; Boeckx, Pascal; Boon, Nico

    2014-04-01

    Biological treatment using methane-oxidizing bacteria (MOB) immobilized on six porous carrier materials have been used to mitigate methane emission. Experiments were performed with different MOB inoculated in building materials at high (~20 % (v/v)) and low (~100 ppmv) methane mixing ratios. Methylocystis parvus in autoclaved aerated concrete (AAC) exhibited the highest methane removal rate at high (28.5 ± 3.8 μg CH₄ g⁻¹ building material h⁻¹) and low (1.7 ± 0.4 μg CH₄ g⁻¹ building material h⁻¹) methane mixing ratio. Due to the higher volume of pores with diameter >5 μm compared to other materials tested, AAC was able to adsorb more bacteria which might explain for the higher methane removal observed. The total methane and carbon dioxide-carbon in the headspace was decreased for 65.2 ± 10.9 % when M. parvus in Ytong was incubated for 100 h. This study showed that immobilized MOB on building materials could be used to remove methane from the air and also act as carbon sink. PMID:24337222

  8. Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments.

    PubMed

    Heyer, Jürgen; Galchenko, Valery F; Dunfield, Peter F

    2002-09-01

    Type II methane-oxidizing bacteria (MOB) were isolated from diverse environments, including rice paddies, pristine and polluted freshwaters and sediments, mangrove roots, upland soils, brackish water ecosystems, moors, oil wells, water purification systems and livestock manure. Isolates were identified based on morphological traits as either Methylocystis spp., Methylosinus sporium or Methylosinus trichosporium. Molecular phylogenies were constructed based on nearly complete 16S rRNA gene sequences, and on partial sequences of genes encoding PmoA (a subunit of particulate methane monooxygenase), MxaF (a subunit of methanol dehydrogenase) and MmoX (a subunit of soluble methane monooxygenase). The maximum pairwise 16S rDNA difference between isolates was 4.2%, and considerable variability was evident within the Methylocystis (maximum difference 3.6%). Due to this variability, some of the published 'specific' oligonucleotide primers for type II MOB exhibit multiple mismatches with gene sequences from some isolates. The phylogenetic tree constructed from pmoA gene sequences closely mirrored that constructed from 16S rDNA sequences, and both supported the presently accepted taxonomy of type II MOB. Contrary to previously published phylogenetic trees, morphologically distinguishable species were generally monophyletic based on pmoA or 16S rRNA gene sequences. This was not true for phylogenies constructed from mmoX and mxaF gene sequences. The phylogeny of mxaF gene sequences suggested that horizontal transfer of this gene may have occurred across type II MOB species. Soluble methane monooxygenase could not be detected in many Methylocystis strains either by an enzyme activity test (oxidation of naphthalene) or by PCR-based amplification of an mmoX gene. PMID:12213929

  9. Field and experimental evidence for low-O2 affinity of aerobic methane oxidizers in coastal waters

    NASA Astrophysics Data System (ADS)

    Steinle, Lea; Maltby, Johanna; Bange, Hermann; Kock, Annette; Lehmann, Moritz F.; Treude, Tina; Niemann, Helge

    2015-04-01

    The coastal ocean accounts for more than 75 % of the global oceanic methane emissions. An important process in mitigating methane emissions from the seawater to the atmosphere is aerobic methane oxidation (MOx). Coastal oceans are highly dynamic systems, in particular with regard to the variability of temperature, salinity, and oxygen concentrations, all of which are potential key environmental factors controlling MOx. We conducted a two-year time-series study of MOx measurements in the water column of a coastal inlet in the southwestern Baltic Sea (Eckernförde Bay, Boknis Eck Time Series Station, 54°31.823 N, 10°02.764 E, 28 m water depth; www.bokniseck.de). Physicochemical parameters at this station have been monitored since 1957. Seasonal stratification during summer/autumn leads to intermittent oxygen depletion (hypoxic to anoxic) in bottom waters in the later part of the stratification period. The duration of these low-oxygen events increased since the 1970s (Lennartz et al., 2014). Furthermore, the organic-rich seafloor continuously produces methane, which leads to gas ebullition followed by accumulation of dissolved methane in bottom waters (up to 470 nM) and supersaturation (with respect to the atmospheric equilibrium) in surface waters (up to 27 nM). MOx communities were most active in bottom waters (1-5 nM/day), which usually contain the lowest oxygen concentrations (sometimes below the in situ detection limit of ~1 µM). In order to better understand the effect of low oxygen concentrations, and thus of hypoxic and suboxic events, on MOx in coastal systems, we conducted lab-based experiments, during which we adjusted oxygen concentrations to values between 0.2 - 220 µM in methane-rich (~100 nM) Eckernförde Bay waters. These samples were then incubated with trace amounts of tritium-labeled methane to assess first order rate constants of methane oxidation. Highest MOx rates were detected at oxygen concentrations of ~0.5 µM (considerably higher than at

  10. Growth of Anaerobic Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in a High-Pressure Membrane Capsule Bioreactor

    PubMed Central

    Gieteling, Jarno; Widjaja-Greefkes, H. C. Aura; Plugge, Caroline M.; Stams, Alfons J. M.; Lens, Piet N. L.; Meulepas, Roel J. W.

    2014-01-01

    Communities of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) grow slowly, which limits the ability to perform physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated SRB are affected by it. Here, we report on the growth of ANME-SRB in a membrane capsule bioreactor inoculated with Eckernförde Bay sediment that combines high-pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2-μm-pore-size membrane. The results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. The rates of oxidation of labeled methane were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was enriched only at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2 and Eel-1 groups and the Desulfuromonadales and not to the typically found SEEP-SRB1 group. The increase of ANME-2a/b occurred in parallel with the increase of SEEP-SRB2, which was previously found to be associated only with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence the growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at a high methane partial pressure. PMID:25501484

  11. Growth of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a high-pressure membrane capsule bioreactor.

    PubMed

    Timmers, Peer H A; Gieteling, Jarno; Widjaja-Greefkes, H C Aura; Plugge, Caroline M; Stams, Alfons J M; Lens, Piet N L; Meulepas, Roel J W

    2015-02-01

    Communities of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) grow slowly, which limits the ability to perform physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated SRB are affected by it. Here, we report on the growth of ANME-SRB in a membrane capsule bioreactor inoculated with Eckernförde Bay sediment that combines high-pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2-m-pore-size membrane. The results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. The rates of oxidation of labeled methane were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was enriched only at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2 and Eel-1 groups and the Desulfuromonadales and not to the typically found SEEP-SRB1 group. The increase of ANME-2a/b occurred in parallel with the increase of SEEP-SRB2, which was previously found to be associated only with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence the growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at a high methane partial pressure. PMID:25501484

  12. Methane-Oxidizing Bacteria in a California Upland Grassland Soil: Diversity and Response to Simulated Global Change

    PubMed Central

    Horz, Hans-Peter; Rich, Virginia; Avrahami, Sharon; Bohannan, Brendan J. M.

    2005-01-01

    We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to “RA 14” or “WB5FH-A,” which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of nonsynonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors. PMID:15870356

  13. Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.

    PubMed

    Ding, Jing; Fu, Liang; Ding, Zhao-Wei; Lu, Yong-Ze; Cheng, Shuk H; Zeng, Raymond J

    2016-01-01

    The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the functional microbes in environments. Therefore, the coexistence of DAMO archaea and bacteria in a paddy field was evaluated in this study. Next-generation sequencing showed that the two orders, Methanosarcinales and Nitrospirales, to which DAMO archaea and DAMO bacteria belong, were detected in the four soil samples. Then the in vitro experiments demonstrated both of nitrite- and nitrate-dependent DAMO activities, which confirmed the coexistence of DAMO archaea and DAMO bacteria. It was the first report about the coexistence of DAMO archaea and bacteria in a paddy field. Furthermore, anammox bacteria were detected in two of the four samples. The in vitro experiments did not show anammox activity in the initial period but showed low anammox activity after 20 days' enrichment. These results implicated that anammox bacteria may coexist with DAMO microorganisms in this field, but at a very low percentage. PMID:26394860

  14. Depth-related coupling relation between methane-oxidizing bacteria (MOBs) and sulfate-reducing bacteria (SRBs) in a marine sediment core from the Dongsha region, the South China Sea.

    PubMed

    Xu, Xiao-Ming; Fu, Shao-Ying; Zhu, Qing; Xiao, Xi; Yuan, Jian-Ping; Peng, Juan; Wu, Chou-Fei; Wang, Jiang-Hai

    2014-12-01

    The vertical distributions of methane-oxidizing bacteria (MOBs) and sulfate-reducing bacteria (SRBs) in the marine sediment core of DH-CL14 from the Dongsha region, the South China Sea, were investigated. To enumerate MOBs and SRBs, their specific genes of pmoA and apsA were quantified by a culture-independent molecular biological technique, real-time polymerase chain reaction (RT-PCR). The result shows that the pmoA gene copies per gram of sediments reached the maximum of 1,118,679 at the depth of 140-160 cm. Overall considering the detection precision, sample amount, measurement cost, and sensitivity to the seepage of methane from the oil/gas reservoirs or gas hydrates, we suggest that the depth of 140-160 cm may be the optimal sampling position for the marine microbial exploration of oils, gases, and gas hydrates in the Dongsha region. The data of the pmoA and apsA gene copies exhibit an evident coupling relation between MOBs and SRBs as illustrated in their vertical distributions in this sediment core, which may well be interpreted by a high sulfate concentration inhibiting methane production and further leading to the reduction of MOBs. In comparison with the numbers of the pmoA and apsA copies at the same sediment depth, we find out that there were two methane-oxidizing mechanisms of aerobic and anaerobic oxidation in this sediment core, i.e., the aerobic oxidation with free oxygen dominantly occurred above the depth of 210-230 cm, while the anaerobic oxidation with the other electron acceptors such as sulfates and manganese-iron oxides happened below the depth of 210-230 cm. PMID:25064353

  15. Molecular and isotopic insights into methane oxidation in Lake Kivu

    NASA Astrophysics Data System (ADS)

    Zigah, P. K.; Wehrli, B.; Schubert, C. J.

    2013-12-01

    Lake Kivu is a meromictic lake in the East African Rift Valley, located between the Republic of Rwanda and the Democratic Republic of Congo. The hypolimnion is permanently stratified and contain an unusually high amount of dissolved methane (CH4; ~ 60 km3) and carbon dioxide (CO2; ~300 km3) at standard temperature and pressure. While microbial-mediated methane oxidation is an important sink of methane in the lake, little is known about the distribution of microbes involved in the methane oxidation. To provide insights into methanotrophy in the lake, we analyzed depth profile of CH4, δ13C-CH4 and δ13C-DIC, δ13C-POC and the biomarkers of methanotrophic archaea and bacteria and their stable carbon isotopic composition from suspended particulate matter isolated from the lake water column. Our preliminary data show enhanced methane oxidation in oxic-anoxic transition zone in the water column. Depth distribution of diagnostic methanotrophic archaeal biomarkers such as archaeol and hydroxyarchaeol suggest archaea might be involved in anaerobic methane oxidation. Phospholipid fatty acids and diplopterol distribution and carbon isotopic signatures indicate bacteria-mediated anaerobic (and aerobic) methane oxidation in the lake.

  16. Conversion of biogas to bioproducts by algae and methane oxidizing bacteria.

    PubMed

    van der Ha, David; Nachtergaele, Leen; Kerckhof, Frederiek-Maarten; Rameiyanti, Devi; Bossier, Peter; Verstraete, Willy; Boon, Nico

    2012-12-18

    Biogas produced by anaerobic digestion is typically converted into electricity and low value heat. In this study, biogas is microbially transformed into valuable bioproducts. As proof of principle, the production of feed additives, i.e. lipids and polyhydroxybutyrate, out of biogas was evaluated. In a first stage, the CO₂ in a synthetic biogas was photosynthetically fixed by an algae Scenedesmus sp. culture at an average rate of 192 ± 9 mg CO₂ L⁻¹ liquid d⁻¹, resulting in concomitant O₂ production. After N-depletion, more than 30% of the 220 ± 7 mg lipids g⁻¹ total organic carbon were unsaturated. In a second stage, the theoretical resulting gas mixture of 60% CH₄ and 40% O₂ was treated by a methane oxidizing Methylocystis parvus culture, with oxidation rates up to 452 ± 7 mg⁻¹ CH₄-C L⁻¹ liquid d⁻¹. By repeated N-limitation, concentrations of 295 ± 50 mg intracellular polyhydroxybutyrate g⁻¹ cell dry weight were achieved. Finally, a one-stage approach with controlled coculturing of both microbial groups resulted in harvestable bioflocs. This is the first time that a total microbial conversion of both greenhouse gases into biomass was achieved without external O₂ provision. Based on these results, a biotechnological approach is discussed whereby all kinds of biogas can be transformed into valuable bioproducts. PMID:23186036

  17. [Comparative characterization of cultured methane-oxidizing bacteria by serological and molecular methods].

    PubMed

    Slobodova, N V; Kolganova, T V; Bulygina, E S; Kuznetsov, B B; Turova, T P; Kravchenko, I K

    2006-01-01

    Three stable methane-oxidizing enrichment cultures, SB26, SB31, and SB31A were analyzed by transmission electron microscopy and by serological and molecular techniques. Electron microscopy revealed the presence of both type I and type II methanotrophs in SB31 and SB31A enrichments; only type II methanotrophs were found in SB26 enrichment. Methylosinus trichosporium was detected in all three enrichments by the application of species-specific antibodies. Additionally, Methylocystis echinoides was found in SB26 culture; Methylococcus capsulatus, in SB31 and SB31A; and Methylomonas methanica, in SB31. The analysis with pmoA and nifH gene sequences as phylogenetic markers revealed the presence of Methylosinus/Methylocystis group in all communities. Moreover, the analysis of pmoA sequences revealed the presence of Methylomonas in SB31. Methylocella was detected in SB31 and SB31A enrichments only by nifH analysis. It was concluded that the simultaneous application of different approaches reveals more reliable information on the diversity of methanotrophs. PMID:16871808

  18. Anaerobic Oxidization of Methane in a Minerotrophic Peatland: Enrichment of Nitrite-Dependent Methane-Oxidizing Bacteria

    PubMed Central

    Zhu, Baoli; van Dijk, Gijs; Fritz, Christian; Smolders, Alfons J. P.; Pol, Arjan; Jetten, Mike S. M.

    2012-01-01

    The importance of anaerobic oxidation of methane (AOM) as a methane sink in freshwater systems is largely unexplored, particularly in peat ecosystems. Nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and reported to be catalyzed by the bacterium “Candidatus Methylomirabilis oxyfera,” which is affiliated with the NC10 phylum. So far, several “Ca. Methylomirabilis oxyfera” enrichment cultures have been obtained using a limited number of freshwater sediments or wastewater treatment sludge as the inoculum. In this study, using stable isotope measurements and porewater profiles, we investigated the potential of n-damo in a minerotrophic peatland in the south of the Netherlands that is infiltrated by nitrate-rich ground water. Methane and nitrate profiles suggested that all methane produced was oxidized before reaching the oxic layer, and NC10 bacteria could be active in the transition zone where countergradients of methane and nitrate occur. Quantitative PCR showed high NC10 bacterial cell numbers at this methane-nitrate transition zone. This soil section was used to enrich the prevalent NC10 bacteria in a continuous culture supplied with methane and nitrite at an in situ pH of 6.2. An enrichment of nitrite-reducing methanotrophic NC10 bacteria was successfully obtained. Phylogenetic analysis of retrieved 16S rRNA and pmoA genes showed that the enriched bacteria were very similar to the ones found in situ and constituted a new branch of NC10 bacteria with an identity of less than 96 and 90% to the 16S rRNA and pmoA genes of “Ca. Methylomirabilis oxyfera,” respectively. The results of this study expand our knowledge of the diversity and distribution of NC10 bacteria in the environment and highlight their potential contribution to nitrogen and methane cycles. PMID:23042166

  19. Carbon isotope fractionation during microbial methane oxidation

    NASA Astrophysics Data System (ADS)

    Barker, James F.; Fritz, Peter

    1981-09-01

    Methane, a common trace constituent of groundwaters, occasionally makes up more than 20% of the total carbon in groundwaters1,2. In aerobic environments CH4-rich waters can enable microbial food chain supporting a mixed culture of bacteria with methane oxidation as the primary energy source to develop3. Such processes may influence the isotopic composition of the residual methane and because 13C/12C analyses have been used to characterize the genesis of methanes found in different environments, an understanding of the magnitude of such effects is necessary. In addition, carbon dioxide produced by the methane-utilizing bacteria can be added to the inorganic carbon pool of affected groundwaters. We found carbon dioxide experimentally produced by methane-utilizing bacteria to be enriched in 12C by 5.0-29.6‰, relative to the residual methane. Where methane-bearing groundwaters discharged into aerobic environments microbial methane oxidation occurred, with the residual methane becoming progressively enriched in 13C. Various models have been proposed to explain the 13C/12C and 14C content of the dissolved inorganic carbon (DIC) of groundwaters in terms of additions or losses during flow in the subsurface4,5. The knowledge of both stable carbon isotope ratios in various pools and the magnitude of carbon isotope fractionation during various processes allows geochemists to use the 13C/12C ratio of the DIC along with water chemistry to estimate corrected 14C groundwater ages4,5. We show here that a knowledge of the carbon isotope fractionation between CH4 and CO2 during microbial methane-utilization could modify such models for application to groundwaters affected by microbial methane oxidation.

  20. 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

  1. 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

  2. Rare Branched Fatty Acids Characterize the Lipid Composition of the Intra-Aerobic Methane Oxidizer “Candidatus Methylomirabilis oxyfera”

    PubMed Central

    Zhu, Baoli; Rijpstra, W. Irene C.; Jetten, Mike S. M.; Ettwig, Katharina F.; Sinninghe Damsté, Jaap S.

    2012-01-01

    The recently described bacterium “Candidatus Methylomirabilis oxyfera” couples the oxidation of the important greenhouse gas methane to the reduction of nitrite. The ecological significance of “Ca. Methylomirabilis oxyfera” is still underexplored, as our ability to identify the presence of this bacterium is thus far limited to DNA-based techniques. Here, we investigated the lipid composition of “Ca. Methylomirabilis oxyfera” to identify new, gene-independent biomarkers for the environmental detection of this bacterium. Multiple “Ca. Methylomirabilis oxyfera” enrichment cultures were investigated. In all cultures, the lipid profile was dominated up to 46% by the fatty acid (FA) 10-methylhexadecanoic acid (10MeC16:0). Furthermore, a unique FA was identified that has not been reported elsewhere: the monounsaturated 10-methylhexadecenoic acid with a double bond at the Δ7 position (10MeC16:1Δ7), which comprised up to 10% of the total FA profile. We propose that the typical branched fatty acids 10MeC16:0 and 10MeC16:1Δ7 are key and characteristic components of the lipid profile of “Ca. Methylomirabilis oxyfera.” The successful detection of these fatty acids in a peatland from which one of the enrichment cultures originated supports the potential of these unique lipids as biomarkers for the process of nitrite-dependent methane oxidation in the environment. PMID:23042164

  3. Methane oxidation coupled to oxygenic photosynthesis in anoxic waters

    PubMed Central

    Milucka, Jana; Kirf, Mathias; Lu, Lu; Krupke, Andreas; Lam, Phyllis; Littmann, Sten; Kuypers, Marcel MM; Schubert, Carsten J

    2015-01-01

    Freshwater lakes represent large methane sources that, in contrast to the Ocean, significantly contribute to non-anthropogenic methane emissions to the atmosphere. Particularly mixed lakes are major methane emitters, while permanently and seasonally stratified lakes with anoxic bottom waters are often characterized by strongly reduced methane emissions. The causes for this reduced methane flux from anoxic lake waters are not fully understood. Here we identified the microorganisms and processes responsible for the near complete consumption of methane in the anoxic waters of a permanently stratified lake, Lago di Cadagno. Interestingly, known anaerobic methanotrophs could not be detected in these waters. Instead, we found abundant gamma-proteobacterial aerobic methane-oxidizing bacteria active in the anoxic waters. In vitro incubations revealed that, among all the tested potential electron acceptors, only the addition of oxygen enhanced the rates of methane oxidation. An equally pronounced stimulation was also observed when the anoxic water samples were incubated in the light. Our combined results from molecular, biogeochemical and single-cell analyses indicate that methane removal at the anoxic chemocline of Lago di Cadagno is due to true aerobic oxidation of methane fuelled by in situ oxygen production by photosynthetic algae. A similar mechanism could be active in seasonally stratified lakes and marine basins such as the Black Sea, where light penetrates to the anoxic chemocline. Given the widespread occurrence of seasonally stratified anoxic lakes, aerobic methane oxidation coupled to oxygenic photosynthesis might have an important but so far neglected role in methane emissions from lakes. PMID:25679533

  4. Non-linear dynamics of stable carbon and hydrogen isotope signatures based on a biological kinetic model of aerobic enzymatic methane oxidation.

    PubMed

    Vavilin, Vasily A; Rytov, Sergey V; Shim, Natalia; Vogt, Carsten

    2016-06-01

    The non-linear dynamics of stable carbon and hydrogen isotope signatures during methane oxidation by the methanotrophic bacteria Methylosinus sporium strain 5 (NCIMB 11126) and Methylocaldum gracile strain 14 L (NCIMB 11912) under copper-rich (8.9 µM Cu(2+)), copper-limited (0.3 µM Cu(2+)) or copper-regular (1.1 µM Cu(2+)) conditions has been described mathematically. The model was calibrated by experimental data of methane quantities and carbon and hydrogen isotope signatures of methane measured previously in laboratory microcosms reported by Feisthauer et al. [ 1 ] M. gracile initially oxidizes methane by a particulate methane monooxygenase and assimilates formaldehyde via the ribulose monophosphate pathway, whereas M. sporium expresses a soluble methane monooxygenase under copper-limited conditions and uses the serine pathway for carbon assimilation. The model shows that during methane solubilization dominant carbon and hydrogen isotope fractionation occurs. An increase of biomass due to growth of methanotrophs causes an increase of particulate or soluble monooxygenase that, in turn, decreases soluble methane concentration intensifying methane solubilization. The specific maximum rate of methane oxidation υm was proved to be equal to 4.0 and 1.3 mM mM(-1) h(-1) for M. sporium under copper-rich and copper-limited conditions, respectively, and 0.5 mM mM(-1) h(-1) for M. gracile. The model shows that methane oxidation cannot be described by traditional first-order kinetics. The kinetic isotope fractionation ceases when methane concentrations decrease close to the threshold value. Applicability of the non-linear model was confirmed by dynamics of carbon isotope signature for carbon dioxide that was depleted and later enriched in (13)C. Contrasting to the common Rayleigh linear graph, the dynamic curves allow identifying inappropriate isotope data due to inaccurate substrate concentration analyses. The non-linear model pretty adequately described experimental

  5. Lipid and carbon isotopic evidence of methane-oxidizing and sulfate-reducing bacteria in association with gas hydrates from the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Zhang, Chuanlun L.; Li, Yiliang; Wall, Judy D.; Larsen, Lise; Sassen, Roger; Huang, Yongsong; Wang, Yi; Peacock, Aaron; White, David C.; Horita, Juske; Cole, David R.

    2002-03-01

    An integrated lipid biomarker carbon isotope approach reveals new insight to microbial methane oxidation in the Gulf of Mexico gas-hydrate system. Hydrate-bearing and hydrate-free sediments were collected from the Gulf of Mexico slope using a research submersible. Phospholipid fatty acids consist mainly of C16 C18 compounds, which are largely derived from bacteria. The phospholipid fatty acids suggest that total biomass is enhanced 11 30-fold in gas-hydrate bearing sediment compared to hydrate-free sediment. Lipid biomarkers indicative of sulfate-reducing bacteria are strongly depleted in 13C (δ13C = -48‰ to -70‰) in the hydrate-bearing samples, suggesting that they are involved in the oxidation of methane (δ13C = -47‰ for thermogenic methane and -70‰ for biogenic methane). Isotopic properties of other biomarkers suggest that sulfur-oxidizing bacteria (Beggiatoa) may also contribute to the lipid pool in hydrate-bearing samples, which are characterized by less negative δ13C values (to -11.2‰). In the hydrate-free sample, fatty acid biomarkers have δ13C values of -27.6‰ to -39.6‰, indicating that crude oil (average ˜-27‰) or terrestrial organic carbon (average ˜-20‰) are the likely carbon sources. Our results provide the first lipid biomarker stable isotope evidence that sulfate- reducing bacteria play an important role in anaerobic methane oxidation in the Gulf of Mexico gas hydrates. The coupled activities of methane-oxidizing and sulfate-reducing organisms contribute to the development of ecosystems in deep-sea environments and result in sequestration of carbon as buried organic carbon and authigenic carbonates. These have implications for studying climate change based on carbon budgets.

  6. Variability in aerobic methane oxidation over the past 1.2 Myrs recorded in microbial biomarker signatures from Congo fan sediments

    NASA Astrophysics Data System (ADS)

    Talbot, Helen M.; Handley, Luke; Spencer-Jones, Charlotte L.; Dinga, Bienvenu Jean; Schefuß, Enno; Mann, Paul J.; Poulsen, John R.; Spencer, Robert G. M.; Wabakanghanzi, Jose N.; Wagner, Thomas

    2014-05-01

    Methane (CH4) is a strong greenhouse gas known to have perturbed global climate in the past, especially when released in large quantities over short time periods from continental or marine sources. It is therefore crucial to understand and, if possible, quantify the individual and combined response of these variable methane sources to natural climate variability. However, past changes in the stability of greenhouse gas reservoirs remain uncertain and poorly constrained by geological evidence. Here, we present a record from the Congo fan of a highly specific bacteriohopanepolyol (BHP) biomarker for aerobic methane oxidation (AMO), 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol), that identifies discrete periods of increased AMO as far back as 1.2 Ma. Fluctuations in the concentration of aminopentol, and other 35-aminoBHPs, follow a pattern that correlates with late Quaternary glacial-interglacial climate cycles, with highest concentrations during warm periods. We discuss possible sources of aminopentol, and the methane consumed by the precursor methanotrophs, within the context of the Congo River setting, including supply of methane oxidation markers from terrestrial watersheds and/or marine sources (gas hydrate and/or deep subsurface gas reservoir). Compound-specific carbon isotope values of -30‰ to -40‰ for BHPs in ODP 1075 and strong similarities between the BHP signature of the core and surface sediments from the Congo estuary and floodplain wetlands from the interior of the Congo River Basin, support a methanotrophic and likely terrigenous origin of the 35-aminoBHPs found in the fan sediments. This new evidence supports a causal connection between marine sediment BHP records of tropical deep sea fans and wetland settings in the feeding river catchments, and thus tropical continental hydrology. Further research is needed to better constrain the different sources and pathways of methane emission. However, this study identifies the large potential

  7. 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

  8. 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. PMID:26696968

  9. 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 Central

    Reim, Andreas; Lüke, Claudia; Krause, Sascha; Pratscher, Jennifer; Frenzel, Peter

    2012-01-01

    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. PMID:22695859

  10. Changes in Activity and Community Structure of Methane-Oxidizing Bacteria over the Growth Period of Rice

    PubMed Central

    Eller, Gundula; Frenzel, Peter

    2001-01-01

    The activity and community structure of methanotrophs in compartmented microcosms were investigated over the growth period of rice plants. In situ methane oxidation was important only during the vegetative growth phase of the plants and later became negligible. The in situ activity was not directly correlated with methanotrophic cell counts, which increased even after the decrease in in situ activity, possibly due to the presence of both vegetative cells and resting stages. By dividing the microcosms into two soil and two root compartments it was possible to locate methanotrophic growth and activity, which was greatest in the rhizoplane of the rice plants. Molecular analysis by denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH) with family-specific probes revealed the presence of both families of methanotrophs in soil and root compartments over the whole season. Changes in community structure were detected only for members of the Methylococcaceae and could be associated only with changes in the genus Methylobacter and not with changes in the dominance of different genera in the family Methylococcaceae. For the family Methylocystaceae stable communities in all compartments for the whole season were observed. FISH analysis revealed evidence of in situ dominance of the Methylocystaceae in all compartments. The numbers of Methylococcaceae cells were relatively high only in the rhizoplane, demonstrating the importance of rice roots for growth and maintenance of methanotrophic diversity in the soil. PMID:11375143

  11. Molecular Fingerprint and Dominant Environmental Factors of Nitrite-Dependent Anaerobic Methane-Oxidizing Bacteria in Sediments from the Yellow River Estuary, China

    PubMed Central

    Yan, Pengze; Li, Mingcong; Wei, Guangshan; Li, Han; Gao, Zheng

    2015-01-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) is performed by “Candidatus Methylomirabilis oxyfera” (M. oxyfera), which connects the carbon and nitrogen global nutrient cycles. In the present study, M. oxyfera-like bacteria sequences were successfully recovered from Yellow River Estuary sediments using specific primers for 16S rRNA and pmoA genes. A M. oxyfera-like sequences analysis based on the 16S rRNA gene revealed greater diversity compared with the pmoA gene; the 16S rRNA gene sequences retrieved from the Yellow River Estuary sediments belong to groups A as well as B and were mainly found in freshwater habitats. Quantitative PCR showed that 16S rRNA gene abundance varied from 9.28±0.11×103 to 2.10±0.13×105 copies g-1 (dry weight), and the pmoA gene abundance ranged from 8.63±0.50×103 to 1.83±0.18×105 copies g-1 (dry weight). A correlation analysis showed that the total organic carbon (TOC) and ammonium (NH4+) as well as the ratio of total phosphorus to total nitrogen (TP/TN) influenced the M. oxyfera-like bacteria distribution in the Yellow River Estuary sediments. These findings will aid in understanding the n-damo bacterial distribution pattern as well as their correlation with surrounding environmental factors in temperate estuarine ecosystems. PMID:26368535

  12. [Research progress in microbial methane oxidation coupled to denitrification].

    PubMed

    Zhu, Jing; Yuan, Meng-Dong; Liu, Jing-Jing; Huang, Xiao-Xiao; Wu, Wei-Xiang

    2013-12-01

    Methane oxidation coupled to denitrification is an essential bond to connect carbon- and nitrogen cycling. To deeply research this process will improve our understanding on the biochemical cycling of global carbon and nitrogen. As an exogenous gaseous carbon source of denitrification, methane can both regulate the balance of atmospheric methane to effectively mitigate the greenhouse effect caused by methane, and reduce the cost of exogenous carbon source input in traditional wastewater denitrification treatment process. As a result, great attention has being paid to the mechanical study of the process. This paper mainly discussed the two types of methane oxidation coupled to denitrification, i. e., aerobic methane oxidation coupled to denitrification (AME-D) and anaerobic methane oxidation coupled to denitrification (ANME-D), with the focus on the microbiological coupling mechanisms and related affecting factors. The existing problems in the engineering application of methane oxidation coupled to denitrification were pointed out, and the application prospects were approached. PMID:24697087

  13. 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

  14. Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer

    PubMed Central

    Kojima, Hisaya; Tokizawa, Riho; Kogure, Kouhei; Kobayashi, Yuki; Itoh, Masayuki; Shiah, Fuh-Kwo; Okuda, Noboru; Fukui, Manabu

    2014-01-01

    Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer ‘Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of ‘M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition–fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems. PMID:25098653

  15. Use of Molecular Fossils for the Interpretation of Paleoenvironments on Early Earth: The Synthesis of Lipid Biomarkers by Methane-Oxidizing Bacteria

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    Over the course of Earth's history, the most important biological influence has come from the evolution of oxygenic photosynthesis and the development of an oxygen-rich biosphere. Although the availability of free oxygen had profound effects on subsequent biological and planetary evolution, clear paleobiological evidence of the timing of this transition is lacking. Recent technical advances in the microanalysis of organic matter has made it possible to detect residual molecules (biomarkers) in proterozoic (2.5 to 0.6 billion years) sedimentary rock characteristic of specific groups of microorganisms. When coupled with the carbon isotopic fractionations characteristic of biological systems and the new field of compound specific isotope analysis, biomarkers could prove to be a powerful tool for decoding ancient biochemistry from the geological record. We have been studying the carbon isotope fractionations associated with the synthesis of organic biomarker molecules in several types of methane-oxidizing bacteria that should have been key to carbon cycling in paleoenvironments after the evolution of oxygenic photosynthesis.

  16. Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer

    NASA Astrophysics Data System (ADS)

    Kojima, Hisaya; Tokizawa, Riho; Kogure, Kouhei; Kobayashi, Yuki; Itoh, Masayuki; Shiah, Fuh-Kwo; Okuda, Noboru; Fukui, Manabu

    2014-07-01

    Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer `Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of `M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition-fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems.

  17. Spectral and thermodynamic properties of methanobactin from γ-proteobacterial methane oxidizing bacteria: a case for copper competition on a molecular level.

    PubMed

    Choi, Dong W; Bandow, Nathan L; McEllistrem, Marcus T; Semrau, Jeremy D; Antholine, William E; Hartsel, Scott C; Gallagher, Warren; Zea, Corbin J; Pohl, Nicole L; Zahn, James A; DiSpirito, Alan A

    2010-12-01

    Methanobactin (mb) is a low molecular mass copper-binding molecule analogous to iron-binding siderophores. The molecule is produced by many methanotrophic or methane oxidizing bacteria (MOB), but has only been characterized to date in one MOB, Methylosinus trichosporium OB3b. To explore the potential molecular diversity in this novel class of metal binding compound, the spectral (UV-visible, fluorescent, and electron paramagnetic resonance) and thermodynamic properties of mb from two γ-proteobacterial MOB, Methylococcus capsulatus Bath and Methylomicrobium album BG8, were determined and compared to the mb from the α-proteobacterial MOB, M. trichosporium OB3b. The mb from both γ-proteobacterial MOB differed from the mb from M. trichosporium OB3b in molecular mass and spectral properties. Compared to mb from M. trichosporium OB3b, the extracellular concentrations were low, as were copper-binding constants of mb from both γ-proteobacterial MOB. In addition, the mb from M. trichosporium OB3b removed Cu(I) from the mb of both γ-proteobacterial MOB. Taken together the results suggest mb may be a factor in regulating methanotrophic community structure in copper-limited environments. PMID:20817303

  18. Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake

    PubMed Central

    Deutzmann, Joerg S.; Stief, Peter; Brandes, Josephin; Schink, Bernhard

    2014-01-01

    Anaerobic methane oxidation coupled to denitrification, also known as “nitrate/nitrite-dependent anaerobic methane oxidation” (n-damo), was discovered in 2006. Since then, only a few studies have identified this process and the associated microorganisms in natural environments. In aquatic sediments, the close proximity of oxygen- and nitrate-consumption zones can mask n-damo as aerobic methane oxidation. We therefore investigated the vertical distribution and the abundance of denitrifying methanotrophs related to Candidatus Methylomirabilis oxyfera with cultivation-independent molecular techniques in the sediments of Lake Constance. Additionally, the vertical distribution of methane oxidation and nitrate consumption zones was inferred from high-resolution microsensor profiles in undisturbed sediment cores. M. oxyfera-like bacteria were virtually absent at shallow-water sites (littoral sediment) and were very abundant at deep-water sites (profundal sediment). In profundal sediment, the vertical distribution of M. oxyfera-like bacteria showed a distinct peak in anoxic layers that coincided with the zone of methane oxidation and nitrate consumption, a strong indication for n-damo carried out by M. oxyfera-like bacteria. Both potential n-damo rates calculated from cell densities (660–4,890 µmol CH4⋅m−2⋅d−1) and actual rates calculated from microsensor profiles (31–437 µmol CH4⋅m−2⋅d−1) were sufficiently high to prevent methane release from profundal sediment solely by this process. Additionally, when nitrate was added to sediment cores exposed to anoxic conditions, the n-damo zone reestablished well below the sediment surface, completely preventing methane release from the sediment. We conclude that the previously overlooked n-damo process can be the major methane sink in stable freshwater environments if nitrate is available in anoxic zones. PMID:25472842

  19. Degradation kinetics of chlorinated aliphatic hydrocarbons by methane oxidizers naturally-associated with wetland plant roots

    NASA Astrophysics Data System (ADS)

    Powell, C. L.; Goltz, M. N.; Agrawal, A.

    2014-12-01

    Chlorinated aliphatic hydrocarbons (CAHs) are common groundwater contaminants that can be removed from the environment by natural attenuation processes. CAH biodegradation can occur in wetland environments by reductive dechlorination as well as oxidation pathways. In particular, CAH oxidation may occur in vegetated wetlands, by microorganisms that are naturally associated with the roots of wetland plants. The main objective of this study was to evaluate the cometabolic degradation kinetics of the CAHs, cis-1,2-dichloroethene (cisDCE), trichloroethene (TCE), and 1,1,1-trichloroethane (1,1,1TCA), by methane-oxidizing bacteria associated with the roots of a typical wetland plant in soil-free system. Laboratory microcosms with washed live roots investigated aerobic, cometabolic degradation of CAHs by the root-associated methane-oxidizing bacteria at initial aqueous [CH4] ~ 1.9 mg L- 1, and initial aqueous [CAH] ~ 150 μg L- 1; cisDCE and TCE (in the presence of 1,1,1TCA) degraded significantly, with a removal efficiency of approximately 90% and 46%, respectively. 1,1,1TCA degradation was not observed in the presence of active methane oxidizers. The pseudo first-order degradation rate-constants of TCE and cisDCE were 0.12 ± 0.01 and 0.59 ± 0.07 d- 1, respectively, which are comparable to published values. However, their biomass-normalized degradation rate constants obtained in this study were significantly smaller than pure-culture studies, yet they were comparable to values reported for biofilm systems. The study suggests that CAH removal in wetland plant roots may be comparable to processes within biofilms. This has led us to speculate that the active biomass may be on the root surface as a biofilm. The cisDCE and TCE mass losses due to methane oxidizers in this study offer insight into the role of shallow, vegetated wetlands as an environmental sink for such xenobiotic compounds.

  20. The regulation of methane oxidation in soil

    NASA Technical Reports Server (NTRS)

    Mancinelli, R. L.

    1995-01-01

    The atmospheric concentration of methane, a greenhouse gas, has more than doubled during the past 200 years. Consequently, identifying the factors influencing the flux of methane into the atmosphere is becoming increasingly important. Methanotrophs, microaerophilic organisms widespread in aerobic soils and sediments, oxidize methane to derive energy and carbon for biomass. In so doing, they play an important role in mitigating the flux of methane into the atmosphere. Several physico-chemical factors influence rates of methane oxidation in soil, including soil diffusivity; water potential; and levels of oxygen, methane, ammonium, nitrate, nitrite, and copper. Most of these factors exert their influence through interactions with methane monooxygenase (MMO), the enzyme that catalyzes the reaction converting methane to methanol, the first step in methane oxidation. Although biological factors such as competition and predation undoubtedly play a role in regulating the methanotroph population in soils, and thereby limit the amount of methane consumed by methanotrophs, the significance of these factors is unknown. Obtaining a better understanding of the ecology of methanotrophs will help elucidate the mechanisms that regulate soil methane oxidation.

  1. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion.

    PubMed

    Lawton, Thomas J; Rosenzweig, Amy C

    2016-08-01

    Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock. PMID:27366961

  2. Potential methane production and methane oxidation rates in peatland ecosystems of the Appalachian Mountains, United States

    SciTech Connect

    Yavitt, J.B.; Lang, G.E.; Downey, D.M. )

    1988-09-01

    Potential rates of methane production and carbon dioxide production were measured on 11 dates in 1986 in peat from six plant communities typical of moss-dominated peatlands in the Appalachian Mountains. Annual methane production ranged from 2.7 to 17.5 mol/sq m, and annual carbon dioxide production ranged from 30.6 to 79.0 mol/sq m. The wide range in methane production values among the communities found within a single peatland indicates that obtaining one production value for a peatland may not be appropriate. Low temperature constrained the potential for methane production in winter, while the chemical quality of the peat substrate appears to control methane production in the summer. Methane oxidation was measured throughout the peat profile to a depth of 30 cm. Values for methane oxidation ranged from 0.08 to 18.7 microM/hr among the six plant communities. Aerobic methane-oxidizing bacteria probably mediated most of the activity. On a daily basis during the summer, between 11 and 100% of the methane produced is susceptible to oxidation within the peat column. Pools of dissolved methane and dissolved carbon dioxide in pore waters were less than 0.2 and less than 1.0 mol/sq m, respectively, indicating that methane does not accumulate in the pore waters. Peatlands have been considered as an important source of biologically produced methane. Despite the high rates of methane production, the high rates of methane oxidation dampen the potential emission of methane to the atmosphere. 41 refs., 7 figs., 4 tabs.

  3. Aerobic Denitrifying Bacteria That Produce Low Levels of Nitrous Oxide

    PubMed Central

    Takaya, Naoki; Catalan-Sakairi, Maria Antonina B.; Sakaguchi, Yasushi; Kato, Isao; Zhou, Zhemin; Shoun, Hirofumi

    2003-01-01

    Most denitrifiers produce nitrous oxide (N2O) instead of dinitrogen (N2) under aerobic conditions. We isolated and characterized novel aerobic denitrifiers that produce low levels of N2O under aerobic conditions. We monitored the denitrification activities of two of the isolates, strains TR2 and K50, in batch and continuous cultures. Both strains reduced nitrate (NO3−) to N2 at rates of 0.9 and 0.03 μmol min−1 unit of optical density at 540 nm−1 at dissolved oxygen (O2) (DO) concentrations of 39 and 38 μmol liter−1, respectively. At the same DO level, the typical denitrifier Pseudomonas stutzeri and the previously described aerobic denitrifier Paracoccus denitrificans did not produce N2 but evolved more than 10-fold more N2O than strains TR2 and K50 evolved. The isolates denitrified NO3− with concomitant consumption of O2. These results indicated that strains TR2 and K50 are aerobic denitrifiers. These two isolates were taxonomically placed in the β subclass of the class Proteobacteria and were identified as P. stutzeri TR2 and Pseudomonas sp. strain K50. These strains should be useful for future investigations of the mechanisms of denitrifying bacteria that regulate N2O emission, the single-stage process for nitrogen removal, and microbial N2O emission into the ecosystem. PMID:12788710

  4. 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

  5. Soil and sediment bacteria capable of aerobic nitrate respiration.

    PubMed Central

    Carter, J P; Hsaio, Y H; Spiro, S; Richardson, D J

    1995-01-01

    Several laboratory strains of gram-negative bacteria are known to be able to respire nitrate in the presence of oxygen, although the physiological advantage gained from this process is not entirely clear. The contribution that aerobic nitrate respiration makes to the environmental nitrogen cycle has not been studied. As a first step in addressing this question, a strategy which allows for the isolation of organisms capable of reducing nitrate to nitrite following aerobic growth has been developed. Twenty-nine such strains have been isolated from three soils and a freshwater sediment and shown to comprise members of three genera (Pseudomonas, Aeromonas, and Moraxella). All of these strains expressed a nitrate reductase with an active site located in the periplasmic compartment. Twenty-two of the strains showed significant rates of nitrate respiration in the presence of oxygen when assayed with physiological electron donors. Also isolated was one member of the gram-positive genus Arthrobacter, which was likewise able to respire nitrate in the presence of oxygen but appeared to express a different type of nitrate reductase. In the four environments studied, culturable bacteria capable of aerobic nitrate respiration were isolated in significant numbers (10(4) to 10(7) per g of soil or sediment) and in three cases were as abundant as, or more abundant than, culturable bacteria capable of denitrification. Thus, it seems likely that the corespiration of nitrate and oxygen may indeed make a significant contribution to the flux of nitrate to nitrite in the environment. PMID:7487017

  6. Interactions between nitrogen cycling and methane oxidation in the pelagic waters of the Gulf of Mexico.

    NASA Astrophysics Data System (ADS)

    Joye, S. B.; Weber, S.; Battles, J.; Montoya, J. P.

    2014-12-01

    Methane is an important greenhouse gas that plays a critical role in climate variation. Although a variety of marine methane sources and sinks have been identified, key aspects of the fate of methane in the ocean remain poorly constrained. At cold seeps in the Gulf of Mexico and elsewhere, methane is introduced into the overlying water column via fluid escape from the seabed. We quantified the fate of methane in the water column overlying seafloor cold seeps, in a brine basin, and at several control sites. Our goals were to determine the factors that regulated methane consumption and assimilation and to explore how these controlling factors varied among and between sites. In particular, we examined the impact of nitrogen availability on methane oxidation and studied the ability of methane oxidizing bacteria to fix molecular nitrogen. Methane oxidation rates were highest in the methane rich bottom waters of natural hydrocabron seeps. At these sites, inorganic nitrogen addition stimulated methane oxidation in laboratory experiments. In vitro shipboard experiments revealed that rates of methane oxidation and nitrogen fixation were correlated strongly, suggesting that nitrogen fixation may have been mediated by methanotrophic bacteria. The highest rates of methane oxidation and nitrogen fixation were observed in the deepwater above at natural hydrocarbon seeps. Rates of methane oxidation were substantial along the chemocline of a brine basin but in these ammonium-rich brines, addition of inorganic nitrogen had little impact on methane oxidation suggesting that methanotrophy in these waters were not nitrogen limited. Control sites exhibited the lowest methane concentrations and methane oxidation rates but even these waters exhibited substantial potential for methane oxidation when methane and inorganic nitrogen concentrations were increased. Together, these data suggest that the availability of inorganic nitrogen plays a critical role in regulating methane oxidation in

  7. Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1.

    PubMed

    Kits, K Dimitri; Klotz, Martin G; Stein, Lisa Y

    2015-09-01

    Obligate methanotrophs belonging to the Phyla Proteobacteria and Verrucomicrobia require oxygen for respiration and methane oxidation; nevertheless, aerobic methanotrophs are abundant and active in low oxygen environments. While genomes of some aerobic methanotrophs encode putative nitrogen oxide reductases, it is not understood whether these metabolic modules are used for NOx detoxification, denitrification or other purposes. Here we demonstrate using microsensor measurements that a gammaproteobacterial methanotroph Methylomonas denitrificans sp. nov. strain FJG1(T) couples methane oxidation to nitrate reduction under oxygen limitation, releasing nitrous oxide as a terminal product. Illumina RNA-Seq data revealed differential expression of genes encoding a denitrification pathway previously unknown to methanotrophs as well as the pxmABC operon in M. denitrificans sp. nov. strain FJG1(T) in response to hypoxia. Physiological and transcriptome data indicate that genetic inventory encoding the denitrification pathway is upregulated only upon availability of nitrate under oxygen limitation. In addition, quantitation of ATP levels demonstrates that the denitrification pathway employs inventory such as nitrate reductase NarGH serving M. denitrificans sp. nov. strain FJG1(T) to conserve energy during oxygen limitation. This study unravelled an unexpected metabolic flexibility of aerobic methanotrophs, thereby assigning these bacteria a new role at the metabolic intersection of the carbon and nitrogen cycles. PMID:25580993

  8. 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.

  9. 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.

  10. Degradation kinetics of chlorinated aliphatic hydrocarbons by methane oxidizers naturally-associated with wetland plant roots.

    PubMed

    Powell, C L; Goltz, M N; Agrawal, A

    2014-12-01

    Chlorinated aliphatic hydrocarbons (CAHs) are common groundwater contaminants that can be removed from the environment by natural attenuation processes. CAH biodegradation can occur in wetland environments by reductive dechlorination as well as oxidation pathways. In particular, CAH oxidation may occur in vegetated wetlands, by microorganisms that are naturally associated with the roots of wetland plants. The main objective of this study was to evaluate the cometabolic degradation kinetics of the CAHs, cis-1,2-dichloroethene (cisDCE), trichloroethene (TCE), and 1,1,1-trichloroethane (1,1,1TCA), by methane-oxidizing bacteria associated with the roots of a typical wetland plant in soil-free system. Laboratory microcosms with washed live roots investigated aerobic, cometabolic degradation of CAHs by the root-associated methane-oxidizing bacteria at initial aqueous [CH4] ~1.9mgL(-1), and initial aqueous [CAH] ~150μgL(-1); cisDCE and TCE (in the presence of 1,1,1TCA) degraded significantly, with a removal efficiency of approximately 90% and 46%, respectively. 1,1,1TCA degradation was not observed in the presence of active methane oxidizers. The pseudo first-order degradation rate-constants of TCE and cisDCE were 0.12±0.01 and 0.59±0.07d(-1), respectively, which are comparable to published values. However, their biomass-normalized degradation rate constants obtained in this study were significantly smaller than pure-culture studies, yet they were comparable to values reported for biofilm systems. The study suggests that CAH removal in wetland plant roots may be comparable to processes within biofilms. This has led us to speculate that the active biomass may be on the root surface as a biofilm. The cisDCE and TCE mass losses due to methane oxidizers in this study offer insight into the role of shallow, vegetated wetlands as an environmental sink for such xenobiotic compounds. PMID:25444117

  11. 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. PMID:12238371

  12. Phosphatase activity of aerobic and facultative anaerobic bacteria.

    PubMed

    Pácová, Z; Kocur, M

    1978-10-01

    1115 strains of aerobic and facultatively anaerobic bacteria were tested for phosphatase activity by a conventional plate method and a microtest. The microtest was devised to allow results to be read after 4 h cultivation. Phosphatase activity was found in wide range of species and strains. Besides staphylococci, where the test for phosphatase is successfully used, it may be applied as one of the valuable tests for the differentiation of the following species: Bacillus cereus, B. licheniformis, Aeromonas spp., Vibrio parahaemolyticus, Actinobacillus spp., Pasteurella spp., Xanthomonas spp., Flavobacterium spp., Alteromonas putrefaciens, Pseudomonas maltophilia, Ps. cepacia, and some other species of Pseudomonas. The species which gave uniformly negative phosphatase reaction were as follows: Staph. saprophyticus, Acinetobacter calcoaceticus, Alcaligenes faecalis, and Bordetella bronchiseptica. PMID:216188

  13. Poplar lignin decomposition by gram-negative aerobic bacteria

    SciTech Connect

    Odier, E.; Janin, G.; Monties, B.

    1981-02-01

    Eleven gram-negative aerobic bacteria (Pseudomonadaceae and Neisseriaceae) out of 122 soil isolates were selected for their ability to assimilate poplar dioxane lignin without a cosubstrate. Dioxane lignin and milled wood lignin degradation rates ranged between 20 and 40% of initial content after 7 days in mineral medium, as determined by a loss of absorbance at 280 nm; 10 strains could degrade in situ lignin, as evidenced by the decrease of the acetyl bromide lignin content of microtome wood sections. No degradation of wood polysaccharides was detected. Lignin biodegradation by Pseudomonas 106 was confirmed by 14CO2 release from labeled poplar wood, although in lower yields compared with results obtained through chemical analysis based on acetyl bromide residual lignin determination. (Refs. 31).

  14. Field and laboratory studies of methane oxidation in an anoxic marine sediment: Evidence for a methanogen-sulfate reducer consortium

    SciTech Connect

    Hoehler, T.M.; Alperin, M.J.; Albert, D.B.

    1994-12-01

    Field and laboratory studies of anoxic sediments from Cape Lookout Bight, North Carolina, suggest that anaerobic methane oxidation is mediated by a consortium of methanogenic and sulfate-reducing bacteria. A seasonal survey of methane oxidation and CO{sub 2} reduction rates indicates that methane production was confined to sulfate-depleted sediments at all times of year, while methane oxidation occurred in two modes. In the summer, methane oxidation was confined to sulfate-depleted sediments and occurred at rates lower than those of CO{sub 2} reduction. In the winter, net methane oxidation occurred in an interval at the base of the sulfate-containing zone. Sediment incubation experiments suggest both methanogens and sulfate reducers were responsible for the observed methane oxidation. In one incubation experiment both modes of oxidation were partially inhibited by 2-bromoethanesulfonic acid (a specific inhibitor of methanogens). This evidence, along with the apparent confinement of methane oxidation to sulfate-depleted sediments in the summer, indicates that methanogenic bacteria are involved in methane oxidation. In a second incubation experiment, net methane oxidation was induced by adding sulfate to homogenized methanogenic sediments, suggesting that sulfate reducers also a play a role in the process. We hypothesize that methanogens oxidize methane and produce hydrogen via a reversal of CO{sub 2} reduction. The hydrogen is efficiently removed and maintained at low concentrations by sulfate reducers. Pore water H{sub 2} concentrations in the sediment incubation experiments (while net methane oxidation was occurring) were low enough that methanogenic bacteria could derive sufficient energy for growth from the oxidation of methane. The methanogen-sulfate reducer consortium may also be a feasible mechanism for previously documented anaerobic methane oxidation in both freshwater and marine environments. 63 refs., 6 refs.

  15. Evidence for the Cooccurrence of Nitrite-Dependent Anaerobic Ammonium and Methane Oxidation Processes in a Flooded Paddy Field

    PubMed Central

    Shen, Li-dong; Liu, Shuai; Huang, Qian; Lian, Xu; He, Zhan-fei; Geng, Sha; Jin, Ren-cun; He, Yun-feng; Lou, Li-ping; Xu, Xiang-yang; Zheng, Ping

    2014-01-01

    Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two of the most recent discoveries in the microbial nitrogen cycle. In the present study, we provide direct evidence for the cooccurrence of the anammox and n-damo processes in a flooded paddy field in southeastern China. Stable isotope experiments showed that the potential anammox rates ranged from 5.6 to 22.7 nmol N2 g−1 (dry weight) day−1 and the potential n-damo rates varied from 0.2 to 2.1 nmol CO2 g−1 (dry weight) day−1 in different layers of soil cores. Quantitative PCR showed that the abundance of anammox bacteria ranged from 1.0 × 105 to 2.0 × 106 copies g−1 (dry weight) in different layers of soil cores and the abundance of n-damo bacteria varied from 3.8 × 105 to 6.1 × 106 copies g−1 (dry weight). Phylogenetic analyses of the recovered 16S rRNA gene sequences showed that anammox bacteria affiliated with “Candidatus Brocadia” and “Candidatus Kuenenia” and n-damo bacteria related to “Candidatus Methylomirabilis oxyfera” were present in the soil cores. It is estimated that a total loss of 50.7 g N m−2 per year could be linked to the anammox process, which is at intermediate levels for the nitrogen flux ranges of aerobic ammonium oxidation and denitrification reported in wetland soils. In addition, it is estimated that a total of 0.14 g CH4 m−2 per year could be oxidized via the n-damo process, while this rate is at the lower end of the aerobic methane oxidation rates reported in wetland soils. PMID:25261523

  16. Evidence for the cooccurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in a flooded paddy field.

    PubMed

    Shen, Li-Dong; Liu, Shuai; Huang, Qian; Lian, Xu; He, Zhan-Fei; Geng, Sha; Jin, Ren-Cun; He, Yun-Feng; Lou, Li-Ping; Xu, Xiang-Yang; Zheng, Ping; Hu, Bao-Lan

    2014-12-01

    Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two of the most recent discoveries in the microbial nitrogen cycle. In the present study, we provide direct evidence for the cooccurrence of the anammox and n-damo processes in a flooded paddy field in southeastern China. Stable isotope experiments showed that the potential anammox rates ranged from 5.6 to 22.7 nmol N2 g(-1) (dry weight) day(-1) and the potential n-damo rates varied from 0.2 to 2.1 nmol CO2 g(-1) (dry weight) day(-1) in different layers of soil cores. Quantitative PCR showed that the abundance of anammox bacteria ranged from 1.0 × 10(5) to 2.0 × 10(6) copies g(-1) (dry weight) in different layers of soil cores and the abundance of n-damo bacteria varied from 3.8 × 10(5) to 6.1 × 10(6) copies g(-1) (dry weight). Phylogenetic analyses of the recovered 16S rRNA gene sequences showed that anammox bacteria affiliated with "Candidatus Brocadia" and "Candidatus Kuenenia" and n-damo bacteria related to "Candidatus Methylomirabilis oxyfera" were present in the soil cores. It is estimated that a total loss of 50.7 g N m(-2) per year could be linked to the anammox process, which is at intermediate levels for the nitrogen flux ranges of aerobic ammonium oxidation and denitrification reported in wetland soils. In addition, it is estimated that a total of 0.14 g CH4 m(-2) per year could be oxidized via the n-damo process, while this rate is at the lower end of the aerobic methane oxidation rates reported in wetland soils. PMID:25261523

  17. Methane oxidation in Saanich Inlet during summer stratification

    NASA Technical Reports Server (NTRS)

    Ward, B. B.; Kilpatrick, K. A.; Wopat, A. E.; Minnich, E. C.; Lidstrom, M. E.

    1989-01-01

    Saanich Inlet, British Columbia, an fjord on the southeast coast of Vancouver Island, typically stratifies in summer, leading to the formation of an oxic-anoxic interface in the water column and accumulation of methane in the deep water. The results of methane concentration measurements in the water column of the inlet at various times throughout the summer months in 1983 are presented. Methane gradients and calculated diffusive fluxes across the oxic-anoxic interface increased as the summer progressed. Methane distribution and consumption in Saanich Inlet were studied in more detail during August 1986. At this time, a typical summer stratification with an oxic-anoxic interface around 140 m was present. At the interface, steep gradients in nutrient concentrations, bacterial abundance and methane concentration were observed. Methane oxidation was detected in the aerobic surface waters and in the anaerobic deep layer, but highest rates occurred in a narrow layer at the oxic-anoxic interface. Estimated methane oxidation rates were suffcient to consume 100 percent of the methane provided by diffusive flux from the anoxic layer. Methane oxidation is thus a mechanism whereby atmospheric flux from anoxic waters is minimized.

  18. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep.

    PubMed

    Heijs, Sander K; Haese, Ralf R; van der Wielen, Paul W J J; Forney, Larry J; van Elsas, Jan Dirk

    2007-04-01

    This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22-34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0-6 cm). Communities in the middle layer (6-22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study. PMID:17431711

  19. In-vitro activity of newer quinolones against aerobic bacteria.

    PubMed

    Auckenthaler, R; Michéa-Hamzehpour, M; Pechère, J C

    1986-04-01

    Nalidixic and five newer 4-quinolones, ciprofloxacin, enoxacin, norfloxacin, ofloxacin and pefloxacin were tested against 576 recent clinical aerobic bacterial isolates. The 4-quinolones were regularly active (MIC90 less than 4 mg/l) against the following bacteria: Staphylococcus aureus, S. epidermidis, S. saprophyticus, different Enterobacteriaceae, Haemophilus influenzae, Campylobacter jejuni, Pseudomonas aeruginosa, Agrobacter spp., Aeromonas spp., Plesiomonas spp., Neisseria meningitidis. Other bacteria were usually intermediately susceptible or resistant: different streptococci, Listeria monocytogenes, Nocardia asteroides, P. maltophilia, Achromobacter xylosoxydans and Alcaligenes denitrificans. Ciprofloxacin was the most potent compound, followed by ofloxacin and pefloxacin, norfloxacin and enoxacin being less active. All the 4-quinolones were much more active than nalidixic acid. The MBC/MIC ratios of the 4-quinolones were between 1 and 2 with a majority of strains, and between 2 and 3 with Streptococcus agalactiae, Str. faecalis and L. monocytogenes. A two- to eight-fold increase of MIC was observed by increasing the inoculum 10,000-fold with most of the strains tested. Susceptible bacterial population of Klebsiella pneumoniae, Enterobacter cloacae, Serratia marcescens and P. aeruginosa contained more clones resistant to nalidixic acid (10(4) to 10(8) at four times the MIC) than to 4-quinolones (10(5) to 10(9) at four times the MIC). Supplementing the media with MgSO4 produced smaller inhibition zone diameters with a disc diffusion method than those obtained with non-supplemented agar, with all quinolone or strains. Less regular effect, or no effect was obtained after supplementation with ZnSO4 or Ca(NO3)2. PMID:2940214

  20. Unexpected Microbial Diversity in Anaerobically Methane-oxidizing Mats of the Black Sea

    NASA Astrophysics Data System (ADS)

    Friedrich, M. W.; Pommerenke, B.; Seifert, R.; Krueger, M.

    2007-12-01

    Sediments of the Black Sea harbour consortia of anaerobically methane-oxidizing microorganisms in dense microbial mats, incrusted in large chimney structures consisting of carbonate precipitate. A number of convincing facts collected previously suggests that anaerobically methane-oxidizing Archaea (ANME) as well as delta- proteobacterial sulphate-reducing bacteria are the key players in anaerobic methane oxidation in Black Sea Mats: their presence has been shown by fluorescent-in-situ hybridization (FISH) with 16S rRNA-targeting probes, lipid biomarkers have typical, low delta13C ratios in archaeal and bacterial lipids, a methyl coenzyme M reductase-like protein was purified from the mat, and mat samples exhibit anaerobic methane oxidation. Here, we show that the diversity of Bacteria in both, pink and black mat samples, is larger than previously known. T-RFLP analysis of 16S rRNA and 16S rRNA genes and cloning and sequencing of randomly selected clones revealed the presence of taxa hitherto unknown to be present in anaerobically methane-oxidizing consortia. Besides the previously known delta-proteobacterial sulphate reducers, clones fell into 7 and 5 different phyla in pink and black coloured mats, respectively. Our findings suggest that the turnover of carbon in anaerobically methane-oxidizing communities might involve a larger diversity of microorganisms than was previously assumed.

  1. 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. PMID:20819367

  2. Methane oxidation linked to chlorite dismutation

    PubMed Central

    Miller, Laurence G.; Baesman, Shaun M.; Carlström, Charlotte I.; Coates, John D.; Oremland, Ronald S.

    2014-01-01

    We examined the potential for CH4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO−2) dismutation. Although dissimilatory reduction of ClO−4 and ClO−3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO−2 amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO−2. We also observed complete removal of 0.2 kPa CH4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO−2. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO−2 and CH4 consumption was established in soils and cultures, no upstream connection with either ClO−4 or ClO−3 was discerned. This result suggests that the release of O2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs. PMID:24987389

  3. Methane oxidation linked to chlorite dismutation

    USGS Publications Warehouse

    Miller, Laurence G.; Baesman, Shaun M.; Carlström, Charlotte I.; Coates, John D.; Oremland, Ronald S.

    2014-01-01

    We examined the potential for CH4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO−2) dismutation. Although dissimilatory reduction of ClO−4 and ClO−3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO−2 amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO−2. We also observed complete removal of 0.2 kPa CH4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO−2. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO−2 and CH4 consumption was established in soils and cultures, no upstream connection with either ClO−4 or ClO−3 was discerned. This result suggests that the release of O2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs.

  4. Methane oxidation linked to chlorite dismutation.

    PubMed

    Miller, Laurence G; Baesman, Shaun M; Carlström, Charlotte I; Coates, John D; Oremland, Ronald S

    2014-01-01

    We examined the potential for CH4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO(-) 2) dismutation. Although dissimilatory reduction of ClO(-) 4 and ClO(-) 3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO(-) 2 amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO(-) 2. We also observed complete removal of 0.2 kPa CH4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO(-) 2. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO(-) 2 and CH4 consumption was established in soils and cultures, no upstream connection with either ClO(-) 4 or ClO(-) 3 was discerned. This result suggests that the release of O2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs. PMID:24987389

  5. Microbial Methane Oxidation Rates in Guandu Wetland of northern Taiwan

    NASA Astrophysics Data System (ADS)

    Yu, Zih-Huei; Wang, Pei-Ling; Lin, Li-Hung

    2016-04-01

    Wetland is one of the major sources of atmospheric methane. The exact magnitude of methane emission is essentially controlled by microbial processes. Besides of methanogenesis, methanotrophy oxidizes methane with the reduction of various electron acceptors under oxic or anoxic conditions. The interplay of these microbial activities determines the final methane flux under different circumstances. In a tidal wetland, the cyclic flooding and recession of tide render oxygen and sulfate the dominant electron acceptors for methane oxidation. However, the details have not been fully examined, especially for the linkage between potential methane oxidation rates and in situ condition. In this study, a sub-tropical wetland in northern Taiwan, Guandu, was chosen to examine the tidal effect on microbial methane regulation. Several sediment cores were retrieved during high tide and low tide period and their geochemical profiles were characterized to demonstrate in situ microbial activities. Incubation experiments were conducted to estimate potential aerobic and anaerobic methane oxidation rates in surface and core sediments. Sediment cores collected in high tide and low tide period showed different geochemical characteristics, owning to tidal inundation. Chloride and sulfate concentration were lower during low tide period. A spike of enhanced sulfate at middle depth intervals was sandwiched by two sulfate depleted zones above and underneath. Methane was accumulated significantly with two methane depletion zones nearly mirroring the sulfate spike zone identified. During the high tide period, sulfate decreased slightly with depth with methane production inhibited at shallow depths. However, a methane consumption zone still occurred near the surface. Potential aerobic methane oxidation rates were estimated between 0.7 to 1.1 μmole/g/d, showing no difference between the samples collected at high tide or low tide period. However, a lag phase was widely observed and the lag phase

  6. 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

  7. 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.

  8. Velvet pad surface sampling of anaerobic and aerobic bacteria: an in vitro laboratory model.

    PubMed Central

    Raahave, D; Friis-Møller, A

    1982-01-01

    Velvet pads have been evaluated in an experimental, laboratory model, simulating intraoperative sampling of Staphylococcus epidermis, Escherichia coli and Bacteroides fragilis. After sampling, the pad was placed in a transport medium and kept in an anaerobic atmosphere, before being shaken and rinsed, followed by anaerobic and aerobic culture. This technique permitted quantitatively high recoveries of the test bacteria. Velvet pad sampling could be a measure to determine the density of aerobic and anaerobic bacteria during operation in an effort to predict the risk of postoperative wound sepsis. Images PMID:6757273

  9. Comparison of Two Techniques to Calculate Methane Oxidation rates in Samples Obtained From the Hudson Canyon Seep Field in the North Atlantic

    NASA Astrophysics Data System (ADS)

    Leonte, M.; Kessler, J. D.; Chepigin, A.; Kellermann, M. Y.; Arrington, E.; Valentine, D. L.; Sylva, S.

    2014-12-01

    Aerobic methane oxidation, or methanotrophy, is the dominant process by which methane is removed from the water column in oceanic environments. Therefore, accurately quantifying methane oxidation rates is crucial when constructing methane budgets on a local or global scale. Here we present a comparison of two techniques used to determine methane oxidation rates based on samples obtained over the Hudson Canyon seep field in the North Atlantic. Traditional methane oxidation rate measurements require inoculation of water samples with isotopically labeled methane and tracking the changes to methane concentrations and isotopes as the samples are incubated. However, the addition of methane above background levels is thought to increase the potential for methane oxidation in the sample. A new technique to calculate methane oxidation rates is based on kinetic isotope models and incorporates direct measurements of methane concentrations, methane 13C isotopes, and water current velocity. Acoustic instrumentation (ADCP) aboard the R/V Endeavor was used to obtain water current velocity data while water samples were collected for methane concentration and isotopic ratio analysis. Methane δ13C measurements allow us to attribute changes in methane concentration to either water dispersion or bacterial methane oxidation. The data obtained from this cruise will tell us a comprehensive story of methane removal processes from this active seep field. The kinetic isotope models will allow us to estimate the total flux of methane from the seep site and calculate methane oxidation rates at different depths and locations away from seafloor plumes.

  10. A four-helix bundle stores copper for methane oxidation.

    PubMed

    Vita, Nicolas; Platsaki, Semeli; Baslé, Arnaud; Allen, Stephen J; Paterson, Neil G; Crombie, Andrew T; Murrell, J Colin; Waldron, Kevin J; Dennison, Christopher

    2015-09-01

    Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase. Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper. Methane monooxygenases are nature's primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock. Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location. PMID:26308900

  11. Anaerobic methane oxidation on the Amazon shelf

    SciTech Connect

    Blair, N.E.; Aller, R.C.

    1995-09-01

    Anaerobic methane oxidation on the Amazon shelf is strongly controlled by dynamic physical sedimentation processes. Rapidly accumulating, physically reworked deltaic sediments characteristic of much of the shelf typically support what appear to be low rates of steady state anaerobic methane oxidation at depths of 5-8 m below the sediment-water interface. Methane oxidation in these cases is responsible for < {approximately}10% of the {Sigma}CO{sub 2} inventory in the oxidation zone and is limited largely by the steady-state diffusive flux of methane into the overlying sulfate reduction zone. In contrast, a large area of the shelf has been extensively eroded, reexposing once deeply buried (>10 m) methane-charged sediment directly to seawater. In this nonsteady-state situation, methane is a major source of recently produced {Sigma}CO{sub 2} and an important reductant for sulfate. These observations suggest that authigenic sedimentary carbonates derived from anaerobic methane oxidation may sometimes reflect physically enhanced nonsteady-state exposure of methane to sulfate in otherwise biogeochemically unreactive deposits. The concentration profiles of CH{sub 4}, SO{sub 4}{sup =}, and {Sigma}CO{sub 2} in the eroded deposit were reproduced by a coupled reaction-transport model. This area of the shelf was reexposed to seawater approximately 5-10 years ago based on the model results and the assumption that the erosion of the deposit occurred as a single event that has now ceased. The necessary second order rate constant for anaerobic methane oxidation was {le}0.1 mM{sup -1} d{sup -1}.

  12. Inhibitory effects of sulfur compounds on methane oxidation by a methane-oxidizing consortium.

    PubMed

    Lee, Eun-Hee; Moon, Kyung-Eun; Kim, Tae Gwan; Lee, Sang-Don; Cho, Kyung-Suk

    2015-12-01

    Kinetic and enzymatic inhibition experiments were performed to investigate the effects of methanethiol (MT) and hydrogen sulfide (H2S) on methane oxidation by a methane-oxidizing consortium. In the coexistence of MT and H2S, the oxidation of methane was delayed until MT and H2S were completely degraded. MT and H2S could be degraded, both with and without methane. The kinetic analysis revealed that the methane-oxidizing consortium showed a maximum methane oxidation rate (Vmax) of 3.7 mmol g-dry cell weight (DCW)(-1) h(-1) and a saturation constant (Km) of 184.1 μM. MT and H2S show competitive inhibition on methane oxidation, with inhibition values (Ki) of 1504.8 and 359.8 μM, respectively. MT was primary removed by particulate methane monooxygenases (pMMO) of the consortium, while H2S was degraded by the other microorganisms or enzymes in the consortium. DNA and mRNA transcript levels of the pmoA gene expressions were decreased to ∼10(6) and 10(3)pmoA gene copy number g-DCW(-1) after MT and H2S degradation, respectively; however, both the amount of the DNA and mRNA transcript recovered their initial levels of ∼10(7) and 10(5)pmoA gene copy number g-DCW(-1) after methane oxidation, respectively. The gene expression results indicate that the pmoA gene could be rapidly reproducible after methane oxidation. This study provides comprehensive information of kinetic interactions between methane and sulfur compounds. PMID:26143035

  13. Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary

    PubMed Central

    Stegman, Monica R; Cottrell, Matthew T; Kirchman, David L

    2014-01-01

    Aerobic anoxygenic phototrophic (AAP) bacteria are well known to be abundant in estuaries, coastal regions and in the open ocean, but little is known about their activity in any aquatic ecosystem. To explore the activity of AAP bacteria in the Delaware estuary and coastal waters, single-cell 3H-leucine incorporation by these bacteria was examined with a new approach that combines infrared epifluorescence microscopy and microautoradiography. The approach was used on samples from the Delaware coast from August through December and on transects through the Delaware estuary in August and November 2011. The percent of active AAP bacteria was up to twofold higher than the percentage of active cells in the rest of the bacterial community in the estuary. Likewise, the silver grain area around active AAP bacteria in microautoradiography preparations was larger than the area around cells in the rest of the bacterial community, indicating higher rates of leucine consumption by AAP bacteria. The cell size of AAP bacteria was 50% bigger than the size of other bacteria, about the same difference on average as measured for activity. The abundance of AAP bacteria was negatively correlated and their activity positively correlated with light availability in the water column, although light did not affect 3H-leucine incorporation in light–dark experiments. Our results suggest that AAP bacteria are bigger and more active than other bacteria, and likely contribute more to organic carbon fluxes than indicated by their abundance. PMID:24824666

  14. Root-Associated Methane Oxidation and Methanogenesis: Key Determinants of Wetland Methane Emissions

    NASA Technical Reports Server (NTRS)

    King, G. M.

    1997-01-01

    During the award period, we have assessed the extent and controls of methane oxidation in north temperate wetlands. It is evident that wetlands have been a major global source of atmospheric methane in the past, and are so at present. It is also evident that microbial methane oxidation consumes a variable fraction of total wetland methane production, perhaps 10%-90%. Methane oxidation is thus a potentially important control of wetland methane emission. Our efforts have been designed to determine the extent of the process, its controls, and possible relationships to changes that might be expected in wetlands as a consequence of anthropogenic or climate-related disturbances. Current work, has emphasized controls of methane oxidation associated with rooted aquatic plants. As for the sediment-water interface, we have observed that oxygen availability is a primary limiting factor. Our conclusion is based on several different lines of evidence obtained from in vitro and in situ analyses. First, we have measured the kinetics of methane oxidation by intact plant roots harboring methane-oxidizing bacteria, as well as the kinetics of the methanotrophs themselves. Values for the half-saturation constant (apparent K(sub m)) are approximately 5 microns. These values are roughly equivalent to, or much less than porewater methane concentrations, indicating that uptake is likely saturated with respect to methane, and that some other parameter must limit activity. Methane concentrations in the lacunar spaces at the base of plant stems are also comparable to the half-saturation constants (when expressed as equivalent dissolved concentrations), providing further support for limitation of uptake by parameters other than methane.

  15. [The phylogenetic diversity of aerobic organotrophic bacteria from the Dagan high-temperature oil field].

    PubMed

    Nazina, T N; Sokolova, D Sh; Shestakova, N M; Grigor'ian, A A; Mikhaĭlova, E M; Babich, T L; Lysenko, A M; Turova, T P; Poltaraus, A B; Feng, Tsin'syan; Ni, Fangtian; Beliaev, S S

    2005-01-01

    The distribution and species diversity of aerobic organotrophic bacteria in the Dagan high-temperature oil field (China), which is exploited via flooding, have been studied. Twenty-two strains of the most characteristic thermophilic and mesophilic aerobic organotrophic bacteria have been isolated from the oil stratum. It has been found that, in a laboratory, the mesophilic and thermophilic isolates grow in the temperature, pH, and salinity ranges characteristic of the injection well near-bottom zones or of the oil stratum, respectively, and assimilate a wide range of hydrocarbons, fatty acids, lower alcohols, and crude oil, thus exhibiting adaptation to the environment. Using comparative phylogenetic 16S rRNA analysis, the taxonomic affiliation of the isolates has been established. The aerobic microbial community includes gram-positive bacteria with a high and low G+C content of DNA, and gamma and beta subclasses of Proteobacteria. The thermophilic bacteria belong to the genera Geobacillus and Thermoactinomyces, and the mesophilic strains belong to the genera Bacillus, Micrococcus, Cellulomonas, Pseudomonas, and Acinetobacter. The microbial community of the oil stratum is dominated by known species of the genus Geobacillus (G. subterraneus, G. stearothermophilus, and G. thermoglucosidasius) and a novel species "Geobacillus jurassicus." A number of novel thermophilic oil-oxidizing bacilli have been isolated. PMID:16119855

  16. The biochemistry of methane oxidation.

    PubMed

    Hakemian, Amanda S; Rosenzweig, Amy C

    2007-01-01

    Methanotrophic bacteria oxidize methane to methanol in the first step of their metabolic pathway. Two forms of methane monooxygenase (MMO) enzymes catalyze this reaction: soluble MMO (sMMO) and membrane-bound or particulate MMO (pMMO). pMMO is expressed when copper is available, and its active site is believed to contain copper. Whereas sMMO is well characterized, most aspects of pMMO biochemistry remain unknown and somewhat controversial. This review emphasizes advances in the past two to three years related to pMMO and to copper uptake and copper-dependent regulation in methanotrophs. The pMMO metal centers have been characterized spectroscopically, and the first pMMO crystal structure has been determined. Significant effort has been devoted to improving in vitro pMMO activity. Proteins involved in sMMO regulation and additional copper-regulated proteins have been identified, and the Methylococcus capsulatus (Bath) genome has been sequenced. Finally, methanobactin (mb), a small copper chelator proposed to facilitate copper uptake, has been characterized. PMID:17328677

  17. Methane Oxidation by Nitrosococcus oceanus and Nitrosomonas europaea†

    PubMed Central

    Jones, Ronald D.; Morita, Richard Y.

    1983-01-01

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

  18. Seasonal Oxygen Dynamics in a Thermokarst Bog in Interior Alaska: Implications for Rates of Methane Oxidation

    NASA Astrophysics Data System (ADS)

    Neumann, R. B.; Moorberg, C.; Wong, A.; Waldrop, M. P.; Turetsky, M. R.

    2015-12-01

    Methane is a potent greenhouse gas, and wetlands represent the largest natural source of methane to the atmosphere. However, much of the methane generated in anoxic wetlands never gets emitted to the atmosphere; up to >90% of generated methane can get oxidized to carbon dioxide. Thus, oxidation is an important methane sink and changes in the rate of methane oxidation can affect wetland methane emissions. Most methane is aerobically oxidized at oxic-anoxic interfaces where rates of oxidation strongly depend on methane and oxygen concentrations. In wetlands, oxygen is often the limiting substrate. To improve understanding of belowground oxygen dynamics and its impact on methane oxidation, we deployed two planar optical oxygen sensors in a thermokarst bog in interior Alaska. Previous work at this site indicated that, similar to other sites, rates of methane oxidation decrease over the growing season. We used the sensors to track spatial and temporal patterns of oxygen concentrations over the growing season. We coupled these in-situ oxygen measurements with periodic oxygen injection experiments performed against the sensor to quantify belowground rates of oxygen consumption. We found that over the season, the thickness of the oxygenated water layer at the peatland surface decreased. Previous research has indicated that in sphagnum-dominated peatlands, like the one studied here, rates of methane oxidation are highest at or slightly below the water table. It is in these saturated but oxygenated locations that both methane and oxygen are available. Thus, a seasonal reduction in the thickness of the oxygenated water layer could restrict methane oxidation. The decrease in thickness of the oxygenated layer coincided with an increase in the rate of oxygen consumption during our oxygen injection experiments. The increase in oxygen consumption was not explained by temperature; we infer it was due to an increase in substrate availability for oxygen consuming reactions and

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

    PubMed Central

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

    2006-01-01

    The abundance of aerobic anoxygenic phototrophic (AAP) 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 Ocean but only 5% or less in the Pacific Ocean. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than that of Prochlorococcus spp. and 10-fold higher than that of Synechococcus spp. In contrast, Prochlorococcus spp. 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. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP bacterial genera (Erythrobacter and Roseobacter spp.). Concentrations of bacteriochlorophyll a (BChl a) were low (∼1%) compared to those of chlorophyll a in the North Atlantic. 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, the pigment content of AAP bacteria approached that of Prochlorococcus in shelf break water. Our results suggest that AAP bacteria can be quite abundant in some oceanic regimes and that their distribution in the water column is consistent with phototrophy. PMID:16391092

  20. 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.

  1. 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

  2. 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

  3. Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production.

    PubMed

    Garcia-Chaves, Maria C; Cottrell, Matthew T; Kirchman, David L; Ruiz-González, Clara; Del Giorgio, Paul A

    2016-07-01

    Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance. PMID:26771928

  4. 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. PMID:26566932

  5. Role of phosphate solubilizing bacteria on rock phosphate solubility and growth of aerobic rice.

    PubMed

    Panhwar, Q A; Radziah, O; Zaharah, A R; Sariah, M; Razi, I Mohd

    2011-09-01

    Use of phosphate-solubilizing bacteria (PSB) as inoculants has concurrently increased phosphorous uptake in plants and improved yields in several crop species. The ability of PSB to improve growth of aerobic rice (Oryza sativa L.) through enhanced phosphorus (P) uptake from Christmas island rock phosphate (RP) was studied in glasshouse experiments. Two isolated PSB strains; Bacillus spp. PSB9 and PSB16, were evaluated with RP treatments at 0, 30 and 60 kg ha(-1). Surface sterilized seeds of aerobic rice were planted in plastic pots containing 3 kg soil and the effect of treatments incorporated at planting were observed over 60 days of growth. The isolated PSB strains (PSB9 and PSB16) solubilized significantly high amounts of P (20.05-24.08 mg kg(-1)) compared to non-inoculated (19-23.10 mg kg(-1)) treatments. Significantly higher P solubilization (24.08 mg kg(-1)) and plant P uptake (5.31 mg plant(-1)) was observed with the PSB16 strain at the highest P level of 60 kg ha(-1). The higher amounts of soluble P in the soil solution increased P uptake in plants and resulted in higher plant biomass (21.48 g plant(-1)). PSB strains also increased plant height (80 cm) and improved root morphology in aerobic rice. The results showed that inoculation of aerobic rice with PSB improved phosphate solubilizing activity of incorporated RP. PMID:22319876

  6. Enrichment of denitrifying anaerobic methane oxidizing microorganisms.

    PubMed

    Hu, Shihu; Zeng, Raymond J; Burow, Luke C; Lant, Paul; Keller, Jurg; Yuan, Zhiguo

    2009-10-01

    The microorganisms responsible for anaerobic oxidation of methane (AOM) coupled to denitrification have not been clearly elucidated. Three recent publications suggested it can be achieved by a denitrifying bacterium with or without the involvement of anaerobic methanotrophic archaea. A key factor limiting the progress in this research field is the shortage of enrichment cultures performing denitrifying anaerobic methane oxidation (DAMO). In this study, DAMO cultures were enriched from mixed inoculum including sediment from a freshwater lake, anaerobic digester sludge and return activated sludge from a sewage treatment plant. Two reactors, operated at 35°C and at 22°C, respectively, showed simultaneous methane oxidation and nitrate reduction after several months of operation. Analysis of 16S rRNA gene clone libraries from the 35°C enrichment showed the presence of an archaeon closely related to other DAMO archaea and a dominated bacterium belonging to the yet uncultivated NC10 phylum. This culture preferred nitrite to nitrate as the electron acceptor. The present study suggests that the archaea are rather methanotrophs than methanogens. The highest denitrification rate achieved was 2.35 mmol NO3 (-) -N gVSS(-1)  day(-1) . The culture enriched at 22°C contained the same NC10 bacterium observed in the culture enriched at 35°C but no archaea. PMID:23765890

  7. 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

  8. Influence of bovine lactoferrin on the growth of selected probiotic bacteria under aerobic conditions.

    PubMed

    Chen, Po-Wen; Ku, Yu-We; Chu, Fang-Yi

    2014-10-01

    Bovine lactoferrin (bLf) is a natural glycoprotein, and it shows broad-spectrum antimicrobial activity. However, reports on the influences of bLf on probiotic bacteria have been mixed. We examined the effects of apo-bLf (between 0.25 and 128 mg/mL) on both aerobic and anaerobic cultures of probiotics. We found that bLf had similar effects on the growth of probiotics under aerobic or anaerobic conditions, and that it actively and significantly (at concentrations of >0.25 mg/mL) retarded the growth rate of Bifidobacterium bifidum (ATCC 29521), B. longum (ATCC 15707), B. lactis (BCRC 17394), B. infantis (ATCC 15697), Lactobacillus reuteri (ATCC 23272), L. rhamnosus (ATCC 53103), and L. coryniformis (ATCC 25602) in a dose-dependent manner. Otherwise, minimal inhibitory concentrations (MICs) were 128 or >128 mg/mL against B. bifidum, B. longum, B. lactis, L. reuteri, and L. rhamnosus (ATCC 53103). With regard to MICs, bLf showed at least four-fold lower inhibitory effect on probiotics than on pathogens. Intriguingly, bLf (>0.25 mg/mL) significantly enhanced the growth of Rhamnosus (ATCC 7469) and L. acidophilus (BCRC 14065) by approximately 40-200 %, during their late periods of growth. Supernatants produced from aerobic but not anaerobic cultures of L. acidophilus reduced the growth of Escherichia coli by about 20 %. Thus, bLf displayed a dose-dependent inhibitory effect on the growth of most probiotic strains under either aerobic or anaerobic conditions. An antibacterial supernatant prepared from the aerobic cultures may have significant practical use. PMID:24916115

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

    PubMed Central

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

    1977-01-01

    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. PMID:328525

  10. 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. PMID:26461264

  11. 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

  12. 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

  13. Improving the aeration of critical fine-grained landfill top cover material by vegetation to increase the microbial methane oxidation efficiency.

    PubMed

    Bohn, Sonja; Brunke, Paul; Gebert, Julia; Jager, Johannes

    2011-05-01

    The natural methane oxidation potential of methanotrophic bacteria in landfill top covers is a sustainable and inexpensive method to reduce methane emissions to the atmosphere. Basically, the activity of methanotrophic bacteria is limited by the availability of oxygen in the soil. A column study was carried out to determine whether and to what extent vegetation can improve soil aeration and maintain the methane oxidation process. Tested soils were clayey silt and mature compost. The first soil is critical in light of surface crusting due to vertical erosion of an integral part of fine-grained material, blocking pores required for the gas exchange. The second soil, mature compost, is known for its good methane oxidation characteristics, due to high air-filled porosity, favorable water retention capacity and high nutrient supply. The assortment of plants consisted of a grass mixture, Canadian goldenrod and a mixture of leguminous plants. The compost offered an excellent methane oxidation potential of 100% up to a CH(4)-input of 5.6l CH(4)m(-2)h(-1). Whereas the oxidation potential was strongly diminished in the bare control column filled with clayey silt even at low CH(4)-loads. By contrast the planted clayey silt showed an increased methane oxidation potential compared to the bare column. The spreading root system forms secondary macro-pores, and hence amplifies the air diffusivity and sustain the oxygen supply to the methanotrophic bacteria. Water is produced during methane oxidation, causing leachate. Vegetation reduces the leachate by evapotranspiration. Furthermore, leguminous plants support the enrichment of soil with nitrogen compounds and thus improving the methane oxidation process. In conclusion, vegetation is relevant for the increase of oxygen diffusion into the soil and subsequently enhances effective methane oxidation in landfill cover soils. PMID:21169005

  14. Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability.

    PubMed

    Henneberger, Ruth; Chiri, Eleonora; Bodelier, Paul E L; Frenzel, Peter; Lüke, Claudia; Schroth, Martin H

    2015-05-01

    Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body. PMID:25186436

  15. Nitrate-dependent anaerobic methane oxidation in a freshwater sediment

    NASA Astrophysics Data System (ADS)

    Norði, Katrin á.; Thamdrup, Bo

    2014-05-01

    Anaerobic oxidation of methane coupled to denitrification (DAOM) is a novel process of potential importance to the regulation of methane emissions from freshwater environments. We established nitrate-enriched microcosms of sediment from a freshwater pond in order to quantify the role of this process in a simulated natural redox zonation. The microcosms were allowed to acclimate to nitrate levels of 1-2 mmol L-1 in the overlying water for 16 months leading to a nitrate penetration of 4 cm. The nitrate enrichment significantly stimulated AOM relative to controls, and based on the similar concentrations of sulfate and reactive Fe(III) in the control sediment we conclude that the observed AOM was coupled to denitrification. DAOM occurred at rates that were two orders of magnitude lower than aerobic methane oxidation rates reported in freshwater sediments, and the process appeared to be limited by nitrate or nitrite even at millimolar nitrate concentrations. By contrast, ammonium was efficiently consumed at the base of the nitrate zone, presumably by the anammox process. Although DAOM was stimulated by nitrate enrichment, there were no significant differences between the methane emission from the control and nitrate-enriched microcosms. Our results provide the first experimental evaluation of the kinetics of DAOM in whole sediment cores and indicate that AOM coupled to denitrification can consume a substantial part of the methane flux in nitrate-rich environments. Because it is much less efficient in scavenging methane than its aerobic counterpart, the anaerobic process will, however, mainly be of significance in the regulation of methane emission from oxygen-depleted systems.

  16. 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. PMID:27297837

  17. Role of ammonia-oxidizing bacteria in micropollutant removal from wastewater with aerobic granular sludge.

    PubMed

    Margot, Jonas; Lochmatter, Samuel; Barry, D A; Holliger, Christof

    2016-01-01

    Nitrifying wastewater treatment plants (WWTPs) are more efficient than non-nitrifying WWTPs to remove several micropollutants such as pharmaceuticals and pesticides. This may be related to the activity of nitrifying organisms, such as ammonia-oxidizing bacteria (AOBs), which could possibly co-metabolically oxidize micropollutants with their ammonia monooxygenase (AMO). The role of AOBs in micropollutant removal was investigated with aerobic granular sludge (AGS), a promising technology for municipal WWTPs. Two identical laboratory-scale AGS sequencing batch reactors (AGS-SBRs) were operated with or without nitrification (inhibition of AMOs) to assess their potential for micropollutant removal. Of the 36 micropollutants studied at 1 μg l(-1) in synthetic wastewater, nine were over 80% removed, but 17 were eliminated by less than 20%. Five substances (bisphenol A, naproxen, irgarol, terbutryn and iohexol) were removed better in the reactor with nitrification, probably due to co-oxidation catalysed by AMOs. However, for the removal of all other micropollutants, AOBs did not seem to play a significant role. Many compounds were better removed in aerobic condition, suggesting that aerobic heterotrophic organisms were involved in the degradation. As the AGS-SBRs did not favour the growth of such organisms, their potential for micropollutant removal appeared to be lower than that of conventional nitrifying WWTPs. PMID:26877039

  18. Methanobactin and the Link between Copper and Bacterial Methane Oxidation.

    PubMed

    DiSpirito, Alan A; Semrau, Jeremy D; Murrell, J Colin; Gallagher, Warren H; Dennison, Christopher; Vuilleumier, Stéphane

    2016-06-01

    Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu(2+) to Cu(1+). In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs. PMID:26984926

  19. Diverse Arrangement of Photosynthetic Gene Clusters in Aerobic Anoxygenic Phototrophic Bacteria

    PubMed Central

    Zheng, Qiang; Zhang, Rui; Koblížek, Michal; Boldareva, Ekaterina N.; Yurkov, Vladimir; Yan, Shi; Jiao, Nianzhi

    2011-01-01

    Background Aerobic anoxygenic photototrophic (AAP) bacteria represent an important group of marine microorganisms inhabiting the euphotic zone of the ocean. They harvest light using bacteriochlorophyll (BChl) a and are thought to be important players in carbon cycling in the ocean. Methodology/Principal Findings Aerobic anoxygenic phototrophic (AAP) bacteria represent an important part of marine microbial communities. Their photosynthetic apparatus is encoded by a number of genes organized in a so-called photosynthetic gene cluster (PGC). In this study, the organization of PGCs was analyzed in ten AAP species belonging to the orders Rhodobacterales, Sphingomonadales and the NOR5/OM60 clade. Sphingomonadales contained comparatively smaller PGCs with an approximately size of 39 kb whereas the average size of PGCs in Rhodobacterales and NOR5/OM60 clade was about 45 kb. The distribution of four arrangements, based on the permutation and combination of the two conserved regions bchFNBHLM-LhaA-puhABC and crtF-bchCXYZ, does not correspond to the phylogenetic affiliation of individual AAP bacterial species. While PGCs of all analyzed species contained the same set of genes for bacteriochlorophyll synthesis and assembly of photosynthetic centers, they differed largely in the carotenoid biosynthetic genes. Spheroidenone, spirilloxanthin, and zeaxanthin biosynthetic pathways were found in each clade respectively. All of the carotenoid biosynthetic genes were found in the PGCs of Rhodobacterales, however Sphingomonadales and NOR5/OM60 strains contained some of the carotenoid biosynthetic pathway genes outside of the PGC. Conclusions/Significance Our investigations shed light on the evolution and functional implications in PGCs of marine aerobic anoxygenic phototrophs, and support the notion that AAP are a heterogenous physiological group phylogenetically scattered among Proteobacteria. PMID:21949847

  20. Enrichment of Denitrifying Methane-Oxidizing Microorganisms Using Up-Flow Continuous Reactors and Batch Cultures

    PubMed Central

    Hatamoto, Masashi; Kimura, Masafumi; Sato, Takafumi; Koizumi, Masato; Takahashi, Masanobu; Kawakami, Shuji; Araki, Nobuo; Yamaguchi, Takashi

    2014-01-01

    Denitrifying anaerobic methane oxidizing (DAMO) microorganisms were enriched from paddy field soils using continuous-flow and batch cultures fed with nitrate or nitrite as a sole electron acceptor. After several months of cultivation, the continuous-flow cultures using nitrite showed remarkable simultaneous methane oxidation and nitrite reduction and DAMO bacteria belonging to phylum NC10 were enriched. A maximum volumetric nitrite consumption rate of 70.4±3.4 mg-N·L−1·day−1 was achieved with very short hydraulic retention time of 2.1 hour. In the culture, about 68% of total microbial cells were bacteria and no archaeal cells were detected by fluorescence in situ hybridization. In the nitrate-fed continuous-flow cultures, 58% of total microbial cells were bacteria while archaeal cells accounted for 7% of total cell numbers. Phylogenetic analysis of pmoA gene sequence showed that enriched DAMO bacteria in the continuous-flow cultivation had over 98% sequence similarity to DAMO bacteria in the inoculum. In contrast, for batch culture, the enriched pmoA gene sequences had 89–91% sequence similarity to DAMO bacteria in the inoculum. These results indicate that electron acceptor and cultivation method strongly affect the microbial community structures of DAMO consortia. PMID:25545013

  1. In vitro susceptibility tests for cationic peptides: comparison of broth microdilution methods for bacteria that grow aerobically.

    PubMed

    Giacometti, A; Cirioni, O; Barchiesi, F; Del Prete, M S; Fortuna, M; Caselli, F; Scalise, G

    2000-06-01

    The in vitro susceptibilities of 90 clinical isolates of gram-positive and gram-negative aerobic bacteria to six cationic peptides, buforin II, cecropin P1, indolicidin, magainin II, nisin, and ranalexin, were evaluated by two broth microdilution methods. The first method was performed according to the procedures outlined by the National Committee for Clinical Laboratory Standards for bacteria that grow aerobically, while the second was performed according to the procedures recently proposed by the R. E. W. Hancock laboratory for testing antimicrobial peptides. Overall, the first method produced MICs two- and fourfold higher than the second method. PMID:10817731

  2. 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

  3. 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.

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

    PubMed

    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

  5. Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary.

    PubMed

    Cottrell, Matthew T; Ras, Josephine; Kirchman, David L

    2010-07-01

    Photoheterotrophic microbes use organic substrates and light energy to satisfy their demand for carbon and energy and seem to be well adapted to eutrophic estuarine and oligotrophic oceanic environments. One type of photoheterotroph, aerobic anoxygenic phototrophic (AAP) bacteria, is especially abundant in particle-rich, turbid estuaries. To explore questions regarding the controls of these photoheterotrophic bacteria, we examined their abundance by epifluorescence microscopy, concentrations of the light-harvesting pigment, bacteriochlorophyll a (BChl a) and the diversity of pufM and 16S ribosomal RNA (rRNA) genes in the Chesapeake Bay. Concentrations of BChl a varied substantially, much more so than AAP bacterial abundance, along the estuarine salinity gradient. The BChl a concentration was correlated with turbidity only when oceanic and estuarine waters were considered together. Concentrations of BChl a and BChl a quotas were higher in particle-associated than in free-living AAP bacterial communities and appear to reflect physiological adaptation, not different AAP bacterial communities; pufM genes did not differ between particle-associated and free-living communities. In contrast, particle-associated and free-living bacterial communities were significantly different, on the basis of the analysis of 16S rRNA genes. The BChl a quota of AAP bacteria was not correlated with turbidity, suggesting that pigment synthesis varies in direct response to particles, not light attenuation. The AAP bacteria seem to synthesize more BChl a when dissolved and particulate substrates are available than when only dissolved materials are accessible, which has implications for understanding the impact of substrates on the level of photoheterotrophy compared with heterotrophy in AAP bacteria. PMID:20182527

  6. Microcosm Approach to Understanding Methane-oxidizing Communities and the Role of Nitrogen Sources

    NASA Astrophysics Data System (ADS)

    Chistoserdova, L.; Hernandez, M. E.; Oshkin, I.

    2014-12-01

    We will report our observations on the dynamics of bacterial communities in response to methane and nitrate stimuli in laboratory microcosm incubations prepared with Lake Washington sediment samples. The experiments were designed to test our hypothesis of methane oxidation as a communal function, with the specific contents of the communities being determined by environmental factors such as oxygen concentration and the nature of the nitrogen source. We first measure taxonomic compositions of long-term oxygenated enrichment cultures and determine that, while dominated by Methylococcaceae bacteria, these cultures also contain accompanying types belonging to a limited number of bacterial taxa, both methylotrophs and non-methylotrophs. We then follow with the short-term community dynamics, under different oxygen tension regimens ('high' to 'low'), different nitrogen source regimens (added nitrate versus no nitrate) and different temperature ranges (10 to 30 oC). We observe rapid loss of species diversity in all incubations, but the composition of the communities depends on the specific environmental factors. Methylobacter represents the major methane-oxidizing partner in the communities incubated at low temperatures while Methylomonas and Methylocystis are more competitive at higher temperatures. All methanotrophs respond positively to nitrate. The non-methanotroph members of the communities reveal different trajectories in response to different oxygen tensions over time, with Methylotenera species persisting under 'low' and Methylophilus species persisting under 'high' oxygen tensions. Metagenomic sequencing reveals successions of different types of the major methane-oxidizing species as well as accompanying species. These types differ in their physiological details such as central carbon meand nitrate metabolism. A broad range of denitrifying capabilities in the organisms forming these stable methane-oxidizing communities is evident from genomic analysis. Our results

  7. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

    A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.

  8. Ammonium-oxidizing bacteria facilitate aerobic degradation of sulfanilic acid in activated sludge.

    PubMed

    Chen, Gang; Ginige, Maneesha P; Kaksonen, Anna H; Cheng, Ka Yu

    2014-01-01

    Sulfanilic acid (SA) is a toxic sulfonated aromatic amine commonly found in anaerobically treated azo dye contaminated effluents. Aerobic acclimatization of SA-degrading mixed microbial culture could lead to co-enrichment of ammonium-oxidizing bacteria (AOB) because of the concomitant release of ammonium from SA oxidation. To what extent the co-enriched AOB would affect SA oxidation at various ammonium concentrations was unclear. Here, a series of batch kinetic experiments were conducted to evaluate the effect of AOB on aerobic SA degradation in an acclimatized activated sludge culture capable of oxidizing SA and ammonium simultaneously. To account for the effect of AOB on SA degradation, allylthiourea was used to inhibit AOB activity in the culture. The results indicated that specific SA degradation rate of the mixed culture was negatively correlated with the initial ammonium concentration (0-93 mM, R²= 0.99). The presence of AOB accelerated SA degradation by reducing the inhibitory effect of ammonium (≥ 10 mM). The Haldane substrate inhibition model was used to correlate substrate concentration (SA and ammonium) and oxygen uptake rate. This study revealed, for the first time, that AOB could facilitate SA degradation at high concentration of ammonium (≥ 10 mM) in an enriched activated sludge culture. PMID:25259503

  9. 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.

  10. Antimicrobial Resistance and Resistance Genes in Aerobic Bacteria Isolated from Pork at Slaughter.

    PubMed

    Li, Lili; Olsen, Rikke Heidemann; Ye, Lei; Yan, He; Nie, Qing; Meng, Hecheng; Shi, Lei

    2016-04-01

    The aim of this study was to investigate the phenotypic and genotypic antimicrobial resistance, integrons, and transferability of resistance markers in 243 aerobic bacteria recovered from pork at slaughter in the People's Republic of China. The organisms belonged to 22 genera of gram-negative bacteria (92.2%) and gram-positive bacteria (7.8%). High levels of resistance were detected to tetracycline, trimethoprim-sulfamethoxazole, and ampicillin (36.2 to 54.3%), and lower levels were detected to nitrofurantoin, cefotaxime, gentamicin, ciprofloxacin, and chloramphenicol (7.8 to 29.2%). Across species, genes conferring antimicrobial resistance were observed with the following frequencies: blaTEM, 40.7%; blaCMY-2, 15.2%; blaCTX-M, 11.5%; sul2, 27.2%; sul1, 14.4%; tet(A), 5.4%; tet(L), 5.4%; tet(M), 5.0%; tet(E), 3.7%; tet(C), 3.3%; tet(S), 2.5%; and tet(K), 0.8%. Various antimicrobial resistance genes were found in new carriers: blaTEM in Lactococcus garvieae, Myroides odoratimimus, Aeromonas hydrophila, Staphylococcus sciuri, Raoultella terrigena, Macrococcus caseolyticus, Acinetobacter ursingii, Sphingobacterium sp., and Oceanobacillus sp.; blaCMY-2 in Lactococcus lactis, Klebsiella oxytoca, Serratia marcescens, Acinetobacter baumannii, and Myroides phaeus; tet(L) in M. caseolyticus; sul1 in Vibrio cincinnatiensis; sul2 in Acinetobacter bereziniae, Acinetobacter johnsonii, and V. cincinnatiensis; and the class 1 integron and gene cassette aadA2 in V. cincinnatiensis. Approximately 6.6% of isolates contained class 1 integrons, and one isolate harbored class 2 integrons. Plasmid associated intI1 and androgen receptor- encoding genes were transferred into Escherichia coli J53 and E. coli DH5α by conjugation and transformation experiments, respectively. Our study highlights the importance of aerobic bacteria from pork as reservoirs for antimicrobial resistance genes and mobile genetic elements that can readily be transferred intra- and interspecies. PMID:27052863

  11. Low-level 14C methane oxidation rate measurements modified for remote field settings

    NASA Astrophysics Data System (ADS)

    Pack, M. A.; Pohlman, J.; Ruppel, C. D.; Xu, X.

    2012-12-01

    Aerobic methane oxidation limits atmospheric methane emissions from degraded subsea permafrost and dissociated methane hydrates in high latitude oceans. Methane oxidation rate measurements are a crucial tool for investigating the efficacy of this process, but are logistically challenging when working on small research vessels in remote settings. We modified a low-level 14C-CH4 oxidation rate measurement for use in the Beaufort Sea above hydrate bearing sediments during August 2012. Application of the more common 3H-CH4 rate measurement that uses 106 times more radioactivity was not practical because the R/V Ukpik cannot accommodate a radiation van. The low-level 14C measurement does not require a radiation van, but careful isolation of the 14C-label is essential to avoid contaminating natural abundance 14C measurements. We used 14C-CH4 with a total activity of 1.1 μCi, which is far below the 100 μCi permitting level. In addition, we modified field procedures to simplify and shorten sample processing. The original low-level 14C-CH4 method requires 6 steps in the field: (1) collect water samples in glass serum bottles, (2) inject 14C-CH4 into bottles, (3) incubate for 24 hours, (4) filter to separate the methanotrophic bacterial cells from the aqueous sample, (5) kill the filtrate with sodium hydroxide (NaOH), and (6) purge with nitrogen to remove unused 14C-CH4. Onshore, the 14C-CH4 respired to carbon dioxide or incorporated into cell material by methanotrophic bacteria during incubation is quantified by accelerator mass spectrometry (AMS). We conducted an experiment to test the possibility of storing samples for purging and filtering back onshore (steps 4 and 6). We subjected a series of water samples to steps 1-3 & 5, and preserved with mercuric chloride (HgCl2) instead of NaOH because HgCl2 is less likely to break down cell material during storage. The 14C-content of the carbon dioxide in samples preserved with HgCl2 and stored for up to 2 weeks was stable

  12. 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 ...

  13. 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...

  14. 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

  15. A four-helix bundle stores copper for methane oxidation

    PubMed Central

    Vita, Nicolas; Platsaki, Semeli; Baslé, Arnaud; Allen, Stephen J.; Paterson, Neil G.; Crombie, Andrew T.; Murrell, J. Colin; Waldron, Kevin J.; Dennison, Christopher

    2015-01-01

    Methane-oxidising bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase (pMMO)1,2. Certain methanotrophs are also able to switch to using the iron-containing soluble MMO (sMMO) to catalyse methane oxidation, with this switchover regulated by copper3,4. MMOs are Nature’s primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and MMOs have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock5,6. We have discovered and characterised a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for pMMO. Csp1 is a tetramer of 4-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realised. Cytosolic homologues of Csp1 are present in diverse bacteria thus challenging the dogma that such organisms do not use copper in this location. PMID:26308900

  16. Methane oxidation over dual redox catalysts

    SciTech Connect

    Klier, K.; Herman, R.G.; Sojka, Z.; DiCosimo, J.I.; DeTavernier, S.

    1992-06-01

    Catalytic oxidation of methane to partial oxidation products, primarily formaldehyde and C[sub 2] hydrocarbons, was found to be directed by the catalyst used. In this project, it was discovered that a moderate oxidative coupling catalyst for C[sub 2] hydrocarbons, zinc oxide, is modified by addition of small amounts of Cu and Fe dopants to yield fair yields of formaldehyde. A similar effect was observed with Cu/Sn/ZnO catalysts, and the presence of a redox Lewis acid, Fe[sup III] or Sn[sup IV], was found to be essential for the selectivity switch from C[sub 2] coupling products to formaldehyde. The principle of double doping with an oxygen activator (Cu) and the redox Lewis acid (Fe, Sn) was pursued further by synthesizing and testing the CuFe-ZSM-5 zeolite catalyst. The Cu[sup II](ion exchanged) Fe[sup III](framework)-ZSM-5 also displayed activity for formaldehyde synthesis, with space time yields exceeding 100 g/h-kg catalyst. However, the selectivity was low and earlier claims in the literature of selective oxidation of methane to methanol over CuFe-ZSM-5 were not reproduced. A new active and selective catalytic system (M=Sb,Bi,Sn)/SrO/La[sub 2]O[sub 3] has been discovered for potentially commercially attractive process for the conversion of methane to C[sub 2] hydrocarbons, (ii) a new principle has been demonstrated for selectivity switching from C[sub 2] hydrocarbon products to formaldehyde in methane oxidations over Cu,Fe-doped zinc oxide and ZSM-5, and (iii) a new approach has been initiated for using ultrafine metal dispersions for low temperature activation of methane for selective conversions. Item (iii) continues being supported by AMOCO while further developments related to items (i) and (ii) are the objective of our continued effort under the METC-AMOCO proposed joint program.

  17. 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. PMID:26654073

  18. Distribution and Physiology of Aerobic Bacteria Containing Bacteriochlorophyll a on the East and West Coasts of Australia †

    PubMed Central

    Shiba, Tsuneo; Shioi, Yuzo; Takamiya, Ken-Ichiro; Sutton, David C.; Wilkinson, Clive R.

    1991-01-01

    Aerobic heterotrophic bacteria containing bacteriochlorophyll were isolated from specimens from a wide variety of marine environments on the west (Shark Bay, Lake Clifton, Lake Heyward, and Perth) and east (near Townsville and Brisbane) coasts of Australia. The bacteria were found in a high proportion (10 to 30%) of the total heterotrophic bacterial strains isolated from marine algae, seagrasses, stromatolites, the epiphytes on stromatolites, seawater, and sands; in some cases they constituted up to 49% of the total. This is much higher than the previous report of 6% from Japan. A high percentage, 13%, was also found in the seawater of Hamelin Pool, at Shark Bay, where the salinity was 66%. The number of these bacteria was generally low in seawater and sands, with a few exceptions. There were no aerobic bacteriochlorophyll-containing bacteria on sponges or corals. The isolated strains were orange or pink, and most had absorption maxima around 800 and 850 to 870 nm, the latter range being the absorption of bacteriochlorophyll a in vivo. The maximum bacteriochlorophyll content was 1 nmol/mg (dry weight) of bacterial cells. Most of the bacteria did not grow phototrophically under anaerobic conditions in a broth medium containing succinate. Cells and cell extracts grown under aerobic conditions had photochemical activities such as reversible photooxidations of the reaction center and cytochrome(s). Some strains showed denitrifying activity. The optimal salinity for bacterial growth varied between strains. PMID:16348398

  19. Plutonium Oxidation State Distribution under Aerobic and Anaerobic Subsurface Conditions for Metal-Reducing Bacteria

    NASA Astrophysics Data System (ADS)

    Reed, D. T.; Swanson, J.; Khaing, H.; Deo, R.; Rittmann, B.

    2009-12-01

    The fate and potential mobility of plutonium in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium is the near-surface contaminant of concern at several DOE sites and continues to be the contaminant of concern for the permanent disposal of nuclear waste. The mobility of plutonium is highly dependent on its redox distribution at its contamination source and along its potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. The redox distribution of plutonium in the presence of facultative metal reducing bacteria (specifically Shewanella and Geobacter species) was established in a concurrent experimental and modeling study under aerobic and anaerobic conditions. Pu(VI), although relatively soluble under oxidizing conditions at near-neutral pH, does not persist under a wide range of the oxic and anoxic conditions investigated in microbiologically active systems. Pu(V) complexes, which exhibit high chemical toxicity towards microorganisms, are relatively stable under oxic conditions but are reduced by metal reducing bacteria under anaerobic conditions. These facultative metal-reducing bacteria led to the rapid reduction of higher valent plutonium to form Pu(III/IV) species depending on nature of the starting plutonium species and chelating agents present in solution. Redox cycling of these lower oxidation states is likely a critical step in the formation of pseudo colloids that may lead to long-range subsurface transport. The CCBATCH biogeochemical model is used to explain the redox mechanisms and final speciation of the plutonium oxidation state distributions observed. These results for microbiologically active systems are interpreted in the context of their importance in defining the overall migration

  20. Survey on Atmospheric Methane Oxidation in Young Glacier-Forefield Soils

    NASA Astrophysics Data System (ADS)

    Schroth, M. H.; Nauer, P.; Zeyer, J. A.

    2010-12-01

    The capacity of soils to act as a sink for atmospheric methane has been observed in a variety of environments. Atmospheric methane oxidation is mediated by thus far uncultivated methanotrophic bacteria, commonly termed “high-affinity” methanotrophs. Despite their ubiquity, relatively little is known about their activity and abundance in pioneer ecosystems and their role in primary succession. In alpine environments, receding glaciers provide a unique opportunity to investigate soil development and establishment of microbial communities. In a field survey we assayed the forefields of several Swiss glaciers for activity and abundance of high-affinity methanotrophs. The forefields differed in exposition, altitude, local climate and specific physical and geochemical parameters. At each forefield, sampling was performed at locations without vegetation cover where glacier retreat occurred less than 20 years ago. At each location we obtained a soil-air profile and collected soil for molecular-biological and chemical analyses. In addition, we quantified soil bulk density and water content to estimate the effective gas-diffusion coefficient of methane. Using this value we quantified rate coefficients of methane oxidation by fitting a diffusion-consumption model to soil-methane concentration data. At selected locations, we applied surface gas push-pull tests (GPPTs) to independently estimate first-order rate coefficients of methane oxidation. A top-closed steel cylinder previously emplaced in the soil was employed to allow for sufficiently long reaction times during GPPTs. To further increase the GPPTs’ sensitivity at locations with low activity, we injected 13C-methane and measured the evolution of δ13C of extracted carbon dioxide. We will present results from soil-methane concentration profiles and GPPTs, which indicated little methane oxidation activity in forefields on siliceous bedrock, but generally higher activity in forefields on calcareous bedrock, as well as

  1. Field-Scale Inhibition and Recovery of Atmospheric-Methane Oxidation in Soil

    NASA Astrophysics Data System (ADS)

    Schroth, M. H.; Dax, A.; Genter, F.; Henneberger, R.

    2015-12-01

    Aerobic methane (CH4) oxidation in upland soils is the only known terrestrial sink for atmospheric CH4. It is mediated by methane-oxidizing bacteria (MOB) that possess a high-affinity form of the enzyme methane monooxygenase (MMO), allowing utilization of CH4 at near-atmospheric, low concentrations (≤ 1.9 µL/L). As cultivation attempts for high-affinity MOB have shown little success to date, there remains much speculation regarding their functioning in different environmental systems. For quantification of microbial functions at the field scale, inhibition experiments are often used as a control and to verify that observed substrate turnover is microbially mediated. Targeting MMO, several compounds have been proposed as inhibitors of CH4 oxidation. However, previous inhibition experiments were mostly conducted in systems dominated by low-affinity MOB, which mediate CH4 oxidation at elevated CH4 concentrations. On the contrary, inhibition experiments targeting high-affinity MOB are scare, particularly at the field scale. We present results of field-scale experiments to investigate effectiveness of and recovery from inhibition of atmospheric CH4 oxidation using the competitive inhibitors CH3F and CH2F2, as well as the non-competitive inhibitor C2H2. The latter is of particular interest, because C2H2 irreversibly binds to MMO, requiring de-novo synthesis of MMO for recovery of CH4 oxidation activity. Experiments were conducted during both winter and summer seasons in a sandy soil. Atmospheric CH4 oxidation was quantified in regular intervals at reference and treatment locations using the soil-profile method with concurrent measurements of soil-water contents and -temperature. Whereas C2H2 inhibition was highly effective in both seasons, the time required for recovery to the level of the reference location was much shorter during the summer experiment (~1 mo compared with 4 mo during winter). Our data provide new insights into the physiology of high-affinity MOB.

  2. Dynamics of atmospheric-methane oxidation in glacier-forefield soils

    NASA Astrophysics Data System (ADS)

    Chiri, Eleonora; Nauer, Philipp A.; Rainer, Edda-Marie; Henneberger, Ruth; Zeyer, Josef; Schroth, Martin H.

    2015-04-01

    Mature upland soils are currently considered the sole terrestrial sink for atmospheric methane (CH4). But little is known about CH4 dynamics in young, developing soil ecosystems such as glacier forefields formed by progressive glacial retreat. Glacier forefields are situated on diverse bedrock types, exhibit a continuum of soil age (chronosequence), and are comprised of various geomorphological landforms, which may differ in physicochemical properties. These features may affect activity and community structure of aerobic methane-oxidizing bacteria (MOB) catalyzing atmospheric CH4 oxidation. Moreover, MOB activity and community structure may be affected by environmental parameters subject to seasonal variability such as soil temperature, water content, and nutrient availability. The aim of this study was to assess spatial and seasonal variability in atmospheric CH4 oxidation in glacier-forefield soils derived from siliceous and calcareous bedrock. Specifically, we quantified soil-atmosphere CH4 flux and CH4 oxidation activity using the soil-gas-profile method and static flux chambers in soils of different age and belonging to different landforms. In these soils MOB abundance and variation in community structure were assessed by targeting the functional gene pmoA using quantitative PCR, TRFLP-based cluster analysis, and high-throughput DNA-sequencing technology. Seasonal variability in atmospheric CH4 oxidation was assessed based on the same attributes measured with high temporal resolution throughout one snow-free season. Most glacier-forefield soils acted as a sink for atmospheric CH4 regardless of bedrock type, and CH4 flux (-0.082 to -2.2 mg CH4 m-2 d-1) and MOB abundance (2.4×103 to 5.5×105 pmoA genecopies (g soil w.w.)-1) increased significantly with soil age. Cluster analysis revealed variations in MOB community composition related to bedrock type rather than soil age, suggesting that distinct MOB communities provided a similar ecosystem service in soils on

  3. Identifying active methane-oxidizers in thawed Arctic permafrost by proteomics

    NASA Astrophysics Data System (ADS)

    Lau, C. M.; Stackhouse, B. T.; Chourey, K.; Hettich, R. L.; Vishnivetskaya, T. A.; Pfiffner, S. M.; Layton, A. C.; Mykytczuk, N. C.; Whyte, L.; Onstott, T. C.

    2012-12-01

    characterization identified ~350 proteins, confirmed enhanced microbial activities and significant shift in community structure within the microcosms. Although the activity of Shewanella sp. was suppressed by the incubation conditions, other bacteria were activated. This was shown by at least 3-fold increase in the number of identified proteins, which were primarily players in cellular energy metabolism. Among them, Geobacter sp. and methane-oxidizers, Bradyrhizobium sp., Methylosinus sp. and Methylocystis sp. appear dominant. In order to advance the protein database for better biodiversity and functional identification, we are currently using duo extraction protocols and consolidating metagenome data obtained from the same soil samples. A depth profile (from active to permafrost layer) for methanotrophs is being determined by examining pristine cores, thawed cryosols as well as enrichment cultures. The proteome information from these samples will be presented, which will be complemented by molecular studies.

  4. Analyses of Spatial Distributions of Sulfate-Reducing Bacteria and Their Activity in Aerobic Wastewater Biofilms

    PubMed Central

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

    1999-01-01

    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 O2, H2S, NO2−, NO3−, NH4+, 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 (approximately 109 to 1010 cells per cm3 of biofilm) were evenly distributed throughout the biofilm, even in the oxic surface. The probe SRB660-stained Desulfobulbus spp. were found to be numerically important members of SRB populations (approximately 108 to 109 cells per cm3). The result of microelectrode measurements showed that a high sulfate-reducing activity was found in a narrow anaerobic zone located about 150 to 300 μm below the biofilm surface and above which an intensive sulfide oxidation zone was found. The biogeochemical measurements showed that elemental sulfur (S0) was an important intermediate of the sulfide reoxidation in such thin wastewater biofilms (approximately 1,500 μm), 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. PMID:10543829

  5. Rapid high-throughput assessment of aerobic bacteria in complex samples by fluorescence-based oxygen respirometry.

    PubMed

    O'Mahony, Fiach C; Papkovsky, Dmitri B

    2006-02-01

    A simple method has been developed for the analysis of aerobic bacteria in complex samples such as broth and food homogenates. It employs commercial phosphorescent oxygen-sensitive probes to monitor oxygen consumption of samples containing bacteria using standard microtiter plates and fluorescence plate readers. As bacteria grow in aqueous medium, at certain points they begin to deplete dissolved oxygen, which is seen as an increase in probe fluorescence above baseline signal. The time required to reach threshold signal is used to either enumerate bacteria based on a predetermined calibration or to assess the effects of various effectors on the growth of test bacteria by comparison with an untreated control. This method allows for the sensitive (down to a single cell), rapid (0.5 to 12 h) enumeration of aerobic bacteria without the need to conduct lengthy (48 to 72 h) and tedious colony counts on agar plates. It also allows for screening a wide range of chemical and environmental samples for their toxicity. These assays have been validated with different bacteria, including Escherichia coli, Micrococcus luteus, and Pseudomonas fluorescens, with the enumeration of total viable counts in broth and industrial food samples (packaged ham, chicken, and mince meat), and comparison with established agar plating and optical-density-at-600-nm assays has been given. PMID:16461677

  6. 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

  7. 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

  8. Linking methane oxidation with perchlorate reduction: a microbial base for possible Martian life

    NASA Astrophysics Data System (ADS)

    Miller, L. G.; Carlstrom, C.; Baesman, S. M.; Coates, J. D.; Oremland, R. S.

    2011-12-01

    Recent observations of methane (CH4) and perchlorate (ClO4-) within the atmosphere and surface of Mars, respectively, provide impetus for establishing a metabolic linkage between these compounds whereby CH4 acts as an electron donor and perchlorate acts as an electron acceptor. Direct linkage through anaerobic oxidation of methane (AOM) has not been observed. However, indirect syntrophic oxygenase-dependent oxidation of CH4 with an aerobic methane oxidizer is feasible. The pathway for anaerobic dissimilatory perchlorate reduction includes 3 steps. The first 2 are sequential reductions of (1) perchlorate to chlorate and (2) chlorate to chlorite, mediated by perchlorate reductase. The third step is disproportionation of chlorite to chloride and molecular oxygen, mediated by chlorite dismutase. Utilization of thusly derived oxygen by hydrocarbon-degrading organisms in anoxic environments was first demonstrated by Coates et. al. (1998)1, however the link to aerobic methane oxidation was not examined at that time. Here, we systematically explore the potential for several species of aerobic methanotrophs to couple with chlorite during dissimilatory perchlorate reduction. In one experiment, 0.5 kPa CH4 was completely removed in one day from the headspace of combined cell suspensions of Dechloromonas agitata strain CKB and Methylococcus capsulatus in the presence of 5 mM chlorite. Oxidation of labeled 14CH4 to 14CO2 under similar conditions was later confirmed. Another experiment demonstrated complete removal of 0.2 kPa CH4 over several days by Methylobacter albus strain BG8 with strain CKB in the presence of 5 mM chlorite. Finally, we observed complete removal of 0.2 kPa CH4 in bottles containing natural soil (enriched in methanotrophs by CH4 additions over several weeks) and strain CKB and in the presence of 10 mM chlorite. This soil, collected from a pristine lake shoreline, demonstrated endogenous methane, perchlorate, chlorate and chlorite uptake. Other soil and

  9. Kinetics of methane oxidation in selected mineral soils

    NASA Astrophysics Data System (ADS)

    Walkiewicz, A.; Bulak, P.; Brzeziñska, M.; Włodarczyk, T.; Polakowski, C.

    2012-10-01

    The kinetic parameters of methane oxidation in three mineral soils were measured under laboratory conditions. Incubationswere preceded by a 24-day preincubationwith 10%vol. of methane. All soils showed potential to the consumption of added methane. None of the soils, however, consumed atmospheric CH4. Methane oxidation followed the Michaelis-Menten kinetics, with relatively low values of parameters for Eutric Cambisol, while high values for Haplic Podzol, and especially for Mollic Gleysol which showed the highest methanotrophic activity and much lower affinity to methane. The high values of parameters for methane oxidation are typical for organic soils and mineral soils from landfill cover. The possibility of the involvement of nitrifying microorganisms, which inhabit the ammonia-fertilized agricultural soils should be verified.

  10. Scrutinizing compost properties and their impact on methane oxidation efficiency.

    PubMed

    Huber-Humer, Marion; Tintner, Johannes; Böhm, Katharina; Lechner, Peter

    2011-05-01

    Methane emissions from active or closed landfills can be reduced by means of microbial methane oxidation enhanced by properly designed landfill covers and engineered biocovers. Composts produced using different waste materials have already been proven to support methane oxidation, and may represent a low-cost alternative to other suitable substrates such as sandy or humic-rich soils, which are frequently not available in sufficient amounts or are too costly. In the present study a data set of 30 different compost materials (different age and input materials) and mixtures, as well as seven soils and mineral substrates were tested to assess methane oxidation rate under similar conditions in a laboratory column set-up. Multivariate data analysis (discriminant analysis) was applied to predict the influence of 21 different parameters (chemical, maturation and physical) on methane oxidation rate in a PLS-DA model. The results show that bulk density, total nutrient content (nitrogen and phosphorus), as well as the quantity and quality (with respect to maturity) of organic matter determined methane oxidation rate in this data set. The model explained 50% of the data variation, indicating how characterisation of oxidation rate by single, even diverse conventional parameters was limited. Thus for the first time, Fourier Transform Infrared (FTIR) spectroscopy was applied to a series of samples to better determine the characteristics of methane-oxidising materials. The initial data obtained in this study appear to be most promising. The prediction of specific methane oxidation rate of a potential biocover material from FTIR spectra and multivariate data analyses is a target to be focused on in the future. PMID:21036026

  11. Organic Osmolytes in Aerobic Bacteria from Mono Lake, an Alkaline, Moderately Hypersaline Environment

    PubMed Central

    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. PMID:16535487

  12. Cultivation of aerobic chemoorganotrophic proteobacteria and gram-positive bacteria from a hot spring microbial mat.

    PubMed Central

    Nold, S C; Kopczynski, E D; Ward, D M

    1996-01-01

    The diversity of aerobic chemoorganotrophic bacteria inhabiting the Octopus Spring cyanobacterial mat community (Yellowstone National Park) was examined by using serial-dilution enrichment culture and a variety of enrichment conditions to cultivate the numerically significant microbial populations. The most abundant bacterial populations cultivated from dilutions to extinction were obtained from enrichment flasks which contained 9.0 x 10(2) primary producer (Synechococcus spp.) cells in the inoculum. Two isolates exhibited 16S rRNA nucleotide sequences typical of beta-proteobacteria. One of these isolates contained a 16S rRNA sequence identical to a sequence type previously observed in the mat by molecular retrieval techniques. Both are distantly related to a new sequence directly retrieved from the mat and contributed by a beta-proteobacterial community member. Phenotypically diverse gram-positive isolates genetically similar to Bacillus flavothermus were obtained from a variety of dilutions and enrichment types. These isolates exhibited identical 16S rRNA nucleotide sequences through a variable region of the molecule. Of the three unique sequences observed, only one had been previously retrieved from the mat, illustrating both the inability of the cultivation methods to describe the composition of a microbial community and the limitations of the ability of molecular retrieval techniques to describe populations which may be less abundant in microbial communities. PMID:8899976

  13. Production of wax esters during aerobic growth of marine bacteria on isoprenoid compounds

    PubMed

    Rontani; Bonin; Volkman

    1999-01-01

    This paper describes the production of isoprenoid wax esters during the aerobic degradation of 6,10,14-trimethylpentadecan-2-one and phytol by four bacteria (Acinetobacter sp. strain PHY9, Pseudomonas nautica [IP85/617], Marinobacter sp. strain CAB [DSMZ 11874], and Marinobacter hydrocarbonoclasticus [ATCC 49840]) isolated from the marine environment. Different pathways are proposed to explain the formation of these compounds. In the case of 6,10, 14-trimethylpentadecan-2-one, these esters result from the condensation of some acidic and alcoholic metabolites produced during the biodegradation, while phytol constitutes the alcohol moiety of most of the esters produced during growth on this isoprenoid alcohol. The amount of these esters formed increased considerably in N-limited cultures, in which the ammonium concentration corresponds to conditions often found in marine sediments. This suggests that the bacterial formation of isoprenoid wax esters might be favored in such environments. Although conflicting evidence exists regarding the stability of these esters in sediments, it seems likely that, under some conditions, bacterial esterification can enhance the preservation potential of labile compounds such as phytol. PMID:9872783

  14. 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. PMID:26601890

  15. Halotolerant aerobic heterotrophic bacteria from the Great Salt Plains of Oklahoma.

    PubMed

    Caton, T M; Witte, L R; Ngyuen, H D; Buchheim, J A; Buchheim, M A; Schneegurt, M A

    2004-11-01

    The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus. PMID:15696379

  16. News from the "blowout", a man-made methane pockmark in the North Sea: chemosynthetic communities and microbial methane oxidation

    NASA Astrophysics Data System (ADS)

    Steinle, Lea I.; Wilfert, Philipp; Schmidt, Mark; Bryant, Lee; Haeckel, Matthias; Lehmann, Moritz F.; Linke, Peter; Sommer, Stefan; Treude, Tina; Niemann, Helge

    2013-04-01

    The accidental penetration of a base-Quaternary shallow gas pocket by a drilling rig in 1990 caused a "blowout" in the British sector of the North Sea (57°55.29' N, 01°37.86' E). Large quantities of methane have been seeping out of this man-made pockmark ever since. As the onset of gas seepage is well constrained, this site can be used as a natural laboratory to gain information on the development of methane oxidizing microbial communities at cold seeps. During an expedition with the R/V Celtic Explorer in July and August 2012, we collected sediments by video-guided push-coring with an ROV (Kiel 6000) along a gradient from inside the crater (close to where a jet of methane bubbles enters the water column) outwards. We also sampled the water column in a grid above the blowout at three different depths. In this presentation, we provide evidence for the establishment of methanotrophic communities in the sediment (AOM communities) on a time scale of decades. Furthermore, we will report data on methane concentrations and anaerobic methane oxidation rates in the sediment. Finally, we will also discuss the spatial distribution of methane and aerobic methane oxidation rates in the water column.

  17. 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

    2013-09-01

    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

  18. Spatial variability of soil gas concentration and methane oxidation capacity in landfill covers.

    PubMed

    Röwer, Inga Ute; Geck, Christoph; Gebert, Julia; Pfeiffer, Eva-Maria

    2011-05-01

    In order to devise design criteria for biocovers intended to enhance the microbial oxidation of landfill methane it is critical to understand the factors influencing gas migration and methane oxidation in landfill cover soils. On an old municipal solid waste landfill in north-western Germany soil gas concentrations (10, 40, 90 cm depth), topsoil methane oxidation capacity and soil properties were surveyed at 40 locations along a 16 m grid. As soil properties determine gas flow patterns it was hypothesized that the variability in soil gas composition and the subsequent methanotrophic activity would correspond to the variability of soil properties. Methanotrophic activity was found to be subject to high spatial variability, with values ranging between 0.17 and 9.80 g CH(4)m(-2)h(-1)(.) Considering the current gas production rate of 0.03 g CH(4)m(-2)h(-1), the oxidation capacity at all sampled locations clearly exceeded the flux to the cover, and can be regarded as an effective instrument for mitigating methane fluxes. The methane concentration in the cover showed a high spatial heterogeneity with values between 0.01 and 0.32 vol.% (10 cm depth), 22.52 vol.% (40 cm), and 36.85 vol.% (90 cm). The exposure to methane raised the oxidation capacity, suggested by a statistical correlation to an increase in methane concentration at 90 cm depth. Methane oxidation capacity was further affected by the methanotroph bacteria pH optimum and nutrient availability, and increased with decreasing pH towards neutrality, and increased with soluble ion concentration). Soil methane and carbon dioxide concentration increased with lower flow resistance of the cover, as represented by the soil properties of a reduced bulk density, increase in air capacity and in relative ground level. PMID:20943363

  19. Termites Facilitate Methane Oxidation and Shape the Methanotrophic Community

    PubMed Central

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

    2013-01-01

    Termite-derived methane contributes 3 to 4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (methanotrophs). However, a considerable fraction of the methane produced can be consumed by methanotrophs that inhabit the mound material, yet the methanotroph ecology in these environments is virtually unknown. The potential for methane oxidation was determined using slurry incubations under conditions with high (12%) and in situ (∼0.004%) methane concentrations through a vertical profile of a termite (Macrotermes falciger) mound and a reference soil. Interestingly, the mound material showed higher methanotrophic activity. The methanotroph community structure was determined by means of a pmoA-based diagnostic microarray. Although the methanotrophs in the mound were derived from populations in the reference soil, it appears that termite activity selected for a distinct community. Applying an indicator species analysis revealed that putative atmospheric methane oxidizers (high-indicator-value probes specific for the JR3 cluster) were indicative of the active nest area, whereas methanotrophs belonging to both type I and type II were indicative of the reference soil. We conclude that termites modify their environment, resulting in higher methane oxidation and selecting and/or enriching for a distinct methanotroph population. PMID:24038691

  20. Drug resistance and molecular epidemiology of aerobic bacteria isolated from puerperal infections in Bangladesh.

    PubMed

    Ahmed, Salma; Kawaguchiya, Mitsuyo; Ghosh, Souvik; Paul, Shyamal Kumar; Urushibara, Noriko; Mahmud, Chand; Nahar, Kamrun; Hossain, Mohammad Akram; Kobayashi, Nobumichi

    2015-06-01

    Puerperal infection is a common complication during postnatal period in developing countries. Bacterial species, drug resistance, and genetic characteristics were investigated for a total of 470 isolates from puerperal infections in Bangladesh for a 2-year period (2010-2012). The most common species was Escherichia coli (n=98), followed by Enterococcus faecalis (n=54), Staphylococcus haemolyticus (n=33), Proteus mirabilis (n=32), Staphylococcus aureus (n=27), Klebsiella pneumoniae (n=22), and Enterobacter cloacae (n=21). S. aureus and Acinetobacter baumannii were isolated at a higher frequency from wound infections after cesarean section, while E. coli, E. cloacae, and K. pneumoniae were isolated from community-acquired endometritis and urinary tract infections. Resistance to third-generation cephalosporins was frequent for Enterobacteriacae, and was mainly mediated by blaCTX-M-1 group beta-lactamases. The CTX-M gene in E. coli from the four phylogroups was identified as blaCTX-M-15, and phylogroup B2 isolates with blaCTX-M-15 were classified into ST131 with O25b allele, harboring aac(6')-Ib-cr and various virulence factors. Carbapenemase genes blaNDM-1 and blaNDM-7 were identified in one isolate each of phylogroup A E. coli. Methicillin-resistant S. aureus isolates had type IV or V SCCmec, including isolates of ST361 (CC672), which is related to an emerging ST672 clone in the Indian subcontinent. This study revealed the recent epidemiological status of aerobic bacteria causing puerperal infections in Bangladesh, providing useful information to improve clinical practice and infection control. PMID:25555043

  1. Functional Relationship Between Phytoplankton and Aerobic Anoxygenic Photosynthetic Bacteria: Modes of Coexistence

    NASA Astrophysics Data System (ADS)

    Kolber, Z. S.; Haffa, A.; Klimov, D.

    2006-12-01

    Aerobic Anoxygenic Photosynthetic Bacteria (AAPs) are ubiquitously distributed in the upper ocean. Although they contain bacteriochlorophyll a (BChla), the main absorption bands in the near UV (370 nm) and infrared (800-850 nm) make this pigment impractical in light harvesting below the first few meters of the water column. Instead, they utilize carotenoids as major light harvesting pigments. Since these carotenoids absorb in the 430-550 nm range, phytoplankton and AAPs utilize a similar portion of the available light spectrum. As AAPs cannot utilize water as the electron donor, they transfer electrons between a range of organic/inorganic electron donors and electron acceptors, thus significantly participating in the redox cycle in the upper ocean. We have measured the vertical distribution and photosynthetic properties of both phytoplankton and AAPs in a highly oligotrophic region 800 km SW of Monterey Bay (34N, 129W), and we have consistently observed the presence of a BChla maximum about 30 to 40 meters above the chlorophyll maximum, indicating that phytoplankton and AAPs occupy different ecological niches in the water column. However, the abundance of AAPs generally displayed a maximum at dawn and a minimum at the dusk, indicating a high level of mortality. This diel cycle was observed in 5 micron and 3 micron size fractions, indicating active grazing by small protists. Incubation experiments with natural, mixed population of AAPs and phytoplankton results in an unusually high accumulation of AAPs in DCMU-treated samples, indicating that pigmented protists do contribute significantly to AAP grazing in a tightly-controlled microbial loop. On the other hand, AAP incubations in pure cultures indicate that they biomineralize sulfur, thus affecting the sulfur cycle. All of these observations indicate that the role of AAPs in the upper ocean ecology is defined by their relationship with phototrophic and heterotrophic communities, rather than by their relative

  2. [Antimicrobial susceptibility of clinical isolates of aerobic Gram-positive cocci and anaerobic bacteria in 2006].

    PubMed

    Yamaguchi, Takahiro; Yoshida, Isamu; Itoh, Yoshihisa; Tachibana, Mineji; Takahashi, Choichiro; Kaku, Mitsuo; Kanemitsu, Keiji; Okada, Masahiko; Horikawa, Yoshinori; Shiotani, Joji; Kino, Hiroyoshi; Ono, Yuka; Baba, Hisashi; Matsuo, Shuji; Asari, Seishi; Toyokawa, Masahiro; Matsuoka, Kimiko; Kusano, Nobuchika; Nose, Motoko; Murase, Mitsuharu; Miyamoto, Hitoshi; Saikawa, Tetsunori; Hiramatsu, Kazufumi; Kohno, Shigeru; Yanagihara, Katsunori; Yamane, Nobuhisa; Nakasone, Isamu; Maki, Hideki; Yamano, Yoshinori

    2010-12-01

    The activity of antibacterial agents against aerobic Gram-positive cocci (26 species, 1022 strains) and anaerobic bacteria (23 species, 184 strains) isolated from clinical specimens in 2006 at 16 clinical facilities in Japan were studied using either broth microdilution or agar dilution method. The ratio of methicillin-resistant strains among Staphylococcus aureus and Staphylococcus epidermidis was 53.0% and 65.8%, suggesting that resistant strains were isolated at high frequency. Vancomycin (VCM) and quinupristin/dalfopristin (QPR/DPR) had good antibacterial activity against methicillin-resistant S. aureus and methicillin-resistant S. epidermidis, with MIC90s of < or = 2 micrcog/mL. The ratio of penicillin (PC) intermediate and resistant strains classified by mutations of PC-binding proteins among Streptococcus pneumoniae was 87.6%. Ceftriaxone, cefpirome, cefepime, carbapenem antibiotics, VCM, teicoplanin, linezolid(LZD) and QPR/DPR had MIC90s of < or = 1 microg/mL against PC-intermediate and resistant S. pneumoniae strains. Against all strains of Enterococcus faecalis and Enterococcus faecium, the MICs of VCM and TEIC were under 2 microg/mL, and no resistant strain was detected, suggesting that these agents had excellent activities against these species. 10.9% of E. faecalis strains or 3.5% of E. faecium strains showed intermediate or resistant to LZD. 24.4% of E. faecium strains showed intermediate or resistant to QPR/DPR. Against all strains of Clostridium difficile, the MIC of VCM were under 1 microg/mL, suggesting that VCM had excellent activity against C. difficile. Carbapenems showed good activity against Peptococcaceae, Bacteroides spp., and Prevotella spp. However since several strains of Bacteroides fragilis showed resistant to carbapenems and the susceptibility of this species should be well-focused in the future. PMID:21425596

  3. [Antimicrobial susceptibility of clinical isolates of aerobic gram-positive cocci and anaerobic bacteria in 2008].

    PubMed

    Yoshida, Isamu; Yamaguchi, Takahiro; Kudo, Reiko; Fuji, Rieko; Takahashi, Choichiro; Oota, Reiko; Kaku, Mitsuo; Kunishima, Hiroyuki; Okada, Masahiko; Horikawa, Yoshinori; Shiotani, Joji; Kino, Hiroyoshi; Ono, Yuka; Fujita, Shinichi; Matsuo, Shuji; Kono, Hisashi; Asari, Seishi; Toyokawa, Masahiro; Kusano, Nobuchika; Nose, Motoko; Horii, Toshinobu; Tanimoto, Ayako; Miyamoto, Hitoshi; Saikawa, Tetsunori; Hiramatsu, Kazufumi; Kohno, Shigeru; Yanagihara, Katsunori; Yamane, Nobuhisa; Nakasone, Isamu; Maki, Hideki; Yamano, Yoshinori

    2012-02-01

    The activity of antibacterial agents against aerobic Gram-positive cocci (25 genus or species, 1029 strains) and anaerobic bacteria (21 genus or species, 187 strains) isolated from clinical specimens in 2008 at 16 clinical facilities in Japan were studied using either broth microdilution or agar dilution method. The ratio of methicillin-resistant strains among Staphylococcus aureus and Staphylococcus epidermidis was 59.6% and 81.2%, suggesting that resistant strains were isolated at high frequency. Vancomycin (VCM), linezolid (LZD) and quinupristin/dalfopristin (QPR/DPR) had good antibacterial activity against methicillin-resistant S. aureus and methicillin-resistant S. epidermidis, with MIC90s of < or = 2 microg/mL. The ratio of penicillin (PC) intermediate and resistant strains classified by mutations of PC-binding proteins among Streptococcus pneumoniae was 92.0% that was highest among our previous reports. Cefpirome, carbapenems, VCM, teicoplanin (TEIC), LZD and QPR/DPR had MIC90s of < or = 1 microg/mL against PC-intermediate and resistant S. pneumoniae strains. Against all strains of Enterococcus faecalis and Enterococcus faecium, the MICs of VCM and TEIC were under 2 microg/mL, and no resistant strain was detected, suggesting that these agents had excellent activities against these species. 15.9% of E. faecalis strains and 1.2% of E. faecium strains showed intermediate to LZD. 17.1% of E. faecium strains showed intermediate or resistant to QPR/DPR. Against all strains of Clostridium difficile, the MIC of VCM was under 1 microg/mL, suggesting that VCM had excellent activity. Carbapenems showed good activity against Clostridiales, Bacteroides spp., and Prevotella spp., but one strain of Bacteroides fragilis showed resistant to carbapenems. And so, the susceptibility of this species should be well-focused in the future at detecting continuously. PMID:22808693

  4. Biodiversity and characterization of aerobic spore-forming bacteria in surimi seafood products.

    PubMed

    Coton, M; Denis, C; Cadot, P; Coton, E

    2011-04-01

    The microbial quality and safety of surimi seafood products was assessed by studying the prevalence and biodiversity of aerobic spore-forming bacteria at the beginning and end of shelf life in 100 surimi samples. Low levels of total flora and sporulated flora were numerated at the beginning of storage, however, residual spores were detected in the majority of samples during storage. Furthermore, for 34 samples, total flora counts>10(4) CFU/g were observed at the end of shelf life which could lead to non-compliance with good practice recommendations or product spoilage. In total, 460 strains were isolated, fingerprinted by M13-PCR and grouped into 98 different clusters. Representative strains were then identified at the species level via 16S rRNA gene sequencing. Overall, dominant species belonged to Bacillus simplex, Bacillus subtilis and Bacillus licheniformis; while B. simplex, B. subtilis as well as Sporosarcina aquimarina were clearly the dominant species found in samples with higher total flora counts. Amylolytic and proteolytic activities were very frequent amongst tested strains (80 and 92.5%, respectively). Heat resistance parameters of 4 strains in a surimi-based medium were determined. B. simplex and B. subtilis strains were the most heat resistant (δ(96 °C)= 27.6 and 23.3 min and z(T)=8.6 and 7.9, respectively) which can explain their dominance in surimi samples exhibiting higher microbial counts. The heat resistance data obtained can now be used to model thermal destruction of strains using predictive microbiology tools (Sym'Previus). PMID:21315981

  5. 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. PMID:26314017

  6. 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. PMID:25974213

  7. Anaerobic methane oxidation coupled to nitrite reduction can be a potential methane sink in coastal environments.

    PubMed

    Shen, Li-Dong; Hu, Bao-Lan; Liu, Shuai; Chai, Xiao-Ping; He, Zhan-Fei; Ren, Hong-Xing; Liu, Yan; Geng, Sha; Wang, Wei; Tang, Jing-Liang; Wang, Yi-Ming; Lou, Li-Ping; Xu, Xiang-Yang; Zheng, Ping

    2016-08-01

    In the current study, we investigated nitrite-dependent anaerobic methane oxidation (N-DAMO) as a potential methane sink in the Hangzhou Bay and the adjacent Zhoushan sea area. The potential activity of the N-DAMO process was primarily observed in Hangzhou Bay by means of (13)C-labeling experiments, whereas very low or no potential N-DAMO activity could be detected in the Zhoushan sea area. The measured potential N-DAMO rates ranged from 0.2 to 1.3 nmol (13)CO2 g(-1) (dry sediment) day(-1), and the N-DAMO potentially contributed 2.0-9.4 % to the total microbial methane oxidation in the examined sediments. This indicated that the N-DAMO process may be an alternative pathway in the coastal methane cycle. Phylogenetic analyses confirmed the presence of Candidatus Methylomirabilis oxyfera-like bacteria in all the examined sediments, while the group A members (the dominant bacteria responsible for N-DAMO) were found mainly in Hangzhou Bay. Quantitative PCR showed that the 16S rRNA gene abundance of Candidatus M. oxyfera-like bacteria varied from 5.4 × 10(6) to 5.0 × 10(7) copies g(-1) (dry sediment), with a higher abundance observed in Hangzhou Bay. In addition, the overlying water NO3 (-) concentration and salinity were identified as the most important factors influencing the abundance and potential activity of Candidatus M. oxyfera-like bacteria in the examined sediments. This study showed the evidence of N-DAMO in coastal environments and indicated the importance of N-DAMO as a potential methane sink in coastal environments. PMID:27225473

  8. Experimental evaluation of the metabolic reversibility of ANME-2d between anaerobic methane oxidation and methanogenesis.

    PubMed

    Ding, Jing; Fu, Liang; Ding, Zhao-Wei; Lu, Yong-Ze; Cheng, Shuk H; Zeng, Raymond J

    2016-07-01

    The "reverse methanogenesis" hypothesis as the metabolic pathway of AOM has recently been supported in the novel ANME lineage ANME-2d in denitrifying anaerobic methane oxidation (DAMO). However, no previous studies have experimentally evaluated the reversal of methane oxidation and methane production in this archaea. In the present study, the metabolic reversibility of ANME-2d from AOM to methanogenesis was evaluated using H2/CO2 and acetate as substrates. The results showed that the system produced methane from H2/CO2 but not from acetate. However, the clone library and real-time PCR analysis of the culture showed that both the percentage and quantity of ANME-2d decreased significantly under this condition, while methanogen abundance increased. Further high-throughput sequencing results showed that the archaea community did not change at the fourth day after H2/CO2 was supplied, but changed profoundly after methanogenesis took place for 3 days. The percentage of DAMO archaea in the total archaea decreased obviously, while more methanogens grew up during this period. Comparatively, the bacteria community changed profoundly at the fourth day. These results indicated that ANME-2d might not reverse its metabolism to produce methane from H2/CO2 or acetate. After archaea were returned to DAMO conditions, DAMO activity decreased and the amount of ANME-2d continued to fall, implying that the lineage had suffered from severe injury and required a long recovery time. PMID:27026178

  9. [Surface layers of methanotrophic bacteria].

    PubMed

    Khmelenina, V N; Suzina, N E; Trotsenko, Iu A

    2013-01-01

    Structural and functional characteristics of the regular glycoprotein layers in prokaryotes are analyzed with a special emphasis on aerobic methanotrophic bacteria. S-layers are present at the surfaces of Methylococcus, Methylothermus, and Methylomicrobium cells. Different Methylomicrobium species either synthesize S-layers with planar (p2, p4) symmetry or form cup-shaped or conicalstructures with hexagonal (p6) symmetry. A unique, copper-binding polypeptide 'CorA'/MopE (27/45 kDa), which is coexpressed with the diheme periplasmic cytochrome c peroxidase 'CorB'/Mca (80 kDa) was found in Methylomicrobium album BG8, Methylomicrobium alcaliphilum 20Z, and Methylococcus capsulatus Bath. This tandem of the surface proteins is functionally analogous to a new siderophore, methanobactin. Importantly, no 'CorA'/MopE homologue was found in methanotrophs not forming S-layers. The role of surface proteins in copper metabolism and initial methane oxidation is discussed. PMID:25509389

  10. 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...

  11. Global Change Simulations Affect Potential Methane Oxidation in Upland Soils

    NASA Astrophysics Data System (ADS)

    Blankinship, J. C.; Hungate, B. A.

    2004-12-01

    Atmospheric concentrations of methane (CH4) are higher now than they have ever been during the past 420,000 years. However, concentrations have remained stable since 1999. Emissions associated with livestock husbandry are unlikely to have changed, so some combination of reduced production in wetlands, more efficient capture by landfills, or increased consumption by biological CH4 oxidation in upland soils may be responsible. Methane oxidizing bacteria are ubiquitous in upland soils and little is known about how these bacteria respond to anthropogenic global change, and how they will influence - or already are influencing - the radiative balance of the atmosphere. Might ongoing and future global changes increase biological CH4 oxidation? Soils were sampled from two field experiments to assess changes in rates of CH4 oxidation in response to global change simulations. Potential activities of CH4 oxidizing bacterial communities were measured through laboratory incubations under optimal temperature, soil moisture, and atmospheric CH4 concentrations (~18 ppm, or 10x ambient). The ongoing 6-year multifactorial Jasper Ridge Global Change Experiment (JRGCE) simulates warming, elevated precipitation, elevated atmospheric CO2, elevated atmospheric N deposition, and increased wildfire frequency in an annual grassland in a Mediterranean-type climate in central California. The ongoing 1-year multifactorial Merriam Climate Change Experiment (MCCE) simulates warming, elevated precipitation, and reduced precipitation in four different types of ecosystems along an elevational gradient in a semi-arid climate in northern Arizona. The high desert grassland, pinyon-juniper woodland, ponderosa pine forest, and mixed conifer forest ecosystems range in annual precipitation from 100 to 1000 mm yr-1, and from productivity being strongly water limited to strongly temperature limited. Among JRGCE soils, elevated atmospheric CO2 increased potential CH4 oxidation rates (p=0.052) and wildfire

  12. The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy.

    PubMed

    House, Christopher H; Beal, Emily J; Orphan, Victoria J

    2011-01-01

    On Earth, marine anaerobic methane oxidation (AOM) can be driven by the microbial reduction of sulfate, iron, and manganese. Here, we have further characterized marine sediment incubations to determine if the mineral dependent methane oxidation involves similar microorganisms to those found for sulfate-dependent methane oxidation. Through FISH and FISH-SIMS analyses using 13C and 15N labeled substrates, we find that the most active cells during manganese dependent AOM are primarily mixed and mixed-cluster aggregates of archaea and bacteria. Overall, our control experiment using sulfate showed two active bacterial clusters, two active shell aggregates, one active mixed aggregate, and an active archaeal sarcina, the last of which appeared to take up methane in the absence of a closely-associated bacterial partner. A single example of a shell aggregate appeared to be active in the manganese incubation, along with three mixed aggregates and an archaeal sarcina. These results suggest that the microorganisms (e.g., ANME-2) found active in the manganese-dependent incubations are likely capable of sulfate-dependent AOM. Similar metabolic flexibility for Martian methanotrophs would mean that the same microbial groups could inhabit a diverse set of Martian mineralogical crustal environments. The recently discovered seasonal Martian plumes of methane outgassing could be coupled to the reduction of abundant surface sulfates and extensive metal oxides, providing a feasible metabolism for present and past Mars. In an optimistic scenario Martian methanotrophy consumes much of the periodic methane released supporting on the order of 10,000 microbial cells per cm2 of Martian surface. Alternatively, most of the methane released each year could be oxidized through an abiotic process requiring biological methane oxidation to be more limited. If under this scenario, 1% of this methane flux were oxidized by biology in surface soils or in subsurface aquifers (prior to release), a total

  13. Application of potential phosphate-solubilizing bacteria and organic acids on phosphate solubilization from phosphate rock in aerobic rice.

    PubMed

    Panhwar, Qurban Ali; 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. 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

  15. 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

  16. 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

  17. 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...

  18. 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

  19. Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils.

    PubMed

    Yang, Yuyin; Shan, Jingwen; Zhang, Jingxu; Zhang, Xiaoling; Xie, Shuguang; Liu, Yong

    2014-12-01

    Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment

  20. 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

  1. Rhizosphere activity and methane oxidation in a temperate forest soil

    NASA Astrophysics Data System (ADS)

    Moody, Catherine S.; Subke, Jens-Arne; Voke, Naomi R.; Holden, Robert D.; Ineson, Phil; Arn Teh, Yit

    2010-05-01

    Methane (CH4) concentrations in the Earth's atmosphere have increased dramatically over recent decades. An abundance of studies indicate that the magnitude of natural methane efflux from wetlands is likely to increase due to climate change. However, the role of vegetation and soils in upland methane oxidation are less well understood. Well-aerated soils are known to be sites of methane oxidation, and amongst a range of abiotic environmental parameters, soil moisture has been identified as critical regulator of the methane oxidation rates. However, the role of microbial activity within the soil, particularly C turnover in the plant rhizosphere, has not been investigated as a means for regulating methanotrophy. We combined a continuous soil CO2 efflux system (Li-Cor Biosciences, LI-8100) with a Cavity-Ringdown-Spectroscopy Fast Greenhouse Gas Analyser (Los Gatos Research Inc.) to measure soil CH4 oxidation in a pine forest in NE England. The soil has a shallow organic layer overlaying a well-draining sandy gley soil. Fluxes were measured from three different collar treatments: (1) excluding both root and ectomycorrhizal (EM) hyphae by trenching using deep collars, (2) excluding roots but allowing access by EM hyphae, and (3) unmodified forest soil (i.e. including both roots and EM hyphae). All collars were protected from natural throughfall, and received weekly-averaged amounts of throughfall based on collections in the stand. Data from two months in early summer 2009 indicate that CH4 oxidation in collars with an intact rhizosphere is more than twice that of either of the exclusion treatments (averaging approx. 90 g ha-1 d-1 in that period). We observed higher fluxes when soils were dryer (i.e. with increasing time since watering), indicating a significant influence of moisture. Despite the confounding effects of soil moisture associated with root water uptake in the unmodified soil collars, we argue that rhizosphere activity is an overlooked component in

  2. Isolation of culturable aerobic bacteria and evidence of Kerstersia gyiorum from the blowhole of captive Yangtze finless porpoises.

    PubMed

    Wan, Xiaoling; McLaughlin, Richard William; Zhou, Junying; Hao, Yujiang; Zheng, Jinsong; Wang, Ding

    2016-08-01

    Bacterial respiratory illnesses are problematic in aquatic mammals such as the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP), which is now at a critically endangered status. Yet little is known about the bacteria inhabiting the respiratory tract of YFPs. In this study, we preliminarily characterized the culturable aerobic bacteria from blow samples of captive YFPs. The bacterial diversity was assessed through cultivation by direct exhalation onto Columbia blood agar plates and identification of representative isolates through 16S rRNA gene sequence analysis. In total, eleven bacterial species belonging to four phyla Proteobacteria (71 %), Firmicutes (25 %), Bacteroidetes (3 %) and Actinobacteria (1 %) were identified. Most of these isolates were opportunistic pathogens found in respiratory illnesses in humans and animals. We also reported the first case of Kerstersia gyiorum isolated from an animal. This work provides a preliminary assessment of the bacteria present in the respiratory tract of captive YFPs, which will be an important first step in elucidating the roles of normal microbiota in maintaining respiratory health of YFPs. This study also points out the necessity of future long-term monitoring of blowhole microorganisms in the YFPs and making emergency preparedness plans for respiratory tract infections. These measures can aid in assessing the pathogenic risk of the critically endangered YFP populations. PMID:27251558

  3. Effects of maturity stage and lactic acid bacteria on the fermentation quality and aerobic stability of Siberian wildrye silage.

    PubMed

    Li, Ping; Bai, Shiqie; You, Minghong; Shen, Yixin

    2016-09-01

    It is difficult to make good quality of silage from alpine gramineous from the Qinghai Tibetan plateau. The effects of lactic acid bacteria (LAB) on the fermentation quality and aerobic stability of Siberian wildrye silage were studied in southeast of the Qinghai Tibetan plateau. Siberian wildrye materials were freshly cut at the sprouting stage, flowering stage, and milky stage. Silage was prepared by using a small-scale silage fermentation system (bag silos). Lactobacillus plantarum (LP, 5 × 10(8) cfu/kg FM), Lactobacillus buchneri (LB, 5 × 10(8) cfu/kg FM) and their mixture (LP+LB, 5 × 10(8) cfu/kg FM) as silage additives were separately added to ensiled forages, and no additive served as control (CK). These bag silos were kept at room temperature (<15°C), and the silage qualities were analyzed after 60 days of ensiling. The number of indigenous LAB on fresh materials was less than that of yeasts and molds, and LAB species showed specification adapted to low temperature. LAB inoculated silages had lower (P < 0.05) pH value, NH 3-N/TN and butyric acid content compared with control silage. Silage treated with LB had higher contents of acetic acid, propionic acid, WSC and CP. However, the aerobic stability of silages inoculated with LAB did not differ significantly between stages (P > 0.05). When fermentation characteristics, chemical composition, and aerobic stability were considered, treatment with L. plantarum resulted in high quality of Siberian wildrye silage harvested at the flowering stage in the alpine region. PMID:27625768

  4. Recalcitrance of 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE) to cometabolic degradation by pure cultures of aerobic and anaerobic bacteria.

    PubMed

    Megharaj, M; Jovcic, A; Boul, H L; Thiele, J H

    1997-08-01

    Pure cultures of aerobic and anaerobic bacteria capable of oxidation and reductive dehalogenation of chloroethylenes, and aerobic bacteria involved in biodegradation of polychlorinated biphenyls (PCBs) were screened for their ability to cometabolize the persistent pollutant 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE). Bacterial cultures expressing methane monooxygenase (Methylosinus trichosporium), propane monooxygenase (Mycobacterium vaccae) and biphenyl 2,3-dioxygenase enzymes (Pseudomonas fluorescens and Rhodococcus globerulus), as well as bacteria reductively dechlorinating chloroethylenes (Acetobacterium woodii and Clostridium butyricum) could not degrade DDE. Cell-free extracts of M. trichosporium, M. vaccae, P. fluorescens and R. globerulus were also unable to transform DDE, indicating that cell wall and membrane diffusion barriers were not biodegradation limiting. These studies suggest that these bacteria can not degrade DDE, even when provided with cosubstrates that induce chlorophenyl- and dichloroethylene-group transforming enzymes. PMID:9294241

  5. 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

  6. Isolation and Identification of Aerobic Bacteria Carrying Tetracycline and Sulfonamide Resistance Genes Obtained from a Meat Processing Plant.

    PubMed

    Li, Lili; Ye, Lei; Zhang, Sen; Meng, Hecheng

    2016-06-01

    Microbial contamination in food-processing plants can play a fundamental role in food quality and safety. The purpose of this study was to investigate aerobic bacteria carrying tetracycline and sulfonamide resistance genes from a meat processing plant as possible sources of meat contamination. One hundred swab samples from surfaces of conveyor belts, meat slicers, meat knives, benches, plastic trays, gloves, and aprons were analyzed. A total of 168 isolates belonging to 10 genera were obtained, including Pseudomonas sp. (n = 35), Acinetobacter sp. (n = 30), Aeromonas sp. (n = 20), Myroides sp. (n = 15), Serratia sp. (n = 15), Staphylococcus sp. (n = 14), Enterobacter sp. (n = 11), Escherichia coli (n = 10), Lactococcus sp. (n = 10), and Klebsiella sp. (n = 8). Of the 168 isolates investigated, 60.7% showed resistance to tetracycline and 57.7% to trimethoprim/sulfamethoxazole. The tetracycline resistance genes tetL, tetA, tetB, tetC, tetE, tetM, tetS, tetK, and tetX were found in the frequency of 7.7%, 6.0%, 4.8%, 4.8%, 3.6%, 3.6%, 3.6%, 1.2%, and 0.6%, respectively. Sulfonamide resistance genes sul1 and sul2 were observed in the frequency of 17.9% and 38.1%, respectively. The tetracycline resistance genes tetX was first found in Myroides sp. This investigation demonstrated that food contact surfaces in a meat processing plant may be sources of contamination of aerobic bacteria carrying tetracycline and sulfonamide antibiotic resistance genes. PMID:27100915

  7. Abundance, depth distribution, and composition of aerobic bacteriochlorophyll a-producing bacteria in four basins of the central Baltic Sea.

    PubMed

    Salka, Ivette; Moulisová, Vladimíra; Koblízek, Michal; Jost, Günter; Jürgens, Klaus; Labrenz, Matthias

    2008-07-01

    The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 x 10(5) cells ml(-1) (11% of total prokaryotes) or 1.0 x 10(3) CFU ml(-1) (9 to 10% of total CFU). Environmental pufM clone sequences were grouped into 11 operational taxonomic units phylogenetically related to cultivated members of the Alpha-, Beta-, and Gammaproteobacteria. In spite of varying pufM compositions, five clones were present in all libraries. Of these, Jannaschia-related clones were always found in relative abundances representing 25 to 30% of the total AAP clones. The abundances of the other clones varied. Clones potentially affiliated with typical freshwater Betaproteobacteria sequences were present at three Baltic Sea stations, whereas clones grouping with Loktanella represented 40% of the total cell numbers in the Gotland Basin. For three alphaproteobacterial clones, probable pufM phylogenetic relationships were supported by 16S rRNA gene analyses of Baltic AAP isolates, which showed nearly identical pufM sequences. Our data indicate that the studied AAP assemblages represented a mixture of marine and freshwater taxa, thus characterizing the Baltic Sea as a "melting pot" of abundant, polyphyletic aerobic photoheterotrophic bacteria. PMID:18502937

  8. 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

  9. Occurrence and activity of sulphate reducing bacteria in aerobic activated sludge systems.

    PubMed

    van den Brand, T P H; Roest, K; Chen, G H; Brdjanovic, D; van Loosdrecht, M C M

    2015-03-01

    In the sewage or wastewater treatment plant, biological sulphate reduction can occur spontaneously or be applied beneficially for its treatment. The results of this study can be applied to control SRB in the sewage and WWTP. Therefore, population diversity analyses of SRB for nine activated sludge wastewater treatment plants (WWTP) in the Netherlands and the effect of long-term (months) oxygen exposures on the SRB activity were carried out. T-RFLP and clone sequencing analyses of winter and summer samples revealed that (1) all WWTP have a similar SRB population, (2) there is no seasonal impact (10-20 °C) on the SRB population present in the WWTP and (3) Desulfobacter postgatei, Desulfovibrio desulfuricans and Desulfovibrio intestinalis were the most common and dominant SRB species observed in these samples, and origin from the sewage. Short term activity tests demonstrated that SRB were not active in the aerobic WWTP, but while flushed with N2-gas SRB became slightly active after 3 h. In a laboratory reactor at a dissolved oxygen concentration of <2 %, sulphate reduction occurred and 89 % COD removal was achieved. SRB grew in granules, in order to protect themselves for oxygen exposures. SRB are naturally present in aerobic WWTP, which is due to the formation of granules. PMID:25649202

  10. 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

  11. 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.

  12. 40 CFR Table Hh-4 to Subpart Hh of... - Landfill Methane Oxidation Fractions

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Landfill Methane Oxidation Fractions.... 98, Subpt. HH, Table HH-4 Table HH-4 to Subpart HH of Part 98—Landfill Methane Oxidation Fractions... soil prior to any oxidation and is calculated as follows: ER29NO13.024 Where: MF = Methane flux...

  13. Microbial Methane Oxidation Processes and Technologies for Mitigation of Landfill Gas Emissions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The aim of this paper is to review the present knowledge regarding the microbial methane oxidation in natural or engineered landfill environments with focus on process understanding, engineering experiences and modeling. This review includes seven sections. First, the methane oxidation is put in con...

  14. 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

  15. Microbiology, ecology, and application of the nitrite-dependent anaerobic methane oxidation process

    PubMed Central

    Shen, Li-Dong; He, Zhan-Fei; Zhu, Qun; Chen, Dong-Qing; Lou, Li-Ping; Xu, Xiang-Yang; Zheng, Ping; Hu, Bao-Lan

    2012-01-01

    Nitrite-dependent anaerobic methane oxidation (n-damo), which couples the anaerobic oxidation of methane to denitrification, is a recently discovered process mediated by “Candidatus Methylomirabilis oxyfera.” M. oxyfera is affiliated with the “NC10” phylum, a phylum having no members in pure culture. Based on the isotopic labeling experiments, it is hypothesized that M. oxyfera has an unusual intra-aerobic pathway for the production of oxygen via the dismutation of nitric oxide into dinitrogen gas and oxygen. In addition, the bacterial species has a unique ultrastructure that is distinct from that of other previously described microorganisms. M. oxyfera-like sequences have been recovered from different natural habitats, suggesting that the n-damo process potentially contributes to global carbon and nitrogen cycles. The n-damo process is a process that can reduce the greenhouse effect, as methane is more effective in heat-trapping than carbon dioxide. The n-damo process, which uses methane instead of organic matter to drive denitrification, is also an economical nitrogen removal process because methane is a relatively inexpensive electron donor. This mini-review summarizes the peculiar microbiology of M. oxyfera and discusses the potential ecological importance and engineering application of the n-damo process. PMID:22905032

  16. Plant pathogenic anaerobic bacteria use aromatic polyketides to access aerobic territory.

    PubMed

    Shabuer, Gulimila; Ishida, Keishi; Pidot, Sacha J; Roth, Martin; Dahse, Hans-Martin; Hertweck, Christian

    2015-11-01

    Around 25% of vegetable food is lost worldwide because of infectious plant diseases, including microbe-induced decay of harvested crops. In wet seasons and under humid storage conditions, potato tubers are readily infected and decomposed by anaerobic bacteria (Clostridium puniceum). We found that these anaerobic plant pathogens harbor a gene locus (type II polyketide synthase) to produce unusual polyketide metabolites (clostrubins) with dual functions. The clostrubins, which act as antibiotics against other microbial plant pathogens, enable the anaerobic bacteria to survive an oxygen-rich plant environment. PMID:26542569

  17. Isolation and characterization of poly(3-hydroxybutyrate)-producing bacteria from aerobic sludge.

    PubMed

    Zheng, Bingxin; Lu, Jianjiang; Tong, Yanbin; Li, Hongling; Chen, Qianqian

    2015-01-01

    Polyhydroxyalkanoates (PHAs) are biodegradable and environmentally friendly natural polymers. In this study, we isolated a bacterium strain capable of synthesizing PHAs from the aerobic sludge of a sewage treatment plant. The bacterium was identified as Burkholderia cepacia via physiological and biochemical tests as well as 16S rDNA sequence analysis. Strain WN-H41 produced PHAs, which was identified as P3HB. These PHAs have a number average molecular weight of 2.6 × 10(4) Da, a polydispersity index (PDI) of 2.4, and its thermal properties include a glass transition temperature of 1 °C, a melting temperature of 171 °C, and a decomposition temperature of 280 °C. These properties indicate that P3HB produced by WN-H41 has a high purity and good thermal stability. PMID:25304488

  18. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes

    PubMed Central

    Fauteux, Lisa; Cottrell, Matthew T.; Kirchman, David L.; Borrego, Carles M.; Garcia-Chaves, Maria Carolina; del Giorgio, Paul A.

    2015-01-01

    There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex. PMID:25927833

  19. 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. PMID:25494579

  20. 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. PMID:23805543

  1. Does vegetation affect the methane oxidation efficiency of passive biosystems?

    PubMed

    Ndanga, Éliane M; Bradley, Robert L; Cabral, Alexandre R

    2015-04-01

    It is often reported in the technical literature that the presence of vegetation improves the methane oxidation efficiency of biosystems; however, the phenomena involved and biosystem performance results are still poorly documented, particularly in the field. This triggered a study to assess the importance of vegetation in methane oxidation efficiency (MOE). In this study, 4 large scale columns, each filled with sand, topsoil and a mixture of compost and topsoil were tested under controlled conditions in the laboratory and partially controlled conditions in the field. Four series of laboratory tests and two series of field tests were performed. 4 different plant covers were tested for each series: Trifolium repens L. (White clover), Phleum pratense L. (Timothy grass), a mixture of both, and bare soil as the control biosystem. The study results indicated that up to a loading equal to 100 g CH4/m(2)/d, the type of plant cover did not influence the oxidation rates, and the MOE was quite high (⩾ 95%) in all columns. Beyond this point, the oxidation rate continued to increase, reaching 253 and 179 g CH4/m(2)/d in laboratory and field tests respectively. In the end, the bare soil achieved as high or higher MOEs than vegetated biosystems. Despite the fact that the findings of this study cannot be generalized to other types of biosystems and plants and that the vegetation types tested were not fully grown, it was shown that for the short-term tests performed and the types of substrates and plants used herein, vegetation does not seem to be a key factor for enhancing biosystem performance. This key conclusion does not corroborate the conclusion of the relatively few studies published in the technical literature assessing the importance of vegetation in MOE. PMID:25690413

  2. 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. PMID:12675610

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

    PubMed

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

    2016-04-01

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

  4. Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota.

    PubMed

    Kozlowski, Jessica A; Stieglmeier, Michaela; Schleper, Christa; Klotz, Martin G; Stein, Lisa Y

    2016-08-01

    Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76(T) exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196(T). In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions. PMID:26882267

  5. Population Changes in Enteric Bacteria and Other Microorganisms During Aerobic Thermophilic Windrow Composting1

    PubMed Central

    Savage, Jacob; Chase, Theodore; Macmillan, James D.

    1973-01-01

    Composting of wastes from swine feeding operations was studied. The effects of the frequency of turning the wastes and addition of straw to improve the physical structure were studied to determine the most effective technique to rapidly increase the temperature and, consequently, destroy coliforms and Salmonella. Four different treatments were studied; the results showed that, with addition of 5% (wt/wt) straw and mechanical turning of the compost 20 times per week, the temperature reached 60 C within 3 days and enteric bacteria were destroyed within 14 days. Images PMID:4203338

  6. Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

    PubMed Central

    Liu, Dongyan; Tago, Kanako; Hayatsu, Masahito; Tokida, Takeshi; Sakai, Hidemitsu; Nakamura, Hirofumi; Usui, Yasuhiro; Hasegawa, Toshihiro; Asakawa, Susumu

    2016-01-01

    Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions. PMID:27600710

  7. Site variation in methane oxidation as affected by atmospheric deposition and type of temperate forest ecosystem

    NASA Astrophysics Data System (ADS)

    Brumme, Rainer; Borken, Werner

    1999-06-01

    Factors controlling methane oxidation were analyzed along a soil acidity gradient (pH(H2O) 3.9 to 5.2) under beech and spruce forests in Germany. Mean annual methane oxidation ranged from 0.1 to 2.5 kg CH4 ha-1 yr-1 and was correlated with base saturation (r2 = 0.88), soil pH (r2 = 0.77), total nitrogen (r2 = 0.71), amount of the organic surface horizon (r2 = 0.49) and bulk density of the mineral soil (r2 = 0.43). At lower pHs the formation of an organic surface horizon was promoted. This horizon did not have any methane oxidation capacity and acted like a gas diffusion barrier, which decreased the methane oxidation capacity of the soil. In contrast, on sites at the higher end of the pH range, higher burrowing activity of earthworms increased macroporosity and thereby gas diffusivity and methane oxidation. Gas diffusivity was also affected by litter shape: broad beech leaves reduced methane oxidation more than spruce needles. An increase in methane oxidation of most soil samples following sieving indicates that diffusion is the main limiting factor for methane oxidation. However, this "sieving effect" was less in soils with a pH below 5 than in soils with a pH above 5, which we attribute to a direct effect of soil acidity. We discuss our results using a hierarchical concept for the "short-term" and "long-term" controls on methane oxidation in forest ecosystems.

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-12-01

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

  10. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils.

    PubMed

    Woo, Hannah L; Hazen, Terry C; Simmons, Blake A; DeAngelis, Kristen M

    2014-02-01

    Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal-Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts. PMID:24238986

  11. Formation of Polyhydroxyalkanoate in Aerobic Anoxygenic Phototrophic Bacteria and Its Relationship to Carbon Source and Light Availability▿

    PubMed Central

    Xiao, Na; Jiao, Nianzhi

    2011-01-01

    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 12T, Labrenzia alexandrii DFL 11T, 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 1H 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. PMID:21908634

  12. Microbiologically influenced corrosion of 304 stainless steel by aerobic Pseudomonas NCIMB 2021 bacteria: AFM and XPS study.

    PubMed

    Yuan, S J; Pehkonen, S O

    2007-09-01

    Microbiologically influenced corrosion (MIC) of stainless steel 304 by a marine aerobic Pseudomonas bacterium in a seawater-based medium was investigated by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). AFM was used to observe in situ the proliferation of a sessile Pseudomonas cell by binary fission. The development of a biofilm on the coupon surface and the extent of corrosion damage beneath the biofilm after various exposure times were also characterized by AFM. Results showed that the biofilm formed on the coupon surface increased in thickness and heterogeneity with time, and thus resulting in the occurrence of extensive micro-pitting corrosion; whilst the depth of pits increased linearly with time. The XPS results confirmed that the colonization of Pseudomonas bacteria on the coupon surface induced subtle changes in the alloy elemental composition in the outermost layer of surface films. The most significant feature resulting from microbial colonization on the coupon surface was the depletion of iron (Fe) and the enrichment of chromium (Cr) content as compared to a control coupon exposed to the sterile medium, and the enrichment of Cr increased with time. These compositional changes in the main alloying elements may be correlated with the occurrence of extensive micropitting corrosion on the surface. PMID:17582747

  13. 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. PMID:26449556

  14. 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. PMID:26347735

  15. 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

  16. 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

  17. Alleviation of toxic hexavalent chromium using indigenous aerobic bacteria isolated from contaminated tannery industry sites.

    PubMed

    Pandey, Siddhartha; Singh, Nitin Kumar; Bansal, Ankur Kumar; Arutchelvan, V; Sarkar, Sudipta

    2016-07-01

    In the last decade, much attention has been paid to bioremediation of Cr(VI) using various bacterial species. Cr(VI) remediation by indegeneous bacteria isolated from contaminated sites of a tannery industry located in Tamil Nadu, India, was investigated in this study. Three Cr(VI) resistant bacterial strains (TES-1, TEf-1, and TES-2) were isolated and selected based on their Cr(VI) reduction ability in minimal salt medium. Among these three bacterial strains, TES-1 was found to be most efficient in bioreduction, while TES-2 was only found to be Cr(VI) resistant and showed negligible bioreduction, whereas TEf-1 was observed to be most Cr(VI) tolerant. Potential for bioremediation of TES-1 and TEf-1 was further investigated at different concentrations of Cr(VI) in the range of 50 to 350 mg L(-1). TEf-1 showed prominent synchronous growth throughout the experiment, whereas TES-1 took a longer acclimatization time. Minimum inhibitory concentrations (MIC) of Cr(VI) for TES-1 and TEf-1 were approximated as 600 mg L(-1) and 750 mg L(-1), respectively. The kinetic behavior of Cr(VI) reduction by TES-1 and TEf-1 exhibited zero- and first-order removal kinetics for Cr(VI), respectively. The most efficient strain TES-1 was identified as Streptomyces sp. by gene sequencing of 16S rRNA. PMID:26458110

  18. A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically.

    PubMed

    Koeth, Laura M; DiFranco-Fisher, Jeanna M; McCurdy, Sandra

    2015-01-01

    Antimicrobial susceptibility testing (AST) is performed to assess the in vitro activity of antimicrobial agents against various bacteria. The AST results, which are expressed as minimum inhibitory concentrations (MICs) are used in research for antimicrobial development and monitoring of resistance development and in the clinical setting for antimicrobial therapy guidance. Dalbavancin is a semi-synthetic lipoglycopeptide antimicrobial agent that was approved in May 2014 by the Food and Drug Administration (FDA) for the treatment of acute bacterial skin and skin structure infections caused by Gram-positive organisms. The advantage of dalbavancin over current anti-staphylococcal therapies is its long half-life, which allows for once-weekly dosing. Dalbavancin has activity against Staphylococcus aureus (including both methicillin-susceptible S. aureus [MSSA] and methicillin-resistant S. aureus [MRSA]), coagulase-negative staphylococci, Streptococcus pneumoniae, Streptococcus anginosus group, β-hemolytic streptococci and vancomycin susceptible enterococci. Similar to other recent lipoglycopeptide agents, optimization of CLSI and ISO broth susceptibility test methods includes the use of dimethyl sulfoxide (DMSO) as a solvent when preparing stock solutions and polysorbate 80 (P80) to alleviate adherence of the agent to plastic. Prior to the clinical studies and during the initial development of dalbavancin, susceptibility studies were not performed with the use of P-80 and MIC results tended to be 2-4 fold higher and similarly higher MIC results were obtained with the agar dilution susceptibility method. Dalbavancin was first included in CLSI broth microdilution methodology tables in 2005 and amended in 2006 to clarify use of DMSO and P-80. The broth microdilution (BMD) procedure shown here is specific to dalbavancin and is in accordance with the CLSI and ISO methods, with step-by-step detail and focus on the critical steps added for clarity. PMID:26381422

  19. Spatial Patterns of Iron- and Methane-Oxidizing Bacterial Communities in an Irregularly Flooded, Riparian Wetland

    PubMed Central

    Wang, Juanjuan; Krause, Sascha; Muyzer, Gerard; Meima-Franke, Marion; Laanbroek, Hendrikus J.; Bodelier, Paul L. E.

    2012-01-01

    Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circumneutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR–DGGE and qPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidizers (Ga-FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Ga-FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of Ga-FeOB was assessed using PCR–DGGE and the abundance of both Ga-FeOB and MOB by qPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of Ga-FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Ga-FeOB outnumbered the MOB subgroups suggesting their competitiveness or the prevalence of Fe2+ over CH4 oxidation in this floodplain. PMID:22375139

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

    PubMed

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

    2010-01-01

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

  1. Inhibition of methane oxidation by Methylococcus capsulatus with hydrochlorofluorocarbons and fluorinated methanes

    SciTech Connect

    Matheson, L.J.; Oremland, R.S.; Jahnke, L.L.

    1997-07-01

    Concerns about stratospheric ozone and global warming have focused some inquiries upon the microbial degradation of some atmospheric halocarbons. Little is known about the interaction of hydrochlorofluorocarbons (HCFCs) and hydrofluorocarbons (HFCs). This study examines possible interactions, including the inhibition of methane oxidation by chlorinated solvents, whether oxidation products formed may have inhibitory effects of their own, and whether other fluorinated methanes inhibit methane oxidation by whole cells. 33 refs., 4 figs., 1 tab.

  2. Kinetically driven instabilities and selectivities in methane oxidation

    SciTech Connect

    Park, Y.K.; Vlachos, D.G.

    1997-08-01

    Ignitions, extinctions, and Hopf bifurcations in methane oxidation were studied as a function of pressure and inlet fuel composition. A continuous stirred-tank reactor was modeled with numerical bifurcation techniques, using the 177 reaction/31 species mechanism. Sensitivity and reaction pathway analyses were performed at turning points to identify the most important reactions and reactive species. Then, simulations were compared with experimental data. Multiple ignitions and extinctions as well as oscillations that are purely kinetically driven were found. Ignition to a partially ignited state with considerable reactivity of methane indicates possible narrow operation windows with high selectivities to partial oxidation products. At 0.1 atm, the authors found a selectivity of up to 80% to CO at 70% CH{sub 4} conversion. The ignition to a fully ignited branch is associated with high selectivity to CO{sub 2} and H{sub 2}O. The C2 chemistry inhibits the ignition of methane to the partially ignited branch. The methane ignition temperature exhibits two branches with respect to pressure, with only the low-pressure branch being dominant. Reaction path analysis at ignition conditions shows that the preferred pathway of CH{sub 4} oxidation is to form CO and CO{sub 2} though CH{sub 2}O and CH{sub 2}(s) intermediates. However, at intermediate to high pressures, the recombination of CH{sub 3} to C{sub 2}H{sub 6} also becomes quite significant.

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

  4. Effect of biomass concentration on methane oxidation activity using mature compost and graphite granules as substrata.

    PubMed

    Xie, S; O'Dwyer, T; Freguia, S; Pikaar, I; Clarke, W P

    2016-10-01

    Reported methane oxidation activity (MOA) varies widely for common landfill cover materials. Variation is expected due to differences in surface area, the composition of the substratum and culturing conditions. MOA per methanotrophic cell has been calculated in the study of natural systems such as lake sediments to examine the inherent conditions for methanotrophic activity. In this study, biomass normalised MOA (i.e., MOA per methanotophic cell) was measured on stabilised compost, a commonly used cover in landfills, and on graphite granules, an inert substratum widely used in microbial electrosynthesis studies. After initially enriching methanotrophs on both substrata, biomass normalised MOA was quantified under excess oxygen and limiting methane conditions in 160ml serum vials on both substrata and blends of the substrata. Biomass concentration was measured using the bicinchoninic acid assay for microbial protein. The biomass normalised MOA was consistent across all compost-to-graphite granules blends, but varied with time, reflecting the growth phase of the microorganisms. The biomass normalised MOA ranged from 0.069±0.006μmol CH4/mg dry biomass/h during active growth, to 0.024±0.001μmol CH4/mg dry biomass/h for established biofilms regardless of the substrata employed, indicating the substrata were equally effective in terms of inherent composition. The correlation of MOA with biomass is consistent with studies on methanotrophic activity in natural systems, but biomass normalised MOA varies by over 5 orders of magnitude between studies. This is partially due to different methods being used to quantify biomass, such as pmoA gene quantification and the culture dependent Most Probable Number method, but also indicates that long term exposure of materials to a supply of methane in an aerobic environment, as can occur in natural systems, leads to the enrichment and adaptation of types suitable for those conditions. PMID:27515185

  5. 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

  6. 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

    2016-04-15

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

  7. Laboratory evaluation of a two-stage treatment system for TCE cometabolism by a methane-oxidizing mixed culture

    SciTech Connect

    Smith, L.H.; McCarty, P.L.

    1997-08-20

    The objective of this research was to evaluate several factors affecting the performance of a two-stage treatment system employing methane-oxidizing bacteria for trichloroethylene (TCE) biodegradation. The system consists of a completely mixed growth reactor and a plug-flow transformation reactor in which the TCE is cometabolized. Laboratory studies were conducted with continuous growth reactors and batch experiments simulating transformation reactor conditions. Performance was characterized in terms of TCE transformation capacity (T{sub C}, g TCE/g cells), transformation yield (T{sub Y}, g TCE/g CH{sub 4}), and the rate coefficient ratio k{sub TCE}/K{sub S,TCE} (L/mg-d). The growth reactor variables studied were solids retention time (SRT) and nutrient nitrogen (N) concentration. Formate and methane were evaluated as potential transformation reactor amendments.

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

    SciTech Connect

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

    1994-12-31

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

  9. The role of paraffin oil on the interaction between denitrifying anaerobic methane oxidation and Anammox processes.

    PubMed

    Fu, Liang; Ding, Zhao-Wei; Ding, Jing; Zhang, Fang; Zeng, Raymond J

    2015-10-01

    Methane is sparingly soluble in water, resulting in a slow reaction rate in the denitrifying anaerobic methane oxidation (DAMO) process. The slow rate limits the feasibility of research to examine the interaction between the DAMO and the anaerobic ammonium oxidation (Anammox) process. In this study, optimized 5 % (v/v) paraffin oil was added as a second liquid phase to improve methane solubility in a reactor containing DAMO and Anammox microbes. After just addition, methane solubility was found to increase by 25 % and DAMO activity was enhanced. After a 100-day cultivation, the paraffin reactor showed almost two times higher consumption rates of NO3 (-) (0.2268 mmol/day) and NH4 (+) (0.1403 mmol/day), compared to the control reactor without paraffin oil. The microbes tended to distribute in the oil-water interface. The quantitative (q) PCR result showed the abundance of gene copies of DAMO archaea, DAMO bacteria, and Anammox bacteria in the paraffin reactor were higher than those in the control reactor after 1 month. Fluorescence in situ hybridization revealed that the percentages of the three microbes were 55.5 and 77.6 % in the control and paraffin reactors after 100 days, respectively. A simple model of mass balance was developed to describe the interactions between DAMO and Anammox microbes and validate the activity results. A mechanism was proposed to describe the possible way that paraffin oil enhanced DAMO activity. It is quite clear that paraffin oil enhances not only DAMO activity but also Anammox activity via the interaction between them; both NO3 (-) and NH4 (+) consumption rates were about two times those of the control. PMID:26036704

  10. Nitrate reduction by denitrifying anaerobic methane oxidizing microorganisms can reach a practically useful rate.

    PubMed

    Cai, Chen; Hu, Shihu; Guo, Jianhua; Shi, Ying; Xie, Guo-Jun; Yuan, Zhiguo

    2015-12-15

    Methane in biogas has been proposed to be an electron donor to facilitate complete nitrogen removal using denitrifying anaerobic methane oxidizing (DAMO) microorganisms in an anaerobic ammonium oxidation (anammox) reactor, by reducing the nitrate produced. However, the slow growth and the low activity of DAMO microorganisms cast a serious doubt about the practical usefulness of such a process. In this study, a previously established lab-scale membrane biofilm reactor (MBfR), with biofilms consisting of a coculture of DAMO and anammox microorganisms, was operated to answer if the DAMO reactor can achieve a nitrate reduction rate that can potentially be applied for wastewater treatment. Through progressively increasing nitrate and ammonium loading rates to the reactor, a nitrate removal rate of 684 ± 10 mg-N L(-1) d(-1) was achieved after 453 days of operation. This rate is, to our knowledge, by far the highest reported for DAMO reactors, and far exceeds what is predicted to be required for nitrate removal in a sidestream (5.6-135 mg-N L(-1) d(-1)) or mainstream anammox reactor (3.2-124 mg-N L(-1) d(-1)). Mass balance analysis showed that the nitrite produced by nitrate reduction was jointly reduced by anammox bacteria at a rate of 354 ± 3 mg-N L(-1) d(-1), accompanied by an ammonium removal rate of 268 ± 2 mg-N L(-1) d(-1), and DAMO bacteria at a rate of 330 ± 9 mg-N L(-1) d(-1). This study shows that the nitrate reduction rate achieved by the DAMO process can be high enough for removing nitrate produced by anammox process, which would enable complete nitrogen removal from wastewater. PMID:26414889

  11. Methane oxidation over dual redox catalysts. Final report

    SciTech Connect

    Klier, K.; Herman, R.G.; Sojka, Z.; DiCosimo, J.I.; DeTavernier, S.

    1992-06-01

    Catalytic oxidation of methane to partial oxidation products, primarily formaldehyde and C{sub 2} hydrocarbons, was found to be directed by the catalyst used. In this project, it was discovered that a moderate oxidative coupling catalyst for C{sub 2} hydrocarbons, zinc oxide, is modified by addition of small amounts of Cu and Fe dopants to yield fair yields of formaldehyde. A similar effect was observed with Cu/Sn/ZnO catalysts, and the presence of a redox Lewis acid, Fe{sup III} or Sn{sup IV}, was found to be essential for the selectivity switch from C{sub 2} coupling products to formaldehyde. The principle of double doping with an oxygen activator (Cu) and the redox Lewis acid (Fe, Sn) was pursued further by synthesizing and testing the CuFe-ZSM-5 zeolite catalyst. The Cu{sup II}(ion exchanged) Fe{sup III}(framework)-ZSM-5 also displayed activity for formaldehyde synthesis, with space time yields exceeding 100 g/h-kg catalyst. However, the selectivity was low and earlier claims in the literature of selective oxidation of methane to methanol over CuFe-ZSM-5 were not reproduced. A new active and selective catalytic system (M=Sb,Bi,Sn)/SrO/La{sub 2}O{sub 3} has been discovered for potentially commercially attractive process for the conversion of methane to C{sub 2} hydrocarbons, (ii) a new principle has been demonstrated for selectivity switching from C{sub 2} hydrocarbon products to formaldehyde in methane oxidations over Cu,Fe-doped zinc oxide and ZSM-5, and (iii) a new approach has been initiated for using ultrafine metal dispersions for low temperature activation of methane for selective conversions. Item (iii) continues being supported by AMOCO while further developments related to items (i) and (ii) are the objective of our continued effort under the METC-AMOCO proposed joint program.

  12. Rapid Methane Oxidation in a Landfill Cover Soil †

    PubMed Central

    Whalen, S. C.; Reeburgh, W. S.; Sandbeck, K. A.

    1990-01-01

    Methane oxidation rates observed in a topsoil covering a retired landfill are the highest reported (45 g m−2 day−1) for any environment. This microbial community had the capacity to rapidly oxidize CH4 at concentrations ranging from <1 ppm (microliters per liter) (first-order rate constant [k] = −0.54 h−1) to >104 ppm (k = −2.37 h−1). The physiological characteristics of a methanotroph isolated from the soil (characteristics determined in aqueous medium) and the natural population, however, were similar to those of other natural populations and cultures: the Q10 and optimum temperature were 1.9 and 31°C, respectively, the apparent half-saturation constant was 2.5 to 9.3 μM, and 19 to 69% of oxidized CH4 was assimilated into biomass. The CH4 oxidation rate of this soil under waterlogged (41% [wt/vol] H2O) conditions, 6.1 mg liter−1 day−1, was near rates reported for lake sediment and much lower than the rate of 116 mg liter−1 day−1 in the same soil under moist (11% H2O) conditions. Since there are no large physiological differences between this microbial community and other CH4 oxidizers, we attribute the high CH4 oxidation rate in moist soil to enhanced CH4 transport to the microorganisms; gas-phase molecular diffusion is 104-fold faster than aqueous diffusion. These high CH4 oxidation rates in moist soil have implications that are important in global climate change. Soil CH4 oxidation could become a negative feedback to atmospheric CH4 increases (and warming) in areas that are presently waterlogged but are projected to undergo a reduction in summer soil moisture. PMID:16348346

  13. 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. PMID:19415973

  14. A fully coupled model for water-gas-heat reactive transport with methane oxidation in landfill covers.

    PubMed

    Ng, C W W; Feng, S; Liu, H W

    2015-03-01

    Methane oxidation in landfill covers is a complex process involving water, gas and heat transfer as well as microbial oxidation. The coupled phenomena of microbial oxidation, water, gas, and heat transfer are not fully understood. In this study, a new model is developed that incorporates water-gas-heat coupled reactive transport in unsaturated soil with methane oxidation. Effects of microbial oxidation-generated water and heat are included. The model is calibrated using published data from a laboratory soil column test. Moreover, a series of parametric studies are carried out to investigate the influence of microbial oxidation-generated water and heat, initial water content on methane oxidation efficiency. Computed and measured results of gas concentration and methane oxidation rate are consistent. It is found that the coupling effects between water-gas-heat transfer and methane oxidation are significant. Ignoring microbial oxidation-generated water and heat can result in a significant difference in methane oxidation efficiency by 100%. PMID:25489976

  15. Co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in subtropical acidic forest soils.

    PubMed

    Meng, Han; Wang, Yong-Feng; Chan, Ho-Wang; Wu, Ruo-Nan; Gu, Ji-Dong

    2016-09-01

    Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two new processes of recent discoveries linking the microbial nitrogen and carbon cycles. In this study, 16S ribosomal RNA (rRNA) gene of anammox bacteria and pmoA gene of n-damo bacteria were used to investigate their distribution and diversity in natural acidic and re-vegetated forest soils. The 16S rRNA gene sequences retrieved featured at least three species in two genera known anammox bacteria, namely Candidatus Brocadia anammoxidans, Candidatus Brocadia fulgida, and Candidatus Kuenenia stuttgartiensis while the pmoA gene amplified was affiliated with two species of known n-damo bacteria Candidatus Methylomirabilis oxyfera and a newly established Candidatus Methylomirabilis sp. According to the results, the diversity of anammox bacteria in natural forests was lower than in re-vegetated forests, but no significant difference was observed in n-damo community between them. Quantitative real-time PCR showed that both anammox and n-damo bacteria were more abundant in the lower layer (10-20 cm) than the surface layer (0-5 cm). The abundance of anammox bacteria varied from 2.21 × 10(5) to 3.90 × 10(6) gene copies per gram dry soil, and n-damo bacteria quantities were between 1.69 × 10(5) and 5.07 × 10(6) gene copies per gram dry soil in the two different layers. Both anammox and n-damo bacteria are reported for the first time to co-occur in acidic forest soil in this study, providing a more comprehensive information on more defined microbial processes contributing to C and N cycles in the ecosystems. PMID:27178181

  16. Segregation of biomass in cyclic anaerobic/aerobic granular sludge allows the enrichment of anaerobic ammonium oxidizing bacteria at low temperatures.

    PubMed

    Winkler, Mari K H; Kleerebezem, Robbert; Kuenen, J Gijs; Yang, Jingjing; van Loosdrecht, Mark C M

    2011-09-01

    A cyclic anaerobic/aerobic bubble column reactor was run for 420 days to study the competition for nitrite between nitrite oxidizing bacteria (NOB) and anaerobic ammonium oxidizing bacteria (Anammox) at low temperatures. An anaerobic feeding period with nitrite and ammonium in the influent followed by an aerated period was applied resulting in a biomass specific conversion rate of 0.18 ± 0.02 [gN(2) - N · gVSS(-1)· day(-1)] when the dissolved oxygen concentration was maintained at 1.0 mgO(2) · L(-1). An increase in white granules was observed in the reactor which were mainly located at the top of the settled sludge bed, whereas red granules were located at the bottom. FISH, activity tests, and qPCR techniques revealed that red biomass was dominated by Anammox bacteria and white granules by NOB. Granules from the top of the sludge bed were smaller and therefore had a higher aerobic volume fraction, a lower density, and consequently a slower settling rate. Sludge was manually removed from the top of the settled sludge bed to selectively remove NOB which resulted in an increased overall biomass specific N-conversion rate of 0.32 ± 0.02 [gN(2) - N · gVSS(-1) · day(-1)]. Biomass segregation in granular sludge reactors gives an extra opportunity to select for specific microbial groups by applying a different SRT for different microbial groups. PMID:21744798

  17. In situ measurement of methane oxidation in groundwater by using natural-gradient tracer tests.

    PubMed Central

    Smith, R L; Howes, B L; Garabedian, S P

    1991-01-01

    Methane oxidation was measured in an unconfined sand and gravel aquifer (Cape Cod, Mass.) by using in situ natural-gradient tracer tests at both a pristine, oxygenated site and an anoxic, sewage-contaminated site. The tracer sites were equipped with multilevel sampling devices to create target grids of sampling points; the injectate was prepared with groundwater from the tracer site to maintain the same geochemical conditions. Methane oxidation was calculated from breakthrough curves of methane relative to halide and inert gas (hexafluroethane) tracers and was confirmed by the appearance of 13C-enriched carbon dioxide in experiments in which 13C-enriched methane was used as the tracer. A Vmax for methane oxidation could be calculated when the methane concentration was sufficiently high to result in zero-order kinetics throughout the entire transport interval. Methane breakthrough curves could be simulated by modifying a one-dimensional adevection-dispersion transport model to include a Michaelis-Menten-based consumption term for methane oxidation. The Km values for methane oxidation that gave the best match for the breakthrough curve peaks were 6.0 and 9.0 microM for the uncontaminated and contaminated sites, respectively. Natural-gradient tracer tests are a promising approach for assessing microbial processes and for testing in situ bioremediation potential in groundwater systems. PMID:1892389

  18. In situ measurement of methane oxidation in groundwater by using natural-gradient tracer tests

    USGS Publications Warehouse

    Smith, R.L.; Howes, B.L.; Garabedian, S.P.

    1991-01-01

    Methane oxidation was measured in an unconfined sand and gravel aquifer (Cape Cod, Mass.) by using in situ natural-gradient tracer tests at both a pristine, oxygenated site and an anoxic, sewage-contaminated site. The tracer sites were equipped with multilevel sampling devices to create target grids of sampling points; the injectate was prepared with groundwater from the tracer site to maintain the same geochemical conditions. Methane oxidation was calculated from breakthrough curves of methane relative to halide and inert gas (hexafluoroethane) tracers and was confirmed by the appearance of 13C-enriched carbon dioxide in experiments in which 13C-enriched methane was used as the tracer. A V(max) for methane oxidation could be calculated when the methane concentration was sufficiently high to result in zero-order kinetics throughout the entire transport interval. Methane breakthrough curves could be simulated by modifying a one-dimensional advection-dispersion transport model to include a Michaelis-Menten-based consumption term for methane oxidation. The K(m) values for methane oxidation that gave the best match for the breakthrough curve peaks were 6.0 and 9.0 ??M for the uncontaminated and contaminated sites, respectively. Natural-gradient tracer tests are a promising approach for assessing microbial processes and for testing in situ bioremediation potential in groundwater systems.

  19. Modelling of stable isotope fractionation by methane oxidation and diffusion in landfill cover soils

    SciTech Connect

    Mahieu, Koenraad De Visscher, Alex; Vanrolleghem, Peter A.; Van Cleemput, Oswald

    2008-07-01

    A technique to measure biological methane oxidation in landfill cover soils that is gaining increased interest is the measurement of stable isotope fractionation in the methane. Usually to quantify methane oxidation, only fractionation by oxidation is taken into account. Recently it was shown that neglecting the isotope fractionation by diffusion results in underestimation of the methane oxidation. In this study a simulation model was developed that describes gas transport and methane oxidation in landfill cover soils. The model distinguishes between {sup 12}CH{sub 4}, {sup 13}CH{sub 4}, and {sup 12}CH{sub 3}D explicitly, and includes isotope fractionation by diffusion and oxidation. To evaluate the model, the simulations were compared with column experiments from previous studies. The predicted concentration profiles and isotopic profiles match the measured ones very well, with a root mean square deviation (RMSD) of 1.7 vol% in the concentration and a RMSD of 0.8 per mille in the {delta}{sup 13}C value, with {delta}{sup 13}C the relative {sup 13}C abundance as compared to an international standard. Overall, the comparison shows that a model-based isotope approach for the determination of methane oxidation efficiencies is feasible and superior to existing isotope methods.

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

    PubMed

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

    2008-12-01

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

  1. Does dissolved organic carbon regulate biological methane oxidation in semiarid soils?

    PubMed

    Sullivan, Benjamin W; Selmants, Paul C; Hart, Stephen C

    2013-07-01

    In humid ecosystems, the rate of methane (CH4 ) oxidation by soil-dwelling methane-oxidizing bacteria (MOB) is controlled by soil texture and soil water holding capacity, both of which limit the diffusion of atmospheric CH4 into the soil. However, it remains unclear whether these same mechanisms control CH4 oxidation in more arid soils. This study was designed to measure the proximate controls of potential CH4 oxidation in semiarid soils during different seasons. Using a unique and well-constrained 3-million-year-old semiarid substrate age gradient, we were able to hold state factors constant while exploring the relationship between seasonal potential CH4 oxidation rates and soil texture, soil water holding capacity, and dissolved organic carbon (DOC). We measured unexpectedly higher rates of potential CH4 oxidation in the wet season than the dry season. Although other studies have attributed low CH4 oxidation rates in dry soils to desiccation of MOB, we present several lines of evidence that this may be inaccurate. We found that soil DOC concentration explained CH4 oxidation rates better than soil physical factors that regulate the diffusion of CH4 from the atmosphere into the soil. We show evidence that MOB facultatively incorporated isotopically labeled glucose into their cells, and MOB utilized glucose in a pattern among our study sites that was similar to wet-season CH4 oxidation rates. This evidence suggests that DOC, which is utilized by MOB in other environments with varying effects on CH4 oxidation rates, may be an important regulator of CH4 oxidation rates in semiarid soils. Our collective understanding of the facultative use of DOC by MOB is still in its infancy, but our results suggest it may be an important factor controlling CH4 oxidation in soils from dry ecosystems. PMID:23526765

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

    PubMed Central

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

    2008-01-01

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

  3. Modeling the effects of vegetation on methane oxidation and emissions through soil landfill final covers across different climates.

    PubMed

    Abichou, Tarek; Kormi, Tarek; Yuan, Lei; Johnson, Terry; Francisco, Escobar

    2015-02-01

    Plant roots are reported to enhance the aeration of soil by creating secondary macropores which improve the diffusion of oxygen into soil as well as the supply of methane to bacteria. Therefore, methane oxidation can be improved considerably by the soil structuring processes of vegetation, along with the increase of organic biomass in the soil associated with plant roots. This study consisted of using a numerical model that combines flow of water and heat with gas transport and oxidation in soils, to simulate methane emission and oxidation through simulated vegetated and non-vegetated landfill covers under different climatic conditions. Different simulations were performed using different methane loading flux (5-200 g m(-2) d(-1)) as the bottom boundary. The lowest modeled surface emissions were always obtained with vegetated soil covers for all simulated climates. The largest differences in simulated surface emissions between the vegetated and non-vegetated scenarios occur during the growing season. Higher average yearly percent oxidation was obtained in simulations with vegetated soil covers as compared to non-vegetated scenario. The modeled effects of vegetation on methane surface emissions and percent oxidation were attributed to two separate mechanisms: (1) increase in methane oxidation associated with the change of the physical properties of the upper vegetative layer and (2) increase in organic matter associated with vegetated soil layers. Finally, correlations between percent oxidation and methane loading into simulated vegetated and non-vegetated covers were proposed to allow decision makers to compare vegetated versus non-vegetated soil landfill covers. These results were obtained using a modeling study with several simplifying assumptions that do not capture the complexities of vegetated soils under field conditions. PMID:25475118

  4. Distribution and rate of methane oxidation in sediments of the Florida everglades

    SciTech Connect

    King, G.M.; Roslev, P.; Skovgaard, H. )

    1990-09-01

    Rates of methane emission from intact cores were measured during anoxic dark and oxic light and dark incubations. Rates of methane oxidation were calculated on the basis of oxic incubations by using the anoxic emissions as an estimate of the maximum potential flux. This technique indicated that methane oxidation consumed up to 91% of the maximum potential flux in peat sediments but that oxidation was negligible in marl sediments. Oxygen microprofiles determined for intact cores were comparable to profiles measured in situ. Thus, the laboratory incubations appeared to provide a reasonable approximation of in situ activities. The magnitude of root-associated oxidation rates indicated that belowground plant surfaces may not markedly increase the total capacity for methane consumption. However, the data collectively support the notion that the distribution and activity of methane oxidation have a major impact on the magnitude of atmospheric fluxes from the Everglades.

  5. Inhibition of Methane Oxidation by Methylococcus capsulatus with Hydrochlorofluorocarbons and Fluorinated Methanes.

    PubMed

    Matheson, L J; Jahnke, L L; Oremland, R S

    1997-07-01

    The inhibition of methane oxidation by cell suspensions of Methylococcus capsulatus (Bath) exposed to hydrochlorofluorocarbon 21 (HCFC-21; difluorochloromethane [CHF(inf2)Cl]), HCFC-22 (fluorodichloromethane [CHFCl(inf2)]), and various fluorinated methanes was investigated. HCFC-21 inhibited methane oxidation to a greater extent than HCFC-22, for both the particulate and soluble methane monooxygenases. Among the fluorinated methanes, both methyl fluoride (CH(inf3)F) and difluoromethane (CH(inf2)F(inf2)) were inhibitory while fluoroform (CHF(inf3)) and carbon tetrafluoride (CF(inf4)) were not. The inhibition of methane oxidation by HCFC-21 and HCFC-22 was irreversible, while that by methyl fluoride was reversible. The HCFCs also proved inhibitory to methanol dehydrogenase, which suggests that they disrupt other aspects of C(inf1) catabolism in addition to methane monooxygenase activity. PMID:16535662

  6. Inhibition of Methane Oxidation by Methylococcus capsulatus with Hydrochlorofluorocarbons and Fluorinated Methanes

    PubMed Central

    Matheson, L. J.; Jahnke, L. L.; Oremland, R. S.

    1997-01-01

    The inhibition of methane oxidation by cell suspensions of Methylococcus capsulatus (Bath) exposed to hydrochlorofluorocarbon 21 (HCFC-21; difluorochloromethane [CHF(inf2)Cl]), HCFC-22 (fluorodichloromethane [CHFCl(inf2)]), and various fluorinated methanes was investigated. HCFC-21 inhibited methane oxidation to a greater extent than HCFC-22, for both the particulate and soluble methane monooxygenases. Among the fluorinated methanes, both methyl fluoride (CH(inf3)F) and difluoromethane (CH(inf2)F(inf2)) were inhibitory while fluoroform (CHF(inf3)) and carbon tetrafluoride (CF(inf4)) were not. The inhibition of methane oxidation by HCFC-21 and HCFC-22 was irreversible, while that by methyl fluoride was reversible. The HCFCs also proved inhibitory to methanol dehydrogenase, which suggests that they disrupt other aspects of C(inf1) catabolism in addition to methane monooxygenase activity. PMID:16535662

  7. Inhibition of methane oxidation by Methylococcus capsulatus with hydrochlorofluorocarbons and fluorinated methanes

    USGS Publications Warehouse

    Matheson, L.J.; Jahnke, L.L.; Oremland, R.S.

    1997-01-01

    The inhibition of methane oxidation by cell suspensions of Methylococcus capsulatus (Bath) exposed to hydrochlorofluorocarbon 21 (HCFC-21; difluorochloromethane [CHF2Cl]), HCFC-22 (fluorodichloromethane [CHFCl2]), and various fluorinated methanes was investigated. HCFC-21 inhibited methane oxidation to a greater extent than HCFC-22, for both the particulate and soluble methane monooxygenases. Among the fluorinated methanes, both methyl fluoride (CH3F) and difluoromethane (CH2F2) were inhibitory while fluoroform (CHF3) and carbon tetrafluoride (CF4) were not. The inhibition of methane oxidation by HCFC-21 and HCFC-22 was irreversible, while that by methyl fluoride was reversible. The HCFCs also proved inhibitory to methanol dehydrogenase, which suggests that they disrupt other aspects of C1 catabolism in addition to methane monooxygenase activity.

  8. Methane oxidation in landfill cover soils, is a 10% default value reasonable?

    PubMed

    Chanton, Jeffrey P; Powelson, David K; Green, Roger B

    2009-01-01

    We reviewed literature results from 42 determinations of the fraction of methane oxidized and 30 determinations of methane oxidation rate in a variety of soil types and landfill covers. Both column measurements and in situ field measurements were included. The means for the fraction of methane oxidized on transit across the soil covers ranged from 22 to 55% from clayey to sandy material. Mean values for oxidation rate ranged from 3.7 to 6.4 mol m(-2) d(-1) (52-102 g m(-2) d(-1)) for the different soil types. The overall mean fraction oxidized across all studies was 36% with a standard error of 6%. The overall mean oxidation rate across all studies was 4.5 mol m(-2) d(-1) +/- 1.0 (72 +/- 16 g m(-2)d(-1)). For the subset of 15 studies conducted over an annual cycle the fraction of methane oxidized ranged from 11 to 89% with a mean value of 35 +/- 6%, nearly identical to the overall mean. Nine of these studies were conducted in north Florida at 30 degrees N latitude and had a fraction oxidized of 27 +/- 4%. Five studies were conducted in northern Europe ( approximately 50-55 degrees N) and exhibited an average of 54 +/- 14%. One study, conducted in New Hampshire, had a value of 10%. The results indicate that the fraction of methane oxidized in landfill greater than the default value of 10%. Of the 42 determinations of methane oxidation reported, only four report values of 10% or less. PMID:19244486

  9. 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

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

    PubMed

    Li, Y; Wang, F; Nishino, N

    2016-04-01

    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

  11. Biomarker Evidence for Widespread Anaerobic Methane Oxidation in Mediterranean Sediments by a Consortium of Methanogenic Archaea and Bacteria†

    PubMed Central

    Pancost, Richard D.; Sinninghe Damsté, Jaap S.; de Lint, Saskia; van der Maarel, Marc J. E. C.; Gottschal, Jan C.

    2000-01-01

    Although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. In order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the Mediterranean Ridge were collected via the submersible Nautile. Geochemical data strongly indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate that this reaction is facilitated by a consortium of archaea and bacteria. Specifically, these methane-rich sediments contain high abundances of methanogen-specific biomarkers that are significantly depleted in 13C (δ13C values are as low as −95‰). Biomarkers inferred to derive from sulfate-reducing bacteria and other heterotrophic bacteria are similarly depleted. Consistent with previous work, such depletion can be explained by consumption of 13C-depleted methane by methanogens operating in reverse and as part a consortium of organisms in which sulfate serves as the terminal electron acceptor. Moreover, our results indicate that this process is widespread in Mediterranean mud volcanoes and in some localized settings is the predominant microbiological process. PMID:10698781

  12. Dynamics of development of aerobic and anaerobic bacteria during aeration of an oil-bearing stratum to enhance oil recovery

    SciTech Connect

    Belyaev, S.S.

    1983-03-01

    The distribution and activity of microorganisms in ground formations has been studied in order to assess their use and regulation during oil field exploitation. Experiments were performed on water-flooded oil fields of the Tatar ASSR and revealed some regularity in the distribution of aerobic and anaerobic microflora. Wells were opened after 3, 28 and 68 days after flooding with aerated water supplemented with nitrogen and phosphate salts. Activation of aerobes results in oxidation of residual oil (not released over 3 years of exploitation). The products (CO/sub 2/ fatty acids) of oxidation promote oil recovery. In the longer experiments anaerobic processes, especially methanogenesis from CO/sub 2/ were enhanced.

  13. Anaerobic Methane Oxidation in Soils - revealed using 13C-labelled methane tracers

    NASA Astrophysics Data System (ADS)

    Riekie, G. J.; Baggs, E. M.; Killham, K. S.; Smith, J. U.

    2008-12-01

    In marine sediments, anaerobic methane oxidation is a significant biogeochemical process limiting methane flux from ocean to atmosphere. To date, evidence for anaerobic methane oxidation in terrestrial environments has proved elusive, and its significance is uncertain. In this study, an isotope dilution method specifically designed to detect the process of anaerobic methane oxidation in methanogenic wetland soils is applied. Methane emissions of soils from three contrasting permanently waterlogged sites in Scotland are investigated in strictly anoxic microcosms to which 13C- labelled methane is added, and changes in the concentration and 12C/13C isotope ratios of methane and carbon dioxide are subsequently measured and used to calculate separate the separate components of the methane flux. The method used takes into account the 13C-methane associated with methanogenesis, and the amount of methane dissolved in the soil. The calculations make no prior assumptions about the kinetics of methane production or oxidation. The results indicate that methane oxidation can take place in anoxic soil environments. The clearest evidence for anaerobic methane oxidation is provided by soils from a minerotrophic fen site (pH 6.0) in Bin Forest underlain by ultra-basic and serpentine till. In the fresh soil anoxic microcosms, net consumption methane was observed, and the amount of headspace 13C-CO2 increased at a greater rate than the 12+13C-CO2, further proof of methane oxidation. A net increase in methane was measured in microcosms of soil from Murder Moss, an alkaline site, pH 6.5, with a strong calcareous influence. However, the 13C-CH4 data provided evidence of methane oxidation, both in the disappearance of C- CH4 and appearance of smaller quantities of 13C-CO2. The least alkaline (pH 5.5) microcosms, of Gateside Farm soil - a granitic till - exhibited net methanogenesis and the changes in 13C-CH4 and 13C-CO2 here followed the pattern expected if no methane is consumed

  14. The effects of climate changes on soil methane oxidation in a dry Arctic tundra

    NASA Astrophysics Data System (ADS)

    D'Imperio, Ludovica

    2014-05-01

    The effects of climate changes on soil methane oxidation in a dry Arctic tundra. Ludovica D'Imperio1, Anders Michelsen1, Christian J. Jørgensen1, Bo Elberling1 1Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Denmark At Northern latitudes climatic changes are predicted to be most pronounced resulting in increasing active layer depth and changes in growing season length, vegetation cover and nutrient cycling. As a consequence of increased temperature, large stocks of carbon stored in the permafrost-affected soils could become available for microbial transformations and under anoxic conditions result in increasing methane production affecting net methane (CH4) budget. Arctic tundra soils also serves as an important sink of atmospheric CH4 by microbial oxidation under aerobic conditions. While several process studies have documented the mechanisms behind both production and emissions of CH4 in arctic ecosystems, an important knowledge gap exists with respect to the in situ dynamics of microbial-driven uptake of CH4 in arctic dry lands which may be enhanced as a consequence of global warming and thereby counterbalancing CH4 emissions from Arctic wetlands. In-situ methane measurements were made in a dry Arctic tundra in Disko Island, Western Greenland, during the summer 2013 to assess the role of seasonal and inter-annual variations in temperatures and snow cover. The experimental set-up included snow fences installed in 2012, allowed investigations of the emissions of GHGs from soil under increased winter snow deposition and ambient field conditions. The soil fluxes of CH4 and CO2 were measured using closed chambers in manipulated plots with increased summer temperatures and shrub removal with or without increased winter precipitation. At the control plots, the averaged seasonal CH4 oxidation rates ranged between -0.05 mg CH4 m-2 hr-1 (end of August) and -0.32 mg CH4 m-2 hr-1 (end of June). In the

  15. Perovskite-supported palladium for methane oxidation - structure-activity relationships.

    PubMed

    Eyssler, Arnim; Lu, Ye; Matam, Santhosh Kumar; Weidenkaff, Anke; Ferri, Davide

    2012-01-01

    Palladium is the precious metal of choice for methane oxidation and perovskite-type oxides offer the possibility to stabilize it as PdO, considered crucial for catalytic activity. Pd can adopt different oxidation and coordination states when associated with perovskite-type oxides. Here, we review our work on the effect of perovskite composition on the oxidation and coordination states of Pd and its influence on catalytic activity for methane oxidation in the case of typical Mn, Fe and Co perovskite-based oxidation catalysts. Especially X-ray absorption near edge structure (XANES) spectroscopy is shown to be crucial to fingerprint the different coordination states of Pd. Pd substitutes Fe and Co in the octahedral sites but without modifying catalytic activity with respect to the Pd-free perovskite. On LaMnO(3) palladium is predominantly exposed at the surface thus bestowing catalytic activity for methane oxidation. However, the occupancy of B-cation sites of the perovskite structure by Pd can be exploited to cyclically activate Pd and to protect it from particle growth. This is explicitly demonstrated for La(Fe, Pd)O(3), where catalytic activity for methane oxidation is enhanced under oscillating redox conditions at 500 °C, therefore paving the way to the practical application in three-way catalysts for stoichiometric natural gas engines. PMID:23211725

  16. Cu-ZSM-5: A biomimetic inorganic model for methane oxidation

    PubMed Central

    Vanelderen, Pieter; Hadt, Ryan G.; Smeets, Pieter J.; Solomon, Edward I.; Schoonheydt, Robert A.; Sels, Bert F.

    2012-01-01

    The present work highlights recent advances in elucidating the methane oxidation mechanism of inorganic Cu-ZSM-5 biomimic and in identifying the reactive intermediates that are involved. Such molecular understanding is important in view of upgrading abundantly available methane, but also to comprehend the working mechanism of genuine Cu-containing oxidation enzymes. PMID:23487537

  17. Assessment of the methane oxidation capacity of compacted soils intended for use as landfill cover materials.

    PubMed

    Rachor, Ingke; Gebert, Julia; Gröngröft, Alexander; Pfeiffer, Eva-Maria

    2011-05-01

    The microbial oxidation of methane in engineered cover soils is considered a potent option for the mitigation of emissions from old landfills or sites containing wastes of low methane generation rates. A laboratory column study was conducted in order to derive design criteria that enable construction of an effective methane oxidising cover from the range of soils that are available to the landfill operator. Therefore, the methane oxidation capacity of different soils was assessed under simulated landfill conditions. Five sandy potential landfill top cover materials with varying contents of silt and clay were investigated with respect to methane oxidation and corresponding soil gas composition over a period of four months. The soils were compacted to 95% of their specific proctor density, resulting in bulk densities of 1.4-1.7 g cm(-3), reflecting considerably unfavourable conditions for methane oxidation due to reduced air-filled porosity. The soil water content was adjusted to field capacity, resulting in water contents ranging from 16.2 to 48.5 vol.%. The investigated inlet fluxes ranged from 25 to about 100g CH(4)m(-2)d(-1), covering the methane load proposed to allow for complete oxidation in landfill covers under Western European climate conditions and hence being suggested as a criterion for release from aftercare. The vertical distribution of gas concentrations, methane flux balances as well as stable carbon isotope studies allowed for clear process identifications. Higher inlet fluxes led to a reduction of the aerated zone, an increase in the absolute methane oxidation rate and a decline of the relative proportion of oxidized methane. For each material, a specific maximum oxidation rate was determined, which varied between 20 and 95 g CH(4)m(-2)d(-1) and which was positively correlated to the air-filled porosity of the soil. Methane oxidation efficiencies and gas profile data imply a strong link between oxidation capacity and diffusive ingress of

  18. Assessment of the methane oxidation capacity of compacted soils intended for use as landfill cover materials

    SciTech Connect

    Rachor, Ingke; Gebert, Julia; Groengroeft, Alexander; Pfeiffer, Eva-Maria

    2011-05-15

    The microbial oxidation of methane in engineered cover soils is considered a potent option for the mitigation of emissions from old landfills or sites containing wastes of low methane generation rates. A laboratory column study was conducted in order to derive design criteria that enable construction of an effective methane oxidising cover from the range of soils that are available to the landfill operator. Therefore, the methane oxidation capacity of different soils was assessed under simulated landfill conditions. Five sandy potential landfill top cover materials with varying contents of silt and clay were investigated with respect to methane oxidation and corresponding soil gas composition over a period of four months. The soils were compacted to 95% of their specific proctor density, resulting in bulk densities of 1.4-1.7 g cm{sup -3}, reflecting considerably unfavourable conditions for methane oxidation due to reduced air-filled porosity. The soil water content was adjusted to field capacity, resulting in water contents ranging from 16.2 to 48.5 vol.%. The investigated inlet fluxes ranged from 25 to about 100 g CH{sub 4} m{sup -2} d{sup -1}, covering the methane load proposed to allow for complete oxidation in landfill covers under Western European climate conditions and hence being suggested as a criterion for release from aftercare. The vertical distribution of gas concentrations, methane flux balances as well as stable carbon isotope studies allowed for clear process identifications. Higher inlet fluxes led to a reduction of the aerated zone, an increase in the absolute methane oxidation rate and a decline of the relative proportion of oxidized methane. For each material, a specific maximum oxidation rate was determined, which varied between 20 and 95 g CH{sub 4} m{sup -2} d{sup -1} and which was positively correlated to the air-filled porosity of the soil. Methane oxidation efficiencies and gas profile data imply a strong link between oxidation capacity

  19. Methane Oxidation in Arctic Soils from High- and Flat-Centered Polygons

    NASA Astrophysics Data System (ADS)

    Zheng, J.; Roy Chowdhury, T.; Yang, Z.; Gu, B.; Wullschleger, S. D.; Graham, D. E.

    2015-12-01

    The premise of global warming will cause deeper permafrost thawing, followed by increased carbon mineralization and CH4 formation in saturated tundra soils. Arctic tundra soils also serve as potential sinks for CH4 in response to warming temperature, which might be a key process in the global CH4 budget. Quantification of methane oxidation potential of Arctic tundra is an important component to constrain models assessing the Carbon-climate feedback from high latitude soils. The signature polygonal ground of Arctic tundra generates high level of heterogeneity in soil hydrology and soil thermal regime. Thus, two distinct polygonal features were investigated in this study to evaluate CH4 oxidation potentials under multiple biogeochemical controls. The rates, drivers, and temperature sensitivity of methane oxidation were compared between High- and Flat-Centered Polygons (HCP and FCP, respectively). A significant lag period of CO2 production was observed in soil microcosms from HCP center, which might be attributed to microbial biomass limitations and the slow growth of anaerobic microbial populations that were sensitive to freezing. Prolonged thawing significantly accelerated carbon mineralization and CH4 oxidation rates measured via methane oxidation assays (MOA) from both active and permafrost organic layers of HCP. Soil microcosms from FCP showed higher CO2 production and CH4 oxidation rates in the active organic layer, but not permafrost layer, which might be explained by the anoxic/oxic interface identified by Fe(II) content in active layer. MOAs with temperature manipulation demonstrated high temperature dependence of methane oxidation activity, mediated primarily by soluble methane monooxygenase based upon metagenomic analysis and PCR quantification. Future work will identify key variables controlling methane oxidation rate and develop parameterization that can be incorporated into Arctic terrestrial ecosystem models.

  20. The hydrological context determines the beta-diversity of aerobic anoxygenic phototrophic bacteria in European Arctic seas but does not favor endemism

    PubMed Central

    Lehours, Anne-Catherine; Jeanthon, Christian

    2015-01-01

    Despite an increasing number of studies over the last 15 years, aerobic anoxygenic photoheterotrophic (AAP) bacteria remain a puzzling functional group in terms of physiology, metabolism, and ecology. To contribute to a better knowledge of their environmental distribution, the present study aims at analyzing their diversity and structure at the boundary between the Norwegian, Greenland, and Barents Seas. The polymorphism of a marker gene encoding a sub-unit of the photosynthetic apparatus (pufM gene) was analyzed and attempted to be related to environmental parameters. The Atlantic or Arctic origin of water masses had a strong impact on the AAP bacterial community structure whose populations mostly belonged to the Alpha- and Gammaproteobacteria. A majority (>60%) of pufM sequences were affiliated to the Gammaproteobacteria reasserting that this class often represents the major component of the AAP bacterial community in oceanic regions. Two alphaproteobacterial groups dominate locally suggesting that they can constitute key players in this marine system transiently. We found that temperature is a major determinant of alpha diversity of AAP bacteria in this marine biome with specific clades emerging locally according to the partitioning of water masses. Whereas we expected specific AAP bacterial populations in this peculiar and newly explored ecosystem, most pufM sequences were highly related to sequences retrieved elsewhere. This observation highlights that the studied area does not favor AAP bacteria endemism but also opens new questions about the truthfulness of biogeographical patterns and on the extent of AAP bacterial diversity. PMID:26191046

  1. 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

  2. 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

  3. Abundance, Depth Distribution, and Composition of Aerobic Bacteriochlorophyll a-Producing Bacteria in Four Basins of the Central Baltic Sea▿ †

    PubMed Central

    Salka, Ivette; Moulisová, Vladimíra; Koblížek, Michal; Jost, Günter; Jürgens, Klaus; Labrenz, Matthias

    2008-01-01

    The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 × 105 cells ml−1 (11% of total prokaryotes) or 1.0 × 103 CFU ml−1 (9 to 10% of total CFU). Environmental pufM clone sequences were grouped into 11 operational taxonomic units phylogenetically related to cultivated members of the Alpha-, Beta-, and Gammaproteobacteria. In spite of varying pufM compositions, five clones were present in all libraries. Of these, Jannaschia-related clones were always found in relative abundances representing 25 to 30% of the total AAP clones. The abundances of the other clones varied. Clones potentially affiliated with typical freshwater Betaproteobacteria sequences were present at three Baltic Sea stations, whereas clones grouping with Loktanella represented 40% of the total cell numbers in the Gotland Basin. For three alphaproteobacterial clones, probable pufM phylogenetic relationships were supported by 16S rRNA gene analyses of Baltic AAP isolates, which showed nearly identical pufM sequences. Our data indicate that the studied AAP assemblages represented a mixture of marine and freshwater taxa, thus characterizing the Baltic Sea as a “melting pot” of abundant, polyphyletic aerobic photoheterotrophic bacteria. PMID:18502937

  4. 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. PMID:23947712

  5. The role of molecular hydrogen and methane oxidation in the water vapour budget of the stratosphere

    NASA Technical Reports Server (NTRS)

    Le Texier, H.; Solomon, S.; Garcia, R. R.

    1988-01-01

    The detailed photochemistry of methane oxidation has been studied in a coupled chemical/dynamical model of the middle atmosphere. The photochemistry of formaldehyde plays an important role in determining the production of water vapor from methane oxidation. At high latitudes, the production and transport of molecular hydrogen is particularly important in determining the water vapor distribution. It is shown that the ratio of the methane vertical gradient to the water vapor vertical gradient at any particular latitude should not be expected to be precisely 2, due both to photochemical and dynamical effects. Modeled H2O profiles are compared with measurements from the Limb Infrared Monitor of the Stratosphere (LIMS) experiment at various latitudes. Molecular hydrogen is shown to be responsible for the formation of a secondary maximum displayed by the model water vapor profiles in high latitude summer, a feature also found in the LIMS data.

  6. A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments

    NASA Astrophysics Data System (ADS)

    Hu, Shihu; Zeng, Raymond J.; Haroon, Mohamed F.; Keller, Jurg; Lant, Paul A.; Tyson, Gene W.; Yuan, Zhiguo

    2015-03-01

    This study investigates interactions between recently identified denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (anammox) processes in controlled anoxic laboratory reactors. Two reactors were seeded with the same inocula containing DAMO organisms Candidatus Methanoperedens nitroreducens and Candidatus Methylomirabilis oxyfera, and anammox organism Candidatus Kuenenia stuttgartiensis. Both were fed with ammonium and methane, but one was also fed with nitrate and the other with nitrite, providing anoxic environments with different electron acceptors. After steady state reached in several months, the DAMO process became solely/primarily responsible for nitrate reduction while the anammox process became solely responsible for nitrite reduction in both reactors. 16S rRNA gene amplicon sequencing showed that the nitrate-driven DAMO organism M. nitroreducens dominated both the nitrate-fed (~70%) and the nitrite-fed (~26%) reactors, while the nitrite-driven DAMO organism M. oxyfera disappeared in both communities. The elimination of M. oxyfera from both reactors was likely the results of this organism being outcompeted by anammox bacteria for nitrite. K. stuttgartiensis was detected at relatively low levels (1-3%) in both reactors.

  7. Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands

    PubMed Central

    Hu, Bao-lan; Shen, Li-dong; Lian, Xu; Zhu, Qun; Liu, Shuai; Huang, Qian; He, Zhan-fei; Geng, Sha; Cheng, Dong-qing; Lou, Li-ping; Xu, Xiang-yang; Zheng, Ping; He, Yun-feng

    2014-01-01

    The process of nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and shown to be mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera). Here, evidence for n-damo in three different freshwater wetlands located in southeastern China was obtained using stable isotope measurements, quantitative PCR assays, and 16S rRNA and particulate methane monooxygenase gene clone library analyses. Stable isotope experiments confirmed the occurrence of n-damo in the examined wetlands, and the potential n-damo rates ranged from 0.31 to 5.43 nmol CO2 per gram of dry soil per day at different depths of soil cores. A combined analysis of 16S rRNA and particulate methane monooxygenase genes demonstrated that M. oxyfera-like bacteria were mainly present in the deep soil with a maximum abundance of 3.2 × 107 gene copies per gram of dry soil. It is estimated that ∼0.51 g of CH4 m−2 per year could be linked to the n-damo process in the examined wetlands based on the measured potential n-damo rates. This study presents previously unidentified confirmation that the n-damo process is a previously overlooked microbial methane sink in wetlands, and n-damo has the potential to be a globally important methane sink due to increasing nitrogen pollution. PMID:24616523

  8. A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments

    PubMed Central

    Hu, Shihu; Zeng, Raymond J.; Haroon, Mohamed F.; Keller, Jurg; Lant, Paul A.; Tyson, Gene W.; Yuan, Zhiguo

    2015-01-01

    This study investigates interactions between recently identified denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (anammox) processes in controlled anoxic laboratory reactors. Two reactors were seeded with the same inocula containing DAMO organisms Candidatus Methanoperedens nitroreducens and Candidatus Methylomirabilis oxyfera, and anammox organism Candidatus Kuenenia stuttgartiensis. Both were fed with ammonium and methane, but one was also fed with nitrate and the other with nitrite, providing anoxic environments with different electron acceptors. After steady state reached in several months, the DAMO process became solely/primarily responsible for nitrate reduction while the anammox process became solely responsible for nitrite reduction in both reactors. 16S rRNA gene amplicon sequencing showed that the nitrate-driven DAMO organism M. nitroreducens dominated both the nitrate-fed (~70%) and the nitrite-fed (~26%) reactors, while the nitrite-driven DAMO organism M. oxyfera disappeared in both communities. The elimination of M. oxyfera from both reactors was likely the results of this organism being outcompeted by anammox bacteria for nitrite. K. stuttgartiensis was detected at relatively low levels (1–3%) in both reactors. PMID:25732131

  9. 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...

  10. Management of aerobic vaginitis.

    PubMed

    Tempera, Gianna; Furneri, Pio Maria

    2010-01-01

    Aerobic vaginitis is a new nonclassifiable pathology that is neither specific vaginitis nor bacterial vaginosis. The diversity of this microbiological peculiarity could also explain several therapeutic failures when patients were treated for infections identified as bacterial vaginosis. The diagnosis 'aerobic vaginitis' is essentially based on microscopic examinations using a phase-contrast microscope (at ×400 magnification). The therapeutic choice for 'aerobic vaginitis' should take into consideration an antibiotic characterized by an intrinsic activity against the majority of bacteria of fecal origin, bactericidal effect and poor/absent interference with the vaginal microbiota. Regarding the therapy for aerobic vaginitis when antimicrobial agents are prescribed, not only the antimicrobial spectrum but also the presumed ecological disturbance on the anaerobic and aerobic vaginal and rectal microbiota should be taken into a consideration. Because of their very low impact on the vaginal microbiota, kanamycin or quinolones are to be considered a good choice for therapy. PMID:21051843

  11. 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. PMID:24462420

  12. 2 D patterns of soil gas diffusivity , soil respiration, and methane oxidation in a soil profile

    NASA Astrophysics Data System (ADS)

    Maier, Martin; Schack-Kirchner, Helmer; Lang, Friederike

    2015-04-01

    The apparent gas diffusion coefficient in soil (DS) is an important parameter describing soil aeration, which makes it a key parameter for root growth and gas production and consumption. Horizontal homogeneity in soil profiles is assumed in most studies for soil properties - including DS. This assumption, however, is not valid, even in apparently homogeneous soils, as we know from studies using destructive sampling methods. Using destructive methods may allow catching a glimpse, but a large uncertainty remains, since locations between the sampling positions cannot be analyzed, and measurements cannot be repeated. We developed a new method to determine in situ the apparent soil gas diffusion coefficient in order to examine 2 D pattern of DS and methane oxidation in a soil profile. Different tracer gases (SF6, CF4, C2H6) were injected continuously into the subsoil and measured at several locations in the soil profile. These data allow for modelling inversely the 2 D patterns of DS using Finite Element Modeling. The 2D DS patterns were then combined with naturally occurring CH4 and CO2 concentrations sampled at the same locations to derive the 2D pattern of soil respiration and methane oxidation in the soil profile. We show that methane oxidation and soil respiration zones shift within the soil profile while the gas fluxes at the surface remain rather stable during a the 3 week campaign.

  13. Anaerobic methane oxidation in two tropical freshwater systems

    NASA Astrophysics Data System (ADS)

    Roland, Fleur; Darchambeau, François; Crowe, Sean A.; Borges, Alberto V.

    2014-05-01

    Lake Kivu is one of the East African Great Lakes. It is located at the border between Rwanda and the Democratic Republic of the Congo. It is a deep meromictic lake characterized by huge amounts of methane (CH4) (60 km3 at 0° C and 1 atm) dissolved in its deep waters. Two thirds of the CH4 originates from anoxic bacterial reduction of dissolved carbon dioxide and one third from anaerobic degradation of settling organic material. CH4 then diffuses slowly from the monimolimnion to surface waters where many is oxidised by methanotrophic microorganisms. In Lake Kivu, this biological oxidation of CH4 could occur with different final electron acceptors: oxygen (aerobic oxidation) but also nitrate (NO3-), nitrite, sulfate (SO42-), iron (Fe) or manganese (Mn) in anaerobic conditions. If the anaerobic oxidation of CH4 (AOM) is generally coupled to SO42- reduction in marine waters, electron acceptors of the AOM were rarely investigated in freshwater systems. Five field campaigns were conducted from 2011 to 2013 during periods with contrasted ventilations of the upper water column. The dry season is characterized by a deeper mixing of surface waters ended by a steep gradient of physico-chemical conditions at the redox interface, while during the rainy season the mixed layer is shallower and ended at its deeper part by a NO3- accumulation zone. Sampling was conducted in the main basin of Lake Kivu but also in a particular sub-basin located northeast of the lake, the Kabuno Bay. Both systems are meromictic but differ in terms of morphometry and geochemistry with a shallower permanent chemocline and higher concentrations of CH4, Fe and Mn in the anoxic waters in Kabuno Bay compared to the main lake. Samples were collected for the measurements of CH4 concentrations and the various potential electron acceptors of the AOM. CH4 oxidation rates were measured along vertical profiles at 5 m and 0.5 m depth intervals respectively in the main basin and Kabuno bay water columns. Results

  14. INACTIVATION OF ENTERIC PATHOGENS DURING AEROBIC DIGESTION OF WASTEWATER SLUDGE

    EPA Science Inventory

    The effects of aerobic and anaerobic digestion on enteric viruses, enteric bacteria, total aerobic bacteria, and intestinal parasites were studied under laboratory and field conditions. Under laboratory conditions, the temperature of the sludge digestion was the major factor infl...

  15. 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

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

    PubMed

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

    2016-02-01

    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

  17. Isolation and characterization of aerobic culturable arsenic-resistant bacteria from surfacewater and groundwater of Rautahat District, Nepal.

    PubMed

    Shakya, S; Pradhan, B; Smith, L; Shrestha, J; Tuladhar, S

    2012-03-01

    Arsenic (As) contamination of groundwater is a serious Environmental Health Management issue of drinking water sources especially in Terai region of Nepal. Many studies have reported that due to natural abundance of arsenic in the environment, various bacteria have developed different resistance mechanisms for arsenic compound. In this study, the culturable arsenic-resistant bacteria indigenous to surfacewater as well as groundwater from Rautahat District of Nepal were randomly isolated by standard plate count method on the basis of viable growth on plate count agar amended with arsenate ranging from 0, 0.5, 10, 40, 80 to 160 milligram per liter (mg/l). With respect to the morphological and biochemical tests, nine morphologically distinct potent arsenate tolerant bacteria showed relatedness with Micrococcus varians, Micrococcus roseus, Micrococcus luteus, Pseudomonas maltophilia, Pseudomonas sp., Vibrio parahaemolyticus, Bacillus cereus, Bacillus smithii 1 and Bacillus smithii 2. The isolates were capable of tolerating more than 1000 mg/l of arsenate and 749 mg/l of arsenite. Likewise, bioaccumulation capability was highest with M. roseus (85.61%) and the least with B. smithii (47.88%) indicating the potential of the organisms in arsenic resistance and most probably in bioremediation. PMID:21868146

  18. 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

  19. 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

  20. Matrix Extension Study: Validation of the Compact Dry TC Method for Enumeration of Total Aerobic Bacteria in Selected Foods.

    PubMed

    Mizuochi, Shingo; Nelson, Maria; Baylis, Chris; Jewell, Keith; Green, Becky; Limbum, Rob; Fernandez, Maria Cristina; Salfinger, Yvonne; Chen, Yi

    2016-01-01

    A validation study was conducted to extend the matrix claim for the Nissui Compact Dry Total Count (TC), Performance Tested Method(s)(SM) (PTM) Certification No. 010404, to cooked chicken, lettuce, frozen fish, milk powder, and pasteurized whole milk. The method was originally certified by the AOAC Research Institute Performance Tested Method(s)(SM) Program for raw meat products. The Compact Dry TC is a ready-to-use dry media sheet that is rehydrated by adding 1 mL of diluted sample. A total aerobic colony count can be determined in the sample following 48 h of incubation. Matrix extension studies were conducted by Campden BRI (formerly Campden and Chorleywood Food Research Association Technology Limited), Chipping Campden, UK. Single-laboratory data were collected for cooked chicken, lettuce, frozen fish, and milk powder, whereas a multilaboratory study was conducted on pasteurized milk. Fourteen laboratories participated in the collaborative study. The Compact Dry TC was tested at two time points, 48 ± 3 h and 72 ± 3 h and compared with the current International Organization for Standardization (ISO) method at the time of the study, ISO 4833:2003 (this standard is withdrawn and has been replaced by: ISO 4833-1:2013 and ISO 4833-2:2013), Microbiology of food and animal feeding stuffs-Horizontal method for the enumeration of microorganisms-Colony-count technique at 30°C. The data were logarithmically transformed and evaluated for repeatability (plus reproducibility for pasteurized milk), RSD of repeatability (plus RSD of reproducibility for milk), r(2), and mean difference between methods with 95% confidence interval (CI). A CI outside of (-0.5 to 0.5) on the log10 mean difference was used as the criterion to establish significant statistical difference between methods. No significant differences were found between the Compact Dry TC 48 and 72 h time points, with the exception of one contamination level of cooked chicken and one contamination level of dry milk

  1. Evaluation of the use of PCR and reverse transcriptase PCR for detection of pathogenic bacteria in biosolids from anaerobic digestors and aerobic composters.

    PubMed

    Burtscher, Carola; Wuertz, Stefan

    2003-08-01

    A PCR-based method and a reverse transcriptase PCR (RT-PCR)-based method were developed for the detection of pathogenic bacteria in organic waste, using Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and Staphylococcus aureus as model organisms. In seeded organic waste samples, detection limits of less than 10 cells per g of organic waste were achieved after one-step enrichment of bacteria, isolation, and purification of DNA or RNA before PCR or RT-PCR amplification. To test the reproducibility and reliability of the newly developed methods, 46 unseeded samples were collected from diverse aerobic (composting) facilities and anaerobic digestors and analyzed by both culture-based classical and newly developed PCR-based procedures. No false-positive but some false-negative results were generated by the PCR- or RT-PCR-based methods after one-step enrichment when compared to the classical detection methods. The results indicated that the level of activity of the tested bacteria in unseeded samples was very low compared to that of freshly inoculated cells, preventing samples from reaching the cell density required for PCR-based detection after one-step enrichment. However, for Salmonella spp., a distinct PCR product could be obtained for all 22 nonamended samples that tested positive for Salmonella spp. by the classical detection procedure when a selective two-step enrichment (20 h in peptone water at 37 degrees C and 24 h in Rappaport Vassiliadis medium at 43 degrees C) was performed prior to nucleic acid extraction and PCR. Hence, the classical procedure was shortened, since cell plating and further differentiation of isolated colonies can be omitted, substituted for by highly sensitive and reliable detection based on nucleic acid extraction and PCR. Similarly, 2 of the 22 samples in which Salmonella spp. were detected also tested positive for Listeria monocytogenes according to a two-step enrichment procedure followed by PCR, compared to 3 samples

  2. Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification

    PubMed Central

    Hassan, Junaid; Bergaust, Linda L.; Wheat, I. David; Bakken, Lars R.

    2014-01-01

    In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NOx) to N2 (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O2 is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e−-flow rates to O2 and NOx. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (, h−1) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O2] falls below a critical threshold and terminates (assuming energy-limitation) as [O2] exhausts. With  = 0.005 h−1, the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting (fraction of the cells recruited to denitrification) falls within 0.038–0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a ‘bet-hedging strategy’: switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia

  3. 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

  4. 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. PMID:26291606

  5. Menadione-catalyzed luminol chemiluminescence assay for the rapid detection of viable bacteria in foods under aerobic conditions.

    PubMed

    Kawasaki, S; Yamashoji, S; Asakawa, A; Isshiki, K; Kawamoto, S

    2004-12-01

    A menadione-catalyzed luminol chemiluminescence assay was developed for the rapid detection and estimation of viable bacteria in foods. The principle of this assay is based on the extracellular menadione-catalyzed active oxygen spieces (O2- and H2O2) generated by the activity of NAD(P)H:menadione oxidoreductase in viable cells. This luminol chemiluminescence assay requires 10 min for the incubation of cells with menadione and then 2 s for the measurement of chemiluminescence intensity after an injection of luminol solution without the treatment of cell lysis. This method was evaluated using liquid food samples of milk, vegetable juice, green tea, and coffee spiked with Escherichia coli ATCC 25922. The study result revealed that E. coli contamination at 1 to 10 CFU/ml in these foods could be detected after incubation at 37 degrees C for 7 h in an enrichment medium; however, the green tea and coffee samples requires filtration. This method could be a useful tool for the rapid evaluation of microbial food contamination. PMID:15633684

  6. The potential for hydrocarbon biodegradation and production of extracellular polymeric substances by aerobic bacteria isolated from a Brazilian petroleum reservoir.

    PubMed

    Vasconcellos, S P; Dellagnezze, B M; Wieland, A; Klock, J-H; Santos Neto, E V; Marsaioli, A J; Oliveira, V M; Michaelis, W

    2011-06-01

    Extracellular polymeric substances (EPS) can contribute to the cellular degradation of hydrocarbons and have a huge potential for application in biotechnological processes, such as bioremediation and microbial enhanced oil recovery (MEOR). Four bacterial strains from a Brazilian petroleum reservoir were investigated for EPS production, emulsification ability and biodegradation activity when hydrocarbons were supplied as substrates for microbial growth. Two strains of Bacillus species had the highest EPS production when phenanthrene and n-octadecane were offered as carbon sources, either individually or in a mixture. While Pseudomonas sp. and Dietzia sp., the other two evaluated strains, had the highest hydrocarbon biodegradation indices, EPS production was not detected. Low EPS production may not necessarily be indicative of an absence of emulsifier activity, as indicated by the results of a surface tension reduction assay and emulsification indices for the strain of Dietzia sp. The combined results gathered in this work suggest that a microbial consortium consisting of bacteria with interdependent metabolisms could thrive in petroleum reservoirs, thus overcoming the limitations imposed on each individual species by the harsh conditions found in such environments. PMID:25187151

  7. Enhanced c2 yields from methane oxidative coupling by means of a separative chemical reactor.

    PubMed

    Tonkovich, A L; Carr, R W; Aris, R

    1993-10-01

    Of the processes for converting natural gas into a more useful chemical feedstock, the oxidative coupling of methane to form ethane and ethylene (C(2)) has perhaps been the most intensively investigated in recent years, but it has proved extremely difficult to obtain C(2) yields in excess of 20 to 25%. Methane oxidative coupling was carried out in a separative chemical reactor that simulated a countercurrent chromatographic moving-bed. This reaction gives 65% methane conversion, 80% C(2) selectivity, and a C(2) yield slightly better than 50% with Sm(2)O(3) catalyst at approximately 1000 K. PMID:17841868

  8. 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.

  9. Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)

    PubMed Central

    Vigneron, Adrien; Cruaud, Perrine; Pignet, Patricia; Caprais, Jean-Claude; Cambon-Bonavita, Marie-Anne; Godfroy, Anne; Toffin, Laurent

    2013-01-01

    Cold seeps, located along the Sonora Margin transform fault in the Guaymas Basin, were extensively explored during the ‘BIG' cruise in June 2010. They present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To investigate this mostly unknown cold and hydrocarbon-rich environment, geochemical and microbiological surveys of the sediments underlying two microbial mats and a surrounding macrofaunal habitat were analyzed in detail. The geochemical measurements suggest biogenic methane production and local advective sulfate-rich fluxes in the sediments. The distributions of archaeal communities, particularly those involved in the methane cycle, were investigated at different depths (surface to 18 cm below the sea floor (cmbsf)) using complementary molecular approaches, such as Automated method of Ribosomal Intergenic Spacer Analysis (ARISA), 16S rRNA libraries, fluorescence in situ hybridization and quantitative polymerase chain reaction with new specific primer sets targeting methanogenic and anaerobic methanotrophic lineages. Molecular results indicate that metabolically active archaeal communities were dominated by known clades of anaerobic methane oxidizers (archaeal anaerobic methanotroph (ANME)-1, -2 and -3), including a novel ‘ANME-2c Sonora' lineage. ANME-2c were found to be dominant, metabolically active and physically associated with syntrophic Bacteria in sulfate-rich shallow sediment layers. In contrast, ANME-1 were more prevalent in the deepest sediment samples and presented a versatile behavior in terms of syntrophic association, depending on the sulfate concentration. ANME-3 were concentrated in small aggregates without bacterial partners in a restricted sediment horizon below the first centimetres. These niche specificities and syntrophic behaviors, depending on biological surface assemblages and environmental availability of electron donors, acceptors and carbon substrates, suggest that ANME could support

  10. Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia

    SciTech Connect

    Orphan, Victoria Jeanne

    2014-11-26

    Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet, our ability to effectively study symbionts in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in the form of new methodologies. Developing strategies that establish links between the identity of microorganisms and their metabolic potential, as well as techniques that can probe metabolic networks on a scale that captures individual molecule exchange and processing, is at the forefront of microbial ecology. Understanding the interactions between microorganisms on this level, at a resolution previously intractable, will lead to our greater understanding of carbon turnover and microbial community resilience to environmental perturbations. In this project, we studied an enigmatic syntrophic association between uncultured methane-oxidizing archaea and sulfate-reducing bacteria. This environmental archaeal-bacterial partnership represents a globally important sink for methane in anoxic environments. The specific goals of this project were organized into 3 major tasks designed to address questions relating to the ecophysiology of these syntrophic organisms under changing environmental conditions (e.g. different electron acceptors and nutrients), primarily through the development of microanalytical imaging methods which enable the visualization of the spatial distribution of the partners within aggregates, consumption and exchange of isotopically labeled substrates, and expression of targeted proteins identified via metaproteomics. The advanced tool set developed here to collect, correlate, and analyze these high resolution image and isotope-based datasets from methane-oxidizing consortia has the potential to be widely applicable for studying and modeling patterns of activity and interactions across a broad range of

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

    PubMed

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

    2015-04-01

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

  12. 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

  13. Exploring methane-oxidizing communities for the co-metabolic degradation of organic micropollutants.

    PubMed

    Benner, Jessica; De Smet, Delfien; Ho, Adrian; Kerckhof, Frederiek-Maarten; Vanhaecke, Lynn; Heylen, Kim; Boon, Nico

    2015-04-01

    Methane-oxidizing cultures from five different inocula were enriched to be used for co-metabolic degradation of micropollutants. In a first screening, 18 different compounds were tested for degradation with the cultures as well as with four pure methane-oxidizing bacterial (MOB) strains. The tested compounds included pharmaceuticals, chemical additives, pesticides, and their degradation products. All enriched cultures were successful in the degradation of at least four different pollutants, but the compounds degraded most often were sulfamethoxazole (SMX) and benzotriazole (BTZ). Addition of acetylene, a specific methane monooxygenase (MMO) inhibitor, revealed that SMX and BTZ were mainly degraded co-metabolically by the present MOB. The pure MOB cultures exhibited less degradation potential, while SMX and BTZ were also degraded by three of the four tested pure strains. For MOB, copper (Cu(2+)) concentration is often an important factor, as several species have the ability to express a soluble MMO (sMMO) if the Cu(2+) concentration is low. In literature, this enzyme is often described to have a broader compound range for co-metabolic degradation of pollutants, in particular when it comes to aromatic structures. However, this study indicated that co-metabolic degradation of the aromatic compounds SMX and BTZ was possible at high Cu(2+) concentration, most probably catalyzed by pMMO. PMID:25487887

  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. PMID:26911022

  15. Selective methane oxidation over promoted oxide catalysts. Topical report, September 8, 1992--September 7, 1996

    SciTech Connect

    Klier, K.; Herman, R.G.

    1996-12-31

    The objective of this research was to selectively oxidize methane to C{sub 2} hydrocarbons and to oxygenates, in particular formaldehyde and methanol, in high space time yields using air at the oxidant under milder reaction conditions that heretofore employed over industrially practical oxide catalysts. The research carried out under this US DOE-METC contract was divided into the following three tasks: Task 1, maximizing selective methane oxidation to C{sub 2}{sup +} products over promoted SrO/La{sub 2}O{sub 3} catalysts; Task 2, selective methane oxidation to oxygenates; and Task 3, catalyst characterization and optimization. Principal accomplishments include the following: the 1 wt% SO{sub 4}{sup 2{minus}}/SrO/La{sub 2}O{sub 3} promoted catalyst developed here produced over 2 kg of C{sub 2} hydrocarbons/kg catalyst/hr at 550 C; V{sub 2}O{sub 5}/SiO{sub 2} catalysts have been prepared that produce up to 1.5 kg formaldehyde/kg catalyst/hr at 630 C with low CO{sub 2} selectivities; and a novel dual bed catalyst system has been designed and utilized to produce over 100 g methanol/kg catalyst/hr at 600 C with the presence of steam in the reactant mixture.

  16. 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. PMID:20627391

  17. Methane oxidation in permeable sediments at hydrocarbon seeps in the Santa Barbara Channel, California

    NASA Astrophysics Data System (ADS)

    Treude, T.; Ziebis, W.

    2010-03-01

    A shallow-water area in the Santa Barbara Channel (California), known collectively as the Coal Oil Point seep field, is one the largest natural submarine oil and gas emission areas in the world. Both gas and oil are seeping constantly through a predominantly sandy seabed into the ocean. This study focused on the methanotrophic activity within the surface sediments (0-15 cm) of the permeable seabed in the so-called Brian Seep area at a water depth ~10 m. Detailed investigations of biogeochemical parameters in the sediment surrounding active gas vents indicated that methane seepage through the permeable seabed induces a convective transport of fluids within the surface sediment layer, which results in a deeper penetration of oxidants (oxygen, sulfate) into the sediment, as well as in a faster removal of potentially inhibiting reduced end products (e.g. hydrogen sulfide). Methanotrophic activity was often found close to the sediment-water interface, indicating the involvement of aerobic bacteria. However, biogeochemical data suggests that the majority of methane is consumed by anaerobic oxidation of methane (AOM) coupled to sulfate reduction below the surface layer (>15 cm), where sulfate is still available in high concentrations. This subsurface maximum of AOM activity in permeable sands is in contrast to known deep-sea seep habitats, where upward fluid advection through more fine-grained sediments leads to an accumulation of AOM activity within the top 10 cm of the sediments, because sulfate is rapidly depleted.

  18. Isotopic partitioning of net ecosystem CO2 exchange reveals the importance of methane oxidation in a boreal peatland

    NASA Astrophysics Data System (ADS)

    Hasselquist, Niles; Peichl, Matthias; Öquist, Mats; Crill, Patrick; Nilsson, Mats

    2016-04-01

    the 13CO2 signature derives from a combination of SOM and pore water CH4 and applying a two-source mixing model, we found that roughly one-third of Rh was the result of methane oxidation whereas the remaining two-thirds came from the mineralization of SOM. Given that Rh represented ca. 50% of total Reco during the measurement period, we provide some of the first in situ measurements that highlight the important role methanotrophic bacteria may play in CO2 fluxes in a northern boreal peatland.

  19. Induction of enhanced methane oxidation in compost: Temperature and moisture response

    SciTech Connect

    Mor, Suman . E-mail: sumanmor@yahoo.com; Visscher, Alex de; Ravindra, Khaiwal; Dahiya, R.P.; Chandra, A.; Cleemput, Oswald van

    2006-07-01

    Landfilling is one of the most common ways of municipal solid waste disposal. Degradation of organic waste produces CH{sub 4} and other landfill gases that significantly contribute to global warming. However, before entering the atmosphere, part of the produced CH{sub 4} can be oxidised while passing through the landfill cover. In the present study, the oxidation rate of CH{sub 4} was studied with various types of compost as possible landfill cover. The influence of incubation time, moisture content and temperature on the CH{sub 4} oxidation capacity of different types of compost was examined. It was observed that the influence of moisture content and temperature on methane oxidation is time-dependent. Maximum oxidation rates were observed at moisture contents ranging from 45% to 110% (dry weight basis), while the optimum temperature ranged from 15 to 30 deg. C.

  20. High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions.

    PubMed

    Segarra, K E A; Schubotz, F; Samarkin, V; Yoshinaga, M Y; Hinrichs, K-U; Joye, S B

    2015-01-01

    The role of anaerobic oxidation of methane (AOM) in wetlands, the largest natural source of atmospheric methane, is poorly constrained. Here we report rates of microbially mediated AOM (average rate=20 nmol cm(-3) per day) in three freshwater wetlands that span multiple biogeographical provinces. The observed AOM rates rival those in marine environments. Most AOM activity may have been coupled to sulphate reduction, but other electron acceptors remain feasible. Lipid biomarkers typically associated with anaerobic methane-oxidizing archaea were more enriched in (13)C than those characteristic of marine systems, potentially due to distinct microbial metabolic pathways or dilution with heterotrophic isotope signals. On the basis of this extensive data set, AOM in freshwater wetlands may consume 200 Tg methane per year, reducing their potential methane emissions by over 50%. These findings challenge precepts surrounding wetland carbon cycling and demonstrate the environmental relevance of an anaerobic methane sink in ecosystems traditionally considered strong methane sources. PMID:26123199

  1. Temperature response of methane oxidation and production potentials in peatland ecosystems across Finland

    NASA Astrophysics Data System (ADS)

    Welti, Nina; Korrensalo, Aino; Kerttula, Johanna; Maljanen, Marja; Uljas, Salli; Lohila, Annalea; Laine, Anna; Vesala, Timo; Elliott, David; Tuittila, Eeva-Stiina

    2016-04-01

    It has been suggested that the ecosystems located in the high latitudes are especially sensitive to warming. Therefore, we compared 14 peatland systems throughout Finland along a latitudinal gradient from 69°N to 61°N to examine the response of methane production and methane oxidation with warming climate. Peat samples were taken at the height of the growing season in 2015 from 0 - 10cm below the water table depth. The plant communities in sampling locations were described by estimating cover of each plant species and pH of water was measured. Upon return to the lab, we made two parallel treatments, under anoxic and oxic conditions in order to calculate the CH4 production and consumption potentials of the peat and used three temperatures, 4°C, 17.5°C, and 30°C to examine the temperature effect on the potentials. We hypothesized that there will be an observable response curve in CH4 production and oxidation relative to temperature with a greater response with increasing latitude. In general, increasing temperature increased the potential for CH4 production and oxidation, at some sites, the potential was highest at 17.5°C, indicating that there is an optimum temperature threshold for the in situ methane producing and oxidizing microbial communities. Above this threshold, the peat microbial communities are not able to cope with increasing temperature. This is especially noticeable for methane oxidation at sites above 62°N. As countries are being expected to adequately account for their greenhouse gas budgets with increasing temperature models, knowing where the temperature threshold exists is of critical importance.

  2. Permafrost Thaw Induces Methane Oxidation in Transitional Thaw Stages in a Subarctic Peatland

    NASA Astrophysics Data System (ADS)

    Perryman, C. R.; Kashi, N. N.; Malhotra, A.; McCalley, C. K.; Varner, R. K.

    2015-12-01

    Rising temperatures in the subarctic are accelerating permafrost thaw and increasing methane (CH4) emissions from subarctic peatlands. Methanotrophs in these peatlands can consume/oxidize CH4, potentially mitigating CH4 emissions in these peatlands. Oxidation rates can exceed 90% of CH4 production in some settings, depending on O2 and CH4 availability and environmental conditions. Malhotra and Roulet identified 10 thaw stages in Stordalen Mire near Abisko, Sweden (68°21'N,18°49'E ) with variable vegetation, environmental conditions, and associated CH4 emissions. We investigated potential methane oxidation rates across these thaw stages. Peat cores were extracted from two depths at each stage and incubated in 350ml glass jars at in situ temperatures and CH4 concentrations. Headspace samples were collected from each incubation jar over a 48-hour period and analyzed for CH4 concentration using flame ionization detection gas chromatography (GC-FID). Oxidation rates ranged from <0.1 to 17 μg of CH4 per gram of dry biomass per day. Water table depth and pore water pH were the strongest environmental correlates of oxidation (sample size = 56, p < 0.001). The highest potential oxidation rates were observed in collapsing palsa sites and recently collapsed sedge-dominated open water sites near palsa mounds. Our results suggest that permafrost thaw induces high CH4 oxidation rates by creating conditions ideal for both methanogenic and methanotrophic microbial communities. Our results also reinforce the importance of incorporating transitional thaw stages in landscape level carbon budgets of thawing peatlands emphasized by Malhotra and Roulet. Forthcoming microbial analysis and stable isotope analysis will further elucidate the factors controlling methane oxidation rates at Stordalen Mire.

  3. Carbon and hydrogen isotope fractionation by microbial methane oxidation: Improved determination

    SciTech Connect

    Mahieu, Koenraad . E-mail: Koenraad.Mahieu@Ugent.be; Visscher, Alex De; Vanrolleghem, Peter A.; Cleemput, Oswald Van

    2006-07-01

    Isotope fractionation is a promising tool for quantifying methane oxidation in landfill cover soils. For good quantification an accurate determination of the isotope fractionation factor ({alpha}) of methane oxidation based on independent batch experiments with soil samples from the landfill cover is required. Most studies so far used data analysis methods based on approximations of the Rayleigh model to determine {alpha}. In this study, the two most common approximations were tested, the simplified Rayleigh approach and the Coleman method. To do this, the original model of Rayleigh was described in measurable variables, methane concentration and isotopic abundances, and fitted to batch oxidation data by means of a weighted non-linear errors-in-variables regression technique. The results of this technique were used as a benchmark to which the results of the two conventional approximations were compared. Three types of batch data were used: simulated data, data obtained from the literature, and data obtained from new batch experiments conducted in our laboratory. The Coleman approximation was shown to be acceptable but not recommended for carbon fractionation (error on {alpha} - 1 up to 5%) and unacceptable for hydrogen fractionation (error up to 20%). The difference between the simplified Rayleigh approach and the exact Rayleigh model is much smaller for both carbon and hydrogen fractionation (error on {alpha} - 1 < 0.05%). There is also a small difference when errors in both variables (methane concentration and isotope abundance) are accounted for instead of assuming an error-free independent variable. By means of theoretical calculations general criteria, not limited to methane, {sup 13}C, or D, were developed for the validity of the simplified Rayleigh approach when using labelled compounds.

  4. Biodegradation of individual and multiple chlorinated aliphatic hydrocarbons by methane-oxidizing cultures.

    PubMed Central

    Chang, H L; Alvarez-Cohen, L

    1996-01-01

    The microbial degradation of chlorinated and nonchlorinated methanes, ethanes, and ethanes by a mixed methane-oxidizing culture grown under chemostat and batch conditions is evaluated and compared with that by two pure methanotrophic strains: CAC1 (isolated from the mixed culture) and Methylosinus trichosporium OB3b. With the exception of 1,1-dichloroethylene, the transformation capacity (Tc) for each chlorinated aliphatic hydrocarbon was generally found to be in inverse proportion to its chlorine content within each aliphatic group (i.e., methanes, ethanes, and ethenes), whereas similar trends were not observed for degradation rate constants. Tc trends were similar for all methane-oxidizing cultures tested. None of the cultures were able to degrade the fully chlorinated aliphatics such as perchloroethylene and carbon tetrachloride. Of the four cultures tested, the chemostat-grown mixed culture exhibited the highest Tc for trichloroethylene, cis-1,2-dichloroethylene, tetrachloroethane, 1,1,1-trichloroethane, and 1,2-dichloroethane, whereas the pure batch-grown OB3b culture exhibited the highest Tc for all other compounds tested. The product toxicity of chlorinated aliphatic hydrocarbons in a mixture containing multiple compounds was cumulative and predictable when using parameters measured from the degradation of individual compounds. The Tc for each chlorinated aliphatic hydrocarbon in a mixture (Tcmix) and the total Tc for the mixture (sigma Tcmix) are functions of the individual Tc, the initial substrate concentration (S0), and the first-order rate constant (k/Ks) of each compound in the mixture, indicating the importance of identifying the properties and compositions of all potentially degradable compounds in a contaminant mixture. PMID:8795228

  5. Oxygen as Intermediate in Anoxic Environments: Nitrite-Dependent Methane Oxidation and Beyond

    NASA Astrophysics Data System (ADS)

    Ettwig, K. F.

    2014-12-01

    In recent years the known diversity of hydrocarbon activation mechanisms under anaerobic conditions has been extended by intra-aerobic denitrification, a process in which oxygen is derived from NO and used for substrate activation. For two phylogenetically unrelated bacterial species, the freshwater NC10 phylum bacterium Methylomirabilis oxyfera [1] and the marine γ-proteobacterial strain HdN1 [2] it has been shown that, under anoxic conditions with nitrate and/or nitrite, mono-oxygenases are used for methane and hexadecane oxidation, respectively. No degradation was observed with nitrous oxide (N2O) only. In the anaerobic methanotroph M. oxyfera, which lacks apparent nitrous oxide reductase in its genome, substrate activation in the presence of nitrite was directly associated with both O2 and N2 formation. These findings strongly argue for the role of nitric oxide (NO), or an oxygen species derived from it, in the activation reaction of methane. Although intracellular oxygen generation has been experimentally documented and elegantly explains the utilization of 'aerobic' pathways under anoxic conditions, research about the underlying molecular mechanism has just started. The proposed candidate enzymes for oxygen (or possibly another another reactive intermediate) production from NO, an NO dismutase (NOD) [3], related to quinol-dependent NO reductases (qNORs), is present and highly expressed in both M. oxyfera and strain HdN1. Besides that, several recently sequenced species from the Cytophaga-Flavobacterium-Bacteroides group harbor Nod/Nor genes, but experimential evidence is needed to show if these have NOD activity, are unusual but functional qNORs, or represent transition states between the two. Additionally, for several anaerobic hydrocarbon-degrading organisms the biochemical mechanism of substrate activation has not been elucidated yet: whereas signature genes of anaerobic degradation are missing, monooxygenase genes are present. Also these microorganisms

  6. 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

  7. Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing.

    PubMed

    Deng, Yongcui; Cui, Xiaoyong; Dumont, Marc G

    2016-08-01

    Sedge-dominated wetlands on the Qinghai-Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region. PMID:27369086

  8. 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...

  9. 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

  10. (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

  11. Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions.

    PubMed

    Nielsen, A K; Gerdes, K; Degn, H; Murrell, J C

    1996-05-01

    Methane is oxidized to methanol by the enzyme methane mono-oxygenase (MMO) in methanotrophic bacteria. In previous work, this multicomponent enzyme system has been extensively characterized at the biochemical and molecular level. Copper ions have been shown to irreversibly inhibit MMO activity in vivo and in vitro, but the effect of copper ions on transcription of the genes encoding the soluble (cytoplasmic) MMO (sMMO) has not previously been investigated. To examine more closely the regulation of bacterial methane oxidation and to determine the role of copper in this process, we have investigated transcriptional regulation of the sMMO gene cluster in the methanotrophic bacterium Methylococcus capsulatus (Bath). Using Northern blot analysis and primer extension experiments, it was shown that the six ORFs of the sMMO gene cluster are organized as an operon and the transcripts produced upon expression of this operon have been identified. The synthesis of these transcripts was under control of a single copper-regulated promoter, which is as yet not precisely defined. PMID:8704968

  12. Assessing the role of spatial structure on cell-specific activity and interactions within uncultured methane-oxidizing syntrophic consortia (Invited)

    NASA Astrophysics Data System (ADS)

    Orphan, V. J.; McGlynn, S.; Chadwick, G.; Dekas, A.; Green-Saxena, A.

    2013-12-01

    Sulfate-coupled anaerobic oxidation of methane is catalysed through symbiotic associations between archaea and sulphate-reducing bacteria and represents the dominant sink for methane in the oceans. These methane-oxidizing symbiotic consortia form well-structured multi-celled aggregations in marine methane seeps, where close spatial proximity is believed to be essential for efficient exchange of substrates between syntrophic partners. The nature of this interspecies metabolic relationship is still unknown however there are a number of hypotheses regarding the electron carrying intermediate and ecophysiology of the partners, each of which should be affected by, and influence, the spatial arrangement of archaeal and bacterial cells within aggregates. To advance our understanding of the role of spatial structure within naturally occurring environmental consortia, we are using spatial statistical methods combined with fluorescence in situ hybridization and high-resolution nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) to quantify the effect of spatial organization and intra- and inter-species interactions on cell-specific microbial activity within these diverse archaeal-bacterial partnerships.

  13. Operando XAS study of the influence of CO and NO on methane oxidation by Pd/Al2O3

    NASA Astrophysics Data System (ADS)

    Marchionni, V.; Nachtegaal, M.; Petrov, A.; Kröcher, O.; Ferri, D.

    2016-05-01

    Methane oxidation on Pd/Al2O3 has been investigated using operando X-ray absorption spectroscopy (XAS) at the Pd K-edge. The influence of CO and NO on methane abatement has been addressed performing temperature programmed reaction runs while recording simultaneously XANES spectra. During CO oxidation Pd is reduced while methane conversion is shifted to higher temperature. NO strongly inhibits both CO and CH4 oxidation, despite the higher fraction of oxidized palladium.

  14. Assessing methane oxidation under landfill covers and its contribution to the above atmospheric CO{sub 2} levels: The added value of the isotope ({delta}{sup 13}C and {delta}{sup 18}O CO{sub 2}; {delta}{sup 13}C and {delta}D CH{sub 4}) approach

    SciTech Connect

    Widory, D.; Proust, E.; Bellenfant, G.; Bour, O.

    2012-09-15

    Highlights: Black-Right-Pointing-Pointer Comparison of the isotope and mass balance approaches to evaluate the level of methane oxidation within a landfill. Black-Right-Pointing-Pointer The level of methane oxidation is not homogenous under the landfill cover and is strongly correlated to the methane flux. Black-Right-Pointing-Pointer Isotope tracking of the contribution of the methane oxidation to the CO{sub 2} concentrations in the ambient air. - Abstract: We are presenting here a multi-isotope approach ({delta}{sup 13}C and {delta}{sup 18}O of CO{sub 2}; {delta}{sup 13}C and {delta}D of CH{sub 4}) to assess (i) the level(s) of methane oxidation during waste biodegradation and its migration through a landfill cover in Sonzay (France), and (ii) its contribution to the atmospheric CO{sub 2} levels above the surface. The isotope approach is compared to the more conventional mass balance approach. Results from the two techniques are comparable and show that the CH{sub 4} oxidation under the landfill cover is heterogenous, with low oxidation percentages in samples showing high biogas fluxes, which was expected in clay covers presenting fissures, through which CH{sub 4} is rapidly transported. At shallow depth, more immobile biogas pockets show a higher level of CH{sub 4} oxidation by the methanotrophic bacteria. {delta}{sup 13}C of CO{sub 2} samples taken at different heights (from below the cover up to 8 m above the ground level) were also used to identify and assess the relative contributions of its main sources both under the landfill cover and in the surrounding atmosphere.

  15. Methane oxidation in a boreal climate in an experimental landfill cover composed from mechanically-biologically treated waste.

    PubMed

    Einola, J-K M; Sormunen, K M; Rintala, J A

    2008-12-15

    The present study evaluated microbial methane (CH4) oxidation in a boreally located outdoor landfill lysimeter (volume 112 m3, height 3.9 m) filled with mechanically-biologically treated waste (MBT residual) and containing a cover layer made from the same MBT residual. The calculations based on gas emission and pore gas measurements showed that, between April and October 2005, a significant proportion (> 96%) of the methane produced (< 23 l CH4 m(-2) d(-1)) in the lysimeter was oxidized. Methane was oxidized mainly at the depths of 35-75 cm, as indicated by the upward decrease both in the methane concentration and in the methane-to-carbon dioxide ratio in the pore gas. Lower methane oxidation (< 0.8 CH4 m(-2) d(-1); this was < 22% of the methane produced) was observed only during the coldest time of the year (January 2006), apparently due to the fall in temperature at the depths of 25-70 cm (from 9-25 degrees C during April to October to 2-9 degrees C in January). Unexpectedly, the highest methane oxidation potential (MOP) was observed in samples from the top layer where exposure to methane was low. Overall, the results show that MBT residual is a suitable support medium for methane oxidation in landfill covers in field conditions in a boreal climate. PMID:18823644

  16. Effects of preconditioning the rhizosphere of different plant species on biotic methane oxidation kinetics.

    PubMed

    Ndanga, Éliane M; Lopera, Carolina B; Bradley, Robert L; Cabral, Alexandre R

    2016-09-01

    The rhizosphere is known as the most active biogeochemical layer of the soil. Therefore, it could be a beneficial environment for biotic methane oxidation. The aim of this study was to document - by means of batch incubation tests - the kinetics of CH4 oxidation in rhizosphere soils that were previously exposed to methane. Soils from three pre-exposure to CH4 zones were sampled: the never-before pre-exposed (NEX), the moderately pre-exposed (MEX) and the very pre-exposed (VEX). For each pre-exposure zone, the rhizosphere of several plant species was collected, pre-incubated, placed in glass vials and submitted to CH4 concentrations varying from 0.5% to 10%. The time to the beginning of CH4 consumption and the CH4 oxidation rate were recorded. The results showed that the fastest CH4 consumption occurred for the very pre-exposed rhizosphere. Specifically, a statistically significant difference in CH4 oxidation half-life was found between the rhizosphere of the VEX vegetated with a mixture of different plants and the NEX vegetated with ryegrass. This difference was attributed to the combined effect of the preconditioning level and plant species as well as to the organic matter content. Regardless of the preconditioning level, the oxidation rate values obtained in this study were comparable to those reported in the reviewed literature for mature compost. PMID:27177464

  17. Species and temperature measurements of methane oxidation in a nanosecond repetitively pulsed discharge

    PubMed Central

    Lefkowitz, Joseph K; Guo, Peng; Rousso, Aric; Ju, Yiguang

    2015-01-01

    Speciation and temperature measurements of methane oxidation during a nanosecond repetitively pulsed discharge in a low-temperature flow reactor have been performed. Measurements of temperature and formaldehyde during a burst of pulses were made on a time-dependent basis using tunable diode laser absorption spectroscopy, and measurements of all other major stable species were made downstream of a continuously pulsed discharge using gas chromatography. The major species for a stoichiometric methane/oxygen/helium mixture with 75% dilution are H2O, CO, CO2, H2, CH2O, CH3OH, C2H6, C2H4 and C2H2. A modelling tool to simulate homogeneous plasma combustion kinetics is assembled by combining the ZDPlasKin and CHEMKIN codes. In addition, a kinetic model for plasma-assisted combustion (HP-Mech/plasma) of methane, oxygen and helium mixtures has been assembled to simulate the measurements. Predictions can accurately capture reactant consumption as well as production of the major product species. However, significant disagreement is found for minor species, particularly CH2O and CH3OH. Further analysis revealed that the plasma-activated low-temperature oxidation pathways, particularly those involving CH3O2 radical reactions and methane reactions with O(1D), are responsible for this disagreement. PMID:26170433

  18. Landfill methane oxidation across climate types in the U.S.

    PubMed

    Chanton, Jeffrey; Abichou, Tarek; Langford, Claire; Hater, Gary; Green, Roger; Goldsmith, Doug; Swan, Nathan

    2011-01-01

    Methane oxidation in landfill covers was determined by stable isotope analyses over 37 seasonal sampling events at 20 landfills with intermediate covers over four years. Values were calculated two ways: by assuming no isotopic fractionation during gas transport, which produces a conservative or minimum estimate, and by assuming limited isotopic fractionation with gas transport producing a higher estimate. Thus bracketed, the best assessment of mean oxidation within the soil covers from chamber captured emitted CH(4) was 37.5 ± 3.5%. The fraction of CH(4) oxidized refers to the fraction of CH(4) delivered to the base of the cover that was oxidized to CO(2) and partitioned to microbial biomass instead of being emitted to the atmosphere as CH(4) expressed as a percentage. Air samples were also collected at the surface of the landfill, and represent CH(4) from soil, from leaking infrastructure, and from cover defects. A similar assessment of this data set yields 36.1 ± 7.2% oxidation. Landfills in five climate types were investigated. The fraction oxidized in arid sites was significantly greater than oxidation in mediterranean sites, or cool and warm continental sites. Sub tropical sites had significantly lower CH(4) oxidation than the other types of sites. This relationship may be explained by the observed inverse relationship between cover loading and fractional CH(4) oxidation. PMID:21133420

  19. Bio-tarp alternative daily cover prototypes for methane oxidation atop open landfill cells.

    PubMed

    Adams, Bryn L; Besnard, Fabien; Bogner, Jean; Hilger, Helene

    2011-05-01

    Final landfill covers are highly engineered to prevent methane release into the atmosphere. However, methane production begins soon after waste placement and is an unaddressed source of emissions. The methane oxidation capacity of methanotrophs embedded in a "bio-tarp" was investigated as a means to mitigate methane release from open landfill cells. The bio-tarp would also serve as an alternative daily cover during routine landfill operation. Evaluations of nine synthetic geotextiles identified two that would likely be suitable bio-tarp components. Pilot tarp prototypes were tested in continuous flow systems simulating landfill gas conditions. Multilayered bio-tarp prototypes consisting of alternating layers of the two geotextiles were found to remove 16% of the methane flowing through the bio-tarp. The addition of landfill cover soil, compost, or shale amendments to the bio-tarp increased the methane removal up to 32%. With evidence of methane removal in a laboratory bioreactor, prototypes were evaluated at a local landfill using flux chambers installed atop intermediate cover at a landfill. The multilayered bio-tarp and amended bio-tarp configurations were all found to decrease landfill methane flux; however, the performance efficacy of bio-tarps was not significantly different from controls without methanotrophs. Because highly variable methane fluxes at the field site likely confounded the test results, repeat field testing is recommended under more controlled flux conditions. PMID:21354776

  20. On the relevance of the methane oxidation cycle to ozone hole chemistry

    NASA Technical Reports Server (NTRS)

    Mueller, Rolf; Crutzen, Paul J.

    1994-01-01

    High concentrations of active chlorine are clearly responsible for the observed ozone depletion during the Antarctic polar spring. However, the mechanism behind the activation of chlorine from the reservoirs species HCl and ClONO2 and the maintenance of extremely high levels of active chlorine after polar sunrise is less well understood. Here, we focus on the influence of the methane oxidation cycle on 'ozone hole' chemistry through its effect on HOx and ClOx radicals. We demonstrate the great potential importance of the heterogeneous reaction HCl + HOCl yields Cl2 + H2O and the gasphase reaction ClO + CH3O2 yields ClOO + CH3O under sunlight conditions in polar spring. Under these conditions, the heterogeneous reaction is the main sink for HOx radicals. Through this channel, the HCl reservoir may be almost completely depleted. The gas phase reaction may control the levels of the CH3O2 radical, provided that high levels of ClO exist. Otherwise this radical initiates a sequence of reactions leading to a considerable loss of active chlorine. Moreover, the production of HOx radicals is reduced, and thereby the efficiency of the heterogeneous reaction limited. The two reactions together may accomplish the complete conversion of HCl into active chlorine, thereby leading to a rapid destruction of ozone.

  1. Anaerobic methane oxidation in low-organic content methane seep sediments

    USGS Publications Warehouse

    Pohlman, John W.; Riedel, Michael; Bauer, James E.; Canuel, Elizabeth A.; Paull, Charles K.; Lapham, Laura; Grabowski, Kenneth S.; Coffin, Richard B.; Spence, George D.

    2013-01-01

    Sulfate-dependent anaerobic oxidation of methane (AOM) is the key sedimentary microbial process limiting methane emissions from marine sediments and methane seeps. In this study, we investigate how the presence of low-organic content sediment influences the capacity and efficiency of AOM at Bullseye vent, a gas hydrate-bearing cold seep offshore of Vancouver Island, Canada. The upper 8 m of sediment contains 14C. A fossil origin for the DIC precludes remineralization of non-fossil OM present within the sulfate zone as a significant contributor to pore water DIC, suggesting that nearly all sulfate is available for anaerobic oxidation of fossil seep methane. Methane flux from the SMT to the sediment water interface in a diffusion-dominated flux region of Bullseye vent was, on average, 96% less than at an OM-rich seep in the Gulf of Mexico with a similar methane flux regime. Evidence for enhanced methane oxidation capacity within OM-poor sediments has implications for assessing how climate-sensitive reservoirs of sedimentary methane (e.g., gas hydrate) will respond to ocean warming, particularly along glacially-influenced mid and high latitude continental margins.

  2. Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways

    PubMed Central

    Wang, Feng-Ping; Zhang, Yu; Chen, Ying; He, Ying; Qi, Ji; Hinrichs, Kai-Uwe; Zhang, Xin-Xu; Xiao, Xiang; Boon, Nico

    2014-01-01

    Anaerobic oxidation of methane (AOM) is a crucial process limiting the flux of methane from marine environments to the atmosphere. The process is thought to be mediated by three groups of uncultivated methane-oxidizing archaea (ANME-1, 2 and 3). Although the responsible microbes have been intensively studied for more than a decade, central mechanistic details remain unresolved. On the basis of an integrated analysis of both environmental metatranscriptome and single-aggregate genome of a highly active AOM enrichment dominated by ANME-2a, we provide evidence for a complete and functioning AOM pathway in ANME-2a. All genes required for performing the seven steps of methanogenesis from CO2 were found present and actively expressed. Meanwhile, genes for energy conservation and electron transportation including those encoding F420H2 dehydrogenase (Fpo), the cytoplasmic and membrane-associated Coenzyme B–Coenzyme M heterodisulfide (CoB-S-SCoM) reductase (HdrABC, HdrDE), cytochrome C and the Rhodobacter nitrogen fixation (Rnf) complex were identified and expressed, whereas genes encoding for hydrogenases were absent. Thus, ANME-2a is likely performing AOM through a complete reversal of methanogenesis from CO2 reduction without involvement of canonical hydrogenase. ANME-2a is demonstrated to possess versatile electron transfer pathways that would provide the organism with more flexibility in substrate utilization and capacity for rapid adjustment to fluctuating environments. This work lays the foundation for understanding the environmental niche differentiation, physiology and evolution of different ANME subgroups. PMID:24335827

  3. Comparative in vitro activity of ceftaroline, ceftaroline-avibactam, and other antimicrobial agents against aerobic and anaerobic bacteria cultured from infected diabetic foot wounds.

    PubMed

    Goldstein, Ellie J C; Citron, Diane M; Merriam, C Vreni; Tyrrell, Kerin L

    2013-07-01

    Foot infections are the most common infectious complication of diabetes. Moderate to severe diabetic foot infections (DFI) are typically polymicrobial with both aerobic and anaerobic organisms. The role of MRSA in these wounds has become an increasing concern. To determine if the addition of avibactam, a novel non-beta-lactam beta-lactamase inhibitor, to ceftaroline would be more active than ceftaroline alone, we tested 316 aerobic pathogens and 154 anaerobic recovered from patients with moderate to severe DFI, and compared ceftaroline with and without avibactam to other agents. Testing on aerobes was done by broth microdilution and by agar dilution for anaerobes, according to CLSI M11-A8, and M7-A8 standards. Ceftaroline-avibactam MIC90 for all Staphylococcus spp. including MRSA was 0.5 μg/mL, and for enterococci was 1 μg/mL. The MIC90s for enteric Gram-negative rods was 0.125 μg/mL. The addition of avibactam to ceftaroline reduced the ceftaroline MICs for 2 strains of resistant Enterobacter spp. and for 1 strain of Morganella. Against anaerobic Gram-positive cocci ceftaroline-avibactam had an MIC90 0.125 μg/mL and for clostridia 1 μg/mL. Avibactam improved ceftaroline's MIC90s for Bacteroides fragilis from >32 to 2 μg/mL and for Prevotella spp. from >32 to 1 μg/mL. Ceftaroline alone demonstrates excellent in vitro activity against most of the aerobes found in moderate to severe DFI. The addition of avibactam provides an increased spectrum of activity including the beta-lactamase producing Prevotella, Bacteroides fragilis and ceftaroline resistant gram-negative enteric organisms. PMID:23623385

  4. 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.

  5. Use of a biologically active cover to reduce landfill methane emissions and enhance methane oxidation.

    PubMed

    Stern, Jennifer C; Chanton, Jeff; Abichou, Tarek; Powelson, David; Yuan, Lei; Escoriza, Sharon; Bogner, Jean

    2007-01-01

    Biologically-active landfill cover soils (biocovers) that serve to minimize CH4 emissions by optimizing CH4 oxidation were investigated at a landfill in Florida, USA. The biocover consisted of 50 cm pre-composted yard or garden waste placed over a 10-15 cm gas distribution layer (crushed glass) over a 40-100 cm interim cover. The biocover cells reduced CH4 emissions by a factor of 10 and doubled the percentage of CH4 oxidation relative to control cells. The thickness and moisture-holding capacity of the biocover resulted in increased retention times for transported CH4. This increased retention of CH4 in the biocover resulted in a higher fraction oxidized. Overall rates between the two covers were similar, about 2g CH4 m(-2)d(-1), but because CH4 entered the biocover from below at a slower rate relative to the soil cover, a higher percentage was oxidized. In part, methane oxidation controlled the net flux of CH4 to the atmosphere. The biocover cells became more effective than the control sites in oxidizing CH4 3 months after their initial placement: the mean percent oxidation for the biocover cells was 41% compared to 14% for the control cells (p<0.001). Following the initial 3 months, we also observed 29 (27%) negative CH4 fluxes and 27 (25%) zero fluxes in the biocover cells but only 6 (6%) negative fluxes and 22 (21%) zero fluxes for the control cells. Negative fluxes indicate uptake of atmospheric CH4. If the zero and negative fluxes are assumed to represent 100% oxidation, then the mean percent oxidation for the biocover and control cells, respectively, for the same period would increase to 64% and 30%. PMID:17005386

  6. Linking activity, composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil

    PubMed Central

    Shrestha, Pravin Malla; Kammann, Claudia; Lenhart, Katharina; Dam, Bomba; Liesack, Werner

    2012-01-01

    Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0–10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH4 m−2 h−1. Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 105–1.9 × 106 copies g−1 of soil. Temperature was positively correlated with CH4 uptake rates (P<0.001), but had no effect on methanotrophic population dynamics. The soil moisture was negatively correlated with CH4 uptake rates (P<0.001), but showed a positive correlation with changes in USCα-like diversity (P<0.001) and pmoA gene abundance (P<0.05). These were greatest at low net CH4 uptake rates during winter times and coincided with an overall increase in bacterial 16S rRNA gene abundances (P<0.05). Taken together, soil moisture had a significant but opposed effect on CH4 uptake rates and methanotrophic population dynamics, the latter being increasingly stimulated by soil moisture contents >50 vol% and primarily related to members of the MHP clade. PMID:22189499

  7. Quantification of atmospheric methane oxidation in glacier forefields: Initial survey results

    NASA Astrophysics Data System (ADS)

    Nauer, Philipp A.; Schroth, Martin H.; Pinto, Eric A.; Zeyer, Josef

    2010-05-01

    The oxidation of CH4 by methanotrophic bacteria is the only known terrestrial sink for atmospheric CH4. Aerobic methanotrophs are active in soils and sediments under various environmental conditions. However, little is known about the activity and abundance of methanotrophs in pioneering ecosystems and their role in succession. In alpine environments, receding glaciers pose a unique opportunity to investigate soil development and ecosystem succession. In an initial survey during summer and autumn 2009 we probed several locations in the forefields of four glaciers in the Swiss Alps to quantify the turnover of atmospheric methane in recently exposed soils. Three glacier forefields (the Stein, Steinlimi and Tiefen) are situated on siliceous bedrock, while one (the Griessen) is situated on calcareous bedrock. We sampled soil air from different depths to generate CH4 concentration profiles for qualitative analysis. At selected locations we applied surface Gas Push-Pull Tests (GPPT) to estimate first-order rate coefficients of CH4 oxidation. The test consists of a controlled injection of the reactants CH4 and O2 and the tracer Ar into and out of the soil at the same location. A top-closed steel cylinder previously emplaced in the soil encloses the injected gas mixture to ensure sufficient reaction times. Rate coefficients can be derived from differences of reactant and tracer breakthrough curves. In one GPPT we employed 13C-CH4 and measured the evolution of δ13C of extracted CO2. To confirm rate coefficients obtained by GPPTs we estimated effective soil diffusivity from soil core samples and fitted a diffusion-consumption model to our profile data. A qualitative analysis of the concentration profiles showed little activity in the forefields on siliceous bedrock, with only one out of fifteen locations exhibiting substantially lower CH4 concentrations in the soil compared to the atmosphere. The surface GPPTs with conventional CH4 at the active location were not sensitive

  8. Draft Genome Sequences of Eight Obligate Methane Oxidizers Occupying Distinct Niches Based on Their Nitrogen Metabolism

    PubMed Central

    De Vos, Paul; Vekeman, Bram

    2016-01-01

    The genome sequences of Methylomonas methanica (NCIMB 11130T, R-45363, and R-45371), Methylomonas koyamae (R-45378, R-45383, and R-49807), Methylomonas lenta (R-45370), and Methylosinus sp. (R-45379) were obtained. These aerobic methanotrophs were isolated from terrestrial ecosystems, and their distinct phenotypes related to nitrogen assimilation and dissimilation were previously reported. PMID:27491982

  9. Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria.

    PubMed

    Campbell, Mark A; Nyerges, Györgyi; Kozlowski, Jessica A; Poret-Peterson, Amisha T; Stein, Lisa Y; Klotz, Martin G

    2011-09-01

    Many methane-oxidizing bacteria (MOB) have been shown to aerobically oxidize ammonia and hydroxylamine (NH(2)OH) to produce nitrite and nitrous oxide (N(2)O). Genome sequences of alphaproteobacterial, gammaproteobacterial, and verrucomicrobial methanotrophs revealed the presence of haoAB, cytL, cytS, nirS or nirK, and norCB genes that may be responsible for N(2)O production, and additional haoAB genes were sequenced from two strains of Methylomicrobium album. The haoAB genes of M. album ATCC 33003 were inducible by ammonia and NH(2)OH, similar to haoAB induction by ammonia in Methylococcus capsulatus Bath. Increased expression of genes encoding nitric oxide reductase (cNOR; norCB) was measured upon exposure of M. capsulatus Bath to NaNO(2) and NO-releasing sodium nitroprusside. Only incubations of M. capsulatus Bath with methane, ammonia, and nitrite produced N(2)O. The data suggest a possible pathway of nitrite reduction to NO by reversely operating NH(2)OH oxidoreductase and NO reduction to N(2)O by cNOR independently or in conjunction with ammonia-induced enzymes (i.e. HAO or cytochrome c'-β). Results of this study show that MOB likely have diverse mechanisms for nitrogen oxide metabolism and detoxification of NH(2)OH that involve conventional and unconventional enzymes. PMID:21682764

  10. Identification of methyl coenzyme M reductase A(mcrA) genes associated with methane-oxidizing archaea

    SciTech Connect

    Hallam, Steven J.; Girguis, Peter R.; Preston, Christina M.; Richardson, Paul M.; DeLong, Edward F.

    2003-09-01

    Phylogenetic and stable-isotope analyses implicated two methanogen-like archaeal groups, ANME-1 and ANME-2, as key participants in the process of anaerobic methane oxidation. Although nothing is known about anaerobic methane oxidation at the molecular level, the evolutionary relationship between methane-oxidizing archaea (MOA) and methanogenic archaea raises the possibility that MOA have co-opted key elements of the methanogenic pathway, reversing many of its steps to oxidize methane anaerobically. In order to explore this hypothesis, the existence and genomic conservation of methyl coenzyme M reductase (MCR), the enzyme catalyzing the terminal step in methanogenesis, was studied in ANME-1 and ANME-2 archaea isolated from various marine environments. Clone libraries targeting a conserved region of the alpha subunit of MCR (mcrA) were generated and compared from environmental samples, laboratory-incubated microcosms, and fosmid libraries. Four out of five novel mcrA types identified from these sources were associated with ANME-1 orANME-2 group members. Assignment of mcrA types to specific phylogenetic groups was based on environmental clone recoveries, selective enrichment of specific MOA and mcrA types in a microcosm, phylogenetic congruence between mcrA and small-subunit rRNA tree topologies, and genomic context derived from fosmid sequences. Analysis of the ANME-1 and ANME-2 mcrA sequences suggested the potential for catalytic activity based on conservation of active-site amino acids. These results provide a basis for identifying methanotrophic archaea with mcrA sequences and define a functional genomic link between methanogenic and methanotrophic archaea.

  11. Methane oxidation in a neutral landfill cover soil: Influence of moisture content, temperature, and nitrogen-turnover

    SciTech Connect

    Boeckx, P.; Van Cleemput, O.

    1996-01-01

    Well-managed, aerated cover soils can have a mitigating effect on methane emission from landfills. The influence of moisture content, soil temperature, and N on the methane uptake capacity of a neutral landfill cover soil was examined. A soil moisture content of 15% w/w gave the maximum CH{sub 4} oxidation rate (2.36 ng CH{sub 4}{sup -1}g{sup -1} soil). When wetter, CH{sub 4} consumption was slower (e.g., 1.6 ng CH{sub 4} h{sup -1} g {sup -1} at 30% w/w) because of a limited gas diffusion. At lower soil moisture, microbial activity was reduced and consequently the oxidation capacity decreased (e.g., 0.84 ng CH{sub 4} {sup -1} g{sup -1} at 5% w/w). Optimum temperature was between 25 and 30{degrees}C. The calculated activation energy of the CH{sub 4} oxidation was 56.5 kj K{sup -1} mol{sup -1}. After NH4{sub 4}{sup +} addition, a negative linear correlation was found between the methane oxidation rate and the nitrous oxide flux (R{sup 2} = 0.96 Y1 = 2.7 - 0.44 x Y2). Addition of NO{sub 3}{sup -} had no significant effect on CH{sub 4} oxidation. The effect of organic residue amendments depended on their C/N ratios. Crop residues with a high C/N ratio (wheat [Triticum sativum L.] and maize [Zea mays L.] straw) stimulated N-immobilization and did not affect the methane-oxidizing capacity. On the other hand, addition of crop residues with low C/N ratios (potato [Solanum tuberosum L.] and sugar beet [Beta vulgaris cv. Altissima] leaves) stimulated N-mineralization, resulting in a strong inhibition of the methane oxidation. 38 refs., 4 figs., 2 tabs.

  12. Deep seawater circulation promotes microbial anaerobic methane oxidation at ˜400 meters below seafloor in the Nankai Trough

    NASA Astrophysics Data System (ADS)

    Moreau, J. W.; Lynch, J.; Morono, Y.; Kouduka, M.; Suzuki, Y.; Inagaki, F.; Iodp Expedition 322 Science Party

    2010-12-01

    Microbially-mediated anaerobic oxidation of methane (AOM) in the seafloor significantly impacts the marine carbon cycle, and limits methane flux to the deep oceans. AOM mediated by microbial consortia predominantly utilizes sulfate as the terminal oxidant, although recent studies have demonstrated the potential for methane oxidation coupled to iron, manganese and nitrate reduction. In the Nankai Trough, aqueous biogeochemical data obtained during IODP Expedition 322 revealed concomitant peaks of methane and sulfide, indicative of a deeply buried sulfate-dependent methane oxidation zone located within a depth interval of intercalated mudstone and sandstone 370-450 meters below the seafloor at IODP Site C0012. Site C0012 is located on the west-northwest flank of a basement high (the Kashinosaki Knoll). Preliminary calculations suggest a ˜20% seawater contribution to sedimentary pore fluids at the depth interval of the observed AOM zone, reflecting deep circulation from possibly distant recharge areas. Methane (˜200 uM) is present and the resulting hydrogeochemical conditions promote anaerobic methane-oxidation and sulfide production. Extracted DNA from SMTZ sediments was nearly five times the concentration of any other depth, although comparison of biomass data obtained via fluorescent cell counts and total extracted DNA concentrations across all depths suggest significant challenges to extracting DNA, possibly related to the relative clay content of sediments. Regardless, the biomass associated with the deep AOM zone is very small, and possibly occupies a very transient ecological niche supported by deep hydrogeologic circulation. Ongoing 16S rDNA and dissimilatory sulfite reductase gene sequencing has thus far revealed several Archaeal and delta-Proteobacteria phylotypes closely related to known AOM consortium members.

  13. Differential methane oxidation activity and microbial community composition at cold seeps in the Arctic off western Svalbard

    NASA Astrophysics Data System (ADS)

    Gründger, Friederike; Svenning, Mette M.; Niemann, Helge; Silyakova, Anna; Serov, Pavel; Li Hong, Wei; Wegener, Gunter; Panieri, Giuliana; Carroll, JoLynn

    2016-04-01

    Most models considering climate change related bottom water warming suggest that gas hydrates may become destabilized, leading to the mobilization of methane into seabed and water column ecosystems, and, eventually, into the atmosphere. However, the capacity of methanotrophic microbes retaining methane in sediments and the hydrosphere is not well constrained. Here, we investigate the microbial utilization of methane in sediments and the water column, focusing on cold seeps discovered at the arctic continental margin of western Svalbard. We measured ex situ rates of methane oxidation and sulfate reduction in two active gas flare sites with different geological settings at the Vestnesa Ridge (1204 m water depth) and within a pingolike feature area southwest off Svalbard (PLF; 380 m water depth). Our results show contrarily situations at our two sampling sites: At Vestnesa Ridge we find high methane oxidation rates with values up to 2055 nmol cm‑3 d‑1 at the sediment surface where the sediments are oversaturated with methane. Whereas, methane concentration and oxidation rates are low in the overlying water column (2 pmol cm‑3 d‑1). In contrast, at the sediment surface at PLF methane concentration and oxidation rates are considerably lower (up to 1.8 nmol cm‑3 d‑1). While the overlying bottom water contains high concentration of methane and shows oxidation rates with values of up to 3.8 nmol cm‑3 d‑1. The data on methane oxidation and sulfate reduction activity are compared to the sediment geochemistry and to data from metagenomic analysis identifying the methanotrophic community composition. These results provide unique insight into the dynamic responses of the seabed biological filter at cold seeps in the Arctic off western Svalbard. This study is part of the Centre for Arctic Gas Hydrate, Environment and Climate and was supported by the Research Council of Norway through its Centres of Excellence funding scheme grant No. 223259.

  14. In Situ Analyses of Methane Oxidation Associated with the Roots and Rhizomes of a Bur Reed, Sparganium Eurycarpum, in a Maine Wetland

    NASA Technical Reports Server (NTRS)

    King, Gary M.

    1996-01-01

    Methane oxidation associated with the belowground tissues of a common aquatic macrophyte, the burweed Sparganium euryearpum, was assayed in situ by a chamber technique with acetylene or methyl fluoride as a methanotrophic inhibitor at a headspace concentration of 3 to 4%. Acetylene and methyl fluoride inhibited both methane oxidation and peat methanogenesis. However, inhibition of methanogenesis resulted in no obvious short-term effect on methane fluxes. Since neither inhibitor adversely affected plant metabolism and both inhibited methanotrophy equally well, acetylene was employed for routine assays because of its low cost and ease of use. Root-associated methanotrophy consumed a variable but significant fraction of the total potential methane flux; values varied between 1 and 58% (mean +/- standard deviation, 27.0% +/- 6.0%), with no consistent temporal or spatial pattern during late summer. The absolute amount of methane oxidized was not correlated with the total potential methane flux; this suggested that parameters other than methane availability (e.g., oxygen availability) controlled the rates of methane oxidation. Estimates of diffusive methane flux and oxidation at the peat surface indicated that methane emission occurred primarily through aboveground plant tissues; the absolute magnitude of methane oxidation was also greater in association with roots than at the peat surface. However, the relative extent of oxidation was greater at the latter locus.

  15. Stable isotopes as tracers of methane dynamics in Everglades marshes with and without active populations of methane oxidizing bacteria

    NASA Technical Reports Server (NTRS)

    Happell, James D.; Chanton, Jeffrey P.; Whiting, Gary J.; Showers, William J.

    1993-01-01

    The stable carbon isotopic composition of CH4 is used to study the processes that affect it during transport through plants from sediment to the atmosphere. The enhancement of CH4 flux from Cladium and Eleocharis over the flux from open water or clipped sites indicated that these plants served as gas conduits between the sediments and the atmosphere. Lowering of the water table below the sediment surface caused an Everglades sawgrass marsh to shift from emission of CH4 to consumption of atmospheric CH4. Cladium transported gases passively mainly via molecular diffusion and/or effusion instead of actively via bulk flow. Stable isotropic data gave no evidence that CH4 oxidation was occurring in the rhizosphere of Cladium. Both CH4 stable carbon isotope and flux data indicated a lack of CH4 oxidation at the sediment-water interface in Everglades marl soils and its presence in peat soils where 40 to 92 percent of the flux across the sediment-water interface was oxidized.

  16. ANME-2D Archaea Catalyze Methane Oxidation in Deep Subsurface Sediments Independent of Nitrate Reduction

    NASA Astrophysics Data System (ADS)

    Hernsdorf, A. W.; Amano, Y.; Suzuki, Y.; Ise, K.; Thomas, B. C.; Banfield, J. F.

    2015-12-01

    -reducing/oxidizing archaeon Ferroglobus placidus. Thus, we suggest that ANME2-D may couple methane oxidation to reduction of ferric iron minerals in the sediment and may be generally important as a link between the iron and methane cycles in deep subsurface environments. Such information has important implications for modeling the global carbon cycle.

  17. A field-validated model for landfill methane emissions inclusive of seasonal methane oxidation

    NASA Astrophysics Data System (ADS)

    Bogner, J. E.; Spokas, K.; Chanton, J.

    2010-12-01

    In addition to natural wetlands, atmospheric methane (CH4) has multiple anthropogenic sources with high uncertainties, including rice production, ruminant animals, natural gas leakages, biomass burning, and landfills. For an improved IPCC Tier III methodology for landfill CH4 emissions in California, we have developed a new science-based, field-validated inventory model which decouples emissions from a historical reliance on a theoretical first order kinetic model for CH4 generation potential. The model (CALMIM, CAlifornia Landfill Methane Inventory Model) is a freely-available JAVA tool which estimates net CH4 emissions to the atmosphere for any landfill cover soil over a typical annual cycle, including (1) the effect of engineered gas extraction; (2) the physical effects of daily, intermediate, and final cover materials to retard emissions; and (3) seasonal soil moisture and temperature effects on both gaseous transport and methanotrophic CH4 oxidation. Linking site-specific data with existing globally-validated USDA models for annual climate and soil microclimate (Global TempSim; Global RainSim; Solarcalc; STM2), this model relies on 1-D diffusion as the major driver for emissions. Importantly, unlike current inventory methods based on modeled generation, the driving force for emissions (e.g., the CH4 concentration gradient) can be directly compared to field data. Methane oxidation is scaled to maximum rates over the full range of moisture and temperature conditions based on extensive supporting laboratory studies using California landfill cover soils. Field validation included meteorological data, soil moisture/temperature measurements, and seasonal (wet/dry) CH4 emissions & oxidation measurements for daily, intermediate, and final cover soils over two annual cycles at a northern (Monterey County) and southern California (Los Angeles County) landfill. The model accurately predicted soil temperature and moisture trends for individual cover materials with

  18. Effect of sand and shaking duration on the recovery of aerobic bacteria, coliforms, and Escherichia coli from prechill broiler whole carcass rinsates.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An experiment was conducted to determine the effect of added sand and shaking duration on the recovery of bacteria from broiler carcasses using the whole carcass rinse (WCR) method. In each of 4 replications, 12 eviscerated broiler carcasses were obtained from a commercial processing plant prior to ...

  19. Linking carbon and nitrogen cycling: Environmental transcription of mmoX, pmoA, and nifH by methane oxidizing Proteobacteria in a Sub-Arctic palsa peatland

    NASA Astrophysics Data System (ADS)

    Liebner, Susanne; Svenning, Mette M.

    2013-04-01

    Sub-Arctic terrestrial ecosystems are currently affected by climate change which causes degradation of stored organic carbon and emissions of greenhouse gases from microbial processes. Methane oxidizing bacteria (MOB) mitigate methane emissions and perform an important function in the soil-atmosphere interaction. In this study we investigated presence and environmental transcription of functional genes of MOB along the degradation of permafrost in a Sub-Arctic palsa peatland using molecular approaches. The acidic and oligotrophic peatland hosts a small number of active MOB among a seemingly specialized community. The methanotrophic community displayed a broad functional potential by transcribing genes for key enzymes involved in both carbon and nitrogen metabolisms including particulate and soluble methane monoogygenase (pMMO and sMMO) as well as nitrogenase. Transcription of mmoX that encodes for a subunit of the sMMO suggests an ecological importance of sMMO with a broad substrate range in this peatland. In situ transcripts of mmoX were tracked mainly to Methylocella related Beijerinckiaceae, and to relatives of Methylomonas while Methylocystis constituting the dominant group which utilizes pMMO. These results address interesting questions concerning in-situ substrate preferences of MOB, and the general importance of species that lack a pMMO for mitigating methane emissions. The importance of MOB for the nitrogen budget in this low pH, nitrogen limited habitat was identified by nifH transcripts of native methanotrophs. Hence, methane oxidizing Proteobacteria show an extended functional repertoire and importance for the biogeochemical cycling in this dynamic ecosystem of degrading permafrost.

  20. Methane oxidation associated to submerged brown-mosses buffers methane emissions from Siberian polygonal peatlands

    NASA Astrophysics Data System (ADS)

    Liebner, Susanne; Zeyer, Josef; Knoblauch, Christian

    2010-05-01

    Circumpolar peatlands store roughly 18 % of the globally stored carbon in soils [based on 1, 2]. Also, northern wetlands and tundra are a net source of methane (CH4), an effective greenhouse gas (GHG), with an estimated annual CH4 release of 7.2% [3] or 8.1% [4] of the global total CH4 emission. Although it is definite that Arctic tundra significantly contributes to the global methane emissions in general, regional variations in GHG fluxes are enormous. CH4 fluxes of polygonal tundra within the Siberian Lena Delta, for example, were reported to be low [5, 6], particularly at open water polygonal ponds and small lakes [7] which make up around 10 % of the delta's surface. Low methane emissions from polygonal ponds oppose that Arctic permafrost thaw ponds are generally known to emit large amounts of CH4 [8]. Combining tools of biogeochemistry and molecular microbiology, we identified sinks of CH4 in polygonal ponds from the Lena Delta that were not considered so far in GHG studies from Arctic wetlands. Pore water CH4 profiling in polygonal ponds on Samoylov, a small island in the central part of the Lena Delta, revealed a pronounced zone of CH4 oxidation near the vegetation surface in submerged layers of brown-mosses. Here, potential CH4 oxidation was an order of magnitude higher than in non-submerged mosses and in adjacent bulk soil. We could additionally show that this moss associated methane oxidation (MAMO) is hampered when exposure of light is prevented. Shading of plots with submerged Scorpidium scorpioides inhibited MAMO leading to higher CH4 concentrations and an increase in CH4 fluxes by a factor of ~13. Compared to non-submerged mosses, the submerged mosses also showed significantly lower δ13C values indicating that they use carbon dioxide derived from methane oxidation for photosynthesis. Applying stable isotope probing of DNA, type II methanotrophs were identified to be responsible for the oxidation of CH4 in the submerged Scorpidium scorpioides. Our

  1. Methane oxidation associated to submerged brown-mosses buffers methane emissions from Siberian polygonal peatlands

    NASA Astrophysics Data System (ADS)

    Liebner, Susanne; Zeyer, Josef; Knoblauch, Christian

    2010-05-01

    Circumpolar peatlands store roughly 18 % of the globally stored carbon in soils [based on 1, 2]. Also, northern wetlands and tundra are a net source of methane (CH4), an effective greenhouse gas (GHG), with an estimated annual CH4 release of 7.2% [3] or 8.1% [4] of the global total CH4 emission. Although it is definite that Arctic tundra significantly contributes to the global methane emissions in general, regional variations in GHG fluxes are enormous. CH4 fluxes of polygonal tundra within the Siberian Lena Delta, for example, were reported to be low [5, 6], particularly at open water polygonal ponds and small lakes [7] which make up around 10 % of the delta's surface. Low methane emissions from polygonal ponds oppose that Arctic permafrost thaw ponds are generally known to emit large amounts of CH4 [8]. Combining tools of biogeochemistry and molecular microbiology, we identified sinks of CH4 in polygonal ponds from the Lena Delta that were not considered so far in GHG studies from Arctic wetlands. Pore water CH4 profiling in polygonal ponds on Samoylov, a small island in the central part of the Lena Delta, revealed a pronounced zone of CH4 oxidation near the vegetation surface in submerged layers of brown-mosses. Here, potential CH4 oxidation was an order of magnitude higher than in non-submerged mosses and in adjacent bulk soil. We could additionally show that this moss associated methane oxidation (MAMO) is hampered when exposure of light is prevented. Shading of plots with submerged Scorpidium scorpioides inhibited MAMO leading to higher CH4 concentrations and an increase in CH4 fluxes by a factor of ~13. Compared to non-submerged mosses, the submerged mosses also showed significantly lower δ13C values indicating that they use carbon dioxide derived from methane oxidation for photosynthesis. Applying stable isotope probing of DNA, type II methanotrophs were identified to be responsible for the oxidation of CH4 in the submerged Scorpidium scorpioides. Our

  2. Quantifying Methane Oxidation Rates and Flux During the Deepwater Horizon Oil Spill with Measurements of Methane Stable Isotopic Ratios and Concentrations

    NASA Astrophysics Data System (ADS)

    Du, M.; Kessler, J. D.; Sylva, S.

    2014-12-01

    Several independent techniques have been developed to measure the rate of methane oxidation and the source flux. However, none of these methods measure them concurrently. Here we present a stable isotope model incorporating measurements of methane stable isotopic ratios and concentrations, and current velocity, which can be used to determine methane oxidation rates, as well as the flux from the seafloor. This model was tested on 20 samples taken from 1 to 12 km from the wellhead from 11 June through 20 June 2010 during the Deepwater Horizon oil spill. Results suggest that rate of methane oxidation ranged from 22 to 844 nM d-1 in mid-June 2010 and that the flux from the seafloor was 8.4×107 moles d-1. Both estimated here are in agreement with previous estimates determined independently.

  3. Stable isotope tracing of anaerobic methane oxidation in the gassy sediments of Eckernfoerde Bay, German Baltic Sea

    SciTech Connect

    Martens, C.S.; Albert, D.B.; Alperin, M.J.

    1999-07-01

    Methane concentrations in the pore waters of Eckernfoerde Bay in the German Baltic Sea generally reach gas bubble saturation values within the upper meter of the sediment column. The depth at which saturation occurs is controlled by a balance between rates of methane production, consumption (oxidation), and transport. The relative importance of anaerobic methane oxidation (AMO) in controlling dissolved and gas bubble methane distributions in the bay's sediments is indirectly revealed through methane concentration versus depth profiles, depth variations in the stable C and H isotope composition of methane, and the C isotope composition of total dissolved inorganic carbon ({Sigma}CO{sub 2}). Direct radiotracer measurements indicate that AMO rates of over 15 mM/yr are focused at the base of the sulfate reduction zone. Diagenetic equations that describe the depth destructions of the {delta}{sup 13}C and {delta}D values of methane reproduce isotopic shifts observed throughout the methane oxidation zone and are best fit with kinetic isotope fractionation factors of 1.012 {+-} 0.001 and 1.120 {plus{underscore}minus} 0.020 respectively.

  4. Effect of chlorine, sodium chloride, trisodium phosphate, and ultraviolet radiation on the reduction of Yersinia enterocolitica and mesophilic aerobic bacteria from eggshell surface.

    PubMed

    Favier, G L; Escudero, M E; de Guzman, A M

    2001-10-01

    Eggshell sanitizing practices are necessary to improve microbiological safety of fresh hen eggs and their products. In this work, the effects of 100 mg/liter free chlorine (chl), 3% sodium chloride (NaCl), 1, 5, and 12% trisodium phosphate (TSP) in wash solutions, and UVR (ultraviolet radiation; 4.573 microW/cm2) were studied at different times on uninoculated and Yersinia enterocolitica-inoculated eggs. On uninoculated eggs, the best results were obtained with 100 mg/liter chlorine and UV exposure for >25 min, with reductions of 1.28 and 1.60 log cycles, respectively, compared to the average bacterial count (4.55 log CFU/egg) on the control (untreated eggs). On Y. enterocolitica-inoculated eggs, highest reductions of the average bacterial count (7.35 log CFU/egg) were obtained with 5 and 12% TSP and 100 mg/liter chl. The decrease obtained with 12% TSP (3.74-log reduction) was significantly higher (P < 0.05) than those obtained with the remaining treatments. Y. enterocolitica was more resistant to UVR than the eggshell natural mesophilic aerobic microflora, except when low inoculum (4.39 log CFU/egg) was assayed. Changes in eggshell microstructure were measured by the blue lake staining method. The presence of Yersinia and Salmonella in eggshell natural flora was also investigated. PMID:11601717

  5. The aerobic and anaerobic bacteriology of perirectal abscesses.

    PubMed Central

    Brook, I; Frazier, E H

    1997-01-01

    The microbiology of perirectal abscesses in 144 patients was studied. Aerobic or facultative bacteria only were isolated in 13 (9%) instances, anaerobic bacteria only were isolated in 27 (19%) instances, and mixed aerobic and anaerobic flora were isolated in 104 (72%) instances. A total of 325 anaerobic and 131 aerobic or facultative isolates were recovered (2.2 anaerobic isolates and 0.9 aerobic isolates per specimen). The predominant anaerobes were as follows: Bacteroides fragilis group (85 isolates), Peptostreptococcus spp. (72 isolates), Prevotella spp. (71 isolates), Fusobacterium spp. (21 isolates), Porphyromonas spp. (20 isolates), and Clostridium spp. (15 isolates). The predominant aerobic and facultative bacteria were as follows: Staphylococcus aureus (34 isolates), Streptococcus spp. (28 isolates), and Escherichia coli (19 isolates). These data illustrate the polymicrobial aerobic and anaerobic microbiology of perirectal abscesses. PMID:9350771

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    In the southern basin of Lake Lugano, thermal stratification of the water column during summer and autumn leads to a lack of exchange between surface and deep water masses, and consequently to seasonal bottom water anoxia, associated with high methane concentrations. With the onset of bottom water anoxia, a dense layer of high particulate matter concentration - a so-called benthic nepheloid layer (BNL) - develops in the bottom waters. A sharp redox gradient marks the upper boundary of the BNL. At its maximum, the BNL extends 15 - 30 m from the sediment into the water column. We investigated the identity of the BNL and key environmental factors controlling its formation in the framework of a seasonal study. Compound specific C-isotope measurements and Fluorescence In Situ Hybridisation (FISH) of suspended particulate organic matter, radioactive tracer based measurements of methane oxidation, as well as investigation of geochemical water column parameters were performed in spring and autumn. Our analyses revealed that the microbial biomass within the BNL is dominated by methanotrophic bacteria. Aerobic methane oxidation (MOx) was restricted to a narrow zone at the top of the BNL, reaching maximum rates of up to 1.8 μM/day. The rates of MOx activity effectively consumed most (>99%) of the uprising methane, leading to the formation of a sharp CH4 concentration gradient and a strongly suppressed kinetic isotope effect (ɛ = -2.8o). CH4 oxidation was limited by the diffusive supply of O2 from the upper hypolimnion, implying that methanotrophy is the primary driver of the seasonal expansion of the anoxic bottom water volume, and explaining the vertical migration of the BNL in response to its own O2 consumption. The bulk organic matter extracted from the BNL was strongly depleted in 13C (δ13C < -60o), providing evidence for the incorporation of CH4-derived carbon into the biomass, suggesting that the BNL was composed of MOx-communities. This was further evidenced by four

  7. 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. PMID:17574997

  8. Search for uro-genital tract infections in patients with symptoms of prostatitis. Studies on aerobic and strictly anaerobic bacteria, mycoplasmas, fungi, trichomonads and viruses.

    PubMed

    Mårdh, P A; Colleen, S

    1975-01-01

    Seventy-nine patients with symptoms of nonacute prostatitis and 20 healthy volunteers were examined for uro-genital tract infection with bacteria, mycoplasmas, fungi, trichomonads and viruses. No differences in the results of the bacterial cultures were found between the patients and the controls. In only a few cases were established urinary tract pathogens found, but in no instance were these findings reproducible in later specimens. The cultures of the expressed prostatic fluids and the samples of semen gave no information of the occurrence of bacteria over and above that obtainable from examination of the urethral specimens. Significant bacteriuria was not found in any of the patients. Though Neisseria gonorrhoeae could not be isolated from any of the subjects, immunofluorescent studies revealed such organisms in seminal fluid in 8% of the patients. Nine of the patients had 1 to 3 years been considered successfully treated for gonorrhoea. Five of these nine patients were still found to harbour gonococci, as judged from the immunofluorescent studies. Corynebacterium vaginale was recovered in an equally low frequency (5%) from the patients and the volunteers. There was no significant difference in the incidence of T-mycoplasmas between the patients (46%) and the controls (35%), while Mycoplasma hominis was only found in the patients (10%). Trichomonas vaginalis could not be detected in wet smears of expressed prostatic fluid in any of the subjects, but could be cultured from one such specimen. Metacycline treatment (performed according the double blind cross-over technique) was studied for effects on the bacterial flora. In about 10% of the patients, an earlier not observed relative dominance of gram-negative rods was found on the cultures made after the therapy. Candida albicans was only isolated from the patients. It was found more often after (24%) than before the (15%) treatment. Complement-fixing antibodies to N. gonorrhoeae, cytomegalovirus and Chlamydia

  9. Evaluation of respiration in compost landfill biocovers intended for methane oxidation.

    PubMed

    Scheutz, Charlotte; Pedicone, Alessio; Pedersen, Gitte Bukh; Kjeldsen, Peter

    2011-05-01

    A low-cost alternative approach to reduce landfill gas (LFG) emissions is to integrate compost into the landfill cover design in order to establish a biocover that is optimized for biological oxidation of methane (CH(4)). A laboratory and field investigation was performed to quantify respiration in an experimental compost biocover in terms of oxygen (O(2)) consumption and carbon dioxide (CO(2)) production and emission rates. O(2) consumption and CO(2) production rates were measured in batch and column experiments containing compost sampled from a landfill biowindow at Fakse landfill in Denmark. Column gas concentration profiles were compared to field measurements. Column studies simulating compost respiration in the biowindow showed average CO(2) production and O(2) consumption rates of 107 ± 14 gm(-2)d(-1) and 63 ± 12 gm(-2)d(-1), respectively. Gas profiles from the columns showed elevated CO(2) concentrations throughout the compost layer, and CO(2) concentrations exceeded 20% at a depth of 40 cm below the surface of the biowindow. Overall, the results showed that respiration of compost material placed in biowindows might generate significant CO(2) emissions. In landfill compost covers, methanotrophs carrying out CH(4) oxidation will compete for O(2) with other aerobic microorganisms. If the compost is not mature, a significant portion of the O(2) diffusing into the compost layer will be consumed by non-methanotrophs, thereby limiting CH(4) oxidation. The results of this study however also suggest that the consumption of O(2) in the compost due to aerobic respiration might increase over time as a result of the accumulation of biomass in the compost after prolonged exposure to CH(4). PMID:21292472

  10. Validation of a simple model to predict the performance of methane oxidation systems, using field data from a large scale biocover test field.

    PubMed

    Geck, Christoph; Scharff, Heijo; Pfeiffer, Eva-Maria; Gebert, Julia

    2016-10-01

    On a large scale test field (1060m(2)) methane emissions were monitored over a period of 30months. During this period, the test field was loaded at rates between 14 and 46gCH4m(-2)d(-1). The total area was subdivided into 60 monitoring grid fields at 17.7m(2) each, which were individually surveyed for methane emissions and methane oxidation efficiency. The latter was calculated both from the direct methane mass balance and from the shift of the carbon dioxide - methane ratio between the base of the methane oxidation layer and the emitted gas. The base flux to each grid field was back-calculated from the data on methane oxidation efficiency and emission. Resolution to grid field scale allowed the analysis of the spatial heterogeneity of all considered fluxes. Higher emissions were measured in the upslope area of the test field. This was attributed to the capillary barrier integrated into the test field resulting in a higher diffusivity and gas permeability in the upslope area. Predictions of the methane oxidation potential were estimated with the simple model Methane Oxidation Tool (MOT) using soil temperature, air filled porosity and water tension as input parameters. It was found that the test field could oxidize 84% of the injected methane. The MOT predictions seemed to be realistic albeit the higher range of the predicted oxidations potentials could not be challenged because the load to the field was too low. Spatial and temporal emission patterns were found indicating heterogeneity of fluxes and efficiencies in the test field. No constant share of direct emissions was found as proposed by the MOT albeit the mean share of emissions throughout the monitoring period was in the range of the expected emissions. PMID:27426022

  11. Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System.

    PubMed

    Pinto, Ameet J; Marcus, Daniel N; Ijaz, Umer Zeeshan; Bautista-de Lose Santos, Quyen Melina; Dick, Gregory J; Raskin, Lutgarde

    2016-01-01

    We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation

  12. Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System

    PubMed Central

    Marcus, Daniel N.; Ijaz, Umer Zeeshan; Bautista-de lose Santos, Quyen Melina; Dick, Gregory J.; Raskin, Lutgarde

    2015-01-01

    ABSTRACT We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close

  13. 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. PMID:25636836

  14. 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

  15. Deposition of Biogenic Iron Minerals in a Methane Oxidizing Microbial Mat

    PubMed Central

    Wrede, Christoph; Dreier, Anne; Heller, Christina; Reitner, Joachim; Hoppert, Michael

    2013-01-01

    The syntrophic community between anaerobic methanotrophic archaea and sulfate reducing bacteria forms thick, black layers within multi-layered microbial mats in chimney-like carbonate concretions of methane seeps located in the Black Sea Crimean shelf. The microbial consortium conducts anaerobic oxidation of methane, which leads to the formation of mainly two biomineral by-products, calcium carbonates and iron sulfides, building up these chimneys. Iron sulfides are generated by the microbial reduction of oxidized sulfur compounds in the microbial mats. Here we show that sulfate reducing bacteria deposit biogenic iron sulfides extra- and intracellularly, the latter in magnetosome-like chains. These chains appear to be stable after cell lysis and tend to attach to cell debris within the microbial mat. The particles may be important nuclei for larger iron sulfide mineral aggregates. PMID:23843725

  16. 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.

  17. Molecular and Stable Isotope Investigation of Nitrite Respiring Bacterial Communities Capable of Anaerobic Ammonium Oxidation (ANAMMOX) and Denitrifying Anaerobic Methane Oxidation (DAMO) in Nitrogen Contaminated Groundwater

    NASA Astrophysics Data System (ADS)

    Song, B.; Hirsch, M.; Taylor, J.; Smith, R. L.; Repert, D.; Tobias, C. R.

    2010-12-01

    Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) are two recently discovered N2 production pathways in the microbial nitrogen cycle. ANAMMOX has been relatively well investigated in various aquatic ecosystems, while DAMO has been examined only in freshwater wetlands. However, neither ANAMMOX nor DAMO have been studied in groundwater ecosystems as microbial N removal processes where they could compliment or compete with denitrification to remediate N contaminated aquifers. Thus, we conducted molecular and stable isotope analyses to detect and measure ANAMMOX and DAMO in a nitrogen contaminated aquifer on Cape Cod, Massachusetts. The study site has a plume of nitrogen contaminated groundwater as a result of continuous discharge of treated wastewater over 60 years. Groundwater was collected from multiport sampling devices installed at two sites, near the waste-water disposal location (A) and more than 3 km down gradient (B) along the contamination plume. Biomass was collected from water samples for DNA extraction and 15N tracer incubation experiments. PCR with specific 16S rRNA gene primers detected the presence of ANAMMOX and DAMO bacteria at both sites. Phylogenetic analysis of 16S rRNA genes revealed that the ANAMMOX community at site A was most associated with Kuenenia spp. while site B had a community more closely related to Brocadia spp. The DAMO communities at the two sites were quite different based on 16S rRNA gene analysis. The communities at site B are closely associated with Candidatus “Methylomirabilis oxyfera”, which is the first enriched DAMO culture. Most of the 16S rRNA sequences detected in site A were related to those found in other DAMO enrichment cultures established from a eutrophic ditch sediment. In order to determine active members of ANAMMOX communities, the transcriptional expression of hydrazine oxidase (hzo) and hydrazine hydrolase (hh) genes was examined at both sites. In addition, 15N tracer

  18. 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

  19. Formate dehydrogenase from the methane oxidizer Methylosinus trichosporium OB3b.

    PubMed Central

    Yoch, D C; Chen, Y P; Hardin, M G

    1990-01-01

    Formate dehydrogenase (NAD+ dependent) was isolated from the obligate methanotroph Methylosinus trichosporium OB3b. When the enzyme was isolated anaerobically, two forms of the enzyme were seen on native polyacrylamide gels, DE-52 cellulose and Sephacryl S-300 columns; they were approximately 315,000 and 155,000 daltons. The enzyme showed two subunits on sodium dodecyl sulfate-polyacrylamide gels. The Mr of the alpha-subunit was 53,800 +/- 2,800, and that of the beta-subunit was 102,600 +/- 3,900. The enzyme (Mr 315,000) was composed of these subunits in an apparent alpha 2 beta 2 arrangement. Nonheme iron was present at a concentration ranging from 11 to 18 g-atoms per mol of enzyme (Mr 315,000). Similar levels of acid-labile sulfide were detected. No other metals were found in stoichiometric amounts. When the enzyme was isolated aerobically, there was no cofactor requirement for NAD reduction; however, when isolated anaerobically, activity was 80 to 90% dependent on the addition of flavin mononucleotide (FMN) to the reaction mixture. Furthermore, the addition of formate to an active, anoxic solution of formate dehydrogenase rapidly inactivated it in the absence of an electron acceptor; this activity could be reconstituted approximately 85% by 50 nM FMN. Flavin adenine dinucleotide could not replace FMN in reconstituting enzyme activity. The Kms of formate dehydrogenase for formate, NAD, and FMN were 146, 200, and 0.02 microM, respectively. "Pseudomonas oxalaticus" formate dehydrogenase, which has physical characteristics nearly identical to those of the M. trichosporium enzyme, was also shown to be inactivated under anoxic conditions by formate and reactivated by FMN. The evolutionary significance of this similarity is discussed. Images PMID:2376564

  20. Substantial high-affinity methanotroph populations in Andisols effect high rates of atmospheric methane oxidation.

    PubMed

    Maxfield, Pete J; Hornibrook, Ed R C; Evershed, Richard P

    2009-10-01

    Methanotrophic bacteria in soils derived from volcanic ash (Andisols) were characterized via time series (13) C-phospholipid fatty acid (PLFA) labelling. Three Andisols were incubated under 2 ppmv (13) CH4 for up to 18 weeks, thus enabling high-affinity methanotrophs to be selectively characterized and quantified. PLFA profiles from all soils were broadly similar, but the magnitude of the high-affinity methanotrophic populations determined through (13) C-PLFA-stable isotope probing displayed sizeable differences. Substantial incorporation of (13) C indicated very large high-affinity methanotrophic populations in two of the soils. Such high values are far in excess (10×) of those observed for a range of mineral soils incubated under similar conditions (Bull et al., 2000; Maxfield et al., 2006; 2008a, b). Two of the three Andisols studied also displayed high but variable CH4 oxidation rates ranging from 0.03 to 1.58 nmol CH4 g(-1) d.wt. h(-1) . These findings suggest that Andisols, a previously unstudied soil class with respect to high-affinity methanotrophic bacteria, may oxidize significant amounts of atmospheric methane despite their low areal coverage globally. PMID:23765899

  1. Vertical distribution of methane oxidation and methanotrophic response to elevated methane concentrations in stratified waters of the Arctic fjord Storfjorden (Svalbard, Norway)

    NASA Astrophysics Data System (ADS)

    Mau, S.; Blees, J.; Helmke, E.; Niemann, H.; Damm, E.

    2013-10-01

    The bacterially mediated aerobic methane oxidation (MOx) is a key mechanism in controlling methane (CH4) emissions from the world's oceans to the atmosphere. In this study, we investigated MOx in the Arctic fjord Storfjorden (Svalbard) by applying a combination of radio-tracer-based incubation assays (3H-CH4 and 14C-CH4), stable C-CH4 isotope measurements, and molecular tools (16S rRNA gene Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting, pmoA- and mxaF gene analyses). Storfjorden is stratified in the summertime with melt water (MW) in the upper 60 m of the water column, Arctic water (ArW) between 60 and 100 m, and brine-enriched shelf water (BSW) down to 140 m. CH4 concentrations were supersaturated with respect to the atmospheric equilibrium (about 3-4 nM) throughout the water column, increasing from ∼20 nM at the surface to a maximum of 72 nM at 60 m and decreasing below. MOx rate measurements at near in situ CH4 concentrations (here measured with 3H-CH4 raising the ambient CH4 pool by <2 nM) showed a similar trend: low rates at the sea surface, increasing to a maximum of ∼2.3 nM day-1 at 60 m, followed by a decrease in the deeper ArW/BSW. In contrast, rate measurements with 14C-CH4 (incubations were spiked with ∼450 nM of 14C-CH4, providing an estimate of the CH4 oxidation at elevated concentration) showed comparably low turnover rates (<1 nM day-1) at 60 m, and peak rates were found in ArW/BSW at ∼100 m water depth, concomitant with increasing 13C values in the residual CH4 pool. Our results indicate that the MOx community in the surface MW is adapted to relatively low CH4 concentrations. In contrast, the activity of the deep-water MOx community is relatively low at the ambient, summertime CH4 concentrations but has the potential to increase rapidly in response to CH4 availability. A similar distinction between surface and deep-water MOx is also suggested by our molecular analyses. The DGGE banding patterns of 16S rRNA gene

  2. Comparison of Landfill Methane Oxidation Measured Using Stable Isotope Analysis and CO2/CH4 Fluxes Measured by the Eddy Covariance Method

    NASA Astrophysics Data System (ADS)

    Xu, L.; Chanton, J.; McDermitt, D. K.; Li, J.; Green, R. B.

    2015-12-01

    Methane plays a critical role in the radiation balance and chemistry of the atmosphere. Globally, landfill methane emission contributes about 10-19% of the anthropogenic methane burden into the atmosphere. In the United States, 18% of annual anthropogenic methane emissions come from landfills, which represent the third largest source of anthropogenic methane emissions, behind enteric fermentation and natural gas and oil production. One uncertainty in estimating landfill methane emissions is the fraction of methane oxidized when methane produced under anaerobic conditions passes through the cover soil. We developed a simple stoichiometric model to estimate methane oxidation fraction when the anaerobic CO2 / CH4 production ratio is known, or can be estimated. The model predicts a linear relationship between CO2 emission rates and CH4 emission rates, where the slope depends on anaerobic CO2 / CH4 production ratio and the fraction of methane oxidized, and the intercept depends on non-methane-dependent oxidation processes. The model was tested using carbon dioxide emission rates (fluxes) and methane emission rates (fluxes) measured using the eddy covariance method over a one year period at the Turkey Run landfill in Georgia, USA. The CO2 / CH4 production ratio was estimated by measuring CO2 and CH4 concentrations in air sampled under anaerobic conditions deep inside the landfill. We also used a mass balance approach to independently estimate fractional oxidation based on stable isotope measurements (δ13C of methane) of gas samples taken from deep inside the landfill and just above the landfill surface. Results from the two independent methods agree well. The model will be described and methane oxidation will be discussed in relation to wind direction, location at the landfill, and age of the deposited refuse.

  3. 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;…

  4. Methane oxidation in heavy metal contaminated Mollic Gleysol under oxic and hypoxic conditions.

    PubMed

    Walkiewicz, A; Bulak, P; Brzezińska, M; Wnuk, E; Bieganowski, A

    2016-06-01

    Soils are the largest terrestrial sink for methane (CH4). However, heavy metals may exert toxicity to soil microorganisms, including methanotrophic bacteria. We tested the effect of lead (Pb), zinc (Zn) and nickel (Ni) on CH4 oxidation (1% v/v) and dehydrogenase activity, an index of the activity of the total soil microbial community in Mollic Gleysol soil in oxic and hypoxic conditions (oxia and hypoxia, 20% and 10% v/v O2, respectively). Metals were added in doses corresponding to the amounts permitted of Pb, Zn, Ni in agricultural soils (60, 120, 35 mg kg(-1), respectively), and half and double of these doses. Relatively low metal contents and O2 status reflect the conditions of most agricultural soils of temperate regions. Methane consumption showed high tolerance to heavy metals. The effect of O2 status was stronger than that of metals. CH4 consumption was enhanced under hypoxia, where both the start and the completion of the control and contaminated treatment were faster than under oxic conditions. Dehydrogenase activity, showed higher sensitivity to the contamination (except for low Ni dose), with a stronger effect of heavy metals, than that of the O2 status. PMID:26946175

  5. The influence of methane oxidation on the stable isotopic composition of methane emitted from Florida swamp forests

    SciTech Connect

    Happell, J.D.; Chanton, J.P. ); Showers, W.S. )

    1994-10-01

    This study reports the first measurements of the [delta][sup 13]C of CH[sub 4] emitted from seasonally flooded swamp forests in the southeastern United States. The seasonally averaged [delta][sup 13]C of CH[sub 4] emitted from a north Florida swamp forest located in the St. Marks National Wildlife Refuge was -52.7 [+-] 6.11[per thousand] (error is [+-] one standard deviation throughout, n = 28), a value [sup 13]C-enriched, relative to typical wetland emissions. In an Everglades cypress dome, the average [delta][sup 13]C of emitted CH[sub 4] was -52.5 [+-] 6.7 [per thousand] (n = 3). Consistent with attenuation of CH[sub 4] emission by CH[sub 4] oxidation in these environments, CH[sub 4] emitted via diffusion from the St. Marks swamp forest was enriched in [sup 13]C by 6.4 [+-] 5.8 [per thousand] (n = 28) and D by 57 [+-] 36 [per thousand] (n = 6) relative to sedimentary CH[sub 4]. Emission experiments, performed in situ with inhibitors of aerobic CH[sub 4] oxidizing bacteria, were used to calculate the fractionation factors ([alpha]) for stable carbon and hydrogen isotopes of CH[sub 4] undergoing transport and oxidation. Values ranged from 1.003 to 1.021 and 1.050 to 1.129, respectively. The best estimates for carbon and hydrogen [alpha] values were 1.020 and 1.068, respectively. The [delta] values of produced (sedimentary) CH[sub 4] were relatively constant in the St. Marks subtropical swamp forest. Additionally, because the transport of CH[sub 4] to the atmosphere was dominated by molecular diffusion, variations in the magnitude of CH[sub 4] oxidation appeared to be the primary factor controlling the [delta] values of emitted CH[sub 4]. This contrasts with systems dominated by bubble ebullition, where variations in CH[sub 4] production mechanisms have been hypothesized to be the primary factor controlling the [delta] values of emitted CH[sub 4].

  6. Methane oxidation potential of boreal landfill cover materials: The governing factors and enhancement by nutrient manipulation.

    PubMed

    Maanoja, Susanna T; Rintala, Jukka A

    2015-12-01

    Methanotrophs inhabiting landfill covers are in a crucial role in mitigating CH4 emissions, but the characteristics of the cover material or ambient temperature do not always enable the maximal CH4 oxidation potential (MOP). This study aimed at identifying the factors governing MOPs of different materials used for constructing biocovers and other cover structures. We also tested whether the activity of methanotrophs could be enhanced at cold temperature (4 and 12°C) by improving the nutrient content (NO3(-), PO4(3-), trace elements) of the cover material. Compost samples from biocovers designed to support CH4 oxidation were exhibiting the highest MOPs (4.16 μmol CH4 g dw(-1) h(-1)), but also the soil samples collected from other cover structures were oxidising CH4 (0.41 μmol CH4 g dw(-1) h(-1)). The best predictors for the MOPs were the NO3(-) content and activity of heterotrophic bacteria at 72.8%, which were higher in the compost samples than in the soil samples. The depletion of NO3(-) from the landfill cover material limiting the activity of methanotrophs could not be confirmed by the nutrient manipulation assay at 4°C as the addition of nitrogen decreased the MOPs from 0.090 μmol CH4 g dw(-1) h(-1) to <0.085 μmol CH4 g dw(-1) h(-1). At 12°C, all nutrient additions reduced the MOPs. The inhibition was believed to result from high ionic concentration caused by nutrient addition. At 4°C, the addition of trace elements increased the MOPs (>0.096 μmol CH4 g dw(-1)h(-1)) suggesting that this was attributable to stimulation of the enzymatic activity of the psychrotolerant methanotrophs. PMID:26298483

  7. Anaerobic methane oxidation may be more prevalent in surface soils than was originally thought

    NASA Astrophysics Data System (ADS)

    Gauthier, Mathieu; Bradley, Robert L.; Šimek, Miloslav

    2013-04-01

    Anaerobic oxidation of methane (CH4) (AOM) is a process that was first reported to occur in deep anoxic marine sediments. In this environment, CH4 is oxidized with sulphate (SO42-) as the terminal electron acceptor. It is mediated by a syntrophic consortium formed by SO42- reducing bacteria and anaerobic CH4 oxidizing Archaea, or by the latter alone. Since this landmark discovery, AOM was found to occur in other environments including freshwater lake sediments and water columns, mud volcanoes, landfill leachate, deep buried Holocene sediments and hydrocarbon contaminated aquifers. All of these situations are very specific and point to AOM as being primarily occurring in highly reducing conditions. Thus, observations of AOM in surface soils with fluctuating REDOX conditions are relatively scarce, although a few independent studies have reported AOM in surface peatlands as well as in a forest soil. Furthermore, AOM may follow different pathways, such as via the coupled oxidation of CH4 and reduction of manganese (Mn(IV)) or iron (Fe(III)), or by a lone denitrifying species that converts nitrite to nitric oxide in order to generate O2 that is then used internally to oxidize CH4. Thus, the goal of our study was to determine whether AOM is more prevalent than was thought in hydromorphic surface soils across different environments, and whether the addition of NO3- or SO4= as alternative electron acceptors may stimulate the process. We collected samples from 3 peatland soils in Scotland, 2 acid-sulphate soils in Finland, and shore sediments of 15 drained fish ponds in the Czech Republic. Subsamples were incubated in the absence of O2 and amended with either NO3-, SO42-, or left unamended (control). The net flux of CH4 and CO2 were assessed by gas chromatography after 2, 20, 40 and 60 days. We also used a 13C-CH4 isotope dilution technique to determine gross production and consumption rates of CH4. We detected AOM in all of our soils, with oxidation rates ranging between 0

  8. 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.

  9. 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. PMID:19787350

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

    PubMed

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

    1999-05-01

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

  11. Aerobic and anaerobic microbiology of infections after trauma in children.

    PubMed Central

    Brook, I

    1998-01-01

    OBJECTIVE: To review the recovery of aerobic and anaerobic bacteria from infections after trauma in children over a 20 year period. METHODS: Only specimens that were studied for both aerobic and anaerobic bacteria were included in the analysis. They were collected from seven separate centres in which the microbiology laboratories only accepted specimens that were properly collected without contamination and were submitted in appropriate transport media. Anaerobes and aerobic bacteria were cultured and identified using standard techniques. Clinical records were reviewed to identify post-trauma patients. RESULTS: From 1974 to 1994, 175 specimens obtained from 166 children with trauma showed bacterial growth. The trauma included blunt trauma (71), lacerations (48), bites (42), and open fractures (5). Anaerobic bacteria only were isolated in 38 specimens (22%), aerobic bacteria only in 51 (29%), and mixed aerobic-anaerobic flora in 86 (49%); 363 anaerobic (2.1/specimen) and 158 aerobic or facultative isolates (0.9/specimen) were recovered. The predominant anaerobic bacteria included Peptostreptococcus spp (115 isolates), Prevotella spp (68), Fusobacterium spp (52), B fragilis group (42), and Clostridium spp (21). The predominant aerobic bacteria included Staph aureus (51), E coli (13), Ps aeruginosa (12), Str pyogenes (11) and Klebsiella pneumoniae (9). Principal infections were: abscesses (52), bacteraemia (3), pulmonary infections (30, including aspiration pneumonia, tracheostomy associated pneumonia, empyema, and ventilator associated pneumonia), wounds (36, including cellulitis, post-traumatic wounds, decubitus ulcers, myositis, gastrostomy and tracheostomy site wounds, and fasciitis), bites (42, including 23 animal and 19 human), peritonitis (4), osteomyelitis (5), and sinusitis (3). Staph aureus and Str pyogenes were isolated at all sites. However, organisms of the oropharyngeal flora predominated in infections that originated from head and neck wounds and

  12. The role of microbial diversity in the dynamics and stability of global methane consumption: microbial methane oxidation as a model-system for microbial ecology (ESF EuroDiversity METHECO)

    NASA Astrophysics Data System (ADS)

    Frenzel, P.; Metheco-Team

    2009-04-01

    therefore cannot be ignored in nature conservation and management issues. Investigating this hypothesis is equivalent to assessing the Biodiversity-Ecosystem Functioning relationship (BEF) which has been intensively studied in classical ecology has largely been ignored investigating microbial communities. METHECO is focusing on methane oxidizing bacteria, a well-defined yet sufficiently diverse group of bacteria catalyzing an important ecosystem service: next to carbon dioxide, methane is the most important greenhouse gas adding about 30% to the radiative forcing exerted by carbon dioxide. The emission of methane would be even much higher without the activity of methane-oxidizing bacteria which on a global basis mitigate about 50% of the biologically produced methane. In contrast, methanotrophs in aerated upland soils form the only biological sink for atmospheric methane playing a vital role in the global climate. METHECO is studying diversity and functioning of methanotrophs over a wide range of European ecosystems from the Mediterranean to the Arctic, and from landfills to pristine environments. Our objectives are (i) the definition of meaningful taxonomic units which describe microbial diversity in the habitats studied, (ii) assessing the effects of perturbations on diversity and functioning, (iii) identifying controls of methanotrophic activity and diversity, and (iv) developing a standardized methodology and framework for environmental microbial ecology.

  13. Activities and distribution of methanogenic and methane-oxidizing microbes in marine sediments from the Cascadia Margin.

    PubMed

    Yoshioka, H; Maruyama, A; Nakamura, T; Higashi, Y; Fuse, H; Sakata, S; Bartlett, D H

    2010-06-01

    We investigated methane production and oxidation and the depth distribution and phylogenetic affiliation of a functional gene for methanogenesis, methyl coenzyme M reductase subunit A (mcrA), at two sites of the Integrated Ocean Drilling Program Expedition 311. These sites, U1327 and U1329, are respectively inside and outside the area of gas hydrate distribution on the Cascadia Margin. Radiotracer experiments using (14)C-labelled substrates indicated high potential methane production rates in hydrate-bearing sediments [128-223 m below seafloor (mbsf)] at U1327 and in sediments between 70 and 140 mbsf at U1329. Tracer-free experiments indicated high cumulative methane production in sediments within and below the gas hydrate layer at U1327 and in sediments below 70 mbsf at U1329. Stable tracer experiments using (13)C-labelled methane showed high potential methane oxidation rates in near-surface sediments and in sediments deeper than 100 mbsf at both sites. Results of polymerase chain reaction amplification of mcrA in DNA were mostly consistent with methane production: relatively strong mcrA amplification was detected in the gas hydrate-bearing sediments at U1327, whereas at U1329, it was mainly detected in sediments from around the bottom-simulating reflector (126 mbsf). Phylogenetic analysis of mcrA separated it into four phylotype clusters: two clusters of methanogens, Methanosarcinales and Methanobacteriales, and two clusters of anaerobic methanotrophic archaea, ANME-I and ANME-II groups, supporting the activity measurement results. These results reveal that in situ methanogenesis in deep sediments probably contributes to gas hydrate formation and are inconsistent with the geochemical model that microbial methane currently being generated in shallow sediments migrates downward and contributes to the hydrate formation. At Site U1327, gas hydrates occurred in turbidite sediments, which were absent at Site U1329, suggesting that a geological setting suitable for a

  14. Are termite mounds biofilters for methane? - Challenges and new approaches to quantify methane oxidation in termite mounds

    NASA Astrophysics Data System (ADS)

    Nauer, Philipp A.; Hutley, Lindsay B.; Bristow, Mila; Arndt, Stefan K.

    2015-04-01

    Methane emissions from termites contribute around 3% to global methane in the atmosphere, although the total source estimate for termites is the most uncertain among all sources. In tropical regions, the relative source contribution of termites can be far higher due to the high biomass and relative importance of termites in plant decomposition. Past research focused on net emission measurements and their variability, but little is known about underlying processes governing these emissions. In particular, microbial oxidation of methane (MOX) within termite mounds has rarely been investigated. In well-studied ecosystems featuring an oxic matrix above an anoxic methane-producing habitat (e.g. landfills or sediments), the fraction of oxidized methane (fox) can reach up to 90% of gross production. However, conventional mass-balance approaches to apportion production and consumption processes can be challenging to apply in the complex-structured and almost inaccessible environment of a termite mound. In effect, all field-based data on termite-mound MOX is based on one study that measured isotopic shifts in produced and emitted methane. In this study a closed-system isotope fractionation model was applied and estimated fox ranged from 10% to almost 100%. However, it is shown here that by applying an open-system isotope-pool model, the measured isotopic shifts can also be explained by physical transport of methane alone. Different field-based methods to quantify MOX in termite mounds are proposed which do not rely on assumptions of physical gas transport. A simple approach is the use of specific inhibitors for MOX, e.g. difluoromethane (CH2F2), combined with chamber-based flux measurements before and after their application. Data is presented on the suitability of different inhibitors and first results of their application in the field. Alternatively, gas-tracer methods allow the quantification of methane oxidation and reaction kinetics without knowledge of physical gas

  15. Biomimetic methane oxidation

    NASA Astrophysics Data System (ADS)

    Watkins, B. E.; Droege, M. W.; Taylor, R. T.; Satcher, J. H.

    1992-06-01

    Methane monooxygenase (MMO) is an enzyme found in methanotrophs that catalyses the selective oxidation of methane to methanol. MMO is protein complex one component of which is a binuclear metal center containing oxygenase. We have completed one round of a design/synthesis/evaluation cycle in the development of coordination complexes that mimic the structure/function of the MMO active site. One of these, a binuclear, coordinately-asymmetric copper complex, is capable of oxidizing cyclohexane to a mixture of cyclohexanol and cyclohexanone in the presence of hydrogen peroxide.

  16. Methane oxidation in Swedish landfills quantified with the stable carbon isotope technique in combination with an optical method for emitted methane.

    PubMed

    Börjesson, Gunnar; Samuelsson, Jerker; Chanton, Jeffrey

    2007-10-01

    Methane budgets (production = emissions + oxidation + recovery) were estimated for six landfill sites in Sweden. Methane oxidation was measured in downwind plumes with a stable isotope technique (Chanton, J. P., et al., Environ. Sci Technol. 1999, 33, 3755-3760.) Positions in plumes for isotope sampling as well as methane emissions were determined with an optical instrument (Fourier Transform InfraRed) in combination with N20 as tracer gas (Galle, B., et al., Environ. Sci Technol. 2001, 35, 21-25.) Two landfills had been closed for years prior to the measurements, while four were active. Measurements at comparable soil temperatures showed that the two closed landfills had a significantly higher fraction of oxidized methane (38-42% of emission) relative to the four active landfills (4.6-15% of emission). These results highlight the importance of installing and maintaining effective landfill covers and also indicate that substantial amounts of methane escape from active landfills. Based on these results we recommend that the IPCC default values for methane oxidation in managed landfills could be set to 10% for active sites and 20% for closed sites. Gas recovery was found to be highly variable at the different sites, with values from 14% up to 65% of total methane production. The variance can be attributed to different waste management practices. PMID:17969681

  17. Teaching Aerobic Lifestyles: New Perspectives.

    ERIC Educational Resources Information Center

    Goodrick, G. Ken; Iammarino, Nicholas K.

    1982-01-01

    New approaches to teaching aerobic life-styles in secondary schools are suggested, focusing on three components: (1) the psychological benefits of aerobic activity; (2) alternative aerobic programs at nonschool locations; and (3) the development of an aerobics curriculum to help maintain an active life-style after graduation. (JN)

  18. Sulfate reduction and methane oxidation in continental margin sediments influenced by irrigation (south-east Atlantic off Namibia)

    SciTech Connect

    Fossing, H.; Ferdelman, T.G.; Berg, P.

    2000-03-01

    Sulfate reduction rates (SRR) and concentrations of SO{sub 4}{sup 2{minus}}, H{sub 2}S, pyrite sulfur, total sulfur, CH{sub 4}, and organic carbon were measured with high depth resolution through the entire length of the SO{sub 4}{sup 2{minus}}-zone and well into the CH{sub 4}-xone at two continental slope stations in the eastern South Atlantic (Benguela upwelling area). The sediments were characterized by a high organic carbon content of approx. 7.5% at GeoB 3703 and 3.7% at GeoB 3714. At GeoB 3703 SO{sub 4}{sup 2{minus}} concentrations decreased linearly with depth to about 40 {micro}M at the sulfate-methane transition zone (SMT) at 3.5 m, while at GeoB 3714, SO{sub 4}{sup 2{minus}} remained at sea water concentration in the top 2 m of the sediment and then decreased linearly to about 70 {micro}M at the SMT at 6 m. Direct rate measurements of SRR ({sup 35}SO{sub 4}{sup 2{minus}}) showed that the highest SRR occurred within the surface 3--5 cm with peak rates of up to 20 and 7 nmol SO{sub 4}{sup 2{minus}} cm{sup 3}/day at GeoB 3703 and GeoB 3714, respectively. SRR decreased quasi-exponentially with depth at GeoB 3703 and the cumulative SRR over the length of the SO{sub 4}{sup 2{minus}} zone resulted in an areal SRR of 1114--3493 {micro}mol/m{sup 2} day at GeoB 3703 with more than 80% of the total sulfate reduction proceeding in the top 30 cm sediment. Modeled SRR balanced both methane oxidation rates and measured SRR within the SMT, but severely underestimated by up to 89% the total SRR{sub area} that were obtained from direct measurements. Modeled and measured SRR were reconciled by including solute transport by irrigation described by a non-local pore water exchange function ({alpha}) which had values of up to 0.3 year{sup {minus}1} in the top sediment, and decreased exponentially to zero (i.e., no irrigation) at 2--3 meters (i.e., above SMT). These results suggested that co-existing sulfate reduction processes and linear SO{sub 4}{sup 2{minus}} gradients can be

  19. Aerobic Conditioning Class.

    ERIC Educational Resources Information Center

    Johnson, Neil R.

    1980-01-01

    An aerobic exercise class that focuses on the conditioning of the cardiovascular and muscular systems is presented. Students complete data cards on heart rate, pulse, and exercises to be completed during the forty minute course. (CJ)

  20. [Research advances in aerobic denitrifiers].

    PubMed

    Wang, Wei; Cai, Zu-cong; Zhong, Wen-hui; Wang, Guo-xiang

    2007-11-01

    This paper reviewed the varieties and characteristics of aerobic denitrifiers, their action mechanisms, and the factors affecting aerobic denitrification. Aerobic denitrifiers mainly include Pseudomonas, Alcaligenes, Paracoccus and Bacillus, which are either aerobic or facultative aerobic, and heterotrophic. They can denitrify under aerobic conditions, with the main product being N2O. They can also convert NH4+ -N to gas product. The nitrate reductase which catalyzes the denitrification is periplasmic nitrate reductase rather than membrane-bound nitrate reductase. Dissolved oxygen concentration and C/N ratio are the main factors affecting aerobic denitrification. The main methods for screening aerobic denitrifiers, such as intermittent aeration and selected culture, were also introduced. The research advances in the application of aerobic denitrifiers in aquaculture, waste water processing, and bio-degradation of organic pollutants, as well as the contributions of aerobic denitrifiers to soil nitrogen emission were summarized. PMID:18260473

  1. Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils.

    PubMed

    Lima, Amanda B; Muniz, Aleksander W; Dumont, Marc G

    2014-01-01

    The oxidation of atmospheric CH4 in upland soils is mostly mediated by uncultivated groups of microorganisms that have been identified solely by molecular markers, such as the sequence of the pmoA gene encoding the β-subunit of the particulate methane monooxygenase enzyme. The objective of this work was to compare the activity and diversity of methanotrophs in Amazonian Dark Earth soil (ADE, Hortic Anthrosol) and their adjacent non-anthropic soil. Secondly, the effect of land use in the form of manioc cultivation was examined by comparing secondary forest and plantation soils. CH4 oxidation potentials were measured and the structure of the methanotroph communities assessed by quantitative PCR (qPCR) and amplicon pyrosequencing of pmoA genes. The oxidation potentials at low CH4 concentrations (10 ppm of volume) were relatively high in all the secondary forest sites of both ADE and adjacent soils. CH4 oxidation by the ADE soil only recently converted to a manioc plantation was also relatively high. In contrast, both the adjacent soils used for manioc cultivation and the ADE soil with a long history of agriculture displayed lower CH4 uptake rates. Amplicon pyrosequencing of pmoA genes indicated that USCα, Methylocystis and the tropical upland soil cluster (TUSC) were the dominant groups depending on the site. By qPCR analysis it was found that USCα pmoA genes, which are believed to belong to atmospheric CH4 oxidizers, were more abundant in ADE than adjacent soil. USCα pmoA genes were abundant in both forested and cultivated ADE soil, but were below the qPCR detection limit in manioc plantations of adjacent soil. The results indicate that ADE soils can harbor high abundances of atmospheric CH4 oxidizers and are potential CH4 sinks, but as in other upland soils this activity can be inhibited by the conversion of forest to agricultural plantations. PMID:25374565

  2. Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils

    PubMed Central

    Lima, Amanda B.; Muniz, Aleksander W.; Dumont, Marc G.

    2014-01-01

    The oxidation of atmospheric CH4 in upland soils is mostly mediated by uncultivated groups of microorganisms that have been identified solely by molecular markers, such as the sequence of the pmoA gene encoding the β-subunit of the particulate methane monooxygenase enzyme. The objective of this work was to compare the activity and diversity of methanotrophs in Amazonian Dark Earth soil (ADE, Hortic Anthrosol) and their adjacent non-anthropic soil. Secondly, the effect of land use in the form of manioc cultivation was examined by comparing secondary forest and plantation soils. CH4 oxidation potentials were measured and the structure of the methanotroph communities assessed by quantitative PCR (qPCR) and amplicon pyrosequencing of pmoA genes. The oxidation potentials at low CH4 concentrations (10 ppm of volume) were relatively high in all the secondary forest sites of both ADE and adjacent soils. CH4 oxidation by the ADE soil only recently converted to a manioc plantation was also relatively high. In contrast, both the adjacent soils used for manioc cultivation and the ADE soil with a long history of agriculture displayed lower CH4 uptake rates. Amplicon pyrosequencing of pmoA genes indicated that USCα, Methylocystis and the tropical upland soil cluster (TUSC) were the dominant groups depending on the site. By qPCR analysis it was found that USCα pmoA genes, which are believed to belong to atmospheric CH4 oxidizers, were more abundant in ADE than adjacent soil. USCα pmoA genes were abundant in both forested and cultivated ADE soil, but were below the qPCR detection limit in manioc plantations of adjacent soil. The results indicate that ADE soils can harbor high abundances of atmospheric CH4 oxidizers and are potential CH4 sinks, but as in other upland soils this activity can be inhibited by the conversion of forest to agricultural plantations. PMID:25374565

  3. Hydrogen may be an energy source for endosymbiotic bacteria of the vent mussel Bathymodiolus puteoserpentis

    NASA Astrophysics Data System (ADS)

    Zielinski, F.; Pape, T.; Wenzhöfer, F.; Seifert, R.; Dubilier, N.

    2005-12-01

    (ml gill)-1. The hydrogen concentrations at these sites did not vary greatly either (Irina II 5.9 μM, Quest 4.2 μM). The H2-oxidation rates decreased significantly after removal of B. puteoserpentis from vent fluids for only 1 day suggesting that hydrogen uptake may be regulated by H2-availability or that bacteria were digested by the host due to starvation. The methane-oxidizing symbiont may be responsible for the observed hydrogen consumption. H2-uptake has been shown for the free-living methanotroph Methylococcus capsulatus and its genes coding for a membrane-bound H2-uptake hydrogenase (hupS and hupL) have been cloned and sequenced. We are currently trying to identify the symbiont responsible for H2-consumption by linking the phylogeny of the symbionts with their physiology using simultaneous fluorescence in situ hybridisation of rRNA and mRNA. Furthermore, we plan to analyze the stable isotope composition of hydrogen in the vent fluids and in the mussels.

  4. Enrichment of denitrifying methanotrophic bacteria from Taihu sediments by a membrane biofilm bioreactor at ambient temperature.

    PubMed

    Wang, Shenghui; Wu, Qing; Lei, Ting; Liang, Peng; Huang, Xia

    2016-03-01

    Denitrification coupled to anaerobic methane oxidation is a recently discovered process performed by bacteria affiliated to the NC10 phylum. These microorganisms could play important roles in the energy-efficient way of anaerobic wastewater treatment where residual dissolved methane might be removed at the expense of nitrate or nitrite. The difficulty to enrich these microorganisms due to a slow growth rate, especially at low temperatures, limited its application in engineering field. In this study, an NC10 bacteria community was enriched from Taihu sediments by a membrane biofilm bioreactor at ambient temperature of 10-25 °C. After 13 months enrichment, the maximum denitrification rate of the enriched culture reached 0.54 mM day(-1) for nitrate and 1.06 mM day(-1) for nitrite. Anaerobic methane oxidation coupled denitrification was estimated from the (13)C-labeled CO2 ((13)CO2) production during batch incubations with (13)CH4. Furthermore, analysis of 16S rRNA genes clone library confirmed the presence of NC10 phylum bacteria and fluorescence in situ hybridization showed that NC10 bacteria dominated the reactor. All of the results indicated the NC10 bacteria community was competitive in terms of treating nitrate-contaminated water or wastewater under natural conditions. PMID:26578374

  5. Comparative studies of pelagic microbial methane oxidation within two anoxic basins of the central Baltic Sea (Gotland Deep and Landsort Deep)

    NASA Astrophysics Data System (ADS)

    Jakobs, G.; Rehder, G.; Jost, G.; Kießlich, K.; Labrenz, M.; Schmale, O.

    2013-07-01

    Pelagic methane oxidation was investigated in dependence on differing environmental conditions within the redox zone of the Gotland Deep (GD) and Landsort Deep (LD), central Baltic Sea. The redox zone of both deeps, which indicates the transition between oxic and anoxic conditions, was characterized by a pronounced methane concentration gradient between the deep water (GD: 1233 nM, LD: 2935 nM) and the surface water (GD and LD < 10 nM), together with a 13C CH4 enrichment (δ13C CH4 deep water: GD -84‰, LD -71‰ ; redox zone: GD -60‰, LD -20‰ ; δ13C CH4 vs. Vienna Pee Dee Belemnite standard), clearly indicating microbial methane consumption in that specific depth interval. Expression analysis of the methane monooxygenase identified one active type I methanotrophic bacterium in both redox zones. In contrast, the turnover of methane within the redox zones showed strong differences between the two basins (GD: max. 0.12 nM d-1 and LD: max. 0.61 nM d-1), with a four times higher turnover rate constant (k) in the LD (GD: 0.0022 d-1, LD: 0.0079 d-1). Vertical mixing rates for both deeps were calculated on the base of the methane concentration profile and the consumption of methane in the redox zone (GD: 2.5 × 10-6 m2 s-1 LD: 1.6 × 10-5 m2 s-1). Our study identified vertical transport of methane from the deep water body towards the redox zone as well as differing hydrographic conditions within the oxic/anoxic transition zone of these deeps as major factors that determine the pelagic methane oxidation.

  6. Comparative studies of pelagic microbial methane oxidation within the redox zones of the Gotland Deep and Landsort Deep (central Baltic Sea)

    NASA Astrophysics Data System (ADS)

    Jakobs, G.; Rehder, G.; Jost, G.; Kießlich, K.; Labrenz, M.; Schmale, O.

    2013-12-01

    Pelagic methane oxidation was investigated in dependence on differing hydrographic conditions within the redox zone of the Gotland Deep (GD) and Landsort Deep (LD), central Baltic Sea. The redox zone of both deeps, which indicates the transition between oxic and anoxic conditions, was characterized by a pronounced methane concentration gradient between the deep water (GD: 1233 nM, 223 m; LD: 2935 nM, 422 m) and the surface water (GD and LD < 10 nM). This gradient together with a 13C CH4 enrichment (δ13C CH4 deep water: GD -84‰, LD -71‰; redox zone: GD -60‰, LD -20‰; surface water: GD -47‰, LD -50‰; δ13C CH4 vs. Vienna Pee Dee Belemnite standard), clearly indicating microbial methane consumption within the redox zone. Expression analysis of the methane monooxygenase identified one active type I methanotrophic bacterium in both redox zones. In contrast, the turnover of methane within the redox zones showed strong differences between the two basins (GD: max. 0.12 nM d-1, LD: max. 0.61 nM d-1), with a nearly four-times-lower turnover time of methane in the LD (GD: 455 d, LD: 127 d). Vertical mixing rates for both deeps were calculated on the base of the methane concentration profile and the consumption of methane in the redox zone (GD: 2.5 × 10-6 m2 s-1, LD: 1.6 × 10-5 m2 s-1). Our study identified vertical transport of methane from the deep-water body towards the redox zone as well as differing hydrographic conditions (lateral intrusions and vertical mixing) within the redox zone of these deeps as major factors that determine the pelagic methane oxidation.

  7. A Year in the Life: Annual Patterns of CO2 and CH4 from a Northern Finland Peatland, Including Anaerobic Methane Oxidation and Summer Ebullition Rates

    NASA Astrophysics Data System (ADS)

    Miller, K.; Lipson, D.; Biasi, C.; Dorodnikov, M.; Männistö, M.; Lai, C. T.

    2014-12-01

    The major ecological controls on methane (CH4) and carbon dioxide (CO2) fluxes in northern wetland systems are well known, yet estimates of source/sink magnitudes are often incongruous with measured rates. This mismatch persists because holistic flux datasets are rare, preventing 'whole picture' determinations of flux controls. To combat this, we measured net CO2 and CH4 fluxes from September 2012-2013 within a peatland in northern Lapland, Finland. In addition, we performed in situ manipulations and in vitro soil incubations to quantify anaerobic methane oxidation and methanogenic rates as they related to alternative electron acceptor availability. Average annual fluxes varied substantially between different depressions within the wetland, a pattern that persisted through all seasons. Season was a strong predictor of both CO2 and CH4 flux rates, yet CH4 rates were not related to melt-season 10cm or 30cm soil temperatures, and only poorly predicted with air temperatures. We found evidence for both autumnal and spring thaw CH4 bursts, collectively accounting for 26% of annual CH4 flux, although the autumnal burst was more than 5 fold larger than the spring burst. CH4 ebullition measured throughout the growing season augmented the CH4 source load by a factor of 1.5, and was linked with fine-scale spatial heterogeneity within the wetland. Surprisingly, CH4 flux rates were insensitive to Fe(III) and humic acid soil amendments, both of which amplified CO2 fluxes. Using in vitro incubations, we determined anaerobic methane oxidation and methanogenesis rates. Measured anaerobic oxidation rates showed potential consumption of between 6-39% of the methane produced, contributing approximately 1% of total carbon dioxide flux. Treatments of nitrate, sulfate and ferric iron showed that nitrate suppressed methanogenesis, but were not associated with anaerobic oxidation rates.

  8. Methane Oxidation on Pd-Ceria. A DFT Study of the Combustion Mechanism over Pd, PdO and Pd-ceria Sites

    SciTech Connect

    Mayernick, Adam D.; Janik, Michael J.

    2010-12-24

    Palladium/ceria exhibits unique catalytic activity for hydrocarbon oxidation; however, the chemical and structural properties of active sites on the palladium–ceria surface are difficult to characterize. Strong interactions between palladium and the ceria support stabilize oxidized Pdδ+ species, which may contribute to the significant activity of Pd/ceria for methane oxidation. We present a density functional theory (DFT + U) investigation into methane oxidation over Pd/ceria and quantify the activity of the PdxCe1-xO2(1 1 1) mixed oxide surface in comparison with the PdO(1 0 0) and Pd(1 1 1) surfaces. The methane activation barrier is lowest over the PdxCe1-xO2(1 1 1) surface, even lower than over the Pd(1 1 1) surface or low coordinated stepped or kinked Pd sites. Subsequent reaction steps in complete oxidation, including product desorption and vacancy refilling, are considered to substantiate that methane activation remains the rate-limiting step despite the low barrier over PdxCe1-xO2(1 1 1). The low barrier over the PdxCe1-xO2(1 1 1) surface demonstrates that mixed ceria-noble metal oxides offer the potential for improved hydrocarbon oxidation performance with respect to dispersed noble metal particles on ceria.

  9. 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)

  10. 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...

  11. 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...

  12. 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)

  13. Managing for Improved Aerobic Stability

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aerobic deterioration or spoilage of silage is the result of aerobic microorganisms metabolizing components of the silage using oxygen. In the almost 40 years over which these silage conferences have been held, we have come to recognize the typical pattern of aerobic microbial development by which s...

  14. An analytical model for estimating the reduction of methane emission through landfill cover soils by methane oxidation.

    PubMed

    Yao, Yijun; Su, Yao; Wu, Yun; Liu, Weiping; He, Ruo

    2015-01-01

    Landfill is an important source of atmospheric methane (CH4). In this study, the development and partial validation are presented for an analytical model for predicting the reduction of CH4 emission in landfill cover soils by CH4 oxidation. The model combines an analytic solution of a coupled oxygen (O2) and CH4 soil gas transport in landfill covers with a piecewise first-order aerobic biodegradation, including the influences of environmental factors such as cover soil thickness, CH4 oxidation and CH4 production rate. Comparison of soil gas concentration profiles with a soil column experiment is provided for a partial validation, and then this model is applied to predict the reduction of CH4 emission through landfill covers in several other cases. A discussion is provided to illustrate the roles of soil layer thickness, reaction rate constant for CH4 oxidation and CH4 production rate in determining CH4 emissions. The results suggest that the increase of cover soil thickness cannot always increase CH4 oxidation rates or removal efficiency, which becomes constant if the thickness of landfill cover soil is larger than a limit. PMID:25464331

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

    PubMed

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

    2015-08-15

    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

  16. 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

  17. 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. PMID:26139241

  18. Taxonomy of Aerobic Marine Eubacteria

    PubMed Central

    Baumann, Linda; Baumann, Paul; Mandel, M.; Allen, Richard D.

    1972-01-01

    Two hundred and eighteen strains of nonfermentative marine bacteria were submitted to an extensive morphological, physiological, and nutritional characterization. All the strains were gram-negative, straight or curved rods which were motile by means of polar or peritrichous flagella. A wide variety of organic substrates served as sole sources of carbon and energy. The strains differed extensively in their nutritional versatility, being able to utilize from 11 to 85 carbon compounds. Some strains had an extracellular amylase, gelatinase, lipase, or chitinase and were able to utilize n-hexadecane and to denitrify. None of the strains had a yellow, cell-associated pigment or a constitutive arginine dihydrolase system, nor were they able to hydrolyze cellulose or agar. The results of the physiological and nutritional characterization were submitted to a numerical analysis which clustered the strains into 22 groups on the basis of phenotypic similarities. The majority of these groups were separable by a large number of unrelated phenotypic traits. Analysis of the moles per cent guanine plus cytosine (GC) content in the deoxyribonucleic acid of representative strains indicated that the peritrichously flagellated groups had a GC content of 53.7 to 67.8 moles%; polarly flagellated strains had a GC content of 30.5 to 64.7 moles%. The peritrichously flagellated groups were assigned to the genus Alcaligenes. The polarly flagellated groups, which had a GC content of 43.2 to 48.0 moles%, were placed into a newly created genus, Alteromonas; groups which had a GC content of 57.8 to 64.7 moles% were placed into the genus Pseudomonas; and the remaining groups were left unassigned. Twelve groups were given the following designations: Alteromonas communis, A. vaga, A. macleodii, A. marinopraesens, Pseudomonas doudoroffi, P. marina, P. nautica, Alcaligenes pacificus, A. cupidus, A. venustus, and A. aestus. The problems of assigning species of aerobic marine bacteria to genera are

  19. Taxonomy of aerobic marine eubacteria.

    PubMed

    Baumann, L; Baumann, P; Mandel, M; Allen, R D

    1972-04-01

    Two hundred and eighteen strains of nonfermentative marine bacteria were submitted to an extensive morphological, physiological, and nutritional characterization. All the strains were gram-negative, straight or curved rods which were motile by means of polar or peritrichous flagella. A wide variety of organic substrates served as sole sources of carbon and energy. The strains differed extensively in their nutritional versatility, being able to utilize from 11 to 85 carbon compounds. Some strains had an extracellular amylase, gelatinase, lipase, or chitinase and were able to utilize n-hexadecane and to denitrify. None of the strains had a yellow, cell-associated pigment or a constitutive arginine dihydrolase system, nor were they able to hydrolyze cellulose or agar. The results of the physiological and nutritional characterization were submitted to a numerical analysis which clustered the strains into 22 groups on the basis of phenotypic similarities. The majority of these groups were separable by a large number of unrelated phenotypic traits. Analysis of the moles per cent guanine plus cytosine (GC) content in the deoxyribonucleic acid of representative strains indicated that the peritrichously flagellated groups had a GC content of 53.7 to 67.8 moles%; polarly flagellated strains had a GC content of 30.5 to 64.7 moles%. The peritrichously flagellated groups were assigned to the genus Alcaligenes. The polarly flagellated groups, which had a GC content of 43.2 to 48.0 moles%, were placed into a newly created genus, Alteromonas; groups which had a GC content of 57.8 to 64.7 moles% were placed into the genus Pseudomonas; and the remaining groups were left unassigned. Twelve groups were given the following designations: Alteromonas communis, A. vaga, A. macleodii, A. marinopraesens, Pseudomonas doudoroffi, P. marina, P. nautica, Alcaligenes pacificus, A. cupidus, A. venustus, and A. aestus. The problems of assigning species of aerobic marine bacteria to genera are

  20. Aerobic bacterial catabolism of persistent organic pollutants - potential impact of biotic and abiotic interaction.

    PubMed

    Jeon, Jong-Rok; Murugesan, Kumarasamy; Baldrian, Petr; Schmidt, Stefan; Chang, Yoon-Seok

    2016-04-01

    Several aerobic bacteria possess unique catabolic pathways enabling them to degrade persistent organic pollutants (POPs), including polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs), polybrominated diphenylethers (PBDEs), and polychlorinated biphenyls (PCBs). The catabolic activity of aerobic bacteria employed for removal of POPs in the environment may be modulated by several biotic (i.e. fungi, plants, algae, earthworms, and other bacteria) and abiotic (i.e. zero-valent iron, advanced oxidation, and electricity) agents. This review describes the basic biochemistry of the aerobic bacterial catabolism of selected POPs and discusses how biotic and abiotic agents enhance or inhibit the process. Solutions allowing biotic and abiotic agents to exert physical and chemical assistance to aerobic bacterial catabolism of POPs are also discussed. PMID:26851837

  1. Lipid Biomarkers Indicating Aerobic Methanotrophy at Ancient Marine Methane- Seeps

    NASA Astrophysics Data System (ADS)

    Birgel, D.; Peckmann, J.

    2007-12-01

    The inventory of lipid biomarkers of a number of ancient methane-seep limestones has been studied over the last decade. The molecular fingerprints of the chemosynthesis-based microbial communities tend to be extremely well-preserved in these limestones. The key process at seeps is the anaerobic oxidation of methane, performed by consortia of sulfate-reducing bacteria and methanotrophic archaea. Compounds preserved within modern and ancient seep settings comprise C-13-depleted lipid biomarkers. Besides the occurrence of C-13- depleted isoprenoids (archaea) and n-alkyl-chains (bacteria), C-13-depleted hopanoids have been reported in seep limestones. Here, lipid biomarker data are presented from three ancient methane-seep limestones embedded in Miocene and Campanian strata. These examples provide strong evidence that methane was not solely oxidized by an anaerobic process. In a Miocene limestone, 3-beta-methylated hopanoids were found (delta C-13: -100 per mil). Most likely, 3-beta-methylated hopanepolyols, prevailing in aerobic methanotrophs were the precursor lipids. In another Miocene limestone, a series of C-13-depleted 4-methylated steranes (lanostanes; -80 to -70 per mil) is derived from aerobic methanotrophs. Lanosterol is the most likely precursor of lanostanes, known to be produced by aerobic methanotrophs, some of which are outstanding among bacteria in having the capacity to produce steroids. In a Campanian seep limestone a suite of conspicuous secohexahydrobenzohopanes (-110 to -107 per mil) is found. These hopanoids probably represent early degradation products of seep-endemic aerobic methanotrophs. This interpretation is supported by the presence of "regular" hopanoids that can be discriminated from the unusual secohexahydrobenzohopanes by only moderately low delta C-13 values (-49 to -42 per mil). Structural and carbon isotope data reveal that aerobic methanotrophy is more common at ancient methane- seeps than previously noticed. Our data indicate that

  2. 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

  3. New Routes for Aerobic Biodegradation of Dimethylsulfoniopropionate

    PubMed Central

    Taylor, Barrie F.; Gilchrist, Darrin C.

    1991-01-01

    Dimethylsulfoniopropionate (DMSP), an osmolyte in marine plants, is biodegraded by cleavage of dimethyl sulfide (DMS) or by demethylation to 3-methiolpropionate (MMPA) and 3-mercaptopropionate (MPA). Sequential demethylation has been observed only with anoxic slurries of coastal sediments. Bacteria that grew aerobically on MMPA and DMSP were isolated from marine environments and phytoplankton cultures. Enrichments with DMSP selected for bacteria that generated DMS, whereas MMPA enrichments selected organisms that produced methanethiol (CH3SH) from either DMSP or MMPA. A bacterium isolated on MMPA grew on MMPA and DMSP, but rapid production of CH3SH from DMSP occurred only with DMSP-grown cells. Low levels of MPA accumulated during growth on MMPA, indicating demethylation as well as demethiolation of MMPA. The alternative routes for DMSP biodegradation via MMPA probably impact on net DMS fluxes to the marine atmosphere. PMID:16348607

  4. Mechanically-biologically treated municipal solid waste as a support medium for microbial methane oxidation to mitigate landfill greenhouse emissions.

    PubMed

    Einola, Juha-Kalle M; Karhu, A Elina; Rintala, Jukka A

    2008-01-01

    The residual fraction of mechanically-biologically treated municipal solid waste (MBT residual) was studied in the laboratory to evaluate its suitability and environmental compatibility as a support medium in methane (CH(4)) oxidative biocovers for the mitigation of greenhouse gas emissions from landfills. Two MBT residuals with 5 and 12 months total (aerobic) biological stabilisation times were used in the study. MBT residual appeared to be a favourable medium for CH(4) oxidation as indicated by its area-based CH(4) oxidation rates (12.2-82.3 g CH(4) m(-2) d(-1) at 2-25 degrees C; determined in CH(4)-sparged columns). The CH(4) oxidation potential (determined in batch assays) of the MBT residuals increased during the 124 d column experiment, from <1.6 to a maximum of 104 microg CH(4) g(dw)(-1) h(-1) (dw=dry weight) at 5 degrees C and 578 microg CH(4) g(dw)(-1) h(-1) at 23 degrees C. Nitrous oxide (N(2)O) production in MBT residual (<15 microg N(2)O kg(dw)(-1) d(-1) in the CH(4) oxidative columns) was at the lower end of the range of N(2)O emissions reported for landfills and non-landfill soils, and insignificant as a greenhouse gas source. Also, anaerobic gas production (25.6 l kg(dw)(-1) during 217 d) in batch assays was low, indicating biological stability of the MBT residual. The electrical conductivities (140-250 mS m(-1)), as well as the concentrations of zinc (3.0 mg l(-1)), copper (0.5 mg l(-1)), arsenic (0.3 mg l(-1)), nickel (0.1 mg l(-1)) and lead (0.1 mg l(-1)) in MBT residual eluates from a leaching test (EN-12457-4) with a liquid/solid (L/S) ratio of 10:1, suggest a potential for leachate pollutant emissions which should be considered in plans to utilise MBT residual. In conclusion, the laboratory experiments suggest that MBT residual can be utilised as a support medium for CH(4) oxidation, even at low temperatures, to mitigate greenhouse gas emissions from landfills. PMID:17360174

  5. Assessing methane oxidation under landfill covers and its contribution to the above atmospheric CO₂ levels: the added value of the isotope (δ¹³C and δ¹⁸O CO₂; δ¹³C and δD CH₄) approach.

    PubMed

    Widory, D; Proust, E; Bellenfant, G; Bour, O

    2012-09-01

    We are presenting here a multi-isotope approach (δ¹³C and δ¹⁸O of CO₂; δ¹³C and δD of CH₄) to assess (i) the level(s) of methane oxidation during waste biodegradation and its migration through a landfill cover in Sonzay (France), and (ii) its contribution to the atmospheric CO₂ levels above the surface. The isotope approach is compared to the more conventional mass balance approach. Results from the two techniques are comparable and show that the CH₄ oxidation under the landfill cover is heterogenous, with low oxidation percentages in samples showing high biogas fluxes, which was expected in clay covers presenting fissures, through which CH₄ is rapidly transported. At shallow depth, more immobile biogas pockets show a higher level of CH₄ oxidation by the methanotrophic bacteria. δ¹³C of CO₂ samples taken at different heights (from below the cover up to 8m above the ground level) were also used to identify and assess the relative contributions of its main sources both under the landfill cover and in the surrounding atmosphere. PMID:22608681

  6. Identification of Methane, Ethane, and Propane Oxidizing Bacteria at Marine Hydrocarbon Seeps by Stable Isotope Probing

    NASA Astrophysics Data System (ADS)

    Redmond, M.; Ding, H.; Friedrich, M. W.; Valentine, D. L.

    2008-12-01

    Hydrocarbon seeps emit substantial amounts of oil and natural gas into the marine environment, where they can be oxidized by microorganisms in the sediment and water column. Here, we used stable isotope probing of DNA and lipid biomarkers to identify the microorganisms actively consuming 13C-labeled natural gas compounds in seep sediment samples. Surface sediment was collected from the Coal Oil Point seep field (offshore Santa Barbara, California, USA) and incubated under aerobic conditions with 13C labeled methane, ethane, or propane for up to 37 days, with sediment sub-samples taken at 3-4 intermediate time points. DNA was extracted from sediment and separated by CsCl density gradient centrifugation. The microbial community in each fraction was profiled using T-RFLP, and bacterial 16S rRNA gene clone libraries were constructed from un-incubated hydrocarbon seep sediment and selected isotopically 'heavy' (13C) and 'light' (12C) gradient fractions from ethane incubations. All clone libraries were dominated by sequences from members of the family Rhodobacteraceae (>25% of sequences) and a diverse group of Gammaproteobacteria, including sequences related to those of methylotrophs and to those of bacteria known to consume the longer-chain alkanes present in crude oil. After 14 days of incubation, the relative abundance of Rhodobacteraceae was higher in 'heavy' fractions from the 13C-ethane incubation than in 'light' fractions, suggesting incorporation of 13C label. The Rhodobacteraceae are very diverse metabolically, but have often been observed in abundance in oil contaminated seawater. Several members of this group have been shown to oxidize longer chain alkanes (C10 or higher), but none have been previously linked to the consumption of the gaseous alkanes ethane, propane, and butane. For the final time point, 13C content of phospholipid fatty acids (PLFA) were also analyzed, showing substantial incorporation of 13C over 37 days. In the methane incubation

  7. Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria

    PubMed Central

    Okubo, Takashi; Liu, Dongyan; Tsurumaru, Hirohito; Ikeda, Seishi; Asakawa, Susumu; Tokida, Takeshi; Tago, Kanako; Hayatsu, Masahito; Aoki, Naohiro; Ishimaru, Ken; Ujiie, Kazuhiro; Usui, Yasuhiro; Nakamura, Hirofumi; Sakai, Hidemitsu; Hayashi, Kentaro; Hasegawa, Toshihiro; Minamisawa, Kiwamu

    2015-01-01

    A number of studies have shown that elevated atmospheric CO2 ([CO2]) affects rice yields and grain quality. However, the responses of root-associated bacteria to [CO2] elevation have not been characterized in a large-scale field study. We conducted a free-air CO2 enrichment (FACE) experiment (ambient + 200 μmol.mol−1) using three rice cultivars (Akita 63, Takanari, and Koshihikari) and two experimental lines of Koshihikari [chromosome segment substitution and near-isogenic lines (NILs)] to determine the effects of [CO2] elevation on the community structure of rice root-associated bacteria. Microbial DNA was extracted from rice roots at the panicle formation stage and analyzed by pyrosequencing the bacterial 16S rRNA gene to characterize the members of the bacterial community. Principal coordinate analysis of a weighted UniFrac distance matrix revealed that the community structure was clearly affected by elevated [CO2]. The predominant community members at class level were Alpha-, Beta-, and Gamma-proteobacteria in the control (ambient) and FACE plots. The relative abundance of Methylocystaceae, the major methane-oxidizing bacteria in rice roots, tended to decrease with increasing [CO2] levels. Quantitative PCR revealed a decreased copy number of the methane monooxygenase (pmoA) gene and increased methyl coenzyme M reductase (mcrA) in elevated [CO2]. These results suggest elevated [CO2] suppresses methane oxidation and promotes methanogenesis in rice roots; this process affects the carbon cycle in rice paddy fields. PMID:25750640

  8. Aerobic and Anaerobic Bacteriology of Hidradenitis Suppurativa: A Study of 22 Cases

    PubMed Central

    Katoulis, Alexandros C.; Koumaki, Dimitra; Liakou, Aikaterini I.; Vrioni, Georgia; Koumaki, Vasiliki; Kontogiorgi, Dimitra; Tzima, Korina; Tsakris, Athanasios; Rigopoulos, Dimitris

    2015-01-01

    Introduction Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease of unclear etiology. The role of bacteria in the pathogenesis of disease remains controversial. Materials and Methods Specimens were obtained from 22 HS patients by direct percutaneous needle aspiration. The collected material was cultured in aerobic and anaerobic conditions, and sensitivity tests were performed. Results Of the 22 patients, 32% were culture negative and 68% were culture positive. A total of 16 isolates was obtained, 14 aerobic and 2 anaerobic. Aerobic bacteria were present in 86% of the specimens, whereas only anaerobic bacteria were isolated in 7%. The predominant aerobic species were Proteus mirabilis, Staphylococcus haemolyticus and Staphylococcus lugdunensis. The isolated anaerobic bacteria were Dermacoccus nishinomiyaensis and Propionibacterium granulosum. Conclusion A variety of aerobic and anaerobic bacteria was isolated from the HS lesions of our patients. In contrast to previous studies, fewer patients were found to be culture positive, and Staphylococcus aureus was isolated in only 1 of them. More studies are necessary to elucidate the controversial role of bacteria in the pathogenesis of HS. PMID:27170935

  9. Kinetics of biological methane oxidation in the presence of non-methane organic compounds in landfill bio-covers

    SciTech Connect

    Albanna, Muna; Warith, Mostafa; Fernandes, Leta

    2010-02-15

    In this experimental program, the effects of non-methane organic compounds (NMOCs) on the biological methane (CH{sub 4}) oxidation process were examined. The investigation was performed on compost experiments incubated with CH{sub 4} and selected NMOCs under different environmental conditions. The selected NMOCs had different concentrations and their effects were tested as single compounds and mixtures of compounds. The results from all experimental sets showed a decrease in CH{sub 4} oxidation capacity of the landfill bio-cover with the increase in NMOCs concentrations. For example, in the experiment using compost with 100% moisture content at 35 deg. C without any NMOCs the V{sub max} value was 35.0 mug CH{sub 4}h{sup -1}g{sub wetwt}{sup -1}. This value was reduced to 19.1 mug CH{sub 4}h{sup -1}g{sub wetwt}{sup -1} when mixed NMOCs were present in the batch reactors under the same environmental conditions. The experimental oxidation rates of CH{sub 4} in the presence of single and mixed NMOCs were modeled using the uncompetitive inhibition model and kinetic parameters, including the dissociation constants, were obtained. Additionally, the degradation rates of the NMOCs and co-metabolic abilities of methanotrophic bacteria were estimated.

  10. Kinetics of biological methane oxidation in the presence of non-methane organic compounds in landfill bio-covers.

    PubMed

    Albanna, Muna; Warith, Mostafa; Fernandes, Leta

    2010-02-01

    In this experimental program, the effects of non-methane organic compounds (NMOCs) on the biological methane (CH4) oxidation process were examined. The investigation was performed on compost experiments incubated with CH4 and selected NMOCs under different environmental conditions. The selected NMOCs had different concentrations and their effects were tested as single compounds and mixtures of compounds. The results from all experimental sets showed a decrease in CH4 oxidation capacity of the landfill bio-cover with the increase in NMOCs concentrations. For example, in the experiment using compost with 100% moisture content at 35 degrees C without any NMOCs the V(max) value was 35.0 microg CH4 h(-1)gwet wt(-1). This value was reduced to 19.1 microg CH4 h(-1) gwet wt(-1) when mixed NMOCs were present in the batch reactors under the same environmental conditions. The experimental oxidation rates of CH4 in the presence of single and mixed NMOCs were modeled using the uncompetitive inhibition model and kinetic parameters, including the dissociation constants, were obtained. Additionally, the degradation rates of the NMOCs and co-metabolic abilities of methanotrophic bacteria were estimated. PMID:19896356

  11. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

    SciTech Connect

    Glass, DR. Jennifer; Yu, DR. Hang; Steele, Joshua; Dawson, Katherine; Sun, S; Chourey, Karuna; Pan, Chongle; Hettich, Robert {Bob} L; Orphan, V

    2013-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphiderich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulphidic (> 1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5 270 nM), cobalt (0.5 6 nM), molybdenum (10 5600 nM) and tungsten (0.3 8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.

  12. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulfidic marine sediments

    SciTech Connect

    Glass, DR. Jennifer; Yu, DR. Hang; Steele, Joshua; Dawson, Katherine; Sun, S; Chourey, Karuna; Hettich, Robert {Bob} L; Orphan, V

    2014-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyze important biogeochemical reactions. In anoxic methane- and sulfide-rich environments, microbes may have unique adaptations for metal acquisition and utilization due to decreased bioavailability as a result of metal sulfide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulfidic (>1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5,600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalyzing anaerobic oxidation of methane utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrotolerant microorganisms. Finally, our data suggest that chemical speciation of metals in highly sulfidic porewaters may exert a stronger influence on microbial bioavailability than total concentration

  13. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments.

    PubMed

    Glass, Jennifer B; Yu, Hang; Steele, Joshua A; Dawson, Katherine S; Sun, Shulei; Chourey, Karuna; Pan, Chongle; Hettich, Robert L; Orphan, Victoria J

    2014-06-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (≤ 10°C) and sulphidic (> 1 mM ΣH(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments. PMID:24148160

  14. Aerobic landfill bioreactor

    DOEpatents

    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.

  15. Aerobic landfill bioreactor

    DOEpatents

    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.

  16. CH4/CO2 ratios indicate highly efficient methane oxidation by a pumice landfill cover-soil.

    PubMed

    Pratt, Chris; Walcroft, Adrian S; Deslippe, Julie; Tate, Kevin R

    2013-02-01

    Landfills that generate too little biogas for economic energy recovery can potentially offset methane (CH(4)) emissions through biological oxidation by methanotrophic bacteria in cover soils. This study reports on the CH(4) oxidation efficiency of a 10-year old landfill cap comprising a volcanic pumice soil. Surface CH(4) and CO(2) fluxes were measured using field chambers during three sampling intervals over winter and summer. Methane fluxes were temporally and spatially variable (-0.36 to 3044 mgCH(4)m(-2)h(-1)); but were at least 15 times lower than typical literature CH(4) fluxes reported for older landfills in 45 of the 46 chambers tested. Exposure of soil from this landfill cover to variable CH(4) fluxes in laboratory microcosms revealed a very strong correlation between CH(4) oxidation efficiency and CH(4)/CO(2) ratios, confirming the utility of this relationship for approximating CH(4) oxidation efficiency. CH(4)/CO(2) ratios were applied to gas concentrations from the surface flux chambers and indicated a mean CH(4) oxidation efficiency of 72%. To examine CH(4) oxidation with soil depth, we collected 10 soil depth profiles at random locations across the landfill. Seven profiles exhibited CH(4) removal rates of 70-100% at depths <60 cm, supporting the high oxidation rates observed in the chambers. Based on a conservative 70% CH(4) oxidation efficiency occurring at the site, this cover soil is clearly offsetting far greater CH(4) quantities than the 10% default value currently adopted by the IPCC. PMID:23186636

  17. Anaerobic bacteria

    MedlinePlus

    Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these ... Goldstein EJ. Diseases caused by non-spore forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman's ...

  18. Temporal resilience and dynamics of anaerobic methane-oxidizing microbial communities to short-term changes in methane partial pressures

    NASA Astrophysics Data System (ADS)

    Klasek, S.; Tiantian, Y.; Torres, M. E.; Colwell, F. S.; Wang, F.; Liang, L.

    2015-12-01

    Marine sediments produce tens to hundreds of teragrams of methane annually, which is released from the seabed at thousands of cold seeps distributed globally along continental margins. Around 80-90% of this methane is consumed in shallower sediment layers before reaching the hydrosphere, in a microbially-mediated process known as anaerobic oxidation of methane (AOM) However, cold seeps appear to exhibit temporal variation in gas flux intensity, and AOM filter efficiency at cold seeps generally decreases with fluid flow rate. To our knowledge, the degree to which temporal heterogeneity in subsurface methane flux stimulates AOM community growth and adaptation to increased methane concentrations has not been investigated. Static high-pressure bioreactors were used to incubate sulfate-methane transition zone (SMTZ) and methanogenic zone sediments underlying a Mediterranean mud volcano gas flare under in situ temperature and pressure at 8 MPa methane. Sulfide production rates of 0.4 μmol/cm3/day in both sediment regimes after 4 months of incubation suggested the resilience of the marine subsurface methane filter may extend well below the SMTZ (40 cm). Similar incubations of SMTZ samples from below a gas flare off Svalbard at saturating (3.8 MPa) and 0.2 MPa methane are being sampled after 1 week, 4 weeks, and 4 months; sulfide production rates of 8-18 nmol/cm3/day were first observed after 4 weeks of incubation. Sediment samples at all specified time points for both sets of incubations were collected for nucleic acid extraction and cell fixation. Anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) are expected dominant taxa in enriched and non-enriched communities. 16S rDNA community analysis is expected to reveal additional microbial players involved in the short-term adaptation to higher methane partial pressures in the marine subsurface. Increased AOM community activity (RNA/DNA ratio) and copy numbers of methane cycling transcripts (mcr

  19. Ground heating and methane oxidation processes at shallow depth in Terre Calde di Medolla (Italy): Observations and conceptual model

    NASA Astrophysics Data System (ADS)

    Capaccioni, Bruno; Tassi, Franco; Cremonini, Stefano; Sciarra, Alessandra; Vaselli, Orlando

    2015-05-01

    The toponym "Terre Calde di Medolla" (literally, "Warm Earths of Medolla") refers to a farming area, located near the town of Modena (Emilia-Romagna region, northern Italy), which has always been known by the local population for the relatively high temperatures of the soil. This phenomenon is particularly evident in wintertime when the snow cover over this area rapidly melts. A detailed investigation, carried out after the devastating 2012 Emilia earthquake that affected this area, showed soil temperatures up to 44°C, i.e., 20-25°C above the local background value, together with diffuse soil fluxes of CH4 (0-2432 g × m-2 × d-1) and minor, though significant, CO2 (0-1184 g × m-2 × d-1), especially from subcircular (a few meters in diameter) zones. Ground heating and gas seepage appear spatially correlated, thus suggesting a close relationship between the two phenomena. The anomalous high ground temperature is not associated with an anomalous geothermal gradient or with the uprising of deep-seated hot fluids. According to the lateral and vertical distributions of the temperatures as well as the chemical and isotopic compositions of the soil gases, the most reliable explanation is the exothermic oxidation of diffusely uprising biogenic methane at very shallow levels (<1 m). Such a process occurs in the presence of free oxygen and methanotrophic bacteria and can then explain (i) the observed ground heating up, (ii) the diffuse emission from the soil of CO2 characterized by an extremely negative isotopic (13C/12C) signature, and (iii) the lack of diffuse and low CH4 fluxes. According to these hypotheses, the heating phenomena affecting the shallow groundwater and the ground surface, as described by several witnesses in the area of the May-June 2012 Emilia earthquake, could be related to either a coseismic or postseismic onset of new areas affected by CH4 seepage or an increase in preexisting CH4 fluxes.

  20. Aerobic Fitness and School Children.

    ERIC Educational Resources Information Center

    Hinkle, J. Scott

    1997-01-01

    Provides school counselors with information on aerobic exercise (specifically running) and the psychological, behavioral, and physical benefits children obtained by participating in fitness programs. Recommends collaboration between school counselors and physical education teachers and gives a preliminary discussion of aerobic running and its…

  1. Aerobic Fitness and School Children.

    ERIC Educational Resources Information Center

    Hinkle, J. Scott

    1992-01-01

    Provides school counselors with information regarding aerobic exercise (specifically running), and the psychological, behavioral, and physical benefits children obtain by participating in fitness programs. Presents methods of collaboration between school counselors and physical education teachers. Offers preliminary discussion of aerobic running…

  2. 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…

  3. What are the differences between aerobic and anaerobic toxic effects of sulfonamides on Escherichia coli?

    PubMed

    Qin, Mengnan; Lin, Zhifen; Wang, Dali; Long, Xi; Zheng, Min; Qiu, Yanling

    2016-01-01

    Bacteria in the environment face the threat of antibiotics. However, most studies investigating the toxicity and toxicity mechanisms of antibiotics have been conducted on microorganisms in aerobic conditions, while studies examining the anaerobic toxicity and toxicity mechanisms of antibiotics are still limited. In this study, we determined the aerobic and anaerobic toxicities of sulfonamides (SAs) on Escherichia coli. Next, a comparison of the aerobic and anaerobic toxicities indicated that the SAs could be divided into three groups: Group I: log(1/EC50-anaerobic)>log(1/EC50-aerobic) (EC50-anaerobic/EC50-aerobic, the median effective concentration under anaerobic/aerobic conditions), Group II: log(1/EC50-anaerobic)≈log(1/EC50-aerobic), and Group III: log(1/EC50-anaerobic)aerobic). Furthermore, this division was not based on the reactive oxygen species (ROS) level or the interaction energy (Ebinding) value, which represents the affinity between SAs and dihydropteroate synthase (dhps) but rather on the total binding energy. Furthermore, SAs with greatly similar structures were categorized into different groups. This deep insight into the difference between aerobic and anaerobic toxicities will benefit environmental science, and the results of this study will serve as a reference for the risk assessment of chemicals in the environment. PMID:26748048

  4. Using Optical Oxygen Sensors and Injection Experiments to Determine in situ Microbial Rate Constants for Methane Oxidation and Heterotrophic Respiration in a Boreal Bog and Fen

    NASA Astrophysics Data System (ADS)

    Waldo, N.; Moorberg, C.; Waldrop, M. P.; Turetsky, M. R.; Neumann, R. B.

    2015-12-01

    Wetlands are the largest natural source of methane to the atmosphere, and play a key role in feedback cycles to climate change. In recognition of this, many researchers are developing process-based models of wetland methane emissions at various scales. In these models, the three key biogeochemical reactions are methane production, methane oxidation, and heterotrophic respiration, and they are modeled using Michaelis-Menten kinetics. The majority of Michaelis-Menten rate constants used in models are based on experiments involving slurries of peat incubated in vials. While these slurries provide a highly controlled setting, they are different from in situ conditions in multiple ways; notably they lack live plants and the centimeter-scale heterogeneities that exist in the field. To determine rate constants in a system more representative of in situ conditions, we extracted peat cores intact from a bog and fen located in the Bonanza Creek Experimental Forest near Fairbanks, Alaska and part of the Alaska Peatland Experiment (APEX) research program. Into those cores we injected water with varying concentrations of methane and oxygen at multiple depths. We used planar oxygen sensors installed on the peat cores to collect high resolution, two dimensional oxygen concentration data during the injections and used oxygen consumption rates under various conditions to calculate rate constants. Results were compared to a similar but smaller set of injection experiments conducted against planar oxygen sensors installed in the bog. Results will inform parametrization of microbial processes in wetland models, improving estimates of methane emissions both under current climate conditions and in the future.

  5. Treatment of chlorinated solvents by nitrogen-fixing and nitrate-supplied methane oxidizers in columns packed with unsaturated porous media

    SciTech Connect

    Chu, K.H.; Alvarez-Cohen, L.

    2000-05-01

    This study compares the feasibility of employing nitrogen-fixing and nitrate-supplied methane-oxidizing cultures grown in unsaturated porous media to degrade cis-1,2-dichloroethylene (cDCE) and trichloroethylene (TCE) in gas streams. Both nitrate-supplied and nitrogen-fixing columns degraded TCE completely at a gaseous concentration of 0.7 mg/L for 8--10 days. However, when columns were supplied with 4% CH{sub 4} and 10% O{sub 2}, nitrate-supplied columns were not able to recover after degrading TCE at a gaseous concentration of 0.13 mg/L for 7 days. In contrast, nitrogen-fixing columns recovered after degrading 0.13--0.4 mg/L TCE for 3--10 days and were capable of repeatedly degrading TCE at gaseous concentrations of 0.03--0.14 mg/L TCE for 3--10 days and were capable of repeatedly degrading TCE at gaseous concentrations of 0.03--0.14 mg/L during long-term intermittent operation that was punctuated by appropriate microbial recovery periods. Both nitrate-supplied and nitrogen-fixing columns were capable of degrading cDCE at concentrations of 0.7--1.0 mg/L for 5--10 days, but only the nitrogen-fixing columns recovered from cDCE exposure. The operating period for columns treating a mixture of TCE and cDCE was significantly shorter than that for treatment of TCE or cDCE alone. Several operating curves were developed to facilitate comparisons between operating conditions and to aid in predicting chlorinated solvent removals in such systems. Nitrogen-fixing columns consistently outperformed nitrate-supplied columns, and columns inoculated with a mixed culture outperformed those inoculated with Methylosinus trichosporium OB3b for TCE removal but not for cDCE removal.

  6. Isolation and Characterization of Bacteria That Grow on Methane and Organic Compounds as Sole Sources of Carbon and Energy

    PubMed Central

    Patt, Tom E.; Cole, Gloria C.; Bland, Judith; Hanson, R. S.

    1974-01-01

    Bacteria capable of growth on methane and a variety of complex organic substrates as sole sources of carbon and energy have been isolated. Conditions used to rigorously establish the purity of the cultures are described. One facultative methylotroph has been studied in detail. This organism has peripherally arranged pairs of intracytoplasmic membranes characteristic of obligate methylotrophs. This isolate apparently utilizes the serine pathway of formaldehyde fixation. The location of methane oxidizers in a dimictic lake indicates that these organisms prefer less than saturating levels of dissolved oxygen. Laboratory experiments confirmed the preference of these organisms for atmospheres containing less oxygen than air. Images PMID:4142033

  7. 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

  8. 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.

  9. 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...

  10. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NASA Astrophysics Data System (ADS)

    Zheng, Y.; Huang, R.; Wang, B. Z.; Bodelier, P. L. E.; Jia, Z. J.

    2014-06-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and functional genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity 6-fold during a 19-day incubation period, while ammonia oxidation activity was significantly suppressed in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like MOB, and nitrifying communities appeared to be partially inhibited by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to an equal increase in Methylosarcina and Methylobacter-related type Ia MOB, indicating the differential growth requirements of representatives of these genera. An increase in 13C assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition partially inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, as well as growth of nitrite-oxidizing bacteria. These

  11. Methane oxidation by Nitrosomonas europaea.

    PubMed Central

    Hyman, M R; Wood, P M

    1983-01-01

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

  12. 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. PMID:27415771

  13. 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. PMID:18487407

  14. 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

  15. 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

  16. Dynamics Associated with Prolonged Ensiling and Aerobic Deterioration of Total Mixed Ration Silage Containing Whole Crop Corn.

    PubMed

    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

  17. Isolation of methanotrophic bacteria from termite gut.

    PubMed

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

    2015-10-01

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

  18. 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. PMID:26348286

  19. 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. PMID:23196248

  20. 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)

  1. "Aerobic" Writing: A Writing Practice Model.

    ERIC Educational Resources Information Center

    Crisp, Sally Chandler

    "Aerobic writing" is a writing center strategy designed to keep students in writing "shape." Like aerobic exercise, aerobic writing is sustained for a certain length of time and done on a regular basis at prescribed time intervals. The program requires students to write at least two times a week for approximately an hour each time. Students write,…

  2. 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)

  3. Response of the jejunal mucosa of dogs with aerobic and anaerobic bacterial overgrowth to antibiotic therapy.

    PubMed Central

    Batt, R M; McLean, L; Riley, J E

    1988-01-01

    Dogs with naturally occurring aerobic or anaerobic bacterial overgrowth have been examined before and after antibiotic therapy in order to assess reversibility of damage to the jejunal mucosa. Histological changes in peroral jejunal biopsies were relatively minor before and after treatment, but sucrose density gradient centrifugation revealed specific biochemical abnormalities that responded to antibiotic therapy. Aerobic overgrowth was initially associated with a marked loss of the main brush border component of alkaline phosphatase activity; this recovered following treatment, suggesting that aerobic bacteria may cause reversible damage to the hydrophobic region of the brush border membrane. In contrast, anaerobic overgrowth was initially associated with a marked reduction in brush border density, indicative of a considerable fall in the glycoprotein-to-lipid ratio of the membrane. Density increased from 1.17 to 1.21 g/ml after antibiotic therapy, consistent with recovery from this relatively severe damage to the brush border caused by anaerobic bacteria. Reductions in soluble and peroxisomal catalase activities which could compromise mucosal protection against free radicals in dogs with aerobic overgrowth, and a loss of particulate malate dehydrogenase activity indicative of mitochondrial disruption in dogs with anaerobic overgrowth, were also reversed after treatment. These findings indicate that aerobic and anaerobic bacterial overgrowth can result in contrasting but potentially reversible damage to the jejunal mucosa which would not be detected by conventional investigative procedures. PMID:3371716

  4. Magnetic Bacteria.

    ERIC Educational Resources Information Center

    Nelson, Jane Bray; Nelson, Jim

    1992-01-01

    Describes the history of Richard Blakemore's discovery of magnetotaxic organisms. Discusses possible reasons why the magnetic response in bacteria developed. Proposes research experiments integrating biology and physics in which students investigate problems using cultures of magnetotaxic organisms. (MDH)

  5. Anaerobic bacteria

    MedlinePlus

    Brook I, Goldstein EJ. Diseases caused by non-spore forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman's Cecil Medicine . 25th ed. Philadelphia, PA: Elsevier Saunders; 2015:chap 297. Stedman's Online ...

  6. 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. PMID:26449384

  7. Swimming bacteria power microscopic gears

    PubMed Central

    Sokolov, Andrey; Apodaca, Mario M.; Grzybowski, Bartosz A.; Aranson, Igor S.

    2010-01-01

    Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be “rectified” under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria Bacillus subtilis moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears’ angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms. PMID:20080560

  8. Swimming bacteria power microscopic gears

    SciTech Connect

    Sokolov, Andrey; Apodaca, Mario M.; Grzybowski, Bartosz A.; Aranson, Igor S.

    2010-01-19

    Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be “rectified” under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria Bacillus subtilis moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears’ angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms.

  9. Swimming bacteria power microscopic gears.

    SciTech Connect

    Sokolov, A.; Apodaca, M. M.; Grzybowski, B. A.; Aranson, I. S.; Materials Science Division; Princeton Univ.; Northwestern Univ.

    2010-01-19

    Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be 'rectified' under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria Bacillus subtilis moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms.

  10. Aerobic and anaerobic growth of Paracoccus denitrificans on methanol.

    PubMed

    Bamforth, C W; Quayle, J R

    1978-10-01

    1. The dye-linked methanol dehydrogenase from Paracoccus denitrificans grown aerobically on methanol has been purified and its properties compared with similar enzymes from other bacteria. It was shown to be specific and to have high affinity for primary alcohols and formaldehyde as substrate, ammonia was the best activator and the enzyme could be linked to reduction of phenazine methosulphate. 2. Paracoccus denitrificans could be grown anaerobically on methanol, using nitrate or nitrite as electron acceptor. The methanol dehydrogenase synthesized under these conditions could not be differentiated from the aerobically-synthesized enzyme. 3. Activities of methanol dehydrogenase, formaldehyde dehydrogenase, formate dehydrogenase, nitrate reductase and nitrite reductase were measured under aerobic and anaerobic growth conditions. 4. Difference spectra of reduced and oxidized cytochromes in membrane and supernatant fractions of methanol-grown P. denitrificans were measured. 5. From the results of the spectral and enzymatic analyses it has been suggested that anaerobic growth on methanol/nitrate is made possible by reduction of nitrate to nitrite using electrons derived from the pyridine nucleotide-linked dehydrogenations of formaldehyde and formate, the nitrite so produced then functioning as electron acceptor for methanol dehydrogenase via cytochrome c and nitrite reductase. PMID:718372

  11. WWOX loss activates aerobic glycolysis

    PubMed Central

    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 discussed here, new data suggest that the tumor suppressor WW domain-containing oxidoreductase (WWOX) modulates HIF1α, thereby regulating this metabolic state. PMID:27308416

  12. Elimination of bacteria from dogs with antibiotics*

    PubMed Central

    Hayes, Norman R.; van der Waaij, D.; Cohen, Bennett J.

    1974-01-01

    The effect of oral administration of neomycin cephalothin or kanamycin cephalothin on the aerobic intestinal bacterial flora, was studied in dogs maintained under isolation conditions in a conventional animal room. The dogs were successfully freed of aerobic bacteria with both combinations within two to seven days after the start of antibiotic treatment, and were maintained bacteria free for up to 21 days. Decontamination was attained more rapidly in dogs that were bathed in hexachlorophene surgical soap before and during the first and third days of antibiotic treatment. There was no evidence of toxicity from either of the antibiotic combinations. These results indicate that, as with mice and monkeys, decontamination of dogs with oral antibiotics is feasible. The technique is of potential value in preventing endogenous bacterial infections in canine experimental studies involving use of immunosuppressive agents. PMID:4529233

  13. Development of microorganisms in the chernozem under aerobic and anaerobic conditions

    NASA Astrophysics Data System (ADS)

    Polyanskaya, L. M.; Gorbacheva, M. A.; Milanovskii, E. Yu.; Zvyagintsev, D. G.

    2010-03-01

    A microbial succession was studied under aerobic and anaerobic conditions by means of experiments with microcosms in different horizons of a chernozem. It was revealed that, under aerobic conditions, all the microorganisms grow irrespective of the soil horizon; fungi and bacteria grow at the first succession stages, and actinomycetes grow at the last stages. It was shown that, in the case of a simulated anaerobiosis commonly used to study anaerobic populations of bacteria, the mycelium of micromycetes grows in the upper part of the chernozem’s A horizon. Under anaerobic conditions, the peak of the mycelium development is shifted from the 3rd to 7th days (typical for aerobic conditions) to the 7th to 15th days of incubation. The level of mycelium length’s stabilization under aerobic and anaerobic conditions also differs: it is higher or lower than the initial one, respectively. Under anaerobic conditions, the growth of fungal mycelium, bacteria, and actinomycetes in the lower part of the A horizon and in the B horizon is extremely weak. There was not any observed growth of actinomycetes in all the chernozem’s horizons under anaerobic conditions.

  14. Methods to determine aerobic endurance.

    PubMed

    Bosquet, Laurent; Léger, Luc; Legros, Patrick

    2002-01-01

    Physiological testing of elite athletes requires the correct identification and assessment of sports-specific underlying factors. It is now recognised that performance in long-distance events is determined by maximal oxygen uptake (V(2 max)), energy cost of exercise and the maximal fractional utilisation of V(2 max) in any realised performance or as a corollary a set percentage of V(2 max) that could be endured as long as possible. This later ability is defined as endurance, and more precisely aerobic endurance, since V(2 max) sets the upper limit of aerobic pathway. It should be distinguished from endurance ability or endurance performance, which are synonymous with performance in long-distance events. The present review examines methods available in the literature to assess aerobic endurance. They are numerous and can be classified into two categories, namely direct and indirect methods. Direct methods bring together all indices that allow either a complete or a partial representation of the power-duration relationship, while indirect methods revolve around the determination of the so-called anaerobic threshold (AT). With regard to direct methods, performance in a series of tests provides a more complete and presumably more valid description of the power-duration relationship than performance in a single test, even if both approaches are well correlated with each other. However, the question remains open to determine which systems model should be employed among the several available in the literature, and how to use them in the prescription of training intensities. As for indirect methods, there is quantitative accumulation of data supporting the utilisation of the AT to assess aerobic endurance and to prescribe training intensities. However, it appears that: there is no unique intensity corresponding to the AT, since criteria available in the literature provide inconsistent results; and the non-invasive determination of the AT using ventilatory and heart rate

  15. Genomics of Nitrogen Cycle in Freshwater Lakes with Focus on Methylotrophic Bacteria

    NASA Astrophysics Data System (ADS)

    Chistoserdova, L.

    2014-12-01

    Data will be presented on communities of microbes active in methane oxidation in Lake Washington, Seattle. Metagenomic sequencing of sediment samples reveals dominant presence of Methylobacter, contrary to prior understanding based on cultivation of methanotrophs. Stable isotope probing of microcosms incubated with methane at varying concentrations of oxygen and nitrate uncover a dominant response by Methylobacter species and a correlation between the populations of Methylobacter and Methylotenera, both responding positively to nitrate. We also uncover a propensity of Methylobacter to act in microoxic conditions, in this case transferring carbon down a food chain represented by a variety of bacteria. Functional gene profiling detects upwards shifts in the abundances of nitrogen metabolism genes in response to nitrate, with Methylococcaceae and Methylophilaceae genes being most abundant. We test a hypothesis of cooperative behavior between Methylobacter, Methylotenera and other species using two alternative approaches: a top-down approach in which we incubate native lake sediments under different conditions and observe trajectories of community simplification, and a bottom-up approach in which we construct synthetic communities from pure cultures of bacteria and observe their behavior. We also cultivate Methylobacter as well as multiple species of Methylophilaceae and analyze their genomes. Among the Methylophilaceae, we uncover a remarkable flexibility in terms of both central carbon and nitrogen metabolic pathways. We hypothesize that this diversity may be driven by microniche conditions along the methane and oxygen countergradients, as well as by the availability of nitrogen sources. Our future plans include deciphering the mechanistic details of cooperative behavior in methane oxidation, using Lake Washington communities as a model.

  16. Aerobic granular processes: Current research trends.

    PubMed

    Zhang, Quanguo; Hu, Jianjun; Lee, Duu-Jong

    2016-06-01

    Aerobic granules are large biological aggregates with compact interiors that can be used in efficient wastewater treatment. This mini-review presents new researches on the development of aerobic granular processes, extended treatments for complicated pollutants, granulation mechanisms and enhancements of granule stability in long-term operation or storage, and the reuse of waste biomass as renewable resources. A discussion on the challenges of, and prospects for, the commercialization of aerobic granular process is provided. PMID:26873285

  17. Isolation and biological characteristics of aerobic marine magnetotactic bacterium YSC-1

    NASA Astrophysics Data System (ADS)

    Gao, Jun; Pan, Hongmiao; Yue, Haidong; Song, Tao; Zhao, Yong; Chen, Guanjun; Wu, Longfei; Xiao, Tian

    2006-12-01

    Magnetotactic bacteria h